John S. Garavelli
Center for Bioinformatics & Computational Biology, Delaware Biotechnology Institute, University of Delaware, 15 Innovation Way, Suite 205, Newark, DE 19711-5449, USA
Copyright 2001, 2018 John S. GaravelliThe RESID Database is a comprehensive collection of annotations and structures for protein modifications including amino-terminal, carboxyl-terminal and peptide chain cross-link, pre-, co- and post-translational modifications.amino acids, modified amino acids, protein modifications, protein structureAA000031-Mar-199531-Mar-199520-Apr-2012alpha-amino acidChEBI:33710C 2 H 3 N 1 O 1 +57.05 +57.021464 +IUPAC-IUB Joint Commission on Biochemical Nomenclature (JCBN)Eur. J. Biochem. 138, 9-37, 1984Nomenclature and symbolism for amino acids and peptides. Recommendations 1983.DOI:10.1111/j.1432-1033.1984.tb07877.xPMID:6692818standard three-letter and one-letter symbols, and nomenclatureThis entry represents an unknown or unidentified alpha-amino or alpha-imino carboxylic acid residue.XUnkPSI-MOD:00009AA000131-Mar-199531-Mar-199530-Sep-2010L-alanine2-aminopropionic acid2-azanylpropanoic acidalpha-alaninealpha-aminopropionic acid(2S)-2-aminopropanoic acidCAS:56-41-7ChEBI:46217PDBHET:ALAC 3 H 5 N 1 O 171.0871.037114C 0 H 0 N 0 O 00.000.000000C -1 H 0 N 0 O -2-44.01-43.989829IUPAC-IUB Joint Commission on Biochemical Nomenclature (JCBN)Eur. J. Biochem. 138, 9-37, 1984Nomenclature and symbolism for amino acids and peptides. Recommendations 1983.DOI:10.1111/j.1432-1033.1984.tb07877.xPMID:6692818standard three-letter and one-letter symbols, and nomenclatureJankowski, V.Vanholder, R.van der Giet, M.Tölle, M.Karadogan, S.Gobom, J.Furkert, J.Oksche, A.Krause, E.Tran, T.N.Tepel, M.Schuchardt, M.Schlüter, H.Wiedon, A.Beyermann, M.Bader, M.Todiras, M.Zidek, W.Jankowski, J.Arterioscler. Thromb. Vasc. Biol. 27, 297-302, 2007Mass-spectrometric identification of a novel angiotensin peptide in human plasma.DOI:10.1161/01.ATV.0000253889.09765.5fPMID:17138938identification of an alanine residue apparently arising from a decarboxylated aspartic acid residueAlanine has not been reported to act as an active site residue.AAlaPSI-MOD:00010DPSI-MOD:00869Not availableUniProt has no active site feature annotations for this residueMOD_RES Beta-decarboxylated aspartateAA000231-Mar-199531-Mar-199530-Jun-2010L-arginine2-amino-5-(carbamimidamido)pentanoic acid [tautomer]2-amino-5-guanidinopentanoic acid2-amino-5-guanidinovaleric acid2-amino-5-[(aminoiminomethyl)amino]pentanoic acid [tautomer]2-azanyl-5-[bis(azanyl)methylideneazanyl]pentanoic acidalpha-amino-delta-guanidinovaleric acid(2S)-2-amino-5-[(diaminomethylidene)amino]pentanoic acidCAS:74-79-3ChEBI:29952PDBHET:ARGC 6 H 12 N 4 O 1156.19156.101111Malinowski, D.P.Fridovich, I.Biochemistry 18, 5909-5917, 1979Chemical modification of arginine at the active site of the bovine erythrocyte superoxide dismutase.DOI:10.1021/bi00593a023PMID:518876chemical modification of an active site arginineIUPAC-IUB Joint Commission on Biochemical Nomenclature (JCBN)Eur. J. Biochem. 138, 9-37, 1984Nomenclature and symbolism for amino acids and peptides. Recommendations 1983.DOI:10.1111/j.1432-1033.1984.tb07877.xPMID:6692818standard three-letter and one-letter symbols, and nomenclatureRArgPSI-MOD:00011ACT_SITEAA000331-Mar-199531-Mar-199530-Sep-2010L-asparagine2,4-bis(azanyl)-4-oxobutanoic acid2,4-diamino-4-oxobutanoic acid2-amino-3-carbamoylpropanoic acid2-amino-4-butanediamic acid2-aminosuccinamic acid2-aminosuccinic acid 4-amidealpha-amino-beta-carbamylpropionic acidalpha-aminosuccinamic acidaspartic acid 4-amideaspartic acid beta-amidebeta-asparagine(2S)-2-amino-4-butanediamic acidCAS:70-47-3ChEBI:50347PDBHET:ASNC 4 H 6 N 2 O 2114.10114.042927C 0 H 0 N 0 O 00.000.000000C 0 H 1 N 1 O -1-0.98-0.984016Vauquelin, L.N.Robiquet, P.J.Ann. Chim. 57, 88-93, 1806Découverte d'un nouveau principe végétal dans les Asperges (Asparagus sativus, Linn.) [The discovery of a new plant principle in asparagus (Asparagus sativus, L.)].article in French; isolation and namingDrenth, J.Jansonius, J.N.Koekoek, R.Swen, H.M.Wolthers, B.G.Nature 218, 929-932, 1968Structure of papain.DOI:10.1038/218929a0PMID:5681232asparagine as an active site residue in a thiol proteinaseIUPAC-IUB Joint Commission on Biochemical Nomenclature (JCBN)Eur. J. Biochem. 138, 9-37, 1984Nomenclature and symbolism for amino acids and peptides. Recommendations 1983.DOI:10.1111/j.1432-1033.1984.tb07877.xPMID:6692818standard three-letter and one-letter symbols, and nomenclatureCurnow, A.W.Tumbula, D.L.Pelaschier, J.T.Min, B.Soll, D.Proc. Natl. Acad. Sci. U.S.A. 95, 12838-12843, 1998Glutamyl-tRNA(Gln) amidotransferase in Deinococcus radiodurans may be confined to asparagine biosynthesis.DOI:10.1073/pnas.95.22.12838PMID:9789001"mischarged" aspartyl-tRNA(Asn) is amidated by glutamyl-tRNA(Gln) amidotransferase in Deinococcus radioduransParadisi, F.Dean, J.L.Geoghegan, K.F.Engel, P.C.Biochemistry 44, 3636-3643, 2005Spontaneous chemical reversion of an active site mutation: deamidation of an asparagine residue replacing the catalytic aspartic acid of glutamate dehydrogenase.DOI:10.1021/bi047679uPMID:15736973an Asp to Asn mutation at an enzyme active site seemingly has partial activity; however, the asparagine form is shown to be inactive, and enhanced spontaneous deamidation results in the partial recovery of activityKolodkin-Gal, I.Hazan, R.Gaathon, A.Carmeli, S.Engelberg-Kulka, H.Science 318, 652-655, 2007A linear pentapeptide is a quorum-sensing factor required for mazEF-mediated cell death in Escherichia coli.DOI:10.1126/science.1147248PMID:17962566enzymatic amidation of an aspartic acid residue in a peptide; the enzyme is currently identified by an activity that is different from the new activitySome bacteria or archaea incorporate asparagine produced by the amidation of aspartyl-tRNA(Asn).aspartate--tRNA(Asn) ligase (EC 6.1.1.23)asparaginyl-tRNA synthase (glutamine-hydrolysing) (EC 6.3.5.6)aspartate--ammonia ligase (EC 6.3.1.1)NAsnPSI-MOD:00012DPSI-MOD:01185ACT_SITEMOD_RES Amidated aspartic acidAA000431-Mar-199531-Mar-199531-Mar-2011L-aspartic acid2-azanylbutanedioic acidaminosuccinic acid(2S)-2-aminobutanedioic acidCAS:56-84-8ChEBI:29958PDBHET:ASPC 4 H 5 N 1 O 3115.09115.026943C 0 H 0 N 0 O 00.000.000000C 0 H -1 N -1 O 10.980.984016Blow, D.M.Birktoft, J.J.Hartley, B.S.Nature 221, 337-340, 1969Role of a buried acid group in the mechanism of action of chymotrypsin.DOI:10.1038/221337a0PMID:5764436Birktoft, J.J.Blow, D.M.Henderson, R.Steitz, T.A.Philos. Trans. R. Soc. Lond., B, Biol. Sci. 257, 67-76, 1970I. Serine proteinases. The structure of alpha-chymotrypsin.PMID:4399050X-ray diffractionSepulveda, P.Marciniszyn Jr., J.Liu, D.Tang, J.J. Biol. Chem. 250, 5082-5088, 1975Primary structure of porcine pepsin. III. Amino acid sequence of a cyanogen bromide fragment, CB2A, and the complete structure of porcine pepsin.PMID:1097438Andreeva, N.S.Gustchina, A.E.Fedorov, A.A.Shutzkever, N.E.Volnova, T.V.Adv. Exp. Med. Biol. 95, 23-31, 1977X-ray crystallographic studies of pepsin.PMID:339692X-ray diffraction, 2.7-3.0 angstromsIUPAC-IUB Joint Commission on Biochemical Nomenclature (JCBN)Eur. J. Biochem. 138, 9-37, 1984Nomenclature and symbolism for amino acids and peptides. Recommendations 1983.DOI:10.1111/j.1432-1033.1984.tb07877.xPMID:6692818standard three-letter and one-letter symbols, and nomenclatureStewart, A.E.Arfin, S.M.Bradshaw, R.A.J. Biol. Chem. 269, 23509-23517, 1994Protein NH2-terminal asparagine deamidase. Isolation and characterization of a new enzyme.PMID:8089117enzyme that deamidates amino-terminal asparagineJedrzejewski, P.T.Girod, A.Tholey, A.Koenig, N.Thullner, S.Kinzel, V.Bossemeyer, D.Protein Sci. 7, 457-469, 1998A conserved deamidation site at Asn 2 in the catalytic subunit of mammalian cAMP-dependent protein kinase detected by capillary LC-MS and tandem mass spectrometry.DOI:10.1002/pro.5560070227PMID:9521123chromatographic and mass spectrometric identificationLindner, H.Sarg, B.Hoertnagl, B.Helliger, W.J. Biol. Chem. 273, 13324-13330, 1998The microheterogeneity of the mammalian H1(0) histone. Evidence for an age-dependent deamidation.DOI:10.1074/jbc.273.21.13324PMID:9582379this deamidation may be non-enzymaticSome active site aspartic acids may form transient covalent bonds with substrates that are not distinguished in protein sequence database features.The deamidation of asparagine is coupled with myristoylation of the immediately preceding glycine (see RESID:AA0059).protein NH2-terminal asparagine deamidase (EC 3.5.1.-)DAspPSI-MOD:00013Nincidental to RESID:AA0059PSI-MOD:00684ACT_SITEMOD_RES Deamidated asparagineAA000531-Mar-199531-Mar-199531-May-2018L-cysteine(R)-cysteine2-amino-3-mercaptopropanoic acid2-amino-3-mercaptopropionic acid2-azanyl-3-sulfanylpropanoic acid3-mercapto-L-alaninealpha-amino-beta-mercaptopropanoic acidalpha-amino-beta-mercaptopropionic acidalpha-amino-beta-thiolpropionic acidbeta-mercaptoalaninehalf-cystineL-(+)-cysteinethioserine(2R)-2-amino-3-sulfanylpropanoic acidCAS:4371-52-2CAS:52-90-4ChEBI:29950PDBHET:CYSC 3 H 5 N 1 O 1 S 1103.14103.009185Grau, U.M.Trommer, W.E.Rossmann, M.G.J. Mol. Biol. 151, 289-307, 1981Structure of the active ternary complex of pig heart lactate dehydrogenase with S-lac-NAD at 2.7 angstrom resolution.DOI:10.1016/0022-2836(81)90516-7PMID:7338899X-ray diffraction, 2.7 angstromsIUPAC-IUB Joint Commission on Biochemical Nomenclature (JCBN)Eur. J. Biochem. 138, 9-37, 1984Nomenclature and symbolism for amino acids and peptides. Recommendations 1983.DOI:10.1111/j.1432-1033.1984.tb07877.xPMID:6692818standard three-letter and one-letter symbols, and nomenclatureTakishima, K.Mamiya, G.Protein Seq. Data Anal. 1, 103-106, 1987Location of the essential cysteine residue of jack bean urease.PMID:3447159Wagner, A.F.V.Frey, M.Neugebauer, F.A.Schäfer, D.Knappe, J.Proc. Natl. Acad. Sci. U.S.A. 89, 996-1000, 1992The free radical in pyruvate formate-lyase is located on glycine-734.DOI:10.1073/pnas.89.3.996PMID:1310545evidence for intermediate cysteine thiyl radicalSauerwald, A.Zhu, W.Major, T.A.Roy, H.Palioura, S.Jahn, D.Whitman, W.B.Yates 3rd, J.R.Ibba, M.Söll, D.Science 307, 1969-1972, 2005RNA-dependent cysteine biosynthesis in archaea.DOI:10.1126/science.1108329PMID:15790858Some methanogenic archaea incorporate cysteine produced by the transsulfuration of O-phosphoserine-tRNA(Cys).Some active site cysteines may form transient covalent bonds with substrates that are not distinguished in protein sequence database features.O-phosphoserine--tRNA(Cys) ligaseO-phospho-L-seryl-tRNA:Cys-tRNA synthase (EC 2.5.1.73)O-phospho-L-serine:tRNA(Cys) ligase (AMP-forming) (EC 6.1.1.27)CCysPSI-MOD:00014ACT_SITEACT_SITE Cysteine radical intermediateAA000631-Mar-199531-Mar-199513-Sep-2013L-glutamic acid1-aminopropane-1,3-dicarboxylic acid2-aminoglutaric acid2-azanylpentanedioic acidalpha-aminoglutaric acidglutaminic acid(2S)-2-aminopentanedioic acidCAS:56-86-0ChEBI:29972PDBHET:GLUC 5 H 7 N 1 O 3129.12129.042593C 0 H 0 N 0 O 00.000.000000C 0 H -1 N -1 O 10.980.984016Hartman, F.C.Biochemistry 10, 146-154, 1971Haloacetol phosphates. Characterization of the active site of rabbit muscle triose phosphate isomerase.DOI:10.1021/bi00777a021PMID:4922541Kimmel, M.T.Plummer Jr., T.H.J. Biol. Chem. 247, 7864-7869, 1972Identification of a glutamic acid at the active center of bovine carboxypeptidase B.PMID:4565668Schmid, M.F.Herriott, J.R.J. Mol. Biol. 103, 175-190, 1976Structure of carboxypeptidase B at 2.8 angstrom resolution.DOI:10.1016/0022-2836(76)90058-9PMID:957425X-ray diffraction, 2.8 angstromsIUPAC-IUB Joint Commission on Biochemical Nomenclature (JCBN)Eur. J. Biochem. 138, 9-37, 1984Nomenclature and symbolism for amino acids and peptides. Recommendations 1983.DOI:10.1111/j.1432-1033.1984.tb07877.xPMID:6692818standard three-letter and one-letter symbols, and nomenclatureKatzin, B.J.Collins, E.J.Robertus, J.D.Proteins 10, 251-259, 1991Structure of ricin A-chain at 2.5 angstroms.DOI:10.1002/prot.340100309PMID:1881881X-ray diffraction, 2.5 angstromsSchmidt, G.Sehr, P.Wilm, M.Selzer, J.Mann, M.Aktories, K.Nature 387, 725-729, 1997Gln 63 of Rho is deamidated by Escherichia coli cytotoxic necrotizing factor-1.DOI:10.1038/42735PMID:9192900enzymatic deamidation of glutamineStriebel, F.Imkamp, F.Sutter, M.Steiner, M.Mamedov, A.Weber-Ban, E.Nature Struct. Mol. Biol. 16, 647-651, 2009Bacterial ubiquitin-like modifier Pup is deamidated and conjugated to substrates by distinct but homologous enzymes.DOI:10.1038/nsmb.1597PMID:19448618Pup activated through deamidation of C-terminal glutamine by depupylase/deamidase DopHoriguchi, Y.Inoue, N.Masuda, M.Kashimoto, T.Katahira, J.Sugimoto, N.Matsuda, M.Proc. Natl. Acad. Sci. U.S.A. 94, 11623-11626, 1997Bordetella bronchiseptica dermonecrotizing toxin induces reorganization of actin stress fibers through deamidation of Gln-63 of the GTP-binding protein Rho.DOI:10.1073/pnas.94.21.11623PMID:9326660enzymatic deamidation of glutamineWang, H.Piatkov, K.I.Brower, C.S.Varshavsky, A.Mol. Cell 34, 686-695, 2009Glutamine-specific N-terminal amidase, a component of the N-end rule pathway.DOI:10.1016/j.molcel.2009.04.032PMID:19560421enzymatic deamidation of N-terminal glutamine targets a protein for degradationCui, J.Yao, Q.Li, S.Ding, X.Lu, Q.Mao, H.Liu, L.Zheng, N.Chen, S.Shao, F.Science 329, 1215-1218, 2010Glutamine deamidation and dysfunction of ubiquitin/NEDD8 induced by a bacterial effector family.DOI:10.1126/science.1193844PMID:20688984deamidation of glutamine in host ubiquitin is catalyzed by Cif homolog of enteropathogenic bacteriaCruz-Migoni, A.Hautbergue, G.M.Artymiuk, P.J.Baker, P.J.Bokori-Brown, M.Chang, C.T.Dickman, M.J.Essex-Lopresti, A.Harding, S.V.Mahadi, N.M.Marshall, L.E.Mobbs, G.W.Mohamed, R.Nathan, S.Ngugi, S.A.Ong, C.Ooi, W.F.Partridge, L.J.Phillips, H.L.Raih, M.F.Ruzheinikov, S.Sarkar-Tyson, M.Sedelnikova, S.E.Smither, S.J.Tan, P.Titball, R.W.Wilson, S.A.Rice, D.W.Science 334, 821-824, 2011A Burkholderia pseudomallei toxin inhibits helicase activity of translation factor eIF4A.DOI:10.1126/science.1211915PMID:22076380deamidation of glutamine in host eIF4A is catalyzed by lethal factor 1 of enteropathogenic bacteriaSome active site glutamic acids may form transient covalent bonds with substrates that are not distinguished in protein sequence database features. protein-glutamine glutaminase (EC 3.5.1.44)EGluPSI-MOD:00015QPSI-MOD:00685ACT_SITEMOD_RES Deamidated glutamineAA000731-Mar-199531-Mar-199530-Jun-2012L-glutamine2,5-bis(azanyl)-5-oxopentanoic acid2,5-diamino-5-oxopentanoic acid2-amino-4-carbamoylbutanoic acid2-aminoglutaramic acidalpha-amino-gamma-carbamylbutyric acidglutamic acid 5-amideglutamic acid gamma-amideglutamide(2S)-2-amino-5-pentanediamic acidCAS:56-85-9ChEBI:30011PDBHET:GLNC 5 H 8 N 2 O 2128.13128.058578IUPAC-IUB Joint Commission on Biochemical Nomenclature (JCBN)Eur. J. Biochem. 138, 9-37, 1984Nomenclature and symbolism for amino acids and peptides. Recommendations 1983.DOI:10.1111/j.1432-1033.1984.tb07877.xPMID:6692818standard three-letter and one-letter symbols, and nomenclatureSchon, A.Kannangara, C.G.Gough, S.Soll, D.Nature 331, 187-190, 1988Protein biosynthesis in organelles requires misaminoacylation of tRNA.DOI:10.1038/331187a0PMID:3340166Curnow, A.W.Hong, K.W.Yuan, R.Kim, S.I.Martins, O.Winkler, W.Henkin, T.M.Soll, D.Proc. Natl. Acad. Sci. U.S.A. 94, 11819-11826, 1997Glu-tRNA(Gln) amidotransferase: a novel heterotrimeric enzyme required for correct decoding of glutamine codons during translation.DOI:10.1073/pnas.94.22.11819PMID:9342321Glutamine has not been reported to act as active site residue.Eukaryotic organelles, along with some bacteria and archaea incorporate glutamine produced by the amidation of "missacylated" glutamyl-tRNA(Gln).glutaminyl-tRNA synthase (glutamine-hydrolysing) (EC 6.3.5.7)glutamate--tRNA(Gln) ligase (EC 6.1.1.24)QGlnPSI-MOD:00016Not availableUniProt has no active site feature annotations for this residueAA000831-Mar-199531-Mar-199530-Jun-2010glycineaminoacetic acidazanylethanoic acidglycocollaminoethanoic acidCAS:56-40-6ChEBI:29947PDBHET:GLYC 2 H 3 N 1 O 157.0557.021464IUPAC-IUB Joint Commission on Biochemical Nomenclature (JCBN)Eur. J. Biochem. 138, 9-37, 1984Nomenclature and symbolism for amino acids and peptides. Recommendations 1983.DOI:10.1111/j.1432-1033.1984.tb07877.xPMID:6692818standard three-letter and one-letter symbols, and nomenclatureWagner, A.F.V.Frey, M.Neugebauer, F.A.Schäfer, D.Knappe, J.Proc. Natl. Acad. Sci. U.S.A. 89, 996-1000, 1992The free radical in pyruvate formate-lyase is located on glycine-734.DOI:10.1073/pnas.89.3.996PMID:1310545evidence for stabilized glycine radicalGGlyPSI-MOD:00017MOD_RES Glycine radicalAA000931-Mar-199504-May-200130-Jun-2012L-histidine(2S)-2-amino-3-(1H-imidazol-5-yl)propanoic acid [tautomer]2-azanyl-3-(1H-imidazol-4-yl)propanoic acid2-azanyl-3-(1H-imidazol-5-yl)propanoic acid [tautomer]4-(2-amino-2-carboxyethyl)imidazolealpha-amino-beta-(4-imidazole)propionic acidglyoxaline-5-alanine(2S)-2-amino-3-(1H-imidazol-4-yl)propanoic acidCAS:71-00-1ChEBI:29979PDBHET:HISC 6 H 7 N 3 O 1137.14137.058912Kossel, A.Hoppe-Seyler's Z. Physiol. Chem. 22, 176-187, 1896Ueber die basischen Stoffe des Zellkerns [On the basic substances of the nucleus].DOI:10.1515/bchm2.1897.22.2.176http://vlp.mpiwg-berlin.mpg.de/library/data/lit17105?article in German; isolation, crystallization and namingHedin, S.G.Hoppe-Seyler's Z. Physiol. Chem. 22, 191-195, 1896Zur Kenntniss der Spaltungsproducte der Proteïinkörper [Toward knowledge of the cleavage products of proteins].DOI:10.1515/bchm2.1897.22.2.191http://vlp.mpiwg-berlin.mpg.de/library/data/lit17107?article in German; determination of molecular weight and elemental compositionPauly, H.Hoppe-Seyler's Z. Physiol. Chem. 42, 508-518, 1904Über die Konstitution des Histidins. I. Mitteilung [On the constitution of histidine. I. Communication].DOI:10.1515/bchm2.1904.42.5-6.508http://vlp.mpiwg-berlin.mpg.de/library/data/lit18003?article in German; determination of molecular structurePyman, F.L.J. Chem. Soc. Trans. 99, 1386-1401, 1911CLVII. - The synthesis of histidine.DOI:10.1039/CT9119901386chemical synthesis; proof of structure and relative stereochemistryHeinrikson, R.L.Stein, W.H.Crestfield, A.M.Moore, S.J. Biol. Chem. 240, 2921-2934, 1965The reactivities of the histidine residues at the active site of ribonuclease toward halo acids of different structures.PMID:14342316Wyckoff, H.W.Tsernoglou, D.Hanson, A.W.Knox, J.R.Lee, B.Richards, F.M.J. Biol. Chem. 245, 305-328, 1970The three-dimensional structure of ribonuclease-S. Interpretation of an electron density map at a nominal resolution of 2 A.PMID:5460889X-ray diffraction, 2.0 angstromsBode, W.Schwager, P.J. Mol. Biol. 98, 693-717, 1975The refined crystal structure of bovine beta-trypsin at 1.8 angstrom resolution.DOI:10.1016/S0022-2836(75)80005-2PMID:512X-ray diffraction, 1.8 angstromsSwenson, R.P.Williams Jr., C.H.Massey, V.J. Biol. Chem. 258, 497-502, 1983Identification of the histidine residue in D-amino acid oxidase that is covalently modified during inactivation by 5-dimethylaminonaphthalene-1-sulfonyl chloride.PMID:6129252Dijkstra, B.W.Renetseder, R.Kalk, K.H.Hol, W.G.J.Drenth, J.J. Mol. Biol. 168, 163-179, 1983Structure of porcine pancreatic phospholipase A-2 at 2.6 angstrom resolution and comparison with bovine phospholipase A-2.DOI:10.1016/S0022-2836(83)80328-3PMID:6876174X-ray diffraction, 2.6 angstromsIUPAC-IUB Joint Commission on Biochemical Nomenclature (JCBN)Eur. J. Biochem. 138, 9-37, 1984Nomenclature and symbolism for amino acids and peptides. Recommendations 1983.DOI:10.1111/j.1432-1033.1984.tb07877.xPMID:6692818standard three-letter and one-letter symbols, and nomenclaturevan den Bergh, C.J.Slotboom, A.J.Verheij, H.M.de Haas, G.H.J. Cell. Biochem. 39, 379-390, 1989The role of Asp-49 and other conserved amino acids in phospholipases A2 and their importance for enzymatic activity.DOI:10.1002/jcb.240390404PMID:2722967Some active site histidines may form transient covalent bonds with substrates that are not distinguished in protein sequence database features.HHisPSI-MOD:00018ACT_SITEAA001031-Mar-199531-Mar-199530-Jun-2010L-isoleucine2-azanyl-3-methylpentanoic acid3-methyl-norvalinealpha-amino-beta-methylvaleric acidL-erythro-isoleucine(2S,3S)-2-amino-3-methylpentanoic acidCAS:73-32-5ChEBI:30009PDBHET:ILEC 6 H 11 N 1 O 1113.16113.084064IUPAC-IUB Joint Commission on Biochemical Nomenclature (JCBN)Eur. J. Biochem. 138, 9-37, 1984Nomenclature and symbolism for amino acids and peptides. Recommendations 1983.DOI:10.1111/j.1432-1033.1984.tb07877.xPMID:6692818standard three-letter and one-letter symbols, and nomenclatureThe alpha carboxyl group of a C-terminal isoleucine is predicted to act as a proton acceptor in the active site of an enzyme.IIlePSI-MOD:00019ACT_SITE Proton acceptor; via carboxylateAA001131-Mar-199531-Mar-199530-Jun-2010L-leucine2-azanyl-4-methylpentanoic acid4-methyl-norvalinealpha-amino-gamma-methylvaleric acidalpha-aminoisocaproic acid(2S)-2-amino-4-methylpentanoic acidCAS:61-90-5ChEBI:30006PDBHET:LEUC 6 H 11 N 1 O 1113.16113.084064IUPAC-IUB Joint Commission on Biochemical Nomenclature (JCBN)Eur. J. Biochem. 138, 9-37, 1984Nomenclature and symbolism for amino acids and peptides. Recommendations 1983.DOI:10.1111/j.1432-1033.1984.tb07877.xPMID:6692818standard three-letter and one-letter symbols, and nomenclatureFarazi, T.A.Manchester, J.K.Waksman, G.Gordon, J.I.Biochemistry 40, 9177-9186, 2001Pre-steady-state kinetic studies of Saccharomyces cerevisiae myristoylCoA:protein N-myristoyltransferase mutants identify residues involved in catalysis.DOI:10.1021/bi0107997PMID:11478885the alpha carboxyl group of a C-terminal leucine is reported to act as a proton acceptor in the active site of an enzymeLLeuPSI-MOD:00020ACT_SITE Proton acceptor; via carboxylateAA001231-Mar-199531-Mar-199530-Jun-2010L-lysine2,6-bis(azanyl)hexanoic acid6-amino-L-norleucinealpha,epsilon-diaminocaproic acid(2S)-2,6-diaminohexanoic acidCAS:56-87-1ChEBI:29967PDBHET:LYSC 6 H 12 N 2 O 1128.18128.094963Swenson, R.P.Williams Jr., C.H.Massey, V.J. Biol. Chem. 257, 1937-1944, 1982Chemical modification of D-amino acid oxidase. Amino acid sequence of the tryptic peptides containing tyrosine and lysine residues modified by fluorodinitrobenzene.PMID:6120171IUPAC-IUB Joint Commission on Biochemical Nomenclature (JCBN)Eur. J. Biochem. 138, 9-37, 1984Nomenclature and symbolism for amino acids and peptides. Recommendations 1983.DOI:10.1111/j.1432-1033.1984.tb07877.xPMID:6692818standard three-letter and one-letter symbols, and nomenclatureLusty, C.J.Ratner, S.Proc. Natl. Acad. Sci. U.S.A. 84, 3176-3180, 1987Reaction of argininosuccinase with bromomesaconic acid: role of an essential lysine in the active site.DOI:10.1073/pnas.84.10.3176PMID:3106962Some active site lysines may form transient covalent bonds with substrates that are not distinguished in the protein sequence database features.KLysPSI-MOD:00021ACT_SITEACT_SITE Schiff-base intermediate with substrateAA001331-Mar-199531-Mar-199525-Feb-2011L-methionine2-amino-4-(methylthio)butanoic acid2-amino-4-(methylthio)butyric acid2-azanyl-4-(methylsulfanyl)butanoic acidalpha-amino-gamma-methylmercaptobutyric acidalpha-amino-gamma-methylthiobutyric acidgamma-methylthio-alpha-aminobutyric acidL-(-)-methionineS-methyl-L-homocysteine(2S)-2-amino-4-(methylsulfanyl)butanoic acidCAS:24425-78-3CAS:63-68-3CAS:7005-18-7ChEBI:16044PDBHET:METC 5 H 9 N 1 O 1 S 1131.19131.040485Mueller, J.H.Proc. Soc. Exp. Biol. Med. 19, 161-163, 1922A new sulphur-containing amino acid isolated from casein.identification as a hydrolytic product of casein; isolation; chemical characterizationMueller, J.H.J. Biol. Chem. 56, 157-169, 1923A new sulfur-containing amino-acid isolated from the hydrolytic products of protein.identification as a hydrolytic product of several proteins; isolation; determination of molecular formulaBarger, G.Coyne, F.P.Biochem. J. 22, 1417-1425, 1928CLXXVI. The amino-acid methionine; constitution and synthesis.PMID:16744158determination of structure by synthesis; namingFowler, A.V.Smith, P.J.J. Biol. Chem. 258, 10204-10207, 1983The active site regions of lacZ and ebg beta-galactosidases are homologous.PMID:6411710chemical modification of an active site methionineIUPAC-IUB Joint Commission on Biochemical Nomenclature (JCBN)Eur. J. Biochem. 138, 9-37, 1984Nomenclature and symbolism for amino acids and peptides. Recommendations 1983.DOI:10.1111/j.1432-1033.1984.tb07877.xPMID:6692818standard three-letter and one-letter symbols, and nomenclatureAlthough appropriate, the keyword "thioether bond" normally does not appear for this amino acid, except for certain active site feature annotations.MMetPSI-MOD:00022*thioether bondNot availableUniProt has no active site feature annotations for this residueAA001431-Mar-199531-Mar-199530-Jun-2010L-phenylalanine2-azanyl-3-phenylpropanoic acidalpha-amino-beta-phenylpropionic acid(2S)-2-amino-3-phenylpropanoic acidCAS:63-91-2ChEBI:29997PDBHET:PHEC 9 H 9 N 1 O 1147.18147.068414IUPAC-IUB Joint Commission on Biochemical Nomenclature (JCBN)Eur. J. Biochem. 138, 9-37, 1984Nomenclature and symbolism for amino acids and peptides. Recommendations 1983.DOI:10.1111/j.1432-1033.1984.tb07877.xPMID:6692818standard three-letter and one-letter symbols, and nomenclaturePhenylalanine has not been demonstrated to act as active site residue.FPhePSI-MOD:00023Not availableUniProt has no active site feature annotations for this residueAA001531-Mar-199531-Mar-199530-Sep-2010L-prolinepyrrolidine-2-carboxylic acid(2S)-2-pyrrolidinecarboxylic acidCAS:147-85-3ChEBI:50342PDBHET:PROC 5 H 7 N 1 O 197.1297.052764IUPAC-IUB Joint Commission on Biochemical Nomenclature (JCBN)Eur. J. Biochem. 138, 9-37, 1984Nomenclature and symbolism for amino acids and peptides. Recommendations 1983.DOI:10.1111/j.1432-1033.1984.tb07877.xPMID:6692818standard three-letter and one-letter symbols, and nomenclatureSubramanya, H.S.Roper, D.I.Dauter, Z.Dodson, E.J.Davies, G.J.Wilson, K.S.Wigley, D.B.Biochemistry 35, 792-802, 1996Enzymatic ketonization of 2-hydroxymuconate: specificity and mechanism investigated by the crystal structures of two isomerases.DOI:10.1021/bi951732kPMID:8547259evidence for amino-terminal proline active sitePProPSI-MOD:00024ACT_SITE Proton acceptor; via carboxylateACT_SITE Proton acceptor; via imino nitrogenAA001631-Mar-199531-Mar-199530-Jun-2010L-serine2-azanyl-3-hydroxypropanoic acid3-hydroxy-L-alaninealpha-amino-beta-hydroxypropionic acidbeta-hydroxyalanine(2S)-2-amino-3-hydroxypropanoic acidCAS:56-45-1ChEBI:29999PDBHET:SERC 3 H 5 N 1 O 287.0887.032028Birktoft, J.J.Blow, D.M.Henderson, R.Steitz, T.A.Philos. Trans. R. Soc. Lond., B, Biol. Sci. 257, 67-76, 1970I. Serine proteinases. The structure of alpha-chymotrypsin.PMID:4399050X-ray diffractionIUPAC-IUB Joint Commission on Biochemical Nomenclature (JCBN)Eur. J. Biochem. 138, 9-37, 1984Nomenclature and symbolism for amino acids and peptides. Recommendations 1983.DOI:10.1111/j.1432-1033.1984.tb07877.xPMID:6692818standard three-letter and one-letter symbols, and nomenclatureSSerPSI-MOD:00025ACT_SITEAA001731-Mar-199531-Mar-199531-Dec-2012L-threonine2-azanyl-3-hydroxybutanoic acidalpha-amino-beta-hydroxybutyric acidbeta-methylserineL-threo-threonine(2S,3R)-2-amino-3-hydroxybutanoic acidCAS:72-19-5ChEBI:30013PDBHET:THRC 4 H 7 N 1 O 2101.10101.047678McCoy, R.E.Meyer, C.E.Rose, W.C.J. Biol. Chem. 112, 283-302, 1935Feeding experiments with mixtures of highly purified amino acids. VIII. Isolation and identificaton of a new essential amino acid.identification as an essential dietary amino acid; isolation, purification and structure determinationMeyer, C.E.Rose, W.C.J. Biol. 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Rose.PMID:12218068historical reviewTThrPSI-MOD:00026ACT_SITEAA001831-Mar-199531-Mar-199525-Feb-2011L-tryptophan2-azanyl-3-(1H-indol-3-yl)propanoic acidalpha-amino-beta-(3-indolyl)propionoic acidbeta(3-indolyl)alanine(2S)-2-amino-3-(1H-indol-3-yl)propanoic acidCAS:73-22-3ChEBI:29954PDBHET:TRPC 11 H 10 N 2 O 1186.21186.079313IUPAC-IUB Joint Commission on Biochemical Nomenclature (JCBN)Eur. J. Biochem. 138, 9-37, 1984Nomenclature and symbolism for amino acids and peptides. Recommendations 1983.DOI:10.1111/j.1432-1033.1984.tb07877.xPMID:6692818standard three-letter and one-letter symbols, and nomenclatureLi, Y.F.Heelis, P.F.Sancar, A.Biochemistry 30, 6322-6329, 1991Active site of DNA photolyase: tryptophan-306 is the intrinsic hydrogen atom donor essential for flavin radical photoreduction and DNA repair in vitro.DOI:10.1021/bi00239a034PMID:2059637spectrographic characterizationStarks, C.M.Back, K.Chappell, J.Noel, J.P.Science 277, 1815-1820, 1997Structural basis for cyclic terpene biosynthesis by tobacco 5-epi-aristolochene synthase.DOI:10.1126/science.277.5333.1815PMID:9295271a protonated tryptophan cation active site is proposedWTrpPSI-MOD:00027ACT_SITE Tryptophan radical intermediateSITE Electron transfer via tryptophanyl radicalAA001931-Mar-199531-Mar-199530-Sep-2010L-tyrosine2-azanyl-3-(4-hydoxyphenyl)propanoic acidalpha-amino-beta-(para-hydroxyphenyl)propionic acidp-tyrosinepara-hydroxyphenylalanine(2S)-2-amino-3-(4-hydoxyphenyl)propanoic acidCAS:60-18-4ChEBI:46858PDBHET:TYRC 9 H 9 N 1 O 2163.18163.063329Takahashi, K.Stein, W.H.Moore, S.J. Biol. Chem. 242, 4682-4690, 1967The identification of a glutamic acid residue as part of the active site of ribonuclease T-1.PMID:6061414Takahashi, K.J. Biochem. 69, 331-338, 1971The structure and function of ribonuclese T-1. XII. Further studies on rose bengal-catalyzed photooxidation of ribonuclease T-1- identification of a critical histidine residue.PMID:5550972Swenson, R.P.Williams Jr., C.H.Massey, V.J. Biol. Chem. 257, 1937-1944, 1982Chemical modification of D-amino acid oxidase. Amino acid sequence of the tryptic peptides containing tyrosine and lysine residues modified by fluorodinitrobenzene.PMID:6120171IUPAC-IUB Joint Commission on Biochemical Nomenclature (JCBN)Eur. J. Biochem. 138, 9-37, 1984Nomenclature and symbolism for amino acids and peptides. Recommendations 1983.DOI:10.1111/j.1432-1033.1984.tb07877.xPMID:6692818standard three-letter and one-letter symbols, and nomenclatureLynn, R.M.Bjornsti, M.A.Caron, P.R.Wang, J.C.Proc. Natl. Acad. Sci. U.S.A. 86, 3559-3563, 1989Peptide sequencing and site-directed mutagenesis identify tyrosine-727 as the active site tyrosine of Saccharomyces cerevisiae DNA topoisomerase I.DOI:10.1073/pnas.86.10.3559PMID:2542938Nordlund, P.Sjoeberg, B.M.Eklund, H.Nature 345, 593-598, 1990Three-dimensional structure of the free radical protein of ribonucleotide reductase.DOI:10.1038/345593a0PMID:2190093X-ray diffractionYTyrPSI-MOD:00028ACT_SITEAA002031-Mar-199531-Mar-199530-Jun-2010L-valine2-azanyl-3-methylbutanoic acidalpha-amino-beta-methylbutyric acidalpha-aminoisovaleric acid(2S)-2-amino-3-methylbutanoic acidCAS:72-18-4ChEBI:30015PDBHET:VALC 5 H 9 N 1 O 199.1399.068414IUPAC-IUB Joint Commission on Biochemical Nomenclature (JCBN)Eur. J. Biochem. 138, 9-37, 1984Nomenclature and symbolism for amino acids and peptides. Recommendations 1983.DOI:10.1111/j.1432-1033.1984.tb07877.xPMID:6692818standard three-letter and one-letter symbols, and nomenclatureThe alpha carboxyl group of a C-terminal valine is predicted to act as a proton acceptor in the active site of an enzyme.VValPSI-MOD:00029ACT_SITE Proton acceptor; via carboxylateAA002131-Mar-199531-Mar-199531-May-2013N-formyl-L-methionine2-formamido-4-(methylsulfanyl)butanoic acid2-formylamino-4-(methylthio)butanoic acid2-formylazanyl-4-(methylsulfanyl)butanoic acid(2S)-2-formylamino-4-(methylsulfanyl)butanoic acidCAS:4289-98-9ChEBI:49298PDBHET:FMEC 6 H 10 N 1 O 2 S 1160.21160.043225C 0 H 0 N 0 O 0 S 00.000.000000C 1 H 0 N 0 O 1 S 028.0127.994915Adams, J.M.Capecchi, M.R.Proc. Natl. Acad. Sci. U.S.A. 55, 147-155, 1966N-formylmethionyl-sRNA as the initiator of protein synthesis.DOI:10.1073/pnas.55.1.147PMID:5328638identification of N-formylmethionyl-tRNA as necessary for the initiation of protein synthesis in Escherichia coliWebster, R.E.Engelhardt, D.L.Zinder, N.D.Proc. Natl. Acad. Sci. U.S.A. 55, 155-161, 1966In vitro protein synthesis: chain initiation.DOI:10.1073/pnas.55.1.155PMID:5220863identification of N-formylmethionine as the blocked N-terminal of phage coat protein synthesized by Escherichia coliThach, R.E.Dewey, K.F.Brown, J.C.Doty, P.Science 153, 416-418, 1966Formylmethionine codon AUG as an initiator of polypeptide synthesis.DOI:10.1126/science.153.3734.416PMID:5328567determination that the AUG codon was translated by the N-formylmethionyl-tRNA during the initiation of protein synthesis in Escherichia coliChen, C.-SParthasarathy, R.Acta Crystallogr. B 33, 3332-3336, 1977Structure and conformation of amino acids containing sulfur. V. N-Formyl-L-methionine.DOI:10.1107/S0567740877010942X-ray diffractionLi, Q.X.Dowhan, W.J. Biol. Chem. 263, 11516-11522, 1988Structural characterization of Escherichia coli phosphatidylserine decarboxylase.PMID:3042771identification and removal of formyl group using 25% trifluoroacetic acidHensel, S.Buse, G.Biol. Chem. Hoppe-Seyler 371, 411-422, 1990Studies on cytochrome-C oxidase, XIV: the amino-acid sequence of subunit-I -- Proteinchemical methods for the analysis of a large hydrophobic membrane protein.PMID:2165784HPLC identification of N-formylhomoserine; N-formylmethionine initiates protein synthesis on vertebrate mitochondrial ribosomesPrince, S.M.Papiz, M.Z.Freer, A.A.McDermott, G.Hawthornthwaite-Lawless, A.M.Cogdell, R.J.Isaacs, N.W.J. Mol. Biol. 268, 412-423, 1997Apoprotein structure in the LH2 complex from Rhodopseudomonas acidophila strain 10050: modular assembly and protein pigment interactions.DOI:10.1006/jmbi.1997.0966PMID:9159480X-ray diffraction, 2.50 angstroms; an N-formyl carbonyl group axially ligates the magnesium ion of bacteriochlorophyll a in light-harvesting protein B-800/850 alpha chain; it is probably the hydrated form, N-(dihydroxymethyl)methionineCogdell, R.J.Freer, A.A.Isaacs, N.W.Hawthornthwaite-Lawless, A.M.McDermott, G.Papiz, M.Z.Prince, S.M.submitted to the Protein Data Bank, August 1996Integral membrane peripheral light harvesting complex from Rhodopseudomonas acidophila strain 10050.PDB:1KZUX-ray diffraction, 2.50 angstromsSoulimane, T.Than, M.E.Dewor, M.Huber, R.Buse, G.Protein Sci. 9, 2068-2073, 2000Primary structure of a novel subunit in ba3-cytochrome oxidase from Thermus thermophilus.DOI:10.1110/ps.9.11.2068PMID:11152118mass spectrometric identification of N-formyl-methionine; deformylation with acetyl chlorideNetz, D.J.A.Pohl, R.Beck-Sickinger, A.G.Selmer, T.Pierik, A.J.Bastos, M.C.F.Sahl, H.-G.J. Mol. Biol. 319, 745-756, 2002Biochemical characterisation and genetic analysis of aureocin A53, a new, atypical bacteriocin from Staphylococcus aureus.DOI:10.1016/S0022-2836(02)00368-6PMID:12054867N-formylmethionine detected by mass spectrometry; authors' initials in the PubMed citation are correctedWalker, J.E.Carroll, J.Altman, M.C.Fearnley, I.M.Meth. Enzymol. 456, 111-131, 2009Chapter 6 Mass spectrometric characterization of the thirteen subunits of bovine respiratory complexes that are encoded in mitochondrial DNA.DOI:10.1016/S0076-6879(08)04406-6PMID:19348885top-down mass-spectrometry; all of 13 proteins encoded in bovine mitochondrial DNA retain the N-formylmethionine initiator except cytochrome c oxidase subunit 3 which undergoes partial processing to remove the formyl group or the N-formylmethionineTucker, E.J.Hershman, S.G.Köhrer, C.Belcher-Timme, C.A.Patel, J.Goldberger, O.A.Christodoulou, J.Silberstein, J.M.McKenzie, M.Ryan, M.T.Compton, A.G.Jaffe, J.D.Carr, S.A.Calvo, S.E.RajBhandary, U.L.Thorburn, D.R.Mootha, V.K.Cell Metab. 14, 428-434, 2011Mutations in MTFMT underlie a human disorder of formylation causing impaired mitochondrial translation.DOI:10.1016/j.cmet.2011.07.010PMID:21907147mutations in the gene for human methionyl-tRNA formyltransferase can cause combined severe oxidative phosphorylation deficiency by impairing mitochondrial protein synthesisN-formylmethionine is translated for the initiator codon in bacteria, and there are different tRNA's with specific tRNA synthases for the initiator N-formylmethionine and the elongation methionine forms.In eukaryotic organelles there is only one tRNA for methionine. A portion of the Met-tRNA is N-formylated by mitochondrion specific methionyl-tRNA formyltransferase and recruited by mitochondrial translation initiation factor 2.As an aldehyde, the formyl group readily undergoes hydration. For the hydrated form N-(dihydroxymethyl)-L-methionine of this residue, see RESID:AA0493.Although appropriate, the keyword "thioether bond" normally does not appear for this amino acid.methionine--tRNA ligase (EC 6.1.1.10)methionyl-tRNA formyltransferase (EC 2.1.2.9)Mamino-terminalPSI-MOD:00030Mamino-terminalPSI-MOD:00482*thioether bondblocked amino endformylationpretranslational modificationMOD_RES N-formylmethionineAA002231-Mar-199531-Mar-199531-May-2013L-selenocysteine2-azanyl-3-selanylpropanoic acid3-selenylalanineSeCysselenium cysteine(2R)-2-amino-3-selanylpropanoic acidCAS:10236-58-5ChEBI:30000PDBHET:CSEC 3 H 5 N 1 O 1 Se 1150.05150.953635C 0 H 0 N 0 O 0 Se 00.000.000000C 0 H 0 N 0 O 0 S -1 Se 146.9147.944450Huber, R.E.Criddle, R.S.Arch. Biochem. Biophys. 122, 164-173, 1967Comparison of the chemical properties of selenocysteine and selenocystine with their sulfur analogs.DOI:10.1016/0003-9861(67)90136-1PMID:6076213Turner, D.C.Stadtman, T.C.Arch. Biochem. Biophys. 154, 366-381, 1973Purification of protein components of the clostridial glycine reductase system and characterization of protein A as a selenoprotein.DOI:10.1016/0003-9861(73)90069-6PMID:4734725Cone, J.E.Del Río, R.M.Davis, J.N.Stadtman, T.C.Proc. Natl. Acad. Sci. U.S.A. 73, 2659-2663, 1976Chemical characterization of the selenoprotein component of clostridial glycine reductase: identification of selenocysteine as the organoselenium moiety.DOI:10.1073/pnas.73.8.2659PMID:1066676Condell, R.A.Tappel, A.L.Biochim. Biophys. 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U.S.A. 83, 4650-4654, 1986Nucleotide sequence and expression of the selenocysteine-containing polypeptide of formate dehydrogenase (formate-hydrogen-lyase-linked) from Escherichia coli.PMID:2941757gene sequenceSliwkowski, M.X.Stadtman, T.C.Proc. Natl. Acad. Sci. U.S.A. 85, 368-371, 1988Selenoprotein A of the clostridial glycine reductase complex: purification and amino acid sequence of the selenocysteine-containing peptide.DOI:10.1073/pnas.85.2.368PMID:2963330Hill, K.E.Lloyd, R.S.Yang, J.G.Read, R.Burk, R.F.J. Biol. Chem. 266, 10050-10053, 1991The cDNA for rat selenoprotein P contains 10 TGA codons in the open reading frame.PMID:2037562Dixon, H.B.F.Eur. J. Biochem. 264, 607-609, 1999IUPAC-IUBMB Joint Commission on Biochemical Nomenclature (JCBN) and Nomenclature Committee of IUBMB (NC-IUBMB), newsletter 1999.PMID:10523135http://www.chem.qmul.ac.uk/iubmb/newsletter/1999/item3.html ; the omission of the author in the PubMed citation is correctedJormakka, M.Törnroth, S.Byrne, B.Iwata, S.Science 295, 1863-1868, 2002Molecular basis of proton motive force generation: structure of formate dehydrogenase-N.DOI:10.1126/science.1068186PMID:11884747X-ray diffraction, 1.6 angstromsJormakka, M.Tornroth, S.Byrne, B.Iwata, S.submitted to the Protein Data Bank, January 2002Formate dehydrogenase N from E. coli.PDB:1KQFX-ray diffraction, 1.60 angstromsItoh, Y.Bröcker, M.J.Sekine, S.Hammond, G.Suetsugu, S.Söll, D.Yokoyama, S.Science 340, 75-78, 2013Decameric SelA.tRNA(Sec) ring structure reveals mechanism of bacterial selenocysteine formation.DOI:10.1126/science.1229521PMID:23559248in bacteria selenocysteine is produced by serine acylation to tRNA(Sec) followed by reaction with selenophosphate to form selenocysteinyl-tRNA(Sec)Selenocysteine is translated for the UGA codon in some genetic systems. It has not yet been demonstrated to arise alternatively from a post-translational modification.Although the single letter symbol U is recommended by IUBMB, many software applications fail to recognize it, and some sequence databases may use the single letter symbol C.serine--tRNA ligase (EC 6.1.1.11)L-seryl-tRNA(Sec) selenium transferase, SelA (EC 2.9.1.1)O-phosphoseryl-tRNA(Sec) kinase (EC 2.7.1.164)O-phospho-L-seryl-tRNA(Sec):L-selenocysteinyl-tRNA synthase, SepSecS (EC 2.9.1.2)USecGO:0001514PSI-MOD:00031CPSI-MOD:00686pretranslational modificationseleniumselenocysteineNON_STD SelenocysteineAA002331-Mar-199531-Mar-199530-Apr-2010L-aspartic acid or L-asparagineC 4 H 5 N 1 O 3, C 4 H 6 N 2 O 2115.09, 114.10115.026943, 114.042927Airoldi, L.P.Doonan, S.FEBS Lett. 50, 155-158, 1975A method of distinguishing between aspartic acid and asparagine and between glutamic acid and glutamine during sequence analysis by the dansyl-Edman procedure.DOI:10.1016/0014-5793(75)80478-9PMID:1089562IUPAC-IUB Joint Commission on Biochemical Nomenclature (JCBN)Eur. J. Biochem. 138, 9-37, 1984Nomenclature and symbolism for amino acids and peptides. Recommendations 1983.DOI:10.1111/j.1432-1033.1984.tb07877.xPMID:6692818standard three-letter and one-letter symbols, and nomenclatureThis represents an uncertain amidation of an aspartic acid.BAsxAA002431-Mar-199531-Mar-199530-Apr-2010L-glutamic acid or L-glutamineC 5 H 7 N 1 O 3, C 5 H 8 N 2 O 2129.11, 128.13129.042593, 128.058578Airoldi, L.P.Doonan, S.FEBS Lett. 50, 155-158, 1975A method of distinguishing between aspartic acid and asparagine and between glutamic acid and glutamine during sequence analysis by the dansyl-Edman procedure.DOI:10.1016/0014-5793(75)80478-9PMID:1089562IUPAC-IUB Joint Commission on Biochemical Nomenclature (JCBN)Eur. J. Biochem. 138, 9-37, 1984Nomenclature and symbolism for amino acids and peptides. Recommendations 1983.DOI:10.1111/j.1432-1033.1984.tb07877.xPMID:6692818standard three-letter and one-letter symbols, and nomenclatureThis represents an uncertain amidation of a glutamic acid.ZGlxAA002531-Mar-199531-Mar-199531-May-2018L-cystine2-amino-3-(2-amino-2-carboxy-ethyl)disulfanyl-propanoic acid [misnomer]3,3'-disulfane-1,2-diylbis(2-azanylpropanoic acid)3,3'-dithiobis(2-aminopropanoic acid)3,3'-dithiobisalanine3,3'-dithiodialaninebeta,beta'-diamino-beta,beta'-dicarboxydiethyldisulfidebeta,beta'-dithiodialaninebis(alpha-aminopropionic acid)-beta-disulfidebis(beta-amino-beta-carboxyethyl)disulfidedicysteine(2R,2'R)-3,3'-disulfane-1,2-diylbis(2-aminopropanoic acid)CAS:56-89-3ChEBI:50058PDBHET:CYSC 6 H 8 N 2 O 2 S 2204.26204.002720C 6 H 10 N 2 O 3 S 2222.28222.013284C 0 H -2 N 0 O 0 S 0-2.02-2.015650C 3 H 5 N 1 O 2 S 1119.14119.004099Soderberg, B.O.Sjoberg, B.M.Sonnerstam, U.Branden, C.I.Proc. Natl. Acad. Sci. U.S.A. 75, 5827-5830, 1978Three-dimensional structure of thioredoxin induced by bacteriophage T4.DOI:10.1073/pnas.75.12.5827PMID:366603X-ray diffraction, 2.8 angstroms; redox-active disulfide bondBergenhem, N.Carlsson, U.Strid, L.Biochim. Biophys. Acta 871, 55-60, 1986The existence of glutathione and cysteine disulfide-linked to erythrocyte carbonic anhydrase from tiger shark.DOI:10.1016/0167-4838(86)90132-9PMID:3083866chemical characterizationSørensen, H.H.Thomsen, J.Bayne, S.Højrup, P.Roepstorff, P.Biomed. Environ. Mass Spectrom. 19, 713-720, 1990Strategies for determination of disulphide bridges in proteins using plasma desorption mass spectrometry.DOI:10.1002/bms.1200191110PMID:2076469the spellings of "Sorensen, H.H." and "Hojrup, P." in the PubMed citation are correctedBalhorn, R.Corzett, M.Mazrimas, J.Watkins, B.Biochemistry 30, 175-181, 1991Identification of bull protamine disulfides.DOI:10.1021/bi00215a026PMID:1988019chemical titration and characterization of disulfide bonds; results from this methodology must be carefully evaluatedForman-Kay, J.D.Clore, G.M.Wingfield, P.T.Gronenborn, A.M.Biochemistry 30, 2685-2698, 1991High-resolution three-dimensional structure of reduced recombinant human thioredoxin in solution.DOI:10.1021/bi00224a017PMID:2001356(1)H-NMR and (15)N-NMR analysis; redox-active disulfide bondDörmann, P.Börchers, T.Korf, U.Højrup, P.Roepstorff, P.Spener, F.J. Biol. Chem. 268, 16286-16292, 1993Amino acid exchange and covalent modification by cysteine and glutathione explain isoforms of fatty acid-binding protein occurring in bovine liver.PMID:8344916mass spectrometric detectionYang, C.Y.Gu, Z.W.Blanco-Vaca, F.Gaskell, S.J.Yang, M.Massey, J.B.Gotto Jr., A.M.Pownall, H.J.Biochemistry 33, 12451-12455, 1994Structure of human apolipoprotein D: locations of the intermolecular and intramolecular disulfide links.DOI:10.1021/bi00207a011PMID:7918467mass spectrometric identification of disulfide bondsHadfield, A.Shammas, C.Kryger, G.Ringe, D.Petsko, G.A.Ouyang, J.Viola, R.E.Biochemistry 40, 14475-14483, 2001Active site analysis of the potential antimicrobial target aspartate semialdehyde dehydrogenase.DOI:10.1021/bi015713oPMID:11724560X-ray diffraction, 2.60 angstroms; inhibitor S-methyl cysteine sulfoxide may react with the active site cysteine to form a disulfide bond and release methanol; although not a natural formation of cystine, it is a model for enzymes inhibited by oxidative disulfide formation with free cysteineHadfield, A.T.Kryger, G.Ouyang, J.Ringe, D.Petsko, G.A.Viola, R.E.submitted to the Protein Data Bank, August 2001Aspartate beta-semialdehyde dehydrogenase in complex with NADP and substrate analogue S-methyl cysteine sulfoxide.PDB:1GL3X-ray diffraction, 2.60 angstromsMetanis, N.Keinan, E.Dawson, P.E.J. Am. Chem. Soc. 128, 16684-16691, 2006Synthetic seleno-glutaredoxin 3 analogues are highly reducing oxidoreductases with enhanced catalytic efficiency.DOI:10.1021/ja0661414PMID:17177418comparative redox potentials of cystine, cysteinylselenocysteine and selenocystine in synthetic glutaredoxins with a [C/U]XX[C/U] motifKolarich, D.Weber, A.Turecek, P.L.Schwarz, H.P.Altmann, F.Proteomics 6, 3369-3380, 2006Comprehensive glyco-proteomic analysis of human alpha1-antitrypsin and its charge isoforms.DOI:10.1002/pmic.200500751PMID:16622833mass spectrometric determination of cysteine disulfide bonded to peptidyl cysteineMost extracellular proteins appear to undergo normal disulfide bond formation spontaneously during secretion. Some proteins require assistance from chaperonins and protein disulfide-isomerase.Binding of free cysteine extracellularly is probably not enzymatically catalyzed.The experimental redox potential of cystine in synthetic glutaredoxin 3 is -194 mV. See RESID:AA0358 and RESID:AA0437.The formula and records labeled "CYS2" refers to cystine produced as a disulfide cross-link of two peptidyl cysteine residues.The formula and records labeled "CYS1" refers to cystine produced as a peptidyl cysteine residue disulfide bonded to a free cysteine.protein-disulfide reductase (EC 1.8.1.8)protein disulfide-isomerase (EC 5.3.4.1)autocatalyticC, Ccross-link 2GO:0018316PSI-MOD:00034CPSI-MOD:00765*redox-active centerdisulfide bondACT_SITE Redox-activeDISULFIDDISULFID InterchainDISULFID Interchain (between ... chains)DISULFID Interchain (with C-...)DISULFID Redox-activeMOD_RES S-cysteinyl cysteineAA002631-Mar-199531-Mar-199525-Feb-2011(2S,3R)-3-hydroxyasparagine(2S,3R)-2,4-diamino-3-hydroxy-4-oxobutanoic acid2-azanyl-3-hydroxy-4-butanediamic acidL-erythro-beta-hydroxyasparagine(2S,3R)-2-amino-3-hydroxy-4-butanediamic acidCAS:20790-74-3PDBHET:AHBC 4 H 6 N 2 O 3130.10130.037842C 0 H 0 N 0 O 116.0015.994915Stenflo, J.Lundwall, A.Dahlbäck, B.Proc. Natl. Acad. Sci. U.S.A. 84, 368-372, 1987beta-Hydroxyasparagine in domains homologous to the epidermal growth factor precursor in vitamin K-dependent protein S.DOI:10.1073/pnas.84.2.368PMID:2948188chromatographic detection; the stereochemistry was determined by hydrolysis and comparison with "erythro-beta-hydroxyaspartic acid"Arlaud, G.J.Van Dorsselaer, A.Bell, A.Mancini, M.Aude, C.Gagnon, J.FEBS Lett. 222, 129-134, 1987Identification of erythro-beta-hydroxyasparagine in the EGF-like domain of human C1r.DOI:10.1016/0014-5793(87)80205-3PMID:2820791mass spectrometric detection; the stereochemistry was determined by hydrolysis and comparison with "erythro-beta-hydroxyaspartic acid"Feinberg, H.Uitdehaag, J.C.Davies, J.M.Wallis, R.Drickamer, K.Weis, W.I.EMBO J. 22, 2348-2359, 2003Crystal structure of the CUB1-EGF-CUB2 region of mannose-binding protein associated serine protease-2.DOI:10.1093/emboj/cdg236PMID:12743029X-ray diffraction, 2.70 angstromsFeinberg, H.Uitdehaag, J.C.Davies, J.M.Wallis, R.Drickamer, K.Weis, W.I.submitted to the Protein Data Bank, January 2003Crystal structure of the CUB1-EGF-CUB2 region of MASP2 molecule: mannose-binding protein associated serine protease-2.PDB:1NT0X-ray diffraction, 2.70 angstromsThis diastereomeric form has been found in the EGF domain of many proteins. For the (2S,3S)-diastereomer, see RESID:AA0478.The PDB group code includes models with both the (2S,3R) and the (2S,3S) stereoconfiguration.The Enzyme Commission has not yet distinguished the different stereospecific enzyme activities.peptide-aspartate beta-dioxygenase (EC 1.14.11.16)NGO:0018376PSI-MOD:00035hydroxylationMOD_RES (3R)-3-hydroxyasparagineAA002731-Mar-199531-Mar-199531-May-2018(2S,3R)-3-hydroxyaspartic acid2-amino-3-hydroxysuccinic acid2-azanyl-3-hydroxybutanedioic acid3-hydroxyaspartic acidL-erythro-beta-hydroxyaspartic acid(2S,3R)-2-amino-3-hydroxybutanedioic acidCAS:17576CAS:7298-98-8ChEBI:17576PDBHET:BH2C 4 H 5 N 1 O 4131.09131.021858C 0 H 0 N 0 O 116.0015.994915Kornguth, M.L.Sallach, H.J.Arch. Biochem. Biophys. 91, 39-42, 1960(beta)-Hydroxyaspartic acid: synthesis and separation of its diastereoisomers.PMID:13753215chemical synthesis and diastereomeric separationDrakenberg, T.Fernlund, P.Roepstorff, P.Stenflo, J.Proc. Natl. Acad. Sci. U.S.A. 80, 1802-1806, 1983beta-Hydroxyaspartic acid in vitamin K-dependent protein C.DOI:10.1073/pnas.80.7.1802PMID:6572939mass spectrometric detection; the stereochemistry was determined by hydrolysis and comparison with "erythro-beta-hydroxyaspartic acid"McMullen, B.A.Fujikawa, K.Kisiel, W.Sasagawa, T.Howald, W.N.Kwa, E.Y.Weinstein, B.Biochemistry 22, 2875-2884, 1983Complete amino acid sequence of the light chain of human blood coagulation factor X: evidence for identification of residue 63 as beta-hydroxyaspartic acid.DOI:10.1021/bi00281a016PMID:6871167mass spectrometric and (1)H-NMR identificationKessler, H.Steuernagel, S.Will, M.Jung, G.Kellner, R.Gillessen, D.Kamiyama, T.Helv. Chim. Acta 71, 1924-1929, 1988The structure of the polycyclic nonadecapeptide Ro 09-0198.DOI:10.1002/hlca.19880710811Padmanabhan, K.Padmanabhan, K.P.Tulinsky, A.Park, C.H.Bode, W.Huber, R.Blankenship, D.T.Cardin, A.D.Kisiel, W.J. Mol. Biol. 232, 947-966, 1993Structure of human des(1-45) factor Xa at 2.2 angstroms resolution.DOI:10.1006/jmbi.1993.1441PMID:8355279X-ray diffraction, 2.2 angstromsThis diastereomeric form has been found in the EGF domain of many proteins. For the (2S,3S)-diastereomer, see RESID:AA0579.The Enzyme Commission has not yet distinguished the different stereospecific enzyme activities.peptide-aspartate beta-dioxygenase (EC 1.14.11.16)DGO:0019715PSI-MOD:00036hydroxylationMOD_RES (3R)-3-hydroxyaspartateAA002831-Mar-199531-Mar-199531-Mar-2012(2S,5R)-5-hydroxylysine2,6-bisazanyl-5-hydroxyhexanoic acid2,6-diamino-2,3,4,6-tetradeoxyhexonic acidalpha,epsilon-diamino-delta-hydroxycaproic acidL-erythro-delta-hydroxylysine(2S,5R)-2,6-diamino-5-hydroxyhexanoic acidCAS:1190-94-9ChEBI:18040PDBHET:LYZC 6 H 12 N 2 O 2144.17144.089878C 0 H 0 N 0 O 116.0015.994915Bergstrom, S.Lindstedt, S.Acta Chem. Scand. 5, 157-167, 1951On the isolation and structure of hydroxylysine.DOI:10.3891/acta.chem.scand.05-0157structure of collagen derived compound established as 5-hydroxylysineWitkop, B.Experientia 12, 372-374, 1956The application of Hudson's lactone rule to gamma- and delta-hydroxyamino acids and the question of the configuration of delta-hydroxy-L-lysine from collagen.DOI:10.1007/BF02157272PMID:13375629determination of the relative configurations for the two chiral centers of collagen derived 5-hydroxylysineSpiess, J.Noe, B.D.Proc. Natl. Acad. Sci. U.S.A. 82, 277-281, 1985Processing of an anglerfish somatostatin precursor to a hydroxylysine-containing somatostatin 28.DOI:10.1073/pnas.82.2.277PMID:2857489chromatographic detection of PTH derivativeTeshima, T.Ueki, Y.Nakai, T.Shiba, T.Tetrahedron 42, 829-834, 1986Structure determination of lepidopteran, self-defense substance produced by silkworm.DOI:10.1016/S0040-4020(01)87488-3chromatographic detectionDoust, A.B.Marai, C.N.J.Harrop, S.J.Wilk, K.E.Curmi, P.M.G.Scholes, G.D.J. Mol. Biol. 344, 135-153, 2004Developing a structure-function model for the cryptophyte phycoerythrin 545 using ultrahigh resolution crystallography and ultrafast laser spectroscopy.DOI:10.1016/j.jmb.2004.09.044PMID:15504407X-ray diffraction, 0.97 angstromsDoust, A.B.Marai, C.N.J.Harrop, S.J.Wilk, K.E.Curmi, P.M.G.Scholes, G.D.submitted to the Protein Data Bank, September 2004High resolution crystal structure of phycoerythrin 545 from the marine cryptophyte Rhodomonas CS24.PDB:1XG0X-ray diffraction, 0.97 angstroms; the stereoisomer is (2S,5R)Aguilar, M.B.Lopez-Vera, E.Ortiz, E.Becerril, B.Possani, L.D.Olivera, B.M.Heimer de la Cotera, E.P.Biochemistry 44, 11130-11136, 2005A novel conotoxin from Conus delessertii with posttranslationally modified lysine residues.DOI:10.1021/bi050518lPMID:16101297mass spectrometric detection; chromatographic identification of the PTH derivative (2S,5R) stereoisomerMyllylä, R.Wang, C.Heikkinen, J.Juffer, A.Lampela, O.Risteli, M.Ruotsalainen, H.Salo, A.Sipilä, L.J. Cell. Physiol. 212, 323-329, 2007Expanding the lysyl hydroxylase toolbox: new insights into the localization and activities of lysyl hydroxylase 3 (LH3).DOI:10.1002/jcp.21036PMID:17516569lysyl hydroxylase 3 (LH3) also possesses galactosyl transferase and glucosyl transferase activitiesSome forms of lysyl hydroxylase are multifunctional and possess both galactosyltransferase (EC 2.4.1.50) and glucosyltransferase (EC 2.4.1.66) activities.procollagen-lysine 5-dioxygenase (EC 1.14.11.4)Kincidental to RESID:AA0153GO:0018395PSI-MOD:00037hydroxylationMOD_RES (2S,5R)-5-hydroxylysineMOD_RES 5-hydroxylysinethis UniProt feature is used when the stereochemistry has not been determinedAA002931-Mar-199531-Mar-199531-May-20183-hydroxy-L-proline3-trans-hydroxy-L-prolinebeta-hydroxypyrrolidine-alpha-carboxylic acidL-threo-3-hydroxyproline(2S,3S)-3-hydroxypyrrolidine-2-carboxylic acidCAS:4298-08-2ChEBI:85428PDBHET:HY3C 5 H 7 N 1 O 2113.12113.047678C 0 H 0 N 0 O 116.0015.994915Ogle, J.D.Arlinghaus, R.B.Logan, M.A.J. Biol. Chem. 237, 3667-3673, 19623-Hydroxyproline, a new amino acid of collagen.PMID:13939597mass spectrometric and chemical characterization; the spelling of Logan in the PubMed citation is correctedFietzek, P.P.Rexrodt, F.W.Wendt, P.Stark, M.Kuehn, K.Eur. J. Biochem. 30, 163-168, 1972The covalent structure of collagen. Amino acid sequence of peptide alpha1-CB6-C2.DOI:10.1111/j.1432-1033.1972.tb02083.xPMID:4343807chromatographic detectionWaite, J.H.J. Comp. Physiol. B, Biochem. Syst. Environ. Physiol. 156, 491-496, 1986Mussel glue from Mytilus californianus Conrad: a comparative study.DOI:10.1007/BF00691034PMID:3734192chromatographic detectionKassel, D.B.Biemann, K.Anal. Chem. 62, 1691-1695, 1990Differentiation of hydroxyproline isomers and isobars in peptides by tandem mass spectrometry.DOI:10.1021/ac00214a032PMID:2400108attempts to distinguish from isobaric 4-hydroxyproline (see RESID:AA0030) with tandem mass spectrometryEyre, D.R.Weis, M.Hudson, D.M.Wu, J.J.Kim, L.J. Biol. Chem. 286, 7732-7736, 2011A novel 3-hydroxyproline (3Hyp)-rich motif marks the triple-helical C terminus of tendon type I collagen.DOI:10.1074/jbc.C110.195768PMID:21239503mass spectrometric and chemical characterizationLoenarz, C.Sekirnik, R.Thalhammer, A.Ge, W.Spivakovsky, E.Mackeen, M.M.McDonough, M.A.Cockman, M.E.Kessler, B.M.Ratcliffe, P.J.Wolf, A.Schofield, C.J.Proc. Natl. Acad. Sci. U.S.A. 111, 4019-4024, 2014Hydroxylation of the eukaryotic ribosomal decoding center affects termination efficiency.DOI:10.1073/pnas.1311750111PMID:24550462modification of Saccharomyces cerevisiae ribosomal protein S23 proline-64 to trans-3-hydroxyproline improves translation accuracyKatz, M.J.Acevedo, J.M.Loenarz, C.Galagovsky, D.Liu-Yi, P.Pérez-Pepe, M.Thalhammer, A.Sekirnik, R.Ge, W.Melani, M.Thomas, M.G.Simonetta, S.Boccaccio, G.L.Schofield, C.J.Cockman, M.E.Ratcliffe, P.J.Wappner, P.Proc. Natl. Acad. Sci. U.S.A. 111, 4025-4030, 2014Sudestada1, a Drosophila ribosomal prolyl-hydroxylase required for mRNA translation, cell homeostasis, and organ growth.DOI:10.1073/pnas.1314485111PMID:24550463modification of Drosophila melanogaster ribosomal protein S23 proline-62 to hydroxyproline; the regioisomer and the stereoisomer were not determinedSingleton, R.S.Liu-Yi, P.Formenti, F.Ge, W.Sekirnik, R.Fischer, R.Adam, J.Pollard, P.J.Wolf, A.Thalhammer, A.Loenarz, C.Flashman, E.Yamamoto, A.Coleman, M.L.Kessler, B.M.Wappner, P.Schofield, C.J.Ratcliffe, P.J.Cockman, M.E.Proc. Natl. Acad. Sci. U.S.A. 111, 4031-4036, 2014OGFOD1 catalyzes prolyl hydroxylation of RPS23 and is involved in translation control and stress granule formation.DOI:10.1073/pnas.1314482111PMID:24550447modification of human ribosomal protein S23 proline-62 to hydroxyproline; the regioisomer and the stereoisomer were not determinedThere are at least three different genes for procollagen-proline 3-dioxygenase in mammals with different specificities and patterns of tissue expression. Usually proline 3-hydroxylation occurs at the second position of specific GPP sequences in collagen chains and is preceded by proline 4-hydroxylation of the proline in the third position. See RESID:AA0030.Eukaryotic ribosomal protein S23 can be hydroxylated at a specific proline and the modification affects translation accuracy and termination efficiency.procollagen-proline 3-dioxygenase (EC 1.14.11.7)[ribosomal protein S23]-proline 3-dioxygenase, OGFOD1, Sudestada1, Tpa1p, (EC 1.14.11.-)Pincidental to RESID:AA0030GO:0018400PSI-MOD:00038hydroxylationMOD_RES 3-hydroxyprolineMOD_RES Hydroxyprolinethis UniProt feature is used when the isomeric structure has not been determinedAA003031-Mar-199531-Mar-199531-May-20184-hydroxy-L-proline4-hydroxyproline4-trans-hydroxy-L-prolinegamma-hydroxypyrrolidine-alpha-carboxylic acidL-threo-4-hydroxyproline(2S,4R)-4-hydroxypyrrolidine-2-carboxylic acidCAS:51-35-4ChEBI:61965PDBHET:HYPC 5 H 7 N 1 O 2113.12113.047678C 0 H 0 N 0 O 116.0015.994915Waite, J.H.J. Comp. Physiol. B, Biochem. Syst. Environ. Physiol. 156, 491-496, 1986Mussel glue from Mytilus californianus Conrad: a comparative study.DOI:10.1007/BF00691034PMID:3734192Kassel, D.B.Biemann, K.Anal. Chem. 62, 1691-1695, 1990Differentiation of hydroxyproline isomers and isobars in peptides by tandem mass spectrometry.DOI:10.1021/ac00214a032PMID:2400108attempts to distinguish from isobaric 3-hydroxyproline (see RESID:AA0029) with tandem mass spectrometryJaakkola, P.Mole, D.R.Tian, Y.M.Wilson, M.I.Gielbert, J.Gaskell, S.J.von Kriegsheim, A.Hebestreit, H.F.Mukherji, M.Schofield, C.J.Maxwell, P.H.Pugh, C.W.Ratcliffe, P.J.Science 292, 468-472, 2001Targeting of HIF-alpha to the von Hippel-Lindau ubiquitylation complex by O2-regulated prolyl hydroxylation.DOI:10.1126/science.1059796PMID:11292861mass spectrometric detection; the stereochemistry was not determined; in this protein this is a regulatory modification, apparently competitive with hydoxylation of an asparagine in another domain (see RESID:AA0026)Min, J.H.Yang, H.Ivan, M.Gertler, F.Kaelin Jr., W.G.Pavletich, N.P.Science 296, 1886-1889, 2002Structure of an HIF-1alpha-pVHL complex: hydroxyproline recognition in signaling.DOI:10.1126/science.1073440PMID:12004076X-ray diffraction, 1.85 angstroms; the bound peptide containing (2S,4R)-4-hydroxyproline is syntheticMin, J.-H.Yang, H.Ivan, M.Gertler, F.Kaelin, W. G. Jr.Pavletich, N.P.submitted to the Protein Data Bank, April 2002Structure of a HIF-1A-PVHL-ElonginB-ElonginC Complex.PDB:1LM8X-ray diffraction, 1.85 angstromsprocollagen-proline 4-dioxygenase (EC 1.14.11.2)hypoxia-inducible factor-proline dioxygenase (EC 1.14.11.29)PGO:0018401PSI-MOD:00039hydroxylationMOD_RES 4-hydroxyprolineMOD_RES Hydroxyprolinethis UniProt feature is used when the isomeric structure has not been determinedAA003131-Mar-199531-Mar-199530-Sep-20112-pyrrolidone-5-carboxylic acid2-oxopyrrolidine-5-carboxylic acid5-oxoproline5-oxopyrrolidine-2-carboxylic acid5-pyrrolidone-2-carboxylic acidPCApyroglutamic acid(2S)-5-oxo-2-pyrrolidinecarboxylic acidCAS:98-79-3ChEBI:30652PDBHET:PCAC 5 H 6 N 1 O 2112.11112.039853C 0 H -2 N 0 O -1-18.02-18.010565C 0 H -3 N -1 O 0-17.03-17.026549Sanger, F.Thompson, E.O.Kitai, R.Biochem. J. 59, 509-518, 1955The amide groups of insulin.PMID:14363129observes that an N-terminal glutaminyl residue tends to cyclize to a pyrrolidone carboxylic acid under acid conditionsPodell, D.N.Abraham, G.N.Biochem. Biophys. Res. Commun. 81, 176-185, 1978A technique for the removal of pyroglutamic acid from the amino terminus of proteins using calf liver pyroglutamate amino peptidase.DOI:10.1016/0006-291X(78)91646-7PMID:26343Fischer, W.H.Spiess, J.Proc. Natl. Acad. Sci. U.S.A. 84, 3628-3632, 1987Identification of a mammalian glutaminyl cyclase converting glutaminyl into pyroglutamyl peptides.DOI:10.1073/pnas.84.11.3628PMID:3473473Betancourt, L.Takao, T.Hernandez, L.Padron, G.Shimonishi, Y.J. Mass Spectrom. 34, 169-174, 1999Structural characterization of Acetobacter diazotropicus levansucrase by matrix-assisted laser desorption/ionization mass spectrometry: identification of an N-terminal blocking group and a free-thiol cysteine residue.DOI:10.1002/(SICI)1096-9888(199903)34:3<169::AID-JMS780>3.0.CO;2-4PMID:10214721mass spectrometric detectionGarden, R.W.Moroz, T.P.Gleeson, J.M.Floyd, P.D.Li, L.Rubakhin, S.S.Sweedler, J.V.J. Neurochem. 72, 676-681, 1999Formation of N-pyroglutamyl peptides from N-Glu and N-Gln precursors in Aplysia neurons.PMID:9930740mass spectrometric detection; the source was peptide in single neuron cells; partial conversion of N-terminal glutamate was observed and appeared to be dependent on a temperature sensitive factorThis modification can form artifactually from amino-terminal glutamine under mildly acid conditions, and from amino-terminal glutamic acid under very acid or anhydrous conditions.The presumed enzyme in Aplysia neurons has not been characterized. The reaction probably requires concomitant hydrolysis of a compound such as ATP.glutaminyl-peptide cyclotransferase (EC 2.3.2.5)QGlpamino-terminalGO:0017186PSI-MOD:00040EGlpamino-terminalPSI-MOD:00420blocked amino endpyroglutamic acidMOD_RES Pyrrolidone carboxylic acidMOD_RES Pyrrolidone carboxylic acid (Glu)AA003231-Mar-199531-Mar-199531-May-2018L-gamma-carboxyglutamic acid(3S)-3-azanylpropane-1,1,3-tricarboxylic acid1-carboxyglutamic acid [misnomer]3-amino-1,1,3-propanetricarboxylic acid3-azanylpropane-1,1,3-tricarboxylic acid4-carboxyglutamic acid(3S)-3-aminopropane-1,1,3-tricarboxylic acidCAS:53861-57-7ChEBI:61939PDBHET:CGUC 6 H 7 N 1 O 5173.12173.032422C 1 H 0 N 0 O 244.0143.989829Stenflo, J.Fernlund, P.Egan, W.Roepstorff, P.Proc. Natl. Acad. Sci. U.S.A. 71, 2730-2733, 1974Vitamin K dependent modifications of glutamic acid residues in prothrombin.DOI:10.1073/pnas.71.7.2730PMID:4528109mass spectrometric and (1)H-NMR identificationHauschka, P.V.Henson, E.B.Gallop, P.M.Anal. Biochem. 108, 57-63, 1980Quantitative analysis and comparative decarboxylation of aminomalonic acid, beta-carboxyaspartic acid, and gamma-carboxyglutamic acid.DOI:10.1016/0003-2697(80)90691-0PMID:7457858Smalley, D.M.Preusch, P.C.Anal. Biochem. 172, 241-247, 1988Analysis of gamma-carboxyglutamic acid by reverse phase HPLC of its phenylthiocarbamyl derivative.DOI:10.1016/0003-2697(88)90438-1PMID:3263814Cairns, J.R.Williamson, M.K.Price, P.A.Anal. Biochem. 199, 93-97, 1991Direct identification of gamma-carboxyglutamic acid in the sequencing of vitamin K-dependent proteins.DOI:10.1016/0003-2697(91)90274-WPMID:1807167Nishimoto, S.K.Zhao, J.Dass, C.Anal. Biochem. 216, 159-164, 1994Isolation and characterization of the reaction product of 4-diazobenzenesulfonic acid and gamma-carboxyglutamic acid: modification of the assay for measurement of beta-carboxyaspartic acid.DOI:10.1006/abio.1994.1020PMID:8135347colorimetric detectionMorris, D.P.Stevens, R.D.Wright, D.J.Stafford, D.W.J. Biol. 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Biol. Chem. 269, 28084-28090, 1994The catalytic role of Cys(124) in the dual specificity phosphatase VHR.PMID:7961745Sun, F.Ding, Y.Ji, Q.Liang, Z.Deng, X.Wong, C.C.Yi, C.Zhang, L.Xie, S.Alvarez, S.Hicks, L.M.Luo, C.Jiang, H.Lan, L.He, C.Proc. Natl. Acad. Sci. 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Biochem. 268, 521-530, 2001The ptsH gene from Bacillus thuringiensis israelensis. Characterization of a new phosphorylation site on the protein HPr.DOI:10.1046/j.1432-1327.2001.01878PMID:11168390alternate tele-phosphorylation of a histidine, normally pros-phosphorylated, inactivates an enzyme; methods for distinguishing the isomersIn the older biochemical literature this is usually called histidine-3-phosphate. See also RESID:AA0036.The crystallographic designation for the substituted nitrogen is epsilon-2, E2.protein-histidine tele-kinase (EC 2.7.3.12)HGO:0018106GO:0018327PSI-MOD:00044phosphohistidinephosphoproteinACT_SITE Tele-phosphohistidine intermediateMOD_RES Tele-phosphohistidineACT_SITE Phosphohistidine intermediatethis UniProt feature is used when the isomeric structure has not been determinedMOD_RES Phosphohistidinethis UniProt feature is used when the isomeric structure has not been determinedAA003631-Mar-199504-May-200131-May-20183'-phospho-L-histidine2-azanyl-3-(3-phosphono-3H-imidazol-4-yl)propanoic acidhistidine-1-phosphate [misnomer]histidine-N(delta)-phosphatehistidine-N3'-phosphateN(pi)-phosphohistidineN3-phosphonohistidineND1-phosphonohistidinepros-phosphohistidine(2S)-2-amino-3-(3-phosphono-3H-imidazol-4-yl)propanoic acidCAS:5789-15-1ChEBI:64936PDBHET:HIPC 6 H 8 N 3 O 4 P 1217.12217.025242C 0 H 1 N 0 O 3 P 179.9879.966331Hultquist, D.E.Moyer, R.W.Boyer, P.D.Biochemistry 5, 322-331, 1966The preparation and characterization of 1-phosphohistidine and 3-phosphohistidine.DOI:10.1021/bi00865a041PMID:5938947the diagram page 330 indicates that what the authors would call "1-phosphohistidine" corresponds to pros-phosphohistidineHultquist, D.E.Biochim. 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See also RESID:AA0035.The crystallographic designation for the substituted nitrogen is delta-1, D1.protein-histidine pros-kinase (EC 2.7.3.11)HGO:0018106GO:0018328PSI-MOD:00045phosphohistidinephosphoproteinACT_SITE Pros-phosphohistidine intermediateMOD_RES Pros-phosphohistidineACT_SITE Phosphohistidine intermediatethis UniProt feature is used when the isomeric structure has not been determinedMOD_RES Phosphohistidinethis UniProt feature is used when the isomeric structure has not been determinedAA003731-Mar-199531-Mar-199531-Dec-2011O-phospho-L-serine2-amino-3-hydroxypropanoic acid 3-phosphate2-azanyl-3-(phosphonooxy)propanoic acidO-phosphonoserineO3-phosphoserineserine phosphate ester(2S)-2-amino-3-(phosphonooxy)propanoic acidCAS:407-41-0ChEBI:45522PDBHET:SEPC 3 H 6 N 1 O 5 P 1167.06166.998359C 0 H 1 N 0 O 3 P 179.9879.966331Lipmann, F.A.Levene, P.A.J. Biol. 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Chem. 279, 45919-45925, 2004Crystal structure of ADP-ribosylated ribosomal translocase from Saccharomyces cerevisiae.DOI:10.1074/jbc.M406218200PMID:15316019X-ray diffraction, 2.6 angstroms; resolution of second chiral centerJorgensen, R.Yates, S.P.Nilsson, J.Prentice, G.A.Teal, D.J.Merrill, A.R.Andersen, G.R.submitted to the Protein Data Bank, July 2004Crystal structure of ADP-ribosylated ribosomal translocase from Saccharomyces cerevisiae.PDB:1U2RX-ray diffraction, 2.6 angstromsZhang, Y.Zhu, X.Torelli, A.T.Lee, M.Dzikovski, B.Koralewski, R.M.Wang, E.Freed, J.Krebs, C.Ealick, S.E.Lin, H.Nature 465, 891-896, 2010Diphthamide biosynthesis requires an organic radical generated by an iron-sulphur enzyme.DOI:10.1038/nature09138PMID:20559380Dong, M.Kathiresan, V.Fenwick, M.K.Torelli, A.T.Zhang, Y.Caranto, J.D.Dzikovski, B.Sharma, A.Lancaster, K.M.Freed, J.H.Ealick, S.E.Hoffman, B.M.Lin, H.Science 359, 1247-1250, 2018Organometallic and radical intermediates reveal mechanism of diphthamide biosynthesis.DOI:10.1126/science.aao6595PMID:29590073electron paramagnetic resonance spectroscopy; electron nuclear double-resonance spectroscopyDiphthamide appears to occur uniquely in translation elongation factor eEF-2.2-(3-amino-3-carboxypropyl)histidine synthaseS-adenosyl-L-methionine:L-histidine-[translation elongation factor 2] 2-[(3S)-3-amino-3-carboxypropyl]transferase (EC 2.5.1.108)diphthine synthaseS-adenosyl-L-methionine:2-[(3S)-3-carboxy-3-aminopropyl]-L-histidine-[translation elongation factor 2] methyltransferase (diphthine-[translation elongation factor 2]-forming) (EC 2.1.1.98)diphthine--ammonia ligasediphthine-[translation elongation factor 2]:ammonia ligase (AMP-forming) (EC 6.3.1.14)HGO:0006471GO:0017183PSI-MOD:00049diphthamideMOD_RES DiphthamideAA004131-Mar-199531-Mar-199531-May-2018N-acetyl-L-alanine2-(acetylamino)propanoic acid2-(acetylazanyl)propanoic acidacetylalanine(2S)-2-(acetamido)propanoic acidCAS:97-69-8ChEBI:61920PDBHET:ACEPDBHET:AYAC 5 H 8 N 1 O 2114.12114.055504C 2 H 2 N 0 O 142.0442.010565Coffee, C.J.Bradshaw, R.A.J. Biol. Chem. 248, 3305-3312, 1973Carp muscle calcium-binding protein. I. Characterization of the tryptic peptides and the complete amino acid sequence of component B.PMID:4700462chemical characterization and mass spectrometric identification; the first page number in the PubMed citation is correctedKretsinger, R.H.Nockolds, C.E.J. Biol. Chem. 248, 3313-3326, 1973Carp muscle calcium-binding protein. II. Structure determination and general description.PMID:4700463X-ray diffraction, 1.85 angstromsWittmann-Liebold, B.Greuer, B.FEBS Lett. 95, 91-98, 1978The primary structure of protein S5 from the small subunit of the Escherichia coli ribosome.DOI:10.1016/0014-5793(78)80059-3PMID:363452chemical characterization and mass spectrometric identificationSwain, A.L.Kretsinger, R.H.Amma, E.L.submitted to the Protein Data Bank, January 1990Restrained least squares refinement of native (calcium) and cadmium-substituted carp parvalbumin using X-ray crystallographic data at 1.6-A resolution.PDB:5CPVX-ray diffraction, 1.6 angstromsN-terminal amino-acid Nα-acetyltransferase NatAacetyl-CoA:ribosomal-protein-L-alanine N-acetyltransferase (EC 2.3.1.128)acetyl-CoA:N-terminal-Gly/Ala/Ser/Val/Cys/Thr-[protein] Nα-acetyltransferase (EC 2.3.1.256)Aamino-terminalGO:0017189PSI-MOD:00050acetylated amino endMOD_RES N-acetylalanineAA004231-Mar-199531-Mar-199531-May-2018N-acetyl-L-aspartic acid2-(acetylamino)butanedioic acid2-(acetylazanyl)butanedioic acidacetylaspartic acid(2S)-2-(acetamido)butanedioic acidCAS:997-55-7ChEBI:21547PDBHET:ACEC 6 H 8 N 1 O 4158.13158.045333C 2 H 2 N 0 O 142.0442.010565Kabsch, W.Mannherz, H.G.Suck, D.Pai, E.Holmes, K.C.submitted to the Protein Data Bank, March 1991Atomic structure of the actin: DNase I complex.PDB:1ATNKabsch, W.Mannherz, H.G.Suck, D.Pai, E.F.Holmes, K.C.Nature 347, 37-44, 1990Atomic structure of the actin: DNase I complex.DOI:10.1038/347037a0PMID:2395459X-ray diffraction, 2.8 angstromsMartin, P.Edwards, B.submitted to the Protein Data Bank, April 1992The structure of residues 7-16 of the Aalpha-chain of human fibrinogen bound to bovine thrombin at 2.3-A resolution.PDB:1BBRMartin, P.D.Robertson, W.Turk, D.Huber, R.Bode, W.Edwards, B.F.P.J. Biol. Chem. 267, 7911-7920, 1992The structure of residues 7-16 of the Aalpha-chain of human fibrinogen bound to bovine thrombin at 2.3-angstroms resolution.PMID:1560020X-ray diffraction, 2.3 angstromsDamino-terminalGO:0017190PSI-MOD:00051acetylated amino endMOD_RES N-acetylaspartateAA004331-Mar-199531-Mar-199531-May-2018N-acetyl-L-cysteine2-acetylamino-3-mercaptopropanoic acid2-acetylamino-3-sulfanylpropanoic acid2-acetylazanyl-3-sulfanylpropanoic acidN-acetylcysteine(2R)-2-acetamido-3-sulfanylpropanoic acidCAS:616-91-1ChEBI:28939PDBHET:ACEPDBHET:SC2C 5 H 8 N 1 O 2 S 1146.18146.027574C 2 H 2 N 0 O 1 S 042.0442.010565Grand, R.J.Perry, S.V.Biochem. J. 211, 267-272, 1983Preparation of the alkali and P light chains of chicken gizzard myosin. Amino acid sequence of the alkali light chain.PMID:6870825(1)H-NMR identificationStrauch, A.R.Rubenstein, P.A.J. Biol. Chem. 259, 7224-7229, 1984A vascular smooth muscle alpha-isoactin biosynthetic intermediate in BC3H1 cells. Identification of acetylcysteine at the NH2 terminus.PMID:6725286radioisotope labeling; identification of transient modificationHasegawa, Y.Ueda, Y.Watanabe, M.Morita, F.J. Biochem. 111, 798-803, 1992Studies on amino acid sequences of two isoforms of 17-kDa essential light chain of smooth muscle myosin from porcine aorta media.PMID:1500421mass spectrometric identificationSee also RESID:AA0044.N-terminal amino-acid Nα-acetyltransferase NatAacetyl-CoA:N-terminal-Gly/Ala/Ser/Val/Cys/Thr-[protein] Nα-acetyltransferase (EC 2.3.1.256)Camino-terminalincidental to RESID:AA0223GO:0018275PSI-MOD:00052PSI-MOD:00897acetylated amino endMOD_RES N-acetylcysteineAA004431-Mar-199531-Mar-199531-May-2018N-acetyl-L-glutamic acid2-(acetylamino)pentanedioic acid2-(acetylazanyl)pentanedioic acidacetylglutamic acid(2S)-2-(acetamido)pentanedioic acidCAS:1188-37-0ChEBI:17533PDBHET:ACEC 7 H 10 N 1 O 4172.16172.060983C 2 H 2 N 0 O 142.0442.010565Strauch, A.R.Rubenstein, P.A.J. Biol. Chem. 259, 7224-7229, 1984A vascular smooth muscle alpha-isoactin biosynthetic intermediate in BC3H1 cells. Identification of acetylcysteine at the NH2 terminus.PMID:6725286identification after a transient primary acetylationHill, C.P.Anderson, D.H.Wesson, L.DeGrado, W.F.Eisenberg, D.submitted to the Protein Data Bank, July 1990Crystal structure of alpha1: implications for protein design.PDB:1AL1synthetic peptide; X-ray diffraction, 2.7 angstromsEamino-terminalincidental to RESID:AA0043GO:0018002PSI-MOD:00053acetylated amino endMOD_RES N-acetylglutamateAA004531-Mar-199531-Mar-199531-Dec-2011N-acetyl-L-glutamine2-acetylamino-5-amino-5-oxopentanoic acid2-acetylamino-5-pentanediamic acid2-acetylazanyl-5-azanyl-5-oxopentanoic acidacetylglutamine(2S)-2-acetamido-5-pentanediamic acidCAS:2490-97-3ChEBI:21553PDBHET:ACEC 7 H 11 N 2 O 3171.18171.076967C 2 H 2 N 0 O 142.0442.010565Edmundson, A.B.Harris, D.L.Fan, Z.C.Guddat, L.W.submitted to the Protein Data Bank, February 1993Principles and pitfalls in designing site-directed peptide ligands.PDB:1MCCsynthetic peptide; X-ray diffraction, 2.7 angstromsThe occurrence of this modification has not been confirmed. Formerly, its annotation in sequence databases was due to either the misidentification of 2-pyrrolidone-5-carboxylic acid, or inappropriate homolog comparisons when proteolytic modification was more probable.Qamino-terminalGO:0017192PSI-MOD:00054acetylated amino endNot availablethis dubious modification is not currently annotated in UniProt featuresAA004631-Mar-199531-Mar-199531-May-2018N-acetylglycine(acetylamino)acetic acid(acetylazanyl)ethanoic acid2-(acetylamino)ethanoic acidaceturic acid2-(acetamido)ethanoic acidCAS:543-24-8ChEBI:61888PDBHET:ACEC 4 H 6 N 1 O 2100.10100.039853C 2 H 2 N 0 O 142.0442.010565Luo, Y.Brayer, G.D.submitted to the Protein Data Bank, August 1994High-resolution three-dimensional structure of horse heart cytochrome c.PDB:1HRCX-ray diffraction, 1.9 angstromsDickerson, R.E.Takano, T.Eisenberg, D.Kallai, O.B.Samson, L.Cooper, A.Margoliash, E.J. Biol. Chem. 246, 1511-1535, 1971Ferricytochrome c. I. General features of the horse and bonito proteins at 2.8 A resolution.PMID:5545094X-ray diffraction, 2.8 angstromsTsunasawa, S.Narita, K.J. Biochem. 92, 607-613, 1982Micro-identification of amino-terminal acetylamino acids in proteins.PMID:6754709Palmiter, R.D.Gagnon, J.Walsh, K.A.Proc. Natl. Acad. Sci. U.S.A. 75, 94-98, 1978Ovalbumin: a secreted protein without a transient hydrophobic leader sequence.DOI:10.1073/pnas.75.1.94PMID:272676biosynthesisN-terminal amino-acid Nα-acetyltransferase NatAacetyl-CoA:N-terminal-Gly/Ala/Ser/Val/Cys/Thr-[protein] Nα-acetyltransferase (EC 2.3.1.256)Gamino-terminalGO:0017193PSI-MOD:00055acetylated amino endMOD_RES N-acetylglycineAA004731-Mar-199531-Mar-200131-Dec-2011N-acetyl-L-isoleucine2-acetylamino-3-methylpentanoic acid2-acetylazanyl-3-methylpentanoic acidacetylisoleucine(2S,3S)-2-acetamido-3-methylpentanoic acidCAS:3077-46-1ChEBI:21555C 8 H 14 N 1 O 2156.20156.102454C 2 H 2 N 0 O 142.0442.010565Gowda, L.R.Savithri, H.S.Rao, D.R.J. Biol. Chem. 269, 18789-18793, 1994The complete primary structure of a unique mannose/glucose-specific lectin from field bean (Dolichos lab lab).PMID:8034631the authors say a chain is blocked but do not show that it is acetylatedThe occurrence of this modification has not been confirmed.Iamino-terminalGO:0017194PSI-MOD:00056acetylated amino endNot availablethis dubious modification is not currently annotated in UniProt featuresAA004831-Mar-199531-Mar-199525-Feb-2011N2-acetyl-L-lysine2-acetylamino-6-aminohexanoic acid2-acetylazanyl-6-azanylhexanoic acidN2-acetyllysine(2S)-2-acetamido-6-aminohexanoic acidCAS:1946-82-3C 8 H 15 N 2 O 2171.22171.113353C 2 H 2 N 0 O 142.0442.010565McInnes, C.Sonnichsen, F.D.Kay, C.M.Hodges, R.S.Sykes, B.D.submitted to the Protein Data Bank, August 1993NMR solution structure and flexibility of a peptide antigen representing the receptor binding domain of Pseudomonas aeruginosa.PDB:1PAJsynthetic peptide; (1)H-NMRThe occurrence of this modification has not been confirmed. The common peptide alpha-N-acetyltransferase does not acetylate basic residues.Kamino-terminalGO:0017195PSI-MOD:00057acetylated amino endNot availablethis dubious modification is not currently annotated in UniProt featuresAA004931-Mar-199531-Mar-199531-May-2018N-acetyl-L-methionine2-acetylamino-4-(methylsulfanyl)butanoic acid2-acetylamino-4-(methylthio)butanoic acid2-acetylazanyl-4-(methylsulfanyl)butanoic acidacetylmethioninemethionamine(2S)-2-acetamido-4-(methylsulfanyl)butanoic acidCAS:65-82-7ChEBI:21557PDBHET:ACEPDBHET:AMEC 7 H 12 N 1 O 2 S 1174.24174.058875C 2 H 2 N 0 O 1 S 042.0442.010565Huang, W.Y.Chirala, S.S.Wakil, S.J.Arch. Biochem. Biophys. 314, 45-49, 1994Amino-terminal blocking group and sequence of the animal fatty acid synthase.DOI:10.1006/abbi.1994.1410PMID:7944406chromatographic and chemical characterization; chemical synthesisScott, D.C.Monda, J.K.Bennett, E.J.Harper, J.W.Schulman, B.A.Science 334, 674-678, 2011N-terminal acetylation acts as an avidity enhancer within an interconnected multiprotein complex.DOI:10.1126/science.1209307PMID:21940857mass spectrometric identification; N-acetylmethionine is specifically recognized and required for NEDD8 transferAlthough appropriate, the keyword "thioether bond" normally does not appear for this amino acid.N-terminal methionine N(α)-acetyltransferase NatBacetyl-CoA:N-terminal Met-Asn/Gln/Asp/Glu-[protein] Met-N(α)-acetyltransferase (EC 2.3.1.225)N-terminal methionine N(α)-acetyltransferase NatCacetyl-CoA:N-terminal Met-Leu/Ile/Phe/Trp/Tyr-[protein] Met-N(α)-acetyltransferase (EC 2.3.1.226)N-terminal methionine N(α)-acetyltransferase NatEacetyl-CoA:N-terminal Met-Ala/Ser/Val/Thr/Lys/Leu/Phe/Tyr-[protein] Met-N(α)-acetyltransferase (EC 2.3.1.258)N-terminal methionine N(α)-acetyltransferase NatFacetyl-CoA:N-terminal Met-Lys/Ser/Val/Leu/Gln/Ile/Tyr/Thr-[transmembrane protein] Met-N(α)-acetyltransferase (EC 2.3.1.259)Mamino-terminalGO:0017196PSI-MOD:00058*thioether bondacetylated amino endMOD_RES N-acetylmethionineAA005031-Mar-199531-Mar-199531-Dec-2011N-acetyl-L-proline1-acetylprolineacetylprolineN-acetylproline(2S)-1-acetyl-2-pyrrolidinecarboxylic acidCAS:68-95-1ChEBI:21560PDBHET:ACEC 7 H 10 N 1 O 2140.16140.071154C 2 H 2 N 0 O 142.0442.010565Sielecki, A.R.James, M.N.G.submitted to the Protein Data Bank, May 1990Structures of product and inhibitor complexes of Streptomyces griseus protease A at 1.8 A resolution. A model for serine protease catalysis.PDB:3SGAX-ray diffraction, 1.8 angstromsLim, W.A.Richards, F.M.Fox, R.O.submitted to the Protein Data Bank, March 1995Structural determinants of peptide-binding orientation and of sequence specificity in SH3 domains.PDB:1SEMX-ray diffraction, 2.0 angstromsHoutz, R.L.Stults, J.T.Mulligan, R.M.Tolbert, N.E.Proc. Natl. Acad. Sci. U.S.A. 86, 1855-1859, 1989Post-translational modifications in the large subunit of ribulose bisphosphate carboxylase/oxygenase.DOI:10.1073/pnas.86.6.1855PMID:2928307mass spectrometric identificationPamino-terminalGO:0017197PSI-MOD:00059acetylated amino endMOD_RES N-acetylprolineAA005131-Mar-199531-Mar-199531-May-2018N-acetyl-L-serine2-acetylamino-3-hydroxypropanoic acid2-acetylazanyl-3-hydroxypropanoic acidN-acetylserine(2S)-2-acetamido-3-hydroxypropanoic acidCAS:16354-58-8ChEBI:45441PDBHET:ACEPDBHET:SACC 5 H 8 N 1 O 3130.12130.050418C 2 H 2 N 0 O 142.0442.010565Strickland, W.N.Strickland, M.S.de Groot, P.C.von Holt, C.Eur. J. Biochem. 109, 151-158, 1980The primary structure of histone H2A from the sperm cell of the sea urchin Parechinus angulosus.DOI:10.1111/j.1432-1033.1980.tb04779.xPMID:6997045N-acetylserine converted by N->O acyl shift to remove blockageWellner, D.Panneerselvam, C.Horecker, B.L.Proc. Natl. Acad. Sci. U.S.A. 87, 1947-1949, 1990Sequencing of peptides and proteins with blocked N-terminal amino acids: N-acetylserine or N-acetylthreonine.DOI:10.1073/pnas.87.5.1947PMID:2106685N-acetylserine converted by N->O acyl shift to remove blockageDeclercq, J.P.Tinant, B.Parello, J.Rambaud, J.J. Mol. Biol. 220, 1017-1039, 1991Ionic interactions with parvalbumins: crystal structure determination of pike 4.10 parvalbumin in four different ionic environments.DOI:10.1016/0022-2836(91)90369-HPMID:1880797X-ray diffraction, 1.65 angstromsDeclercq, J.P.Tinant, B.Parello, J.submitted to the Protein Data Bank, January 1995X-ray structure of a new crystal form of pike 4.10 beta parvalbumin.PDB:1PVBX-ray diffraction, 1.75 angstromsN-terminal amino-acid Nα-acetyltransferase NatAacetyl-CoA:N-terminal-Gly/Ala/Ser/Val/Cys/Thr-[protein] Nα-acetyltransferase (EC 2.3.1.256)N-terminal L-serine Nα-acetyltransferase NatDacetyl-CoA:N-terminal-L-seryl-[histone 4/2A] L-serine Nα-acetyltransferase (EC 2.3.1.257)Samino-terminalGO:0017198PSI-MOD:00060PSI-MOD:00648acetylated amino endMOD_RES N-acetylserineAA005231-Mar-199531-Mar-199531-May-2018N-acetyl-L-threonine2-acetylamino-3-hydroxybutanoic acid2-acetylazanyl-3-hydroxybutanoic acidN-acetylthreonineN-methylcarbonylthreonine(2S,3R)-2-acetamido-3-hydroxybutanoic acidCAS:17093-74-2ChEBI:45826PDBHET:ACEC 6 H 10 N 1 O 3144.15144.066068C 2 H 2 N 0 O 142.0442.010565Strickland, W.N.Strickland, M.S.de Groot, P.C.von Holt, C.Eur. J. Biochem. 109, 151-158, 1980The primary structure of histone H2A from the sperm cell of the sea urchin Parechinus angulosus.DOI:10.1111/j.1432-1033.1980.tb04779.xPMID:6997045N-acetylthreonine converted by N->O acyl shift to remove blockageWellner, D.Panneerselvam, C.Horecker, B.L.Proc. Natl. Acad. Sci. U.S.A. 87, 1947-1949, 1990Sequencing of peptides and proteins with blocked N-terminal amino acids: N-acetylserine or N-acetylthreonine.DOI:10.1073/pnas.87.5.1947PMID:2106685N-acetylthreonine converted by N->O acyl shift to remove blockageN-terminal amino-acid Nα-acetyltransferase NatAacetyl-CoA:N-terminal-Gly/Ala/Ser/Val/Cys/Thr-[protein] Nα-acetyltransferase (EC 2.3.1.256)Tamino-terminalGO:0017199PSI-MOD:00061acetylated amino endMOD_RES N-acetylthreonineAA005331-Mar-199531-Mar-199531-Dec-2011N-acetyl-L-tyrosine2-acetylamino-3-(4-hydoxyphenyl)propanoic acid2-acetylazanyl-3-(4-hydoxyphenyl)propanoic acidN-acetyltyrosine(2S)-2-acetamido-3-(4-hydoxyphenyl)propanoic acidCAS:537-55-3ChEBI:21563PDBHET:ACEC 11 H 12 N 1 O 3206.22206.081718C 2 H 2 N 0 O 142.0442.010565Smyth, D.G.Massey, D.E.Zakarian, S.Finnie, M.D.Nature 279, 252-254, 1979Endorphins are stored in biologically active and inactive forms: isolation of alpha-N-acetyl peptides.DOI:10.1038/279252a0PMID:440436mass spectrometric identificationKawauchi, H.Tubokawa, M.Muramoto, K.Biochem. Biophys. Res. Commun. 88, 1249-1254, 1979Isolation and primary structure of endorphin from salmon pituitary glands.DOI:10.1016/0006-291X(79)91114-8PMID:475783chromatographic identification of N-acetyl-O5'-dansyl-tyrosineLee, M.S.Gippert, G.P.Soman, K.V.Case, D.A.Wright, P.E.submitted to the Protein Data Bank, September 1989Three-dimensional solution structure of a single zinc finger DNA-binding domain.PDB:1ZNFsynthetic peptide; conformation by (1)H-NMRLee, M.S.Cavanagh, J.Wright, P.E.FEBS Lett. 254, 159-164, 1989Complete assignment of the (1)H NMR spectrum of a synthetic zinc finger from Xfin. Sequential resonance assignments and secondary structure.DOI:10.1016/0014-5793(89)81030-0PMID:2506074(1)H-NMR characterization, synthetic peptideTong, L.submitted to the Protein Data Bank, November 1995Human P56-Lck tyrosine kinase SH2 Domain in complex with the phosphotyrosyl peptide Ac-PTyr-Glu-Glu-Ile (PYEEI peptide).PDB:1LKKX-ray diffraction, 1.0 angstroms, synthetic peptideYamino-terminalGO:0018000PSI-MOD:00062acetylated amino endMOD_RES N-acetyltyrosineAA005431-Mar-199531-Mar-199531-May-2018N-acetyl-L-valine2-acetylamino-3-methylbutanoic acid2-acetylazanyl-3-methylbutanoic acidN-acetylvaline(2S)-2-acetamido-3-methylbutanoic acidCAS:96-81-1ChEBI:21565PDBHET:ACEC 7 H 12 N 1 O 2142.18142.086804C 2 H 2 N 0 O 142.0442.010565Medzihradszky, K.F.Gibson, B.W.Kaur, S.Yu, Z.H.Medzihradszky, D.Burlingame, A.L.Bass, N.M.Eur. J. Biochem. 203, 327-339, 1992The primary structure of fatty-acid-binding protein from nurse shark liver. Structural and evolutionary relationship to the mammalian fatty-acid-binding protein family.DOI:10.1111/j.1432-1033.1992.tb16553.xPMID:1735421mass spectrometric identificationN-terminal amino-acid Nα-acetyltransferase NatAacetyl-CoA:N-terminal-Gly/Ala/Ser/Val/Cys/Thr-[protein] Nα-acetyltransferase (EC 2.3.1.256)Vamino-terminalGO:0018001PSI-MOD:00063acetylated amino endMOD_RES N-acetylvalineAA005531-Mar-199531-Mar-199531-Dec-2011N6-acetyl-L-lysine6-acetylamino-2-aminohexanoic acid6-acetylazanyl-2-aminohexanoic acidepsilon-acetyllysineN(zeta)-acetyllysine(2S)-6-acetamido-2-aminohexanoic acidCAS:692-04-6ChEBI:61930PDBHET:ALYC 8 H 14 N 2 O 2170.21170.105528C 2 H 2 N 0 O 142.0442.010565Hase, T.Wakabayashi, S.Matsubara, H.Kerscher, L.Oesterhelt, D.Rao, K.K.Hall, D.O.J. Biochem. 83, 1657-1670, 1978Complete amino acid sequence of Halobacterium halobium ferredoxin containing an N(epsilon)-acetyllysine residue.PMID:670159chemical synthesis; chromatographic detectionEdde, B.Rossier, J.Le Caer, J.P.Berwald-Netter, Y.Koulakoff, A.Gros, F.Denoulet, P.J. Cell. Biochem. 46, 134-142, 1991A combination of posttranslational modifications is responsible for the production of neuronal alpha-tubulin heterogeneity.DOI:10.1002/jcb.240460207PMID:1680872chromatographic detection and radioisotope labelingFrolow, F.Harel, M.Sussman, J.L.Shoham, M.submitted to the Protein Data Bank, April 19962Fe-2S Ferredoxin from Haloarcula marismortui.PDB:1DOIX-ray diffraction, 1.9 angstromsLapko, V.N.Smith, D.L.Smith, J.B.Protein Sci. 10, 1130-1136, 2001In vivo carbamylation and acetylation of water-soluble human lens alphaB-crystallin lysine 92.DOI:10.1110/ps.40901PMID:11369851mass spectrometric detection with N6-carboxy-L-lysineHirota, J.Satomi, Y.Yoshikawa, K.Takao, T.Rapid Commun. Mass Spectrom. 17, 371-376, 2003Epsilon-N,N,N-trimethyllysine-specific ions in matrix-assisted laser desorption/ionization-tandem mass spectrometry.DOI:10.1002/rcm.924PMID:12590383attempts to distinguish from nominally isobaric N6,N6,N6-trimethyllysine (see RESID:AA0074)histone acetyltransferase (EC 2.3.1.48)tubulin N-acetyltransferase (EC 2.3.1.108)protein lysine N6-acetyltransferase (EC 2.3.1.-)KGO:0018003PSI-MOD:00064acetyllysineMOD_RES N6-acetyllysineAA005631-Mar-199513-Sep-201313-Sep-2013S-acetyl-L-cysteine2-amino-3-(acetylthio)propanoic acid2-azanyl-3-(acetylsulfanyl)propanoic acidcysteine acetate thioesterS-acetylcysteine(2R)-3-acetylsulfanyl-2-aminopropanoic acidCAS:15312-11-5PDBHET:SCYC 5 H 7 N 1 O 2 S 1145.18145.019749C 2 H 2 N 0 O 1 S 042.0442.010565Wagner, A.F.V.Frey, M.Neugebauer, F.A.Schäfer, D.Knappe, J.Proc. Natl. Acad. Sci. U.S.A. 89, 996-1000, 1992The free radical in pyruvate formate-lyase is located on glycine-734.DOI:10.1073/pnas.89.3.996PMID:1310545evidence for an S-acetylcysteine intermediateCGO:0018219GO:0018326PSI-MOD:00065thioester bondACT_SITE S-acetylcysteine intermediateAA005731-Mar-199531-Mar-199531-May-2018N-formylglycine(formylamino)acetic acid(formylazanyl)ethanoic acid2-formamidoacetic acid2-formamidoethanoic acidN(alpha)-formylglycine(formylamino)ethanoic acidCAS:2491-15-8ChEBI:21717C 3 H 4 N 1 O 286.0786.024203C 1 H 0 N 0 O 128.0127.994915Lübke, K.Matthes, S.Kloss, G.Experientia 27, 765-767, 1971Isolation and structure of N(α)-formyl melittin.DOI:10.1007/BF02136852PMID:5139483blocked N-terminal, apparent mass spectrometric and gas chromatographic detection; a typographic error in the title of the PubMed citation is correctedDianoux, A.C.Tsugita, A.Przybylski, M.FEBS Lett. 174, 151-156, 1984Mass spectral identification of the blocked N-terminal tryptic peptide of the ATPase inhibitor from beef heart mitochondria.PMID:6236102bovine mitochondrial ATPase inhibitor peptide with N-formylglycine supposedly identified by mass-spectrometryRunswick, M.J.Walker, J.E.Gibson, B.W.Williams, D.H.Biochem. J. 235, 515-519, 1986The frayed N-terminal of the inhibitor protein of bovine mitochondrial F1-ATPase.PMID:2874795failure to confirm the presence of N-formylglycine in bovine mitochondrial ATPase inhibitor peptideThis modification should not be confused with L-3-oxoalanine, also referred to as C(alpha)-formylglycine (see RESID:AA0185).Gamino-terminalGO:0018005PSI-MOD:00066blocked amino endformylationMOD_RES N-formylglycineAA005831-Mar-199531-Mar-200125-Feb-2011N-D-glucuronoyl-glycineN-D-glucuronyl-glycine2-(glucuronoylamino)ethanoic acidCAS:62532-50-7C 8 H 12 N 1 O 7234.18234.061377C 6 H 8 N 0 O 6176.12176.032088Lin, T.S.Kolattukudy, P.E.Eur. J. Biochem. 106, 341-351, 1980Structural studies on cutinase, a glycoprotein containing novel amino acids and glucuronic acid amide at the N terminus.DOI:10.1111/j.1432-1033.1980.tb04580.xPMID:7398618chromatographic detection; chemical and spectrographic characterization; demonstration of amide linkageKolattukudy, P.E.Meth. Enzymol. 106, 210-217, 1984Detection of an N-terminal glucuronamide linkage in proteins.DOI:10.1016/0076-6879(84)06022-5PMID:6493057chemical characterizationThe glucuronic acid is linked as an amide, rather than as a glycoside (see RESID:AA0291). The alpha glucuronoyl form is shown.Gamino-terminalGO:0018007PSI-MOD:00067blocked amino endMOD_RES N-D-glucuronoyl glycineAA005931-Mar-199531-Mar-200131-May-2013N-myristoyl-glycineN-(1-oxotetradecyl)glycineN-myristylglycineN-tetradecanoylglycine(tetradecanoylamino)ethanoic acidCAS:14246-55-0PDBHET:MYRC 16 H 30 N 1 O 2 +268.42 +268.227654 +C 14 H 26 N 0 O 1 +210.36 +210.198365 +Ozols, J.Carr, S.A.Strittmatter, P.J. Biol. Chem. 259, 13349-13354, 1984Identification of the NH2-terminal blocking group of NADH-cytochrome b5 reductase as myristic acid and the complete amino acid sequence of the membrane-binding domain.PMID:6436247GC and FAB mass spectrometric characterizationDizhoor, A.M.Ericsson, L.H.Johnson, R.S.Kumar, S.Olshevskaya, E.Zozulya, S.Neubert, T.A.Stryer, L.Hurley, J.B.Walsh, K.A.J. Biol. Chem. 267, 16033-16036, 1992The NH-2 terminus of retinal recoverin is acylated by a small family of fatty acids.PMID:1386601mass spectrometric characterizationNeubert, T.A.Johnson, R.S.Hurley, J.B.Walsh, K.A.J. Biol. Chem. 267, 18274-18277, 1992The rod transducin alpha subunit amino terminus is heterogeneously fatty acylated.PMID:1326520mass spectrometric and chemical characterizationGriffith, J.P.Kim, J.L.Kim, E.E.Sintchak, M.D.Thomson, J.A.Fitzgibbon, M.J.Fleming, M.A.Caron, P.R.Hsiao, K.Navia, M.A.Cell 82, 507-522, 1995X-ray structure of calcineurin inhibited by the immunophilin-immunosuppressant FKBP12-FK506 complex.DOI:10.1016/0092-8674(95)90439-5PMID:7543369X-ray diffraction, 2.5 angstromsGriffith, J.P.Kim, J.L.Kim, E.E.Sintchak, M.D.Thomson, J.A.Fitzgibbon, M.J.Fleming, M.A.Caron, P.R.Hsiao, K.Navia, M.A.submitted to the Protein Data Bank, August 1996Ternary complex of a calcineurin A fragment, calcineurin B, Fkbp12 and the immunosuppressant drug FK506 (tacrolimus).PDB:1TCOX-ray diffraction, 2.5 angstromsMaurer-Stroh, S.Eisenhaber, B.Eisenhaber, F.J. Mol. Biol. 317, 523-540, 2002N-terminal N-myristoylation of proteins: refinement of the sequence motif and its taxon-specific differences.DOI:10.1006/jmbi.2002.5425PMID:11955007Maurer-Stroh, S.Eisenhaber, B.Eisenhaber, F.J. Mol. Biol. 317, 541-557, 2002N-terminal N-myristoylation of proteins: prediction of substrate proteins from amino acid sequence.DOI:10.1006/jmbi.2002.5426PMID:11955008improved profile prediction for the modificationVilas, G.L.Corvi, M.M.Plummer, G.J.Seime, A.M.Lambkin, G.R.Berthiaume, L.G.Proc. Natl. Acad. Sci. U.S.A. 103, 6542-6547, 2006Posttranslational myristoylation of caspase-activated p21-activated protein kinase 2 (PAK2) potentiates late apoptotic events.DOI:10.1073/pnas.0600824103PMID:16617111post-translational myristoylation of a proteolytically produced N-terminal glycineBurnaevskiy, N.Fox, T.G.Plymire, D.A.Ertelt, J.M.Weigele, B.A.Selyunin, A.S.Way, S.S.Patrie, S.M.Alto, N.M.Nature 496, 106-109, 2013Proteolytic elimination of N-myristoyl modifications by the Shigella virulence factor IpaJ.DOI:10.1038/nature12004PMID:23535599peptidase from an infective organism that removes N-myristoyl glycineThe myristyl group represents a mixture of saturated and unsaturated fatty acids. Depending on the membrane composition, fatty acids including C12:0, C14:0, C14:1, and C14:2 may be incorporated.This modification is usually co-translational, occurring as the protein N-terminal emerges from the ribosome and immediately after the initial methionine is cleaved. However, glycine myristoylation can in some cases be performed on an N-terminal glycine produced by a post-translational proteolytic cleavage.The ExPASy Prosite pattern PS00008 should only be used with extreme caution. Because that pattern is not anchored to an N-terminal glycine, it extravagantly overpredicts "myristoylation" sites throughout the entire length of many protein sequences. Glycine myristoylation can only occur once in any protein sequence - at the N-terminal.glycylpeptide N-tetradecanoyltransferase (EC 2.3.1.97)Gamino-terminalGO:0018008PSI-MOD:00068blocked amino endlipoproteinmyristoylationLIPID N-myristoyl glycineAA006031-Mar-199531-Mar-199531-May-2018N-palmitoyl-L-cysteine2-hexadecanamido-3-sulfanylpropanoic acid2-hexadecanoylamino-3-mercaptopropanoic acidN-(1-oxahexadecyl)-L-cysteine(2R)-2-hexadecanoylamino-3-sulfanylpropanoic acidCAS:67603-49-0C 19 H 36 N 1 O 2 S 1 +342.56 +342.246675 +C 16 H 30 N 0 O 1 S 0 +238.41 +238.229666 +Hantke, K.Braun, V.Eur. J. Biochem. 34, 284-296, 1973Covalent binding of lipid to protein.DOI:10.1111/j.1432-1033.1973.tb02757.xPMID:4575979Bouchon, B.Klein, M.Bischoff, R.Van Dorsselaer, A.Roitsch, C.Anal. Biochem. 246, 52-61, 1997Analysis of the lipidated recombinant outer surface protein A from Borrelia burgdorferi by mass spectrometry.DOI:10.1006/abio.1996.9982PMID:9056182mass spectrometric characterizationPepinsky, R.B.Zeng, C.Wen, D.Rayhorn, P.Baker, D.P.Williams, K.P.Bixler, S.A.Ambrose, C.M.Garber, E.A.Miatkowski, K.Taylor, F.R.Wang, E.A.Galdes, A.J. Biol. Chem. 273, 14037-14045, 1998Identification of a palmitic acid-modified form of human Sonic hedgehog.DOI:10.1074/jbc.273.22.14037PMID:9593755chemical characterization and mutational analysis of the modified human protein in fly and other cell linesLe Henaff, M.Fontenelle, C.Arch. Microbiol. 173, 339-345, 2000Chemical analysis of processing of spiralin, the major lipoprotein of Spiroplasma melliferum.DOI:10.1007/s002030000145PMID:10896212chemical characterization of N-palmitoyl cysteine and S-diacylated glyceryl cysteineKulathila, R.Kulathila, R.Indic, M.van den Berg, B.PLoS One 6, e15610, 2011Crystal structure of Escherichia coli CusC, the outer membrane component of a heavy metal efflux pump.DOI:10.1371/journal.pone.0015610PMID:21249122X-ray diffraction, 2.30 angstromsvan den Berg, B.submitted to the Protein Data Bank, November 2010Outer membrane protein cusC.PDB:3PIKX-ray diffraction, 2.30 angstromsIn bacteria, the enzyme producing this modification may use a mixture of saturated and unsaturated fatty acids and act in close association with the enzyme producing S-diacylglycerol-L-cysteine (see RESID:AA0107). The signal peptide that is cleaved immediately before the modified cysteine typically ends in the motif [ILMV]X[AGS]C.In eukaryotes, the enzyme acts in the absence of modification of the cysteine thiol and may proceed after initial S-acylation (see RESID:AA0106) through a cyclic intermediate to the final N-acyl form. The eukaryotic enzyme appears to act more efficiently following formation of a carboxyl-terminal cholesterol ester (see RESID:AA0309).This modification should not be confused with S-palmitoyl-cysteine (see RESID:AA0106).protein S-acyltransferasepalmitoyl-CoA:[protein]-L-cysteine S-palmitoyltransferase (EC 2.3.1.225)Camino-terminalincidental to RESID:AA0107incidental to RESID:AA0309GO:0018009PSI-MOD:00069blocked amino endlipoproteinpalmitoylationLIPID N-palmitoyl cysteineAA006131-Mar-199531-Mar-200131-May-2018N-methyl-L-alanine2-methylazanylpropanoic acidN-methylalanine(2S)-2-methylaminopropanoic acidCAS:3913-67-5ChEBI:61922PDBHET:MAAC 4 H 7 N 1 O 185.1185.052764C 1 H 2 N 0 O 014.0314.015650Chen, R.Chen-Schmeisser, U.Proc. Natl. Acad. Sci. U.S.A. 74, 4905-4908, 1977Isopeptide linkage between N-alpha-monomethylalanine and lysine in ribosomal protein S11 from Escherichia coli.DOI:10.1073/pnas.74.11.4905PMID:337304isopeptide linkage erroneously reported because of previewChen, R.Brosius, J.Wittmann-Liebold, B.Schäfer, W.J. Mol. Biol. 111, 173-181, 1977Occurrence of methylated amino acids as N-termini of proteins from Escherichia coli ribosomes.DOI:10.1016/S0022-2836(77)80121-6PMID:323502chemical characterization and synthesis; chromatographic and mass spectrometric identification; the omission of author "Schäfer, W." in the PubMed citation is correctedKamp, R.Wittmann-Liebold, B.FEBS Lett. 121, 117-122, 1980Primary structure of protein S11 from Escherichia coli ribosomes.DOI:10.1016/0014-5793(80)81278-6PMID:7007074confirmation of monomethylation and premature cleavage during Edman couplingJanzen, C.J.Fernandez, J.P.Deng, H.Diaz, R.Hake, S.B.Cross, G.A.M.FEBS Lett. 580, 2306-2310, 2006Unusual histone modifications in Trypanosoma brucei.DOI:10.1016/j.febslet.2006.03.044PMID:16580668mass-spectrometric identification of N-terminal N-methylalanine; the initials of G.A.M. Cross in the PubMed citation are correctedPolypeptides with monomethylated amino terminals can undergo premature cleavage during the coupling step of an Edman degradation. This can result in "preview" with both a residue and the following residue being seen from the first step on through a sequence.N-terminal RCC1 methyltransferaseprotein N-terminal methyltransferaseS-adenosyl-L-methionine:N-terminal-(A,P,S)PK-[protein] methyltransferase (EC 2.1.1.244)protein N-terminal monomethyltransferaseS-adenosyl-L-methionine:N-terminal-(A,P,S)PK-[protein] monomethyltransferase (EC 2.1.1.299)AGO:0018011GO:0019716PSI-MOD:00070methylated amino endMOD_RES N-methylalanineAA006231-Mar-199531-Mar-199531-May-2018N,N,N-trimethyl-L-alanine(1S)-1-carboxy-N,N,N-trimethylethanazanium(2S)-2-(trimethylammonio)propanoic acidN,N,N-trimethylalanine cationN,N,N-trimethylalaninium(1S)-1-carboxy-N,N,N-trimethylethanaminiumCAS:44802-94-0C 6 H 13 N 1 O 11+115.18115.099165C 3 H 7 N 0 O 01+43.0943.054227Lederer, F.Alix, J.H.Hayes, D.Biochem. Biophys. Res. Commun. 77, 470-480, 1977N-Trimethylalanine, a novel blocking group, found in E. coli ribosomal protein L11.DOI:10.1016/S0006-291X(77)80004-1PMID:332162radioisotope labeling; chromatographic and mass spectrographic identification; chemical synthesisDognin, M.J.Wittmann-Liebold, B.Hoppe-Seyler's Z. Physiol. Chem. 361, 1697-1705, 1980Identification of methylated amino acids during sequence analysis. Application to the Escherichia coli ribosomal protein L11.DOI:10.1515/bchm2.1980.361.2.1697PMID:6778808chromatographic detection; mass spectrometric identification; chemical synthesisHenry, G.D.Dalgarno, D.C.Levine, B.A.Trayer, I.P.Biochem. Soc. Trans. 10, 362-363, 1982Discovery of alpha-N-trimethylalanine in myosin light chains and its role in actomyosin interaction.DOI:10.1042/bst0100362(1)H-NMR identification; chemical synthesisHenry, G.D.Trayer, I.P.Brewer, S.Levine, B.A.Eur. J. Biochem. 148, 75-82, 1985The widespread distribution of alpha-N-trimethylalanine as the N-terminal amino acid of light chains from vertebrate striated muscle myosins.DOI:10.1111/j.1432-1033.1985.tb08809.xPMID:3979397mass spectrometric and (1)H-NMR detectionVanet, A.Plumbridge, J.A.Guerin, M.F.Alix, J.H.Mol. Microbiol. 14, 947-958, 1994Ribosomal protein methylation in Escherichia coli: the gene prmA, encoding the ribosomal protein L11 methyltransferase, is dispensable.DOI:10.1111/j.1365-2958.1994.tb01330.xPMID:7715456Consult FAQ at http://pir.georgetown.edu/resid/faq.shtml#q12 concerning calculation of the difference formula.ribosomal protein L11 methyltransferase prmA (EC 2.1.1.-)N-terminal RCC1 methyltransferaseprotein N-terminal methyltransferaseS-adenosyl-L-methionine:N-terminal-(A,P,S)PK-[protein] methyltransferase (EC 2.1.1.244)Aamino-terminalGO:0018011GO:0018012PSI-MOD:00071blocked amino endmethylated amino endMOD_RES N,N,N-trimethylalanineAA006331-Mar-199531-Mar-200131-May-2018N-methylglycineL-sarcosinemethylaminoacetic acidmethylaminoethanoic acidCAS:107-97-1ChEBI:15611PDBHET:SARC 3 H 5 N 1 O 171.0871.037114C 1 H 2 N 0 O 014.0314.015650Kamitori, S.Takusagawa, F.J. Mol. Biol. 225, 445-456, 1992Crystal structure of the 2:1 complex between d(GAAGCTTC) and the anticancer drug actinomycin D.DOI:10.1016/0022-2836(92)90931-9PMID:1593629X-ray diffraction, 3.0 angstromsBailey, A.O.Panchenko, T.Sathyan, K.M.Petkowski, J.J.Pai, P.J.Bai, D.L.Russell, D.H.Macara, I.G.Shabanowitz, J.Hunt, D.F.Black, B.E.Foltz, D.R.Proc. Natl. Acad. Sci. U.S.A. 110, 11827-11832, 2013Posttranslational modification of CENP-A influences the conformation of centromeric chromatin.DOI:10.1073/pnas.1300325110PMID:23818633mass spectrometric identificationDai, X.Otake, K.You, C.Cai, Q.Wang, Z.Masumoto, H.Wang, Y.J. Proteome Res. 12, 4167-4175, 2013Identification of novel α-n-methylation of CENP-B that regulates its binding to the centromeric DNA.DOI:10.1021/pr400498yPMID:23978223mass spectrometric identificationSarcosine occurs internally in some nonencoded peptides. It has been observed as a minor post-translational modification arising from the incomplete trimethylation of N-terminal glycine. See RESID:AA0619 and RESID:AA0620.Polypeptides with monomethylated amino terminals can undergo premature cleavage during the coupling step of an Edman degradation. This can result in "preview" with both a residue and the following residue being seen from the first step on through a sequence.It is not clear whether the N-terminal methyltransferase responsible for methylating N-terminal glycine is distinguishable from the enzyme activities of EC 2.1.1.244 or EC 2.1.1.299.protein N-terminal methyltransferase (EC 2.1.1.-)GGO:0018013GO:0019736PSI-MOD:00072methylated amino acidmethylated amino endNot availablethis modification is not annotated in UniProt featuresAA006431-Mar-199531-Mar-200131-May-2018N-methyl-L-methionine2-methylamino-4-(methylthio)butanoic acidN-methylmethionine(2S)-2-methylamino-4-(methylsulfanyl)butanoic acidCAS:42537-72-4ChEBI:61886PDBHET:MMEC 6 H 11 N 1 O 1 S 1145.22145.056135C 1 H 2 N 0 O 0 S 014.0314.015650Brosius, J.Chen, R.FEBS Lett. 68, 105-109, 1976The primary structure of protein L16 located at the peptidyltransferase center of Escherichia coli ribosomes.DOI:10.1016/0014-5793(76)80415-2PMID:786730N-methylmethionine observed in Escherichia coli ribosomal protein L16Chen, R.Brosius, J.Wittmann-Liebold, B.Schäfer, W.J. Mol. Biol. 111, 173-181, 1977Occurrence of methylated amino acids as N-termini of proteins from Escherichia coli ribosomes.DOI:10.1016/S0022-2836(77)80121-6DOI:10.1016/S0022-2836(77)80121-6PMID:323502chemical characterization and synthesis; chromatographic and mass spectrometric identification; the omission of author "Schäfer, W." in the PubMed citation is correctedStock, A.Schaeffer, E.Koshland Jr., D.E.Stock, J.J. Biol. Chem. 262, 8011-8014, 1987A second type of protein methylation reaction in bacterial chemotaxis.PMID:3298225radioisotope labeling; chromatographic detection of PTH derivativeForest, K.T.Dunham, S.A.Koomey, M.Tainer, J.A.Mol. Microbiol. 31, 743-752, 1999Crystallographic structure reveals phosphorylated pilin from Neisseria: phosphoserine sites modify type IV pilus surface chemistry and fibre morphology.DOI:10.1046/J.1365-2958.1999.01184.XPMID:10048019X-ray diffraction, 2.60 angstromsForest, K.T.Dunham, S.A.Koomey, M.Tainer, J.A.submitted to the Protein Data Bank, March 1998Crystallographic structure of phosphorylated pilin from Neisseria: phosphoserine sites modify type IV pilus surface chemistry.PDB:1PILX-ray diffraction, 2.60 angstromsTaylor, T.C.Backlund, A.Bjorhall, K.Spreitzer, R.J.Andersson, I.J. Biol. Chem. 276, 48159-48164, 2001First crystal structure of Rubisco from a green alga, Chlamydomonas reinhardtii.DOI:10.1074/jbc.M107765200PMID:11641402X-ray diffraction, 1.40 angstromsTaylor, T.C.Spreitzer, R.J.Andersson, I.submitted to the Protein Data Bank, August 2001Rubisco from Chlamydomonas reinhardtii.PDB:1GK8X-ray diffraction, 1.40 angstromsPolypeptides with monomethylated amino terminals can undergo premature cleavage during the coupling step of an Edman degradation. This can result in "preview" with both a residue and the following residue being seen from the first step on through a sequence.Although appropriate, the keyword "thioether bond" normally does not appear for this amino acid.S-adenosylmethionine--methionyl-peptide N-methyltransferase (EC 2.1.1.-)prepilin peptidase (EC 3.4.23.43)MGO:0018014PSI-MOD:00073*thioether bondmethylated amino endMOD_RES N-methylmethionineAA006531-Mar-199531-Mar-200131-Dec-2011N-methyl-L-phenylalanineN-methylphenylalanine(2S)-2-methylamino-3-phenylpropanoic acidCAS:2566-30-5ChEBI:61884PDBHET:MEAC 10 H 11 N 1 O 1161.20161.084064C 1 H 2 N 0 O 014.0314.015650Hermodson, M.A.Chen, K.C.S.Buchanan, T.M.Biochemistry 17, 442-445, 1978Neisseria pili proteins: amino-terminal amino acid sequences and identification of an unusual amino acid.DOI:10.1021/bi00596a010PMID:413571chromatographic determinationMcKern, N.M.Stewart, D.J.Strike, P.M.J. Protein Chem. 7, 157-164, 1988Amino acid sequences of pilins from serologically distinct strains of Bacteroides nodosus.DOI:10.1007/BF01025245PMID:2577730chromatographic determinationStrom, M.S.Lory, S.J. Biol. Chem. 266, 1656-1664, 1991Amino acid substitutions in pilin of Pseudomonas aeruginosa. Effect on leader peptide cleavage, amino-terminal methylation, and pilus assembly.PMID:1671038the amino-terminal methyltransferase activity of prepilin peptidase is not specific for phenylalanineForest, K.T.Dunham, S.A.Koomey, M.Tainer, J.A.Mol. Microbiol. 31, 743-752, 1999Crystallographic structure reveals phosphorylated pilin from Neisseria: phosphoserine sites modify type IV pilus surface chemistry and fibre morphology.DOI:10.1046/J.1365-2958.1999.01184.XPMID:10048019X-ray diffraction, 2.60 angstromsForest, K.T.Dunham, S.A.Koomey, M.Tainer, J.A.submitted to the Protein Data Bank, March 1998Crystallographic structure of phosphorylated pilin from Neisseria: phosphoserine sites modify type IV pilus surface chemistry.PDB:1PILX-ray diffraction, 2.60 angstromsPolypeptides with monomethylated amino terminals can undergo premature cleavage during the coupling step of an Edman degradation. This can result in "preview" with both a residue and the following residue being seen from the first step on through a sequence.prepilin peptidase (EC 3.4.23.43)FGO:0018015PSI-MOD:00074methylated amino endMOD_RES N-methylphenylalanineAA006631-Mar-199531-Mar-199531-May-2018N,N-dimethyl-L-proline1,1-dimethyl-L-proliniumN,N-dimethyl-L-proliniumstachydrin(2S)-2-carboxy-1,1-dimethylpyrrolidiniumCAS:51705-67-0ChEBI:21451PDBHET:PBEC 7 H 13 N 1 O 11+127.19127.099165C 2 H 5 N 0 O 01+29.0629.038577Pettigrew, G.W.Smith, G.M.Nature 265, 661-662, 1977Novel N-terminal protein blocking group identified as dimethylproline.DOI:10.1038/265661a0PMID:193025(1)H-NMR identificationSmith, G.M.Pettigrew, G.W.Eur. J. Biochem. 110, 123-130, 1980Identification of N,N-dimethylproline as the N-terminal blocking group of Crithidia oncopelti cytochrome c557.DOI:10.1111/j.1432-1033.1980.tb04847.xPMID:6254758chromatographic separation; mass spectrometric, (1)H-NMR and (13)C-NMR identificationMartinage, A.Briand, G.Van Dorsselaer, A.Turner, C.H.Sautiere, P.Eur. J. Biochem. 147, 351-359, 1985Primary structure of histone H2B from gonads of the starfish Asterias rubens. Identification of an N-dimethylproline residue at the amino-terminal.DOI:10.1111/j.1432-1033.1985.tb08757.xPMID:3882426mass spectrometric and (1)H-NMR identificationConsult FAQ at http://pir.georgetown.edu/resid/faq.shtml#q12 concerning calculation of the difference formula.N-terminal RCC1 methyltransferaseprotein N-terminal methyltransferaseS-adenosyl-L-methionine:N-terminal-(A,P,S)PK-[protein] methyltransferase (EC 2.1.1.244)Pamino-terminalGO:0018016GO:0035568PSI-MOD:00075blocked amino endmethylated amino endMOD_RES N,N-dimethylprolineAA006731-Mar-199531-Mar-199531-May-2018N(omega)-,N(omega')-dimethyl-L-arginineN3,N4-dimethylarginineN5-[(methylamino)(methylimino)methyl]ornithineNG,N'G-dimethylargininesymmetric dimethylarginine(2S)-2-amino-5-[((methylamino)(methylimino)methyl)amino]pentanoic acidCAS:30344-00-4ChEBI:61916PDBHET:2MRC 8 H 16 N 4 O 1184.24184.132411C 2 H 4 N 0 O 028.0528.031300Baldwin, G.S.Carnegie, P.R.Biochem. J. 123, 69-74, 1971Isolation and partial characterization of methylated arginines from the encephalitogenic basic protein of myelin.PMID:5128665chromatographic isolation; chemical characterizationScoble, H.A.Whitaker, J.N.Biemann, K.J. Neurochem. 47, 614-616, 1986Analysis of the primary sequence of human myelin basic protein peptides 1-44 and 90-170 by fast atom bombardment mass spectrometry.DOI:10.1111/j.1471-4159.1986.tb04544.xPMID:2426402mass spectrometric analysisZou, Y.Wang, Y.Biochemistry 44, 6293-6301, 2005Tandem mass spectrometry for the examination of the posttranslational modifications of high-mobility group A1 proteins: symmetric and asymmetric dimethylation of Arg25 in HMGA1a protein.DOI:10.1021/bi0475525PMID:15835918mass spectrometric differentiation between symmetric and asymmetric dimethylarginine by neutral loss fragmentsThis modification should not be confused with omega-N,omega-N-dimethyl-L-arginine (see RESID:AA0068) or N2,N2-dimethyl-L-arginine (see RESID:AA0569).[myelin basic protein]-arginine N-methyltransferase (EC 2.1.1.126)RGO:0018216GO:0019918PSI-MOD:00076methylated amino acidMOD_RES Symmetric dimethylarginineMOD_RES Omega-N-methylated arginineAA006831-Mar-199531-Mar-199531-May-2018N(omega)-,N(omega)-dimethyl-L-arginineasymmetric dimethylarginineN5-[(dimethylamino)(imino)methyl]ornithineNG,NG-dimethylarginine(2S)-2-amino-5-([(dimethylamino)(imino)methyl]amino)pentanoic acidCAS:30315-93-6ChEBI:61896PDBHET:DA2C 8 H 16 N 4 O 1184.24184.132411C 2 H 4 N 0 O 028.0528.031300Merrill, B.M.Lopresti, M.B.Stone, K.L.Williams, K.R.Int. J. Pept. Protein Res. 29, 21-39, 1987Amino acid sequence of UP1, an hnRNP-derived single-stranded nucleic acid binding protein from calf thymus.PMID:3032834chromatographic identificationYague, J.Vazquez, J.Lopez de Castro, J.A.Protein Sci. 9, 2210-2217, 2000A post-translational modification of nuclear proteins, N(G),N(G)-dimethyl-Arg, found in a natural HLA class I peptide ligand.DOI:10.1110/ps.9.11.2210PMID:11152131mass spectrometric detectionZou, Y.Wang, Y.Biochemistry 44, 6293-6301, 2005Tandem mass spectrometry for the examination of the posttranslational modifications of high-mobility group A1 proteins: symmetric and asymmetric dimethylation of Arg25 in HMGA1a protein.DOI:10.1021/bi0475525PMID:15835918mass spectrometric differentiation between symmetric and asymmetric dimethylarginine by neutral loss fragmentsKuhn, P.Xu, Q.Cline, E.Zhang, D.Ge, Y.Xu, W.Protein Sci. 18, 1272-1280, 2009Delineating Anopheles gambiae coactivator associated arginine methyltransferase 1 automethylation using top-down high resolution tandem mass spectrometry.DOI:10.1002/pro.139PMID:19472346mass spectrometric detection of an intermolecular autocatalytic modificationThis modification should not be confused with omega-N,omega-N'-dimethyl-L-arginine (see RESID:AA0067) or N2,N2-dimethyl-L-arginine (see RESID:AA0569).histone-arginine N-methyltransferase (EC 2.1.1.125)RGO:0018216GO:0019919PSI-MOD:00077methylated amino acidMOD_RES Asymmetric dimethylarginineMOD_RES Omega-N-methylated arginineAA006931-Mar-199531-Mar-199531-May-2018N(omega)-methyl-L-arginineNG-methylarginine(2S)-2-amino-5-[(imino(methylamino)methyl)amino]pentanoic acidCAS:17035-90-4ChEBI:65309C 7 H 14 N 4 O 1170.22170.116761C 1 H 2 N 0 O 014.0314.015650Baldwin, G.S.Carnegie, P.R.Biochem. J. 123, 69-74, 1971Isolation and partial characterization of methylated arginines from the encephalitogenic basic protein of myelin.PMID:5128665chromatographic isolation; chemical characterizationScoble, H.A.Whitaker, J.N.Biemann, K.J. Neurochem. 47, 614-616, 1986Analysis of the primary sequence of human myelin basic protein peptides 1-44 and 90-170 by fast atom bombardment mass spectrometry.DOI:10.1111/j.1471-4159.1986.tb04544.xPMID:2426402mass spectrometric analysisZou, Y.Wang, Y.Biochemistry 44, 6293-6301, 2005Tandem mass spectrometry for the examination of the posttranslational modifications of high-mobility group A1 proteins: symmetric and asymmetric dimethylation of Arg25 in HMGA1a protein.DOI:10.1021/bi0475525PMID:15835918mass spectrometric differentiation between symmetric and asymmetric dimethylarginine by neutral loss fragmentshistone-arginine N-methyltransferase (EC 2.1.1.125)[myelin basic protein]-arginine N-methyltransferase (EC 2.1.1.126)RGO:0018216GO:0019918GO:0019919PSI-MOD:00078methylated amino acidMOD_RES Omega-N-methylarginineMOD_RES Omega-N-methylated arginineAA007031-Mar-199531-Mar-199531-Dec-2011N4-methyl-L-asparaginebeta-aspartyl methylamidebeta-methylasparagine [misnomer]N(gamma)-methylasparagineN-methylasparagine(2S)-2-amino-N4-methylbutanediamic acidCAS:7175-34-0ChEBI:61960PDBHET:MENC 5 H 8 N 2 O 2128.13128.058578C 1 H 2 N 0 O 014.0314.015650Klotz, A.V.Leary, J.A.Glazer, A.N.J. Biol. Chem. 261, 15891-15894, 1986Post-translational methylation of asparaginyl residues. Identification of beta-71 gamma-N-methylasparagine in allophycocyanin.PMID:3782095mass spectrometric and (1)H-NMR identificationKlotz, A.V.Thomas, B.A.Glazer, A.N.Blacher, R.W.Anal. Biochem. 186, 95-100, 1990Detection of methylated asparagine and glutamine residues in polypeptides.DOI:10.1016/0003-2697(90)90579-XPMID:2356973chemical characterization; chemical synthesis; (1)H-NMR characterization; chromatographic detection; PTH derivativeStec, B.Troxler, R.F.Teeter, M.M.submitted to the Protein Data Bank, June 1995Structure of phycocyanin from Cyanidium caldarium at 1.65A resolution.PDB:1PHNX-ray diffraction, 1.65 angstromsKettenring, J.Colombo, L.Ferrari, P.Tavecchia, P.Nebuloni, M.Vékey, K.Gallo, G.G.Selva, E.J. Antibiot. 44, 702-715, 1991Antibiotic GE2270 a: a novel inhibitor of bacterial protein synthesis. II. Structure elucidation.PMID:1880060mass spectrometric, (1)H-NMR, (13)C-NMR, and IR identificationNGO:0019710PSI-MOD:00079methylated amino acidMOD_RES N4-methylasparagineAA007131-Mar-199531-Mar-199531-May-2018N5-methyl-L-glutamine2-amino-N5-methylpentanediamic acidgamma-methylglutamineN(delta)-methylglutamineN-methylglutamine(2S)-2-amino-5-methylamino-5-oxopentanoic acidCAS:3031-62-7ChEBI:61891PDBHET:MEQC 6 H 10 N 2 O 2142.16142.074228C 1 H 2 N 0 O 014.0314.015650Lhoest, J.Colson, C.Mol. Gen. Genet. 154, 175-180, 1977Genetics of ribosomal protein methylation in Escherichia coli. II. A mutant lacking a new type of methylated amino acid, N5-methylglutamine, in protein L3.DOI:10.1007/BF00330833PMID:331083radioisotope labeling; chromatographic identificationMuranova, T.A.Muranov, A.V.Markova, L.F.Ovchinnikov, Y.A.FEBS Lett. 96, 301-305, 1978The primary structure of ribosomal protein L3 from Escherichia coli 70 S ribosomes.DOI:10.1016/0014-5793(78)80423-2PMID:365579Klotz, A.V.Thomas, B.A.Glazer, A.N.Blacher, R.W.Anal. Biochem. 186, 95-100, 1990Detection of methylated asparagine and glutamine residues in polypeptides.DOI:10.1016/0003-2697(90)90579-XPMID:2356973chemical characterization; chemical synthesis; (1)H-NMR characterization; chromatographic detection; PTH derivativeDincbas-Renqvist, V.Engstrom, A.Mora, L.Heurgue-Hamard, V.Buckingham, R.Ehrenberg, M.EMBO J. 19, 6900-6907, 2000A post-translational modification in the GGQ motif of RF2 from Escherichia coli stimulates termination of translation.DOI:10.1093/emboj/19.24.6900PMID:11118225Tessarz, P.Santos-Rosa, H.Robson, S.C.Sylvestersen, K.B.Nelson, C.J.Nielsen, M.L.Kouzarides, T.Nature 505, 564-568, 2014Glutamine methylation in histone H2A is an RNA-polymerase-I-dedicated modification.DOI:10.1038/nature12819PMID:24352239mass spectrometric identificationQGO:0018019PSI-MOD:00080methylated amino acidMOD_RES N5-methylglutamineAA007231-Mar-199531-Mar-199531-May-2018L-glutamic acid 5-methyl ester(5)-methyl L-hydrogen glutamate2-aminopentanedioic acid 5-methyl ester5-methyl L-2-aminoglutarate5-methyl L-glutamateglutamic acid 5-methyl esterglutamic acid gamma-methyl ester(2S)-2-amino-5-methoxy-5-oxopentanoic acidCAS:1499-55-4ChEBI:82795C 6 H 9 N 1 O 3143.14143.058243C 1 H 2 N 0 O 014.0314.015650C 1 H 1 N -1 O 115.0114.999666Kleene, S.J.Toews, M.L.Adler, J.J. Biol. Chem. 252, 3214-3218, 1977Isolation of glutamic acid methyl ester from an Escherichia coli membrane protein involved in chemotaxis.PMID:16888radioisotope labeling; chromatographic detectionKehry, M.R.Engstroem, P.Dahlquist, F.W.Hazelbauer, G.L.J. Biol. Chem. 258, 5050-5055, 1983Multiple covalent modifications of Trg, a sensory transducer of Escherichia coli.PMID:6300110methylated tryptic peptides were isolatedXiao, H.El Bissati, K.Verdier-Pinard, P.Burd, B.Zhang, H.Kim, K.Fiser, A.Angeletti, R.H.Weiss, L.M.J. Proteome Res. 9, 359-372, 2010Post-translational modifications to Toxoplasma gondii α- and β-tubulins include novel C-terminal methylation.DOI:10.1021/pr900699aPMID:19886702detection of multiple glutamate methylations by mass-spectrometry in negative ion modeGlutamate methylesterase can also act as a glutamine amidohydrolase.protein-glutamate O-methyltransferase (EC 2.1.1.80)EGO:0008983GO:0018390GO:0019712PSI-MOD:00081QGO:0018390GO:0019713PSI-MOD:00657methylated amino acidMOD_RES Glutamate methyl ester (Gln)MOD_RES Glutamate methyl ester (Glu)AA007331-Mar-199531-Mar-200131-May-20183'-methyl-L-histidine1-methylhistidine [misnomer]N(delta)-methylhistidineN(pi)-methylhistidinepros-methylhistidine(2S)-2-amino-3-(3-methyl-3H-imidazol-4-yl)propanoic acidCAS:368-16-1ChEBI:43903PDBHET:MHSC 7 H 9 N 3 O 1151.17151.074562C 1 H 2 N 0 O 014.0314.015650Edmondson, D.E.Kenney, W.C.Singer, T.P.Biochemistry 15, 2937-2945, 1976Structural elucidation and properties of 8alpha-(N1-histidyl)riboflavin: the flavin component of thiamine dehydrogenase and beta-cyclopiazonate oxidocyclase.DOI:10.1021/bi00659a001PMID:8076chemical and spectrographic characterization of both 1'- and 3'-methylhistidine; the authors use biochemical rather than IUPAC numberingIUPAC-IUB Joint Commission on Biochemical Nomenclature (JCBN)Eur. J. Biochem. 138, 9-37, 1984Nomenclature and symbolism for amino acids and peptides. Recommendations 1983.DOI:10.1111/j.1432-1033.1984.tb07877.xPMID:6692818tele-, tau-, and pros-, pi-, nomenclatureMaita, T.Hayashida, M.Tanioka, Y.Komine, Y.Matsuda, G.Proc. Natl. Acad. Sci. U.S.A. 84, 416-420, 1987The primary structure of the myosin head.DOI:10.1073/pnas.84.2.416PMID:3467365identification of 3'-methylhistidine along with methyl- and trimethyllysineRaftery, M.J.Harrison, C.A.Alewood, P.Jones, A.Geczy, C.L.Biochem. J. 316, 285-293, 1996Isolation of the murine S100 protein MRP14 (14 kDa migration-inhibitory-factor-related protein) from activated spleen cells: characterization of post-translational modifications and zinc binding.PMID:8645219mass spectrometric detection; chromatographic identification of PTC derivatives of 1'- and 3'-methylhistidine; the authors' source for the reference standard acknowledges that their name, 1'-methylhistidine, is a misnomer for the IUPAC standard name 3'-methylhistidineSelmer, T.Kahnt, J.Goubeaud, M.Shima, S.Grabarse, W.Ermler, U.Thauer, R.K.J. Biol. Chem. 275, 3755-3760, 2000The biosynthesis of methylated amino acids in the active site region of methyl-coenzyme M reductase.DOI:10.1074/jbc.275.6.3755PMID:10660523mass spectrometric characterization; in methyl-coenzyme M reductase the biosynthetic origin of the methyl group is S-adenosyl methionine, not methyl-coenzyme MIn the older biochemical literature this is usually called 1-methylhistidine. See also RESID:AA0317.The crystallographic designation for the substituted nitrogen is delta-1, D1.protein-L-histidine N-pros-methyltransferase (EC 2.1.1.-)HGO:0018021GO:0042037PSI-MOD:00082methylated amino acidMOD_RES Pros-methylhistidineMOD_RES Methylhistidinethis UniProt feature is used when the isomeric structure has not been determinedAA007431-Mar-199531-Mar-199531-Dec-2013N6,N6,N6-trimethyl-L-lysine2-amino-6-(trimethylammonio)hexanoic acid5-azanyl-5-carboxy-N,N,N-trimethylpentanazaniumepsilon-trimethyllysineN(zeta)-trimethyllysineN6,N6,N6-trimethyllysin-N6-iumN6,N6,N6-trimethyllysine cation(5S)-5-amino-5-carboxy-N,N,N-trimethylpentan-1-aminiumCAS:19253-88-4ChEBI:61961PDBHET:M3LC 9 H 19 N 2 O 11+171.26171.149190C 3 H 7 N 0 O 01+43.0943.054227DeLange, R.J.Glazer, A.N.Smith, E.L.J. Biol. Chem. 244, 1385-1388, 1969Presence and location of an unusual amino acid, epsilon-N-trimethyllysine, in cytochrome c of wheat germ and Neurospora.PMID:4304194Dognin, M.J.Wittmann-Liebold, B.Hoppe-Seyler's Z. Physiol. Chem. 361, 1697-1705, 1980Identification of methylated amino acids during sequence analysis. Application to the Escherichia coli ribosomal protein L11.DOI:10.1515/bchm2.1980.361.2.1697PMID:6778808chromatographic detection; mass spectrometric identificationBloxham, D.P.Parmelee, D.C.Kumar, S.Walsh, K.A.Titani, K.Biochemistry 21, 2028-2036, 1982Complete amino acid sequence of porcine heart citrate synthase.DOI:10.1021/bi00538a009PMID:7093227Babu, Y.S.Bugg, C.E.Cook, W.J.submitted to the Protein Data Bank, May 1988Structure of calmodulin refined at 2.2 A resolution.PDB:3CLNBabu, Y.S.Bugg, C.E.Cook, W.J.J. Mol. Biol. 204, 191-204, 1988Structure of calmodulin refined at 2.2 A resolution.DOI:10.1016/0022-2836(88)90608-0PMID:3145979Sundaralingam, M.submitted to the Protein Data Bank, August 1993Structure of the recombinant Paramecium tetraurelia calmodulin at 1.68 Angstrom resolution.PDB:1OSARao, S.T.Wu, S.Satyshur, K.A.Ling, K.Y.Kung, C.Sundaralingam, M.Protein Sci. 2, 436-447, 1993Structure of Paramecium tetraurelia calmodulin at 1.8 angstroms resolution.DOI:10.1002/pro.5560020316PMID:8453381Hirota, J.Satomi, Y.Yoshikawa, K.Takao, T.Rapid Commun. Mass Spectrom. 17, 371-376, 2003Epsilon-N,N,N-trimethyllysine-specific ions in matrix-assisted laser desorption/ionization-tandem mass spectrometry.DOI:10.1002/rcm.924PMID:12590383attempts to distinguish from nominally isobaric N6-acetyllysine (see RESID:AA0055); the authors say trimethylation "causes an incremental increase in mass of 42.0470 Da from the corresponding MH+ ion"; the correct value to four decimal places is 43.0542 when the difference is taken instead from the neutral parent mass as all other difference calculations areConsult FAQ at http://pir.georgetown.edu/resid/faq.shtml#q12 concerning calculation of the difference formula.histone-lysine N-methyltransferase (EC 2.1.1.43)cytochrome-c-lysine N-methyltransferase (EC 2.1.1.59)calmodulin-lysine N-methyltransferase (EC 2.1.1.60)KGO:0018023GO:0018024PSI-MOD:00083methylated amino acidMOD_RES N6,N6,N6-trimethyllysineMOD_RES N6-methylated lysinethis UniProt feature is used when the extent of methylation has not been determinedAA007531-Mar-199531-Mar-199531-Dec-2013N6,N6-dimethyl-L-lysineepsilon-dimethyllysinelysine derivative Lys(y)N(zeta)-dimethyllysine(2S)-2-amino-6-(dimethylamino)hexanoic acidCAS:2259-86-1ChEBI:61969PDBHET:MLYC 8 H 16 N 2 O 1156.23156.126263C 2 H 4 N 0 O 028.0528.031300Schaefer, W.H.Lukas, T.J.Blair, I.A.Schultz, J.E.Watterson, D.M.J. Biol. Chem. 262, 1025-1029, 1987Amino acid sequence of a novel calmodulin from Paramecium tetraurelia that contains dimethyllysine in the first domain.PMID:3100523mass spectrometric identificationSundaralingam, M.submitted to the Protein Data Bank, August 1993Structure of the recombinant Paramecium tetraurelia calmodulin at 1.68 Angstrom resolution.PDB:1OSARao, S.T.Wu, S.Satyshur, K.A.Ling, K.Y.Kung, C.Sundaralingam, M.Protein Sci. 2, 436-447, 1993Structure of Paramecium tetraurelia calmodulin at 1.8 angstroms resolution.DOI:10.1002/pro.5560020316PMID:8453381Rayment, I.Rypniewski, W.R.Schmidt-Bäse, K.Smith, R.Tomchick, D.R.Benning, M.M.Winkelmann, D.A.Wesenberg, G.Holden, H.M.Science 261, 50-58, 1993Three-dimensional structure of myosin subfragment-1: a molecular motor.DOI:10.1126/science.8316857PMID:8316857chemical method for specific dimthylation of lysineKroeger, N.Deutzmann, R.Sumper, M.Science 286, 1129-1132, 1999Polycationic peptides from diatom biosilica that direct silica nanosphere formation.DOI:10.1126/science.286.5442.1129PMID:10550045chromatographic, mass spectrometric and (1)H-NMR identificationThis modification is readily formed artifactually by reductive methylation using formaldehyde.histone-lysine N-methyltransferase (EC 2.1.1.43)cytochrome-c-lysine N-methyltransferase (EC 2.1.1.59)calmodulin-lysine N-methyltransferase (EC 2.1.1.60)KGO:0018024GO:0018027PSI-MOD:00084methylated amino acidMOD_RES N6,N6-dimethyllysineMOD_RES N6-methylated lysinethis UniProt feature is used when the extent of methylation has not been determinedAA007631-Mar-199531-Mar-199531-Dec-2011N6-methyl-L-lysineepsilon-methyllysineN(zeta)-methyllysine(2S)-2-amino-6-methylaminohexanoic acidCAS:1188-07-4ChEBI:61928PDBHET:MLZC 7 H 14 N 2 O 1142.20142.110613C 1 H 2 N 0 O 014.0314.015650Minami, Y.Wakabayashi, S.Wada, K.Matsubara, H.Kerscher, L.Oesterhelt, D.J. Biochem. 97, 745-753, 1985Amino acid sequence of a ferredoxin from thermoacidophilic archaebacterium, Sulfolobus acidocaldarius. Presence of an N(6)-monomethyllysine and phyletic consideration of archaebacteria.PMID:3926756chromatographic and mass spectrometric identificationhistone-lysine N-methyltransferase (EC 2.1.1.43)cytochrome-c-lysine N-methyltransferase (EC 2.1.1.59)calmodulin-lysine N-methyltransferase (EC 2.1.1.60)KGO:0018024GO:0018026PSI-MOD:00085methylated amino acidMOD_RES N6-methyllysineMOD_RES N6-methylated lysinethis UniProt feature is used when the extent of methylation has not been determinedAA007731-Mar-199531-Mar-199531-May-2013N6-palmitoyl-L-lysine2-amino-6-(hexadecanamido)hexanoic acidepsilon-palmitoyllysineN(zeta)-palmitoyllysineN6-(1-oxohexadecyl)-L-lysine(2S)-2-amino-6-(hexadecanoylamino)hexanoic acidCAS:559012-43-0ChEBI:21895C 22 H 42 N 2 O 2366.59366.324629C 16 H 30 N 0 O 1238.41238.229666Tomasselli, A.G.Hui, J.Fisher, J.Zuercher-Neely, H.Reardon, I.M.Oriaku, E.Kezdy, F.J.Heinrikson, R.L.J. Biol. Chem. 264, 10041-10047, 1989Dimerization and activation of porcine pancreatic phospholipase A2 via substrate level acylation of lysine 56.PMID:2498336the autocatalytic transfer of a fatty acid, normally palmitate, from substrate to lysine is described; octanoate transfer from a chromogenic substrate analog is artifactualHackett, M.Guo, L.Shabanowitz, J.Hunt, D.F.Hewlett, E.L.Science 266, 433-435, 1994Internal lysine palmitoylation in adenylate cyclase toxin from Bordetella pertussis.DOI:10.1126/science.7939682PMID:7939682mass spectrometric identificationStanley, P.Packman, L.C.Koronakis, V.Hughes, C.Science 266, 1992-1996, 1994Fatty acylation of two internal lysine residues required for the toxic activity of Escherichia coli hemolysin.DOI:10.1126/science.7801126PMID:7801126radioisotope labelingJiang, H.Khan, S.Wang, Y.Charron, G.He, B.Sebastian, C.Du, J.Kim, R.Ge, E.Mostoslavsky, R.Hang, H.C.Hao, Q.Lin, H.Nature 496, 110-113, 2013SIRT6 regulates TNF-α secretion through hydrolysis of long-chain fatty acyl lysine.DOI:10.1038/nature12038PMID:23552949hydrolase from an infective organism that preferentially removes myristoyl and palmitoyl groups from N6-acylated lysine peptidespeptidyl-lysine N6-palmitoyltransferase (EC 2.3.1.-)KGO:0018029PSI-MOD:00086lipoproteinpalmitoylationLIPID N6-palmitoyl lysineAA007809-Aug-199509-Aug-199531-May-2013N6-myristoyl-L-lysine2-amino-6-(tetradecanamido)hexanoic acidepsilon-myristoyllysineN(zeta)-myristoyllysineN6-(1-oxotetradecyl)-L-lysine(2S)-2-amino-6-(tetradecanoylamino)hexanoic acidCAS:62471-07-2ChEBI:21894PDBHET:MYKPDBHET:MYRC 20 H 38 N 2 O 2338.54338.293328C 14 H 26 N 0 O 1210.36210.198365Stevenson, F.T.Bursten, S.L.Locksley, R.M.Lovett, D.H.J. Exp. Med. 176, 1053-1062, 1992Myristyl acylation of the tumor necrosis factor alpha precursor on specific lysine residues.DOI:10.1084/jem.176.4.1053PMID:1402651radioisotope labeling; biosynthesis; chromatographic detectionStevenson, F.T.Bursten, S.L.Fanton, C.Locksley, R.M.Lovett, D.H.Proc. Natl. Acad. Sci. U.S.A. 90, 7245-7249, 1993The 31-kDa precursor of interleukin 1alpha is myristoylated on specific lysines within the 16-kDa N-terminal propiece.DOI:10.1073/pnas.90.15.7245PMID:8346241biosynthesis; chemical synthesis; chromatographic detectionWhittingham, J.L.Havelund, S.Jonassen, I.Biochemistry 36, 2826-2831, 1997Crystal structure of a prolonged-acting insulin with albumin-binding properties.DOI:10.1021/bi9625105PMID:9062110crystallographic structure of artifically produced modificationWhittingham, J.L.Havelund, S.Jonassen, I.submitted to the Protein Data Bank, December 1996Structure of insulin.PDB:1XDAX-ray diffraction, 1.80 angstromsJiang, H.Khan, S.Wang, Y.Charron, G.He, B.Sebastian, C.Du, J.Kim, R.Ge, E.Mostoslavsky, R.Hang, H.C.Hao, Q.Lin, H.Nature 496, 110-113, 2013SIRT6 regulates TNF-α secretion through hydrolysis of long-chain fatty acyl lysine.DOI:10.1038/nature12038PMID:23552949hydrolase from an infective organism that preferentially removes myristoyl and palmitoyl groups from N6-acylated lysine peptidespeptidyl-lysine N6-myristoyltransferase (EC 2.3.1.-)KGO:0018028PSI-MOD:00087lipoproteinmyristoylationLIPID N6-myristoyl lysineAA007931-Mar-199531-Mar-199531-Dec-2011O-palmitoyl-L-threonineL-threonine hexadecanoate esterO3-palmitoyl-threoninethreonine palmitate ester(2S,3R)-2-amino-3-(hexadecanoyloxy)butanoic acidCAS:88467-30-5C 20 H 37 N 1 O 3339.52339.277344C 16 H 30 N 0 O 1238.41238.229666Stoffel, W.Hillen, H.Schroeder, W.Deutzmann, R.Hoppe-Seyler's Z. Physiol. Chem. 364, 1455-1466, 1983The primary structure of bovine brain myelin lipophilin (proteolipid apoprotein).DOI:10.1515/bchm2.1983.364.2.1455PMID:6642431chromatographic and mass spectrometric identificationBranton, W.D.Rudnick, M.S.Zhou, Y.Eccleston, E.D.Fields, G.B.Bowers, L.D.Nature 365, 496-497, 1993Fatty acylated toxin structure.DOI:10.1038/365496a0PMID:8413602chromatographic and mass spectrometric identificationThe palmitate represents a mixture of saturated and unsaturated fatty acids.Tincidental to RESID:AA0097GO:0018220PSI-MOD:00088lipoproteinpalmitoylationLIPID O-palmitoyl threonineAA008025-Aug-199525-Aug-199530-Sep-2011O-palmitoyl-L-serineL-serine hexadecanoate esterO3-palmitoyl-serineserine palmitate ester(2S)-2-amino-3-(hexadecanoyloxy)propanoic acidCAS:88815-78-5PDBHET:PLMC 19 H 35 N 1 O 3325.49325.261694C 16 H 30 N 0 O 1238.41238.229666Diehl, H.J.Schaich, M.Budzinski, R.M.Stoffel, W.Proc. Natl. Acad. Sci. 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Soc. 132, 16324-16326, 2010NosA Catalyzing Carboxyl-Terminal Amide Formation in Nosiheptide Maturation via an Enamine Dealkylation on the Serine-Extended Precursor Peptide.DOI:10.1021/ja106571gPMID:21047073serine amide in a bacterial antibiotic is formed by oxidative cleavage of a terminal serine residuepeptidylglycine monooxygenase (EC 1.14.17.3)peptidylamidoglycolate lyase (EC 4.3.2.5)Scarboxyl-terminalGO:0018049PSI-MOD:00105amidated carboxyl endMOD_RES Serine amideAA009731-Mar-199531-Mar-199531-May-2018L-threonine amidethreoninamide(2S,3R)-2-amino-3-hydroxybutanamideCAS:2280-40-2ChEBI:21404PDBHET:NH2C 4 H 9 N 2 O 2117.13117.066403C 0 H 1 N 1 O -1-0.98-0.984016Ramilo, C.A.Zafaralla, G.C.Nadasdi, L.Hammerland, L.G.Yoshikami, D.Gray, W.R.Kristipati, R.Ramachandran, J.Miljanich, G.Olivera, B.M.Biochemistry 31, 9919-9926, 1992Novel alpha- and omega-conotoxins from Conus striatus venom.DOI:10.1021/bi00156a009PMID:1390774chemical synthesispeptidylglycine monooxygenase (EC 1.14.17.3)peptidylamidoglycolate lyase (EC 4.3.2.5)Tcarboxyl-terminalGO:0018050PSI-MOD:00106amidated carboxyl endMOD_RES Threonine amideAA009831-Mar-199531-Mar-199531-May-2018L-tryptophan amidetryptophanamide(2S)-2-amino-3-(1H-indol-3-yl)propanamideCAS:20696-57-5ChEBI:16533PDBHET:NH2C 11 H 12 N 3 O 1202.24202.098037C 0 H 1 N 1 O -1-0.98-0.984016Gäde, G.Goldsworthy, G.J.Schaffer, M.H.Cook, J.C.Rinehart Jr., K.L.Biochem. Biophys. Res. Commun. 134, 723-730, 1986Sequence analyses of adipokinetic hormones II from corpora cardiaca of Schistocerca nitans, Schistocerca gregaria, and Locusta migratoria by fast atom bombardment mass spectrometry.DOI:10.1016/S0006-291X(86)80480-6PMID:3947348mass spectrometric identificationpeptidylglycine monooxygenase (EC 1.14.17.3)peptidylamidoglycolate lyase (EC 4.3.2.5)Wcarboxyl-terminalGO:0018051PSI-MOD:00107amidated carboxyl endMOD_RES Tryptophan amideAA009931-Mar-199531-Mar-199531-May-2018L-tyrosine amidetyrosinamide(2S)-2-amino-3-(4-hydoxyphenyl)propanamideCAS:4985-46-0ChEBI:21412PDBHET:NH2PDBHET:TYCC 9 H 11 N 2 O 2179.20179.082053C 0 H 1 N 1 O -1-0.98-0.984016Olivera, B.M.McIntosh, J.M.Cruz, L.J.Luque, F.A.Gray, W.R.Biochemistry 23, 5087-5090, 1984Purification and sequence of a presynaptic peptide toxin from Conus geographus venom.DOI:10.1021/bi00317a001PMID:6509012chromatographic identification of PTC derivativeConlon, J.M.Schmidt, W.E.Gallwitz, B.Falkmer, S.Thim, L.Regul. Pept. 16, 261-268, 1986Characterization of an amidated form of pancreatic polypeptide from the daddy sculpin (Cottus scorpius).DOI:10.1016/0167-0115(86)90025-XPMID:3562898mass spectrometric characterizationTakamatsu, K.Tatemoto, K.Neurochem. Res. 17, 239-246, 1992Isolation and characterization of two novel peptide amides originating from myelin basic protein in bovine brain.DOI:10.1007/BF00966665PMID:1377792this peptide has a carboxyl-terminal amide probably produced by a non-enzymatic reactionpeptidylglycine monooxygenase (EC 1.14.17.3)peptidylamidoglycolate lyase (EC 4.3.2.5)Ycarboxyl-terminalGO:0018052PSI-MOD:00108amidated carboxyl endMOD_RES Tyrosine amideAA010031-Mar-199531-Mar-199531-May-2018L-valine amidevalinamide(2S)-2-amino-3-methylbutanamideCAS:4540-60-7ChEBI:21418PDBHET:NH2C 5 H 11 N 2 O 1115.16115.087138C 0 H 1 N 1 O -1-0.98-0.984016Mutt, V.Jorpes, J.E.Magnusson, S.Eur. J. Biochem. 15, 513-519, 1970Structure of porcine secretin. The amino acid sequence.DOI:10.1111/j.1432-1033.1970.tb01034.xPMID:5465996Argiolas, A.Pisano, J.J.J. Biol. Chem. 260, 1437-1444, 1985Bombolitins, a new class of mast cell degranulating peptides from the venom of the bumblebee Megabombus pennsylvanicus.PMID:2578459peptidylglycine monooxygenase (EC 1.14.17.3)peptidylamidoglycolate lyase (EC 4.3.2.5)Vcarboxyl-terminalGO:0018053PSI-MOD:00109amidated carboxyl endMOD_RES Valine amideAA010131-Mar-199531-Mar-199530-Jun-2010L-cysteine methyl disulfide2-amino-3-(methyldisulfanediyl)propanoic acid2-amino-3-(methyldithio)propanoic acid2-amino-3-methyldisulfanylpropanoic acid2-azanyl-3-(methyldisulfanediyl)-propanoic acidL-3-(methyldithio)alanineS-methylthio-L-cysteineS-methylthiocysteine(2R)-2-amino-3-(methyldisulfanediyl)propanoic acidCAS:33784-54-2PDBHET:SCHC 4 H 7 N 1 O 1 S 2149.23148.996906C 1 H 2 N 0 O 0 S 146.0945.987721Lo, S.S.Fraser, B.A.Liu, T.Y.J. Biol. Chem. 259, 11041-11045, 1984The mixed disulfide in the zymogen of streptococcal proteinase. Characterization and implication for its biosynthesis.PMID:6381494mass spectrometric detection; isotope labelingKissinger, C.R.Sieker, L.C.Adman, E.T.Jensen, L.H.J. Mol. Biol. 219, 693-715, 1991Refined crystal structure of ferredoxin II from Desulfovibrio gigas at 1.7 A.DOI:10.1016/0022-2836(91)90665-SPMID:2056535X-ray diffraction, 1.7 angstromsKissinger, C.R.Sieker, L.C.Adman, E.T.Jensen, L.H.submitted to the Protein Data Bank, April 1991Refined crystal structure of ferredoxin II from Desulfovibrio gigas at 1.7 A.PDB:1FXDX-ray diffraction, 1.70 angstromsGoodfellow, B.J.Macedo, A.L.Rodrigues, P.Moura, I.Wray, V.Moura, J.J.J. Biol. Inorg. Chem. 4, 421-430, 1999The solution structure of a [3Fe-4S] ferredoxin: oxidised ferredoxin II from Desulfovibrio gigas.DOI:10.1007/s007750050328PMID:10555576Goodfellow, B.J.Macedo, A.L.Rodrigues, P.Wray, V.Moura, I.Moura, J.J.G.submitted to the Protein Data Bank, October 1998The NMR solution structure of the 3Fe ferredoxin II from Desulfovibrio gigas, 15 structures.PDB:1F2GCOSY, TOCSY, and NOESY NMR spectroscopy; the cysteine methyl disulfide modification is not reported for this structureCGO:0018222PSI-MOD:00110disulfide bondMOD_RES Cysteine methyl disulfideAA010231-Mar-199531-Mar-199531-May-2018S-farnesyl-L-cysteine2-amino-3-(3,7,11-trimethyl-2,6,10-dodecatrienylthio)propanoic acid(2R)-2-amino-3-([(2E,6E)-3,7,11-trimethyldodeca-2,6,10-trien-1-yl]sulfanyl)propanoic acidCAS:68000-92-0ChEBI:86019PDBHET:FARC 18 H 29 N 1 O 1 S 1307.50307.196986C 15 H 24 N 0 O 0 S 0204.36204.187801Farnsworth, C.C.Wolda, S.L.Gelb, M.H.Glomset, J.A.J. Biol. Chem. 264, 20422-20429, 1989Human lamin B contains a farnesylated cysteine residue.PMID:2684976radiolabeling; mass spectrometric and chemical characterizationTuinman, A.A.Thomas, D.A.Cook, K.D.Xue, C.B.Naider, F.Becker, J.M.Anal. Biochem. 193, 173-177, 1991Mass spectrometric signature of S-prenylated cysteine peptides.DOI:10.1016/0003-2697(91)90004-DPMID:1872463mass spectrometric identificationHeilmeyer Jr., L.M.G.Serwe, M.Weber, C.Metzger, J.Hoffmann-Posorske, E.Meyer, H.E.Proc. Natl. Acad. Sci. U.S.A. 89, 9554-9558, 1992Farnesylcysteine, a constituent of the alpha and beta subunits of rabbit skeletal muscle phosphorylase kinase: localization by conversion to S-ethylcysteine and by tandem mass spectrometry.DOI:10.1073/pnas.89.20.9554PMID:1409665farnesylation not followed by cleavage of the terminal peptide and methylation of the new carboxyl endLong, S.B.Casey, P.J.Beese, L.S.Nature 419, 645-650, 2002Reaction path of protein farnesyltransferase at atomic resolution.DOI:10.1038/nature00986PMID:12374986X-ray diffraction, 2.10 angstromsLong, S.B.Casey, P.J.Beese, L.S.submitted to the Protein Data Bank, February 2002Protein farnesyltransferase complexed with a farnesylated K-Ras4B peptide product.PDB:1KZPX-ray diffraction, 2.10 angstromsFormation of S-farnesycysteine may be coupled with subsequent cleavage of a carboxy-terminal tripeptide for the CXXX motif and methyl esterification of the farnesylated cysteine. See L-cysteine methyl ester (RESID:AA0105).This modification may be found at the first position in the sequence motif CXX[SAQCMT]* where the second and third positions are usually aliphatic.protein farnesyltransferasefarnesyl-diphosphate:protein-cysteine farnesyltransferase (EC 2.5.1.58)Cincidental to RESID:AA0105GO:0018226PSI-MOD:00111PSI-MOD:01116lipoproteinprenylationthioether bondLIPID S-farnesyl cysteineAA010331-Mar-199531-Mar-199530-Sep-2013S-12-hydroxyfarnesyl-L-cysteine2-amino-3-(12-hydroxy-3,7,11-trimethyl-3,6,10-dodecatrienylthio)propanoic acid(2R)-2-amino-3-([(2E,6E,10Z)-12-hydroxy-3,7,11-trimethyldodeca-2,6,10-trien-1-yl]sulfanyl)propanoic acidC 18 H 29 N 1 O 2 S 1323.50323.191900C 15 H 24 N 0 O 1 S 0220.36220.182715Sakagami, Y.Yoshida, M.Isogai, A.Suzuki, A.Science 212, 1525-1527, 1981Peptidal sex hormones inducing conjugation tube formation in compatible mating-type cells of Tremella mesenterica.DOI:10.1126/science.212.4502.1525PMID:17790543possible identification of 12-hydroxyfarnesylIshibashi, Y.Sakagami, Y.Isogai, A.Suzuki, A.Biochemistry 23, 1399-1404, 1984Structures of tremerogens A-9291-I and A-9291-VIII: peptidal sex hormones of Tremella brasiliensis.DOI:10.1021/bi00302a010mass spectrometric and (1)H-NMR characterizationFormation of S-12-hydroxyfarnesylcysteine may be coupled with subsequent cleavage of a carboxy-terminal tripeptide for the CAAX motif and methyl esterification of the farnesylated cysteine. See L-cysteine methyl ester (RESID:AA0105).Cincidental to RESID:AA0105GO:0018227GO:0042050PSI-MOD:00112PSI-MOD:01133lipoproteinprenylationthioether bondLIPID S-12-hydroxyfarnesyl cysteineAA010431-Mar-199531-Mar-199531-May-2018S-geranylgeranyl-L-cysteine2-amino-3-(3,7,11,15-tetramethyl-2,6,10,14-hexadecatetraenylthio)propanoic acid(2R)-2-amino-3-([(2E,6E,10Z)-12-hydroxy-3,7,11-trimethyldodeca-2,6,10-trien-1-yl]sulfanyl)propanoic acidCAS:131404-69-8ChEBI:86021PDBHET:GERC 23 H 37 N 1 O 1 S 1375.62375.259586C 20 H 32 N 0 O 0 S 0272.48272.250401Morishita, R.Fukada, Y.Kokame, K.Yoshizawa, T.Masuda, K.Niwa, M.Kato, K.Asano, T.Eur. J. Biochem. 210, 1061-1069, 1992Identification and isolation of common and tissue-specific geranylgeranylated gamma subunits of guanine-nucleotide-binding regulatory proteins in various tissues.DOI:10.1111/j.1432-1033.1992.tb17512.xPMID:1483450mass spectrometric and chemical characterizationFor the type I geranylgeranyltransferase the residue may be found at the first position in the sequence motif CXX[LF]* where the second and third positions are usually aliphatic.For the type II geranylgeranyltransferase the residue may be found at the first and final positions in the sequence motif CXC* or at the final two positions in the sequence motif CC*. These motifs are necessary but not sufficient for modification.Formation of S-geranylgeranylcysteine may be coupled with subsequent cleavage of a carboxy-terminal tripeptide for the CAAX motif and methyl esterification of the geranylgeranylated cysteine. Methyl esterification without cleavage occurs for the CXC motif.protein geranylgeranyltransferase type Igeranylgeranyl-diphosphate:protein-cysteine geranyltransferase (EC 2.5.1.59)protein geranylgeranyltransferase type IIgeranylgeranyl-diphosphate:protein-cysteine geranyltransferase (EC 2.5.1.60)Cincidental to RESID:AA0105GO:0018228PSI-MOD:00113PSI-MOD:01119lipoproteinprenylationthioether bondLIPID S-geranylgeranyl cysteineAA010531-Mar-199531-Mar-199531-Dec-2011L-cysteine methyl ester2-amino-3-mercaptopropanoic methyl ester2-amino-3-sulfanylpropanoic methyl estermecysteinemethyl L-cysteinatemethyl (2R)-2-amino-3-sulfanylpropanoateCAS:2485-63-3ChEBI:61989PDBHET:CMTC 4 H 8 N 1 O 2 S 1134.17134.027574C 1 H 2 N 0 O 0 S 014.0314.015650Ota, I.M.Clarke, S.J. Biol. Chem. 264, 12879-12884, 1989Enzymatic methylation of 23-29-kDa bovine retinal rod outer segment membrane proteins. Evidence for methyl ester formation at carboxyl-terminal cysteinyl residues.PMID:2753892chemical and radiolabeling evidence for carboxyl methylation of a C-terminal cysteineTuinman, A.A.Thomas, D.A.Cook, K.D.Xue, C.B.Naider, F.Becker, J.M.Anal. Biochem. 193, 173-177, 1991Mass spectrometric signature of S-prenylated cysteine peptides.DOI:10.1016/0003-2697(91)90004-DPMID:1872463mass spectrometric identificationThe term "carboxyl methylation" applies to this modification. The terms "carboxy methylation" and "carboxymethylation" are sometimes used incorrectly for this modification. Since those terms mean "replacement by a methylcarboxylic acid", they actually refer to a different, artifactual modification.protein-S-isoprenylcysteine O-methyltransferase (EC 2.1.1.100)Ccarboxyl-terminalsecondary to RESID:AA0102secondary to RESID:AA0103secondary to RESID:AA0104GO:0018229PSI-MOD:00114methylated carboxyl endMOD_RES Cysteine methyl esterAA010631-Mar-199531-Mar-199531-May-2018S-palmitoyl-L-cysteine2-amino-3-(hexadecanoylthio)propanoic acidcysteine hexadecanoate thioestercysteine palmitate thioester(2R)-2-amino-3-(hexadecanoylsulfanyl)propanoic acidCAS:114507-35-6ChEBI:74151PDBHET:PLMC 19 H 35 N 1 O 2 S 1341.55341.238850C 16 H 30 N 0 O 1 S 0238.41238.229666Bach, R.Konigsberg, W.H.Nemerson, Y.Biochemistry 27, 4227-4231, 1988Human tissue factor contains thioester-linked palmitate and stearate on the cytoplasmic half-cystine.DOI:10.1021/bi00412a004PMID:3166978chemical characterizationStults, J.T.Griffin, P.R.Lesikar, D.D.Naidu, A.Moffat, B.Benson, B.J.Am. J. Physiol. 261, L118-L125, 1991Lung surfactant protein SP-C from human, bovine, and canine sources contains palmityl cysteine thioester linkages.PMID:1872406mass spectrometric identificationJohansson, J.Szyperski, T.Curstedt, T.Wuthrich, K.Biochemistry 33, 6015-6023, 1994The NMR structure of the pulmonary surfactant-associated polypeptide sp-C in an apolar solvent contains a valyl-rich alpha-helix.DOI:10.1021/bi00185a042PMID:8180229(1)H-NMR identificationSteinert, P.M.Kim, S.Y.Chung, S.I.Marekov, L.N.J. Biol. Chem. 271, 26242-26250, 1996The transglutaminase 1 enzyme is variably acylated by myristate and palmitate during differentiation in epidermal keratinocytes.DOI:10.1074/jbc.271.42.26242PMID:8824274mass spectrometric identification; differential S-palmitoylation and S-myristoylation (see RESID:AA0307)Ducker, C.E.Stettler, E.M.French, K.J.Upson, J.J.Smith, C.D.Oncogene 23, 9230-9237, 2004Huntingtin interacting protein 14 is an oncogenic human protein: palmitoyl acyltransferase.DOI:10.1038/sj.onc.1208171PMID:15489887Huang, K.Yanai, A.Kang, R.Arstikaitis, P.Singaraja, R.R.Metzler, M.Mullard, A.Haigh, B.Gauthier-Campbell, C.Gutekunst, C.A.Hayden, M.R.El-Husseini, A.Neuron 44, 977-986, 2004Huntingtin-interacting protein HIP14 is a palmitoyl transferase involved in palmitoylation and trafficking of multiple neuronal proteins.DOI:10.1016/j.neuron.2004.11.027PMID:15603740Wilson, J.P.Raghavan, A.S.Yang, Y.Y.Charron, G.Hang, H.C.Mol. Cell. Proteomics 10, M110.001198, 2011Proteomic analysis of fatty-acylated proteins in mammalian cells with chemical reporters reveals S-acylation of histone H3 variants.DOI:10.1074/mcp.M110.001198PMID:21076176biotin-tagged reagent; observed S-palmitoylation of several histone 3 varieties, in particular 3.2, in human lymphoma T cell (Jurkat) culturesAlthough the predominant palmitoyl transferase in mammalian systems appears to utilize a mixture of saturated and unsaturated fatty acids, some systems may be more specific in their incorporation of other fatty acids. See RESID:AA0307 and RESID:AA0308.This modification should not be confused with N-palmitoyl-cysteine (see RESID:AA0060).protein S-acyltransferasepalmitoyl-CoA:[protein]-L-cysteine S-palmitoyltransferase (EC 2.3.1.225)CGO:0018230PSI-MOD:00115lipoproteinpalmitoylationthioester bondACT_SITE S-palmitoyl cysteine intermediateLIPID S-palmitoyl cysteineAA010731-Mar-199531-Mar-199531-Mar-2013S-diacylglycerol-L-cysteine2-amino-3-[(S)-2-((Z)-9-octadecenoyloxy)-3-(hexadecanoyloxy)propyl]thiopropanoic acidS-(1-2'-oleoyl-3'-palmitoyl-glycerol)cysteine(2R)-2-amino-3-[(2S)-2-((9Z)-9-octadecenoyloxy)-3-(hexadecanoyloxy)propyl]sulfanylpropanoic acidPDBHET:DGAC 40 H 73 N 1 O 5 S 1680.09679.520945C 37 H 68 N 0 O 4 S 0576.95576.511761Hantke, K.Braun, V.Eur. J. Biochem. 34, 284-296, 1973Covalent binding of lipid to protein.DOI:10.1111/j.1432-1033.1973.tb02757.xPMID:4575979chromatographic and mass spectrometric identification; chemical synthesisWeyer, K.A.Schäfer, D.Lottspeich, F.Michel, H.Biochemistry 26, 2909-2914, 1987The cytochrome subunit of the photosynthetic reaction center from Rhodopseudomonas viridis is a lipoprotein.DOI:10.1021/bi00384a036chromatographic and mass spectrometric identification; this amino-terminal cysteine has a free alpha-amino groupBouchon, B.Klein, M.Bischoff, R.Van Dorsselaer, A.Roitsch, C.Anal. Biochem. 246, 52-61, 1997Analysis of the lipidated recombinant outer surface protein A from Borrelia burgdorferi by mass spectrometry.DOI:10.1006/abio.1996.9982PMID:9056182mass spectrometric characterizationLe Hénaff, M.Fontenelle, C.Arch. Microbiol. 173, 339-345, 2000Chemical analysis of processing of spiralin, the major lipoprotein of Spiroplasma melliferum.DOI:10.1007/s002030000145PMID:10896212chemical characterization of N-palmitoyl cysteine and S-diacylated glyceryl cysteineKulathila, R.Kulathila, R.Indic, M.van den Berg, B.PLoS One 6, e15610, 2011Crystal structure of Escherichia coli CusC, the outer membrane component of a heavy metal efflux pump.DOI:10.1371/journal.pone.0015610PMID:21249122X-ray diffraction, 2.30 angstromsvan den Berg, B.submitted to the Protein Data Bank, November 2010Outer membrane protein cusC.PDB:3PIKX-ray diffraction, 2.30 angstromsThe oleate and palmitate actually represent mixtures of saturated (generally at 3') and unsaturated (generally at 2') fatty acids.The signal peptide that is cleaved immediately before the modified cysteine typically ends in the motif [ILMV]X[AGS]C. Cleavage and formation of this modification may occur without N-palmitoylation, see RESID:AA0060.Cincidental to RESID:AA0060GO:0018231GO:0042050PSI-MOD:00116PSI-MOD:00898PSI-MOD:00899PSI-MOD:01144lipoproteinthioether bondLIPID S-diacylglycerol cysteineAA010831-Mar-199531-Mar-199530-Sep-2011S-(L-isoglutamyl)-L-cysteine(S,R)-2-amino-4-[S-(2-amino-2-carboxyethyl)thiocarboxy]butanoic acid2-amino-5-(2-amino-2-carboxyethyl)thio-5-oxopentanoic acidgamma-(S-cysteinyl)glutamic acid(2S)-2-amino-5-[(2R)-2-amino-2-carboxyethyl]sulfanyl-5-oxopentanoic acidCAS:105580-05-0ChEBI:22021C 8 H 10 N 2 O 3 S 1214.24214.041213C 0 H -3 N -1 O 0 S 0-17.03-17.026549Thomas, M.L.Tack, B.F.Biochemistry 22, 942-947, 1983Identification and alignment of a thiol ester site in the third component of guinea pig complement.DOI:10.1021/bi00273a036PMID:6838833chemical characterizationC, Qcross-link 2GO:0018232PSI-MOD:00117thioester bondCROSSLNK Isoglutamyl cysteine thioester (Cys-Gln)AA010931-Mar-199531-Mar-199531-Mar-20122'-(L-cystein-S-yl)-L-histidine(2S)-2-amino-3-[2-([(2R)-2-amino-2-carboxyethyl]sulfanyl)-1H-imidazol-4-yl]propanoic acidS-(2'-histidyl)cysteine(2R)-2-amino-3-[(4-[(2S)-2-amino-2-carboxyethyl]-1H-imidazol-2-yl)sulfanyl]propanoic acidCAS:77504-36-0C 9 H 10 N 4 O 2 S 1238.26238.052447C 0 H -2 N 0 O 0 S 0-2.02-2.015650Lerch, K.J. Biol. Chem. 257, 6414-6419, 1982Primary structure of tyrosinase from Neurospora crassa. II. Complete amino acid sequence and chemical structure of a tripeptide containing an unusual thioether.PMID:6210696chemical characterizationVirador, V.M.Reyes Grajeda, J.P.Blanco-Labra, A.Mendiola-Olaya, E.Smith, G.M.Moreno, A.Whitaker, J.R.J. Agric. Food Chem. 58, 1189-1201, 2010Cloning, sequencing, purification, and crystal structure of Grenache (Vitis vinifera) polyphenol oxidase.DOI:10.1021/jf902939qPMID:20039636X-ray diffraction, 2.20 angstromsReyes Grajeda, J.P.Virador, V.M.Blanco-Labra, A.Mendiola-Olaya, E.Smith, G.M.Moreno, A.Whitaker, J.R.submitted to the Protein Data Bank, March 2007Crystal structure of Grenache (Vitis vinifera) polyphenol oxidase.PDB:2P3XX-ray diffraction, 2.20 angstromsCysteinylhistidine probably does not have a functional role in the enzymatic activity of Neurospora crassa tyrosinase.C, Hcross-link 2GO:0018233PSI-MOD:00118thioether bondCROSSLNK 2'-(S-cysteinyl)-histidine (Cys-His)AA011031-Mar-199524-Oct-200813-Sep-2013L-lanthionine(R)-S-(2-amino-2-carboxyethyl)-L-cysteine(R,R)-2,6-diamino-4-thiaheptanedioic acid(R,R)-3,3'-thiobis-(2-aminopropanoic acid)(R,R)-bis(2-amino-2-carboxyethyl)sulfide2-amino-3-(2-amino-2-carboxyethyl)sulfanylpropanoic acid3,3'-thiobis-L-alanine(2R,2'R)-3,3'-sulfanediylbis(2-aminopropanoic acid)CAS:922-55-4ChEBI:21347C 6 H 8 N 2 O 2 S 1172.20172.030649C 0 H -2 N 0 O 0 S -1-34.08-33.987721C 0 H -2 N 0 O -1 S 0-18.02-18.010565Sloane, N.H.Unich, K.G.Biochemistry 5, 2658-2665, 1966Studies on amino acids in embryonic tissue. I. L-Lanthionine, a naturally occurring amino acid in the chick embryo.DOI:10.1021/bi00872a026PMID:6007887L-lanthionine and meso-lanthionine were isolated from heat and acid treated samples, and the meso form was assumed to be unnaturalClaesen, J.Bibb, M.Proc. Natl. Acad. Sci. U.S.A. 107, 16297-16302, 2010Genome mining and genetic analysis of cypemycin biosynthesis reveal an unusual class of posttranslationally modified peptides.DOI:10.1073/pnas.1008608107PMID:20805503biosynthesis as an intermediate from two cysteinesTang, W.van der Donk, W.A.Nature Chem. Biol. 9, 157-159, 2013The sequence of the enterococcal cytolysin imparts unusual lanthionine stereochemistry.DOI:10.1038/nchembio.1162PMID:23314913chiral gas chromatographic and mass spectrometric identificationThis diastereomeric form, which retains the conformation of the R chiral center of L-cysteine, does occur naturally but is not common. See RESID:AA0111.C, Ccross-link 2PSI-MOD:01837C, Scross-link 2GO:0018081GO:0018154PSI-MOD:00119lanthioninethioether bondNot availablethis modification is not annotated in UniProt featuresAA011131-Mar-199531-Mar-199513-Sep-2013meso-lanthionine(2R,2'S)-3,3'-thiobis-(2-aminopropanoic acid)(2R,6S)-2,6-diamino-4-thiaheptanedioic acid(2R,6S)-meso-lanthionine(2S)-2-amino-3-[[(2R)-2-amino-2-carboxyethyl]sulfanyl]propanoic acid(2S,6R)-meso-lanthionine [misnomer](R)-S-(2-amino-2-carboxyethyl)-D-cysteine(R,S)-bis(2-amino-2-carboxyethyl)sulfide3,3'-thiobis-meso-alaninecysteine-3-D-alanine thioether(2R,2'S)-3,3'-sulfanediylbis(2-aminopropanoic acid)CAS:922-56-5ChEBI:25013PDBHET:DALC 6 H 8 N 2 O 2 S 1172.20172.030649C 0 H -2 N 0 O -1 S 0-18.02-18.010565Allgaier, H.Jung, G.Werner, R.G.Schneider, U.Zaehner, H.Eur. J. Biochem. 160, 9-22, 1986Epidermin: sequencing of a heterodet tetracyclic 21-peptide amide antibiotic.DOI:10.1111/j.1432-1033.1986.tb09933.xPMID:3769923(1)H-NMR and (13)C-NMR identification; chemical synthesisMartin, N.I.Sprules, T.Carpenter, M.R.Cotter, P.D.Hill, C.Ross, R.P.Vederas, J.C.Biochemistry 43, 3049-3056, 2004Structural characterization of lacticin 3147, a two-peptide lantibiotic with synergistic activity.DOI:10.1021/bi0362065PMID:15023056He, Z.Kisla, D.Zhang, L.Yuan, C.Green-Church, K.B.Yousef, A.E.Appl. Environ. Microbiol. 73, 168-178, 2007Isolation and identification of a Paenibacillus polymyxa strain that coproduces a novel lantibiotic and polymyxin.DOI:10.1128/AEM.02023-06PMID:17071789desulfuration and reduction with nickel dichloride and isotope labeled sodium borohydrideLi, B.Sher, D.Kelly, L.Shi, Y.Huang, K.Knerr, P.J.Joewono, I.Rusch, D.Chisholm, S.W.van der Donk, W.A.Proc. Natl. Acad. Sci. U.S.A. 107, 10430-10435, 2010Catalytic promiscuity in the biosynthesis of cyclic peptide secondary metabolites in planktonic marine cyanobacteria.DOI:10.1073/pnas.0913677107PMID:20479271This diastereomeric form, despite the appearance of the same stereochemical designator, inverts the conformation of the S chiral center of L-serine to a D-alanine skeleton with S chiralty because of the altered prority of the beta-carbon. The stereosymmetry of the meso-form is broken within a peptide chain.peptidyl-phosphoserine/phosphothreonine dehydratase (EC 4.2.1.-)peptidyl-cysteine dehydroalanine/dehydrobutyrine ligase (EC 6.2.-.-)C, Scross-link 2GO:0018081GO:0018155PSI-MOD:00120lanthioninethioether bondCROSSLNK Lanthionine (Cys-Ser)CROSSLNK Lanthionine (Ser-Cys)AA011231-Mar-199531-Mar-199513-Sep-2013(2S,3S,2'R)-3-methyllanthionine(2S,3S,2'R)-2-amino-3-[(2-amino-2-carboxyethyl)thio]butanoic acid(2S,3S,6R)-2,6-diamino-3-methyl-4-thiaheptanedioic acid(2S,3S,6R)-3-methyllanthionine(2S-[2R*,3R*(S*)])-2-amino-3-[(2-amino-2-carboxyethyl)thio]butanoic acid3-methyl-D,L-lanthioninecysteine-3-D-butyrine thioether(2S,3S)-2-amino-3-([(2R)-2-amino-2-carboxyethyl]sulfanyl)butanoic acidCAS:42849-28-5ChEBI:20118PDBHET:DBBC 7 H 10 N 2 O 2 S 1186.23186.046299C 0 H -2 N 0 O -1 S 0-18.02-18.010565Allgaier, H.Jung, G.Werner, R.G.Schneider, U.Zaehner, H.Eur. J. Biochem. 160, 9-22, 1986Epidermin: sequencing of a heterodet tetracyclic 21-peptide amide antibiotic.DOI:10.1111/j.1432-1033.1986.tb09933.xPMID:3769923(1)H-NMR and (13)C-NMR identification; chemical synthesisHe, Z.Kisla, D.Zhang, L.Yuan, C.Green-Church, K.B.Yousef, A.E.Appl. Environ. Microbiol. 73, 168-178, 2007Isolation and identification of a Paenibacillus polymyxa strain that coproduces a novel lantibiotic and polymyxin.DOI:10.1128/AEM.02023-06PMID:17071789desulfuration and reduction with nickel dichloride and isotope labeled sodium borohydrideLi, B.Sher, D.Kelly, L.Shi, Y.Huang, K.Knerr, P.J.Joewono, I.Rusch, D.Chisholm, S.W.van der Donk, W.A.Proc. Natl. Acad. Sci. U.S.A. 107, 10430-10435, 2010Catalytic promiscuity in the biosynthesis of cyclic peptide secondary metabolites in planktonic marine cyanobacteria.DOI:10.1073/pnas.0913677107PMID:20479271There are 3 chiral centers, so there are 8 possible stereoisomers. Bacterial peptidyl-cysteine dehydroalanine/dehydrobutyrine ligase and peptide conformation preferentially produce the (2S,3S,2'R) diastereomer. The cysteine maintains its L configuration (R chirality), while the threonine 2-aminobutanoate skeleton has a D configuration (S chirality). For the (2R,3R,2'R) diastereomer, see RESID:AA0610.peptidyl-phosphoserine/phosphothreonine dehydratase (EC 4.2.1.-)peptidyl-cysteine dehydroalanine/dehydrobutyrine ligase (EC 6.2.-.-)C, Tcross-link 2GO:0018081GO:0018156PSI-MOD:00121lanthioninethioether bondCROSSLNK Beta-methyllanthionine (Cys-Thr)CROSSLNK Beta-methyllanthionine (Thr-Cys)AA011331-Mar-199531-Mar-199531-Mar-20123'-(L-cystein-S-yl)-L-tyrosine2-amino-3-[3-(2-amino-2-carboxyethylthio)-4-hydroxyphenyl]propanoic acid3'-(cystein-S-yl)tyrosineS-(tyros-3'-yl)cysteine(2S)-2-amino-3-(3-[(2R)2-amino-2-carboxyethylsulfanyl]-4-hydroxyphenyl)propanoic acidCOMe:BIM000265C 12 H 12 N 2 O 3 S 1264.30264.056863C 0 H -2 N 0 O 0 S 0-2.02-2.015650Ito, N.Phililips, S.E.V.Stevens, C.Ogel, Z.B.McPherson, M.J.Keen, J.N.Yadav, K.D.S.Knowles, P.F.Nature 350, 87-90, 1991Novel thioether bond revealed by a 1.7 angstrom crystal structure of galactose oxidase.DOI:10.1038/350087a0PMID:2002850Schnell, R.Sandalova, T.Hellman, U.Lindqvist, Y.Schneider, G.J. Biol. Chem. 280, 27319-27328, 2005Siroheme- and [Fe4S4]-dependent NirA from Mycobacterium tuberculosis is a sulfite reductase with a covalent Cys-Tyr bond in the active site.DOI:10.1074/jbc.M502560200PMID:15917234X-ray diffraction, 2.8 angstromsSchnell, R.Sandalova, T.Hellman, U.Lindqvist, Y.Schneider, G.submitted to the Protein Data Bank, April 2005Structure of Mycobacterium tuberculosis NirA protein.PDB:1ZJ8X-ray diffraction, 2.8 angstromsIn galactose oxidase, cysteinyltyrosine may exist as a stable free radical; the bond between the sulfur and the phenyl ring appears to have some double bond character.This modification should not be confused with 3-(S-L-cysteinyl)-L-tyrosine (see RESID:AA0396).C, Ycross-link 2GO:0018234PSI-MOD:00122thioether bondCROSSLNK 3'-(S-cysteinyl)-tyrosine (Cys-Tyr)CROSSLNK 3'-(S-cysteinyl)-tyrosine (Tyr-Cys)AA011431-Mar-199531-Mar-199531-May-2018N6-carboxy-L-lysine2-amino-6-carbamic hexanoic acid2-amino-6-carboxamido hexanoic acid2-azanyl-6-(carboxyazanyl)hexanoic acidlysine NZ-carboxylic acidN6-carbamyllysine [misnomer]N6-carboxylysine(2S)-2-amino-6-(carboxyamino)hexanoic acidCAS:45101-60-8ChEBI:49185PDBHET:FMTPDBHET:KCXC 7 H 12 N 2 O 3172.18172.084792C 1 H 0 N 0 O 244.0143.989829Morrow, J.S.Keim, P.Gurd, F.R.N.J. Biol. Chem. 249, 7484-7494, 1974CO-2 adducts of certain amino acids, peptides, and sperm whale myoglobin studied by carbon 13 and proton nuclear magnetic resonance.PMID:4436319(1)H-NMR and (13)C-NMR identificationStringer, C.D.Hartman, F.C.Biochem. Biophys. Res. Commun. 80, 1043-1048, 1978Sequences of two active-site peptides from spinach ribulosebisphosphate carboxylase/oxygenase.DOI:10.1016/0006-291X(78)91351-7PMID:637859Jabri, E.Carr, M.B.Hausinger, R.P.Karplus, P.A.Science 268, 998-1004, 1995The crystal structure of urease from Klebsiella aerogenes.DOI:10.1126/science.7754395PMID:7754395X-ray diffraction, 2.2 angstromsLapko, V.N.Smith, D.L.Smith, J.B.Protein Sci. 10, 1130-1136, 2001In vivo carbamylation and acetylation of water-soluble human lens alphaB-crystallin lysine 92.DOI:10.1110/ps.40901PMID:11369851mass spectrometric detection of N6-carbamoyllysine with N6-acetyl-L-lysine; the carbamoyl group (mass 43.02) attached to an amine, forming a ureido group, and produced by reaction with cyanate or isocyanate should be carefully distinguished from the carboxy group (mass 44.01) attached to an amine, forming a carbamoyl groupGolemi, D.Maveyraud, L.Vakulenko, S.Samama, J.P.Mobashery, S.Proc. Natl. Acad. Sci. U.S.A. 98, 14280-14285, 2001Critical involvement of a carbamylated lysine in catalytic function of class D beta-lactamases.DOI:10.1073/pnas.241442898PMID:11724923N6-carboxylysine can be produced by artifactual, catalytic or auto-catalytic processes.ribulose-bisphosphate carboxylase activase (EC 6.3.4.-)urease activase (EC 6.3.4.-)KGO:0018235PSI-MOD:00123MOD_RES N6-carboxylysineAA011531-Mar-199531-Mar-199513-Sep-2013N6-(1-carboxyethyl)-L-lysineN6-(1-carboxyethyl)lysineNZ-(1-carboxyethyl)lysine(2S)-2-amino-6-([(1S)-1-carboxyethyl]amino)hexanoic acidCAS:68852-50-6ChEBI:53015PDBHET:MCLC 9 H 16 N 2 O 3200.24200.116092C 3 H 4 N 0 O 272.0672.021129Thompson, J.Miller, S.P.F.J. Biol. Chem. 263, 2064-2069, 1988N6-(1-carboxyethyl)lysine formation by Stretococcus lactis. Purification, synthesis, and stereochemical structure.PMID:3123486chromatographic detection; (1)H-NMR identification; chemical synthesis confirmation of stereochemistryKrook, M.Ghosh, D.Stroemberg, R.Carlquist, M.Joernvall, H.Proc. Natl. Acad. Sci. U.S.A. 90, 502-506, 1993Carboxyethyllysine in a protein: native carbonyl reductase/NADP+-dependent prostaglandin dehydrogenase.DOI:10.1073/pnas.90.2.502PMID:8421682mass spectrometric detection; (1)H-NMR identification; chemical synthesisWermuth, B.Bohren, K.M.Ernst, E.FEBS Lett. 335, 151-154, 1993Autocatalytic modification of human carbonyl reductase by 2-oxocarboxylic acids.DOI:10.1016/0014-5793(93)80719-BPMID:8253186demonstration that the modification can be produced auto-catalyticallyautocatalyticKGO:0018238PSI-MOD:00124MOD_RES N6-1-carboxyethyl lysineAA011631-Mar-199531-Mar-199531-May-2018L-hypusine(2S,9R)-2,11-diazanyl-9-hydroxy-7-azaundecanoic acid(2S,9R)-hypusine2-azanyl-6-[(4-azanyl-2-hydroxybutyl)azanyl]hexanoic acidepsilon-(4-amino-2-hydroxybutyl)-L-lysineN(epsilon)-(4-amino-2-hydroxybutyl)-L-lysineN(zeta)-(4-amino-2-hydroxybutyl)-L-lysineN6-(4-amino-2-hydroxybutyl)-L-lysine(2S)-2-amino-6-([(2R)-4-amino-2-hydroxybutyl]amino)hexanoic acidCAS:34994-11-1ChEBI:64640C 10 H 21 N 3 O 2215.30215.163377C 4 H 9 N 1 O 187.1287.068414Shiba, T.Mizote, H.Kaneko, T.Nakajima, T.Kakimoto, Y.Biochim. 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Sci. 18, 475-479, 1993Is hypusine essential for eukaryotic cell proliferation?DOI:10.1016/0968-0004(93)90010-KPMID:8108861review articleWolff, E.C.Kang, K.R.Kim, Y.S.Park, M.H.Amino Acids 33, 341-350, 2007Posttranslational synthesis of hypusine: evolutionary progression and specificity of the hypusine modification.DOI:10.1007/s00726-007-0525-0PMID:17476569evolutionary considerationsHypusine appears to occur uniquely in translation initiation factor eIF-5A. For the detectable intermediate form, L-deoxyhypusine, in either deoxyhypusine synthase or in initiation factor 5A, eIF5A, see RESID:AA0564.It is highly probable that, like prokaryotic elongation factor EF-P, eIF-5A acts to relieve ribosome stalling during the translation of polyproline and prolylglycine sequences. The hypusine residue may extend into the ribosome active site and assist in catalysis of the petidyl transfer.deoxyhypusine synthase (EC 2.5.1.46)deoxyhypusine monooxygenase (EC 1.14.99.29)KGO:0008612PSI-MOD:00125hydroxylationhypusineMOD_RES HypusineAA011731-Mar-199531-Mar-199531-May-2018N6-biotinyl-L-lysine(3aS-(3aalpha,4beta,6aalpha))-N6-(5-(hexahydro-2-oxo-1H-thieno(3,4-d)imidazol-4-yl)-1-oxopentyl)-L-lysinebiocytinepsilon-N-biotinyllysineN6-biotinyllysineN6-[5-((3aS,4S,6aR)-hexahydro-2-oxo-1H-thieno[3,4-d]imidazol-4-yl)-1-oxopentyl]-L-lysine(2S)-2-amino-6-(5-[(3aS,4S,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanoylamino)hexanoic acidCAS:576-19-2CAS:58-85-5ChEBI:83144COMe:BIM000388PDBHET:BTNC 16 H 26 N 4 O 3 S 1354.47354.172562C 10 H 14 N 2 O 2 S 1226.29226.077599Thampy, K.G.Huang, W.Y.Wakil, S.J.Arch. Biochem. 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Biol. 26, 265-273, 1994The major biotinyl protein from Pisum sativum seeds covalently binds biotin at a novel site.DOI:10.1007/BF00039537PMID:7948875biotin covalently bound at a site differing from the usual biotin binding homologyAthappilly, F.K.Hendrickson, W.A.Structure 3, 1407-1419, 1995Structure of the biotinyl domain of acetyl-coenzyme A carboxylase determined by MAD phasing.DOI:10.1016/S0969-2126(01)00277-5PMID:8747466X-ray diffraction, 1.8 angstromsAthappilly, F.K.Hendrickson, W.A.submitted to the Protein Data Bank, November 1995Structure of the biotinyl domain of acetyl-coenzyme A carboxylase determined by MAD phasing.PDB:1BDOX-ray diffraction, 1.8 angstromsChew, Y.C.Camporeale, G.Kothapalli, N.Sarath, G.Zempleni, J.J. Nutr. Biochem. 17, 225-233, 2006Lysine residues in N-terminal and C-terminal regions of human histone H2A are targets for biotinylation by biotinidase.DOI:10.1016/j.jnutbio.2005.05.003PMID:16109483reports the natural biotinylation of histone lysinesbiotin--protein ligase (EC 6.3.4.-)biotin--[methylmalonyl-CoA-carboxyltransferase] ligase (EC 6.3.4.9)biotin--[propionyl-CoA-carboxylase (ATP-hydrolysing)] ligase (EC 6.3.4.10)biotin--[methylcrotonoyl-CoA-carboxylase] ligase (EC 6.3.4.11)biotin--[acetyl-CoA-carboxylase] ligase (EC 6.3.4.15)KGO:0018054PSI-MOD:00126biotinMOD_RES N6-biotinyllysineAA011831-Mar-199531-Mar-199531-May-2018N6-lipoyl-L-lysine(2S)-2-amino-6-(5-[(3R)-1,2-dithiolan-3-yl]pentanamido)hexanoic acid(2S,6'R)-2-amino-6-(6,8-dithiooctanamido)hexanoic acid2-amino-6-(5-[1,2-dithiolan-3-yl]-1-oxopentyl)aminohexanoic acidN6-6,8-dithiooctanoyllysineN6-lipoyllysine(2S)-2-amino-6-[(5-[(3R)-1,2-dithiolan-3-yl]pentanoyl)amino]hexanoic acidCAS:1200-22-2CAS:1676-89-7ChEBI:14919COMe:BIM000394PDBHET:LPAC 14 H 24 N 2 O 2 S 2316.48316.127920C 8 H 12 N 0 O 1 S 2188.30188.032957Fujiwara, K.Okamura-Ikeda, K.Motokawa, Y.J. Biol. Chem. 261, 8836-8841, 1986Chicken liver H-protein, a component of the glycine cleavage system: amino acid sequence and identification of the N-lipoyllysine residue.PMID:3522581detection of radioisotope labeled N-ethylmaleimide PTH derivativePackman, L.C.Borges, A.Perham, R.N.Biochem. J. 252, 79-86, 1988Amino acid sequence analysis of the lipoyl and peripheral subunit-binding domains in the lipoate acetyltransferase component of the pyruvate dehydrogenase complex from Bacillus stearothermophilus.PMID:3421911mass spectrometric identification of bis-pyridethylated derivativeCohen-Addad, C.Pares, S.Sieker, L.Neuburger, M.Douce, R.Nature Struct. Biol. 2, 63-68, 1995The lipoamide arm in the glycine decarboxylase complex is not freely swinging.DOI:10.1038/nsb0195-63PMID:7719855X-ray diffraction, 2.6 angstromsPares, S.Cohen-Addad, C.Sieker, L.Neuburger, M.Douce, R.submitted to the Protein Data Bank, February 1994H protein of the glycine cleavage system (aminomethyltransferase) (E.C.1.4.4.2).PDB:1HPCX-ray diffraction, 2.6 angstromslipoate--protein ligase[lipoyl-carrier protein]-L-lysine:lipoate ligase (AMP-forming) (EC 6.3.1.20)KGO:0018055PSI-MOD:00127lipoamideredox-active centerMOD_RES N6-lipoyllysineAA011931-Mar-199531-Mar-199530-Jun-2012N6-pyridoxal phosphate-L-lysine(2S)-2-amino-6-[([3-hydroxy-2-methyl-5-phosphonooxymethylpyridin-4-yl]methylidene)amino]hexanoic acidCAS:2440-59-7COMe:BIM000270PDBHET:LLPC 14 H 20 N 3 O 6 P 1357.30357.108972C 8 H 8 N 1 O 5 P 1229.13229.014009Bohney, J.P.Fonda, M.L.Feldhoff, R.C.FEBS Lett. 298, 266-268, 1992Identification of Lys(190) as the primary binding site for pyridoxal 5'-phosphate in human serum albumin.DOI:10.1016/0014-5793(92)80073-PPMID:1544460sequencing after reaction with (3)H-pyridoxal phosphate and borohydride reductionKGO:0018272PSI-MOD:00128phosphoproteinpyridine ringpyridoxal phosphateMOD_RES N6-(pyridoxal phosphate)lysineAA012031-Mar-199531-Mar-199530-Sep-2011N6-retinylidene-L-lysineN6-retinal-L-lysineN6-retinyl-lysine(2S)-2-amino-6-[(2E,4E,6E,8E)-3,7-dimethyl-9-(2,6,6-trimethylcyclohex-1-en-1-yl)-2,4,6,8-nonatetraenylidene]aminohexanoic acidCAS:116-31-4CAS:130443-70-8COMe:BIM000139PDBHET:LYRPDBHET:RETC 26 H 38 N 2 O 1394.60394.298414C 20 H 26 N 0 O 0266.43266.203451Mullen, E.Akhtar, M.Biochem. J. 211, 45-54, 1983Structural studies on membrane-bound bovine rhodopsin.PMID:6870827chemical conversion and identification as carboxymethyllysineKatre, N.V.Wolber, P.K.Stoeckenius, W.Stroud, R.M.Proc. Natl. Acad. Sci. U.S.A. 78, 4068-4072, 1981Attachment site(s) of retinal in bacteriorhodopsin.DOI:10.1073/pnas.78.7.4068PMID:6794028radioisotope labeling; chemical conversion and identification as retinyllysineStandfuss, J.Xie, G.Edwards, P.C.Burghammer, M.Oprian, D.D.Schertler, G.F.X.J. Mol. Biol. 372, 1179-1188, 2007Crystal structure of a thermally stable rhodopsin mutant.DOI:10.1016/j.jmb.2007.03.007PMID:17825322X-ray diffraction, 3.40 angstroms; the initials of "G.F. Schertler" in the PubMed citation are correctedStandfuss, J.Xie, G.Edwards, P.C.Burghammer, M.Oprian, D.D.Schertler, G.F.X.submitted to the Protein Data Bank, September 2006Crystal structure of a rhodopsin stabilizing mutant expressed in mammalian cells.PDB:2J4YX-ray diffraction, 2.60 angstromsThe all-trans form is shown. Light-induced interconversion with the 11-cis (4Z) form in rhodopsin is the basis for light sensing in animals. Light-induced interconversion with the 13-cis (2Z) form in bacteriorhodopsin is utilized for proton pumping in some archaea.KGO:0018273PSI-MOD:00129chromoproteinretinalMOD_RES N6-(retinylidene)lysineAA012131-Mar-199531-Mar-199531-May-2018L-allysine2-amino-5-formylvaleric acid2-amino-adipic acid semialdahyde2-aminoadipate 6-semialdehyde5-formyl-norvaline6-oxonorleucineAASAalpha-amino-adipic acid delta-semialdahyde(2S)-2-amino-6-oxohexanoic acidCAS:1962-83-0CAS:6665-12-9ChEBI:131803C 6 H 9 N 1 O 2127.14127.063329C 0 H -3 N -1 O 1-1.03-1.031634Kang, A.H.Bornstein, P.Piez, K.A.Biochemistry 6, 788-795, 1967The amino acid sequence of peptides from the cross-linking region of rat skin collagen.DOI:10.1021/bi00855a019PMID:5337886chemical characterizationClick, E.M.Bornstein, P.Biochemistry 9, 4699-4706, 1970Isolation and characterization of the cyanogen bromide peptides from the alpha 1 and alpha 2 chains of human skin collagen.DOI:10.1021/bi00826a012PMID:5529814chemical characterizationDiedrich, D.L.Schnaitman, C.A.Proc. Natl. Acad. Sci. U.S.A. 75, 3708-3712, 1978Lysyl-derived aldehydes in outer membrane proteins of Escherichia coli.DOI:10.1073/pnas.75.8.3708PMID:358196mass spectrometric detectionUmeda, H.Kawamorita, K.Suyama, K.Amino Acids 20, 187-199, 2001High-performance liquid chromatographic quantification of allysine as bis-p-cresol derivative in elastin.DOI:10.1007/s007260170059PMID:11332453chromatographic detectionHerranz, N.Dave, N.Millanes-Romero, A.Morey, L.Díaz, V.M.Lórenz-Fonfría, V.Gutierrez-Gallego, R.Jerónimo, C.Di Croce, L.García de Herreros, A.Peiró, S.Mol. Cell 46, 369-376, 2012Lysyl oxidase-like 2 deaminates lysine 4 in histone H3.DOI:10.1016/j.molcel.2012.03.002PMID:22483618mass spectrometric detection; lysyl oxidase-like 2, LOXL2, is reported to convert histone H3-trimethyl-lysine-4 to allysineprotein-lysine 6-oxidase (EC 1.4.3.13)Kincidental to RESID:AA0028GO:0018057PSI-MOD:00130MOD_RES AllysineAA012202-Nov-200102-Nov-200130-Sep-2011L-2-aminoadipic acid2-amino-1,4-butanedicarboxylic acidL-alpha-aminoadipic acid(2S)-2-aminohexanedioic acidCAS:1118-90-7CAS:542-32-5C 6 H 9 N 1 O 3143.14143.058243C 0 H -3 N -1 O 214.9714.963280Hiraoka, B.Y.Fukasawa, K.Fukasawa, K.M.Harada, M.J. Biochem. 88, 373-377, 1980Identification and quantification of alpha-amino adipic acid in bovine dentine phosphoprotein.PMID:7419498chromatographic detectionDiedrich, D.L.Schnaitman, C.A.Proc. Natl. Acad. Sci. U.S.A. 75, 3708-3712, 1978Lysyl-derived aldehydes in outer membrane proteins of Escherichia coli.DOI:10.1073/pnas.75.8.3708PMID:358196mass spectrometric characterizationBailey, A.J.Ranta, M.H.Nicholls, A.C.Partridge, S.M.Elsden, D.F.Biochem. Biophys. Res. Commun. 78, 1403-1410, 1977Isolation of alpha-amino adipic acid from mature dermal collagen and elastin. Evidence for an oxidative pathway in the maturation of collagen and elastin.DOI:10.1016/0006-291X(77)91448-6PMID:336041The oxidation of allysine to 2-aminoadipic acid is not well characterized.protein-lysine 6-oxidase (EC 1.4.3.13)KGO:0019728PSI-MOD:00131Not availablethis modification is not annotated in UniProt featuresAA012331-Mar-199531-Mar-199531-May-2018L-lysinoalanine(2R,9S)-lysinoalaninealaninolysineLALlysino-D-alanineN-epsilon-(2-amino-2-carboxyethyl)-L-lysineN6-(2-amino-2-carboxyethyl)-L-lysine(2S)-2-amino-6-([(2R)-2-amino-2-carboxyethyl]amino)hexanoic acidCAS:18810-04-3C 9 H 15 N 3 O 2197.24197.116427C 9 H 17 N 3 O 3215.25215.126991C 0 H -2 N 0 O -1-18.02-18.010565C 3 H 5 N 1 O 287.0887.032028Naruse, N.Tenmyo, O.Tomita, K.Konishi, M.Miyaki, T.Kawaguchi, H.Fukase, K.Wakamiya, T.Shiba, T.J. Antibiot. 42, 837-845, 1989Lanthiopeptin, a new peptide antibiotic. Production, isolation and properties of lanthiopeptin.PMID:2544544Yamauchi, T.Goto, M.Wu, H.Y.Uo, T.Yoshimura, T.Mihara, H.Kurihara, T.Miyahara, I.Hirotsu, K.Esaki, N.J. Biochem. 145, 421-424, 2009Serine racemase with catalytically active lysinoalanyl residue.DOI:10.1093/jb/mvp010PMID:19155267Hosoda, K.Ohya, M.Kohno, T.Maeda, T.Endo, S.Wakamatsu, K.J. Biochem. 119, 226-230, 1996Structure determination of an immunopotentiator peptide, cinnamycin, complexed with lysophosphatidylethanolamine by 1H-NMR1.PMID:8882709(1)H-NMR identificationHosoda, K.Ohya, M.Kohno, T.Maeda, T.Endo, S.Wakamatsu, K.submitted to the Protein Data Bank, January 2006Structure of cinnamycin complexed with lysophosphatidylethanolamine.PDB:2DDENMRThe formula and records labeled "KSX" refers to a lysinoalanine residue produced as a cross-link between a peptidyl lysine and a peptidyl serine residue. For the cross-link the stereochemistry of the second chiral center has not been resolved; it appears to epimerize rapidly during acid hydrolysis. The (2R,9S) form is shown.The formula and records labeled "LYS" refers to a lysinoalanine residue produced as a peptidyl lysine residue bonded to a free serine. For the lysine modification by D-serine, the diastereomer is (2R,9S).K, Scross-link 2GO:0018274PSI-MOD:00132KPSI-MOD:01838CROSSLNK Lysinoalanine (Ser-Lys)MOD_RES Lysino-D-alanine (Lys)AA012431-Mar-199531-Mar-199513-Sep-2013N6-(L-isoglutamyl)-L-lysine2-azanyl-6-([4-azanyl-4-carboxybutanoyl]azanyl)hexanoic acid5-glutamyl N6-lysineN(epsilon)-(gamma-glutamyl)lysine(2S)-2-amino-6-([(4S)-4-amino-4-carboxybutanoyl]amino)hexanoic acidCAS:17105-15-6ChEBI:21863C 11 H 17 N 3 O 3239.27239.126991C 0 H -3 N -1 O 0-17.03-17.026549C 0 H -2 N 0 O -1-18.02-18.010565Lorand, L.Downey, J.Gotoh, T.Jacobsen, A.Tokura, S.Biochem. Biophys. Res. Commun. 31, 222-230, 1968The transpeptidase system which crosslinks fibrin by gamma-glutamyl-epsilon-lysine bonds.DOI:10.1016/0006-291X(68)90734-1PMID:5656070title typographical errors in the PubMed citation are correctedMatačić, S.Loewy, A.G.Biochem. Biophys. Res. Commun. 30, 356-362, 1968The identification of isopeptide crosslinks in insoluble fibrin.DOI:10.1016/0006-291X(68)90750-XPMID:5637041chemical characterization; the encoding of an author's name in the PubMed citation is corrected to UTF8Simon, M.Green, H.J. Biol. Chem. 263, 18093-18098, 1988The glutamine residues reactive in transglutaminase-catalyzed cross-linking of involucrin.PMID:2461365radioisotope labeling and linkage analysisShimizu, T.Hozumi, K.Horiike, S.Nunomura, K.Ikegami, S.Takao, T.Shimonishi, Y.Nature 380, 32, 1996A covalently crosslinked histone.DOI:10.1038/380032a0PMID:8598899mass spectrometric and linkage analysisKudryashov, D.S.Durer, Z.A.Ytterberg, A.J.Sawaya, M.R.Pashkov, I.Prochazkova, K.Yeates, T.O.Loo, R.R.Loo, J.A.Satchell, K.J.Reisler, E.Proc. Natl. Acad. Sci. U.S.A. 105, 18537-18542, 2008Connecting actin monomers by iso-peptide bond is a toxicity mechanism of the Vibrio cholerae MARTX toxin.DOI:10.1073/pnas.0808082105PMID:19015515mass spectrometric identification; X-ray diffraction, 3.21 angstroms; ATP is required to produce the isopeptide bond between lysine and glutamic acidSawaya, M.R.Kudryashov, D.S.Pashkov, I.Reisler, E.Loo, R.R.submitted to the Protein Data Bank, March 2008Actin dimer cross-linked by V. cholerae MARTX toxin and complexed with gelsolin-segment 1.PDB:3CJBX-ray diffraction, 3.21 angstromsPearce, M.J.Mintseris, J.Ferreyra, J.Gygi, S.P.Darwin, K.H.Science 322, 1104-1107, 2008Ubiquitin-like protein involved in the proteasome pathway of Mycobacterium tuberculosis.DOI:10.1126/science.1163885PMID:18832610identification of prokaryotic ubiquitin-like protein, pup, cross-linkage of terminal glutamine to N6-lysine after deamidationIyer, L.M.Burroughs, A.M.Aravind, L.Biol. Direct 3, 45, 2008Unraveling the biochemistry and provenance of pupylation: a prokaryotic analog of ubiquitination.DOI:10.1186/1745-6150-3-45PMID:18980670the homology of pafa, which activates the C-terminal glutamate of pup, suggests but does not establish that the linkage is through the gamma-carboxyl; the pup homologs in various bacteria have either glutamine or glutamic acid as the C-terminusSutter, M.Damberger, F.F.Imkamp, F.Allain, F.H.Weber-Ban, E.J. Am. Chem. Soc. 132, 5610-5612, 2010Prokaryotic ubiquitin-like protein (Pup) is coupled to substrates via the side chain of its C-terminal glutamate.DOI:10.1021/ja910546xPMID:20355727(1)H-, (13)C-, (15)N-NMR characterization establishes that the bond is through the C5-carboxylCross-linking of pup has been established to be through the gamma-carboxyl group of the C-terminal glutamine or glutamic acid.For the modification of a peptidyl glutamic acid by formation of an isopeptide bond through the gamma-carboxyl group to the N2-amino group of a non-peptidyl lysine, see RESID:AA0505.The structure shown in PubChem for this name is incorrect, being instead alpha-(gamma-glutamyl)-lysine, which is not the product of peptide transamidation.protein-glutamine gamma-glutamyltransferase (EC 2.3.2.13)K, Qcross-link 2GO:0003810GO:0018153PSI-MOD:00133E, Kcross-link 2PSI-MOD:01484isopeptide bondCROSSLNK Isoglutamyl lysine isopeptide (Gln-Lys) (interchain with K-...)CROSSLNK Isoglutamyl lysine isopeptide (Glu-Lys) (interchain with K-...)CROSSLNK Isoglutamyl lysine isopeptide (Lys-Gln)CROSSLNK Isoglutamyl lysine isopeptide (Lys-Gln) (interchain with Q-...)CROSSLNK Isoglutamyl lysine isopeptide (Lys-Glu) (interchain with E-...)CROSSLNK Glutamyl lysine isopeptide (Gln-Lys) (interchain with K-...)this UniProt feature is used when it has not been determined whether the linkage is through the alpha- or gamma-carboxyl groupCROSSLNK Glutamyl lysine isopeptide (Glu-Lys) (interchain with K-...)this UniProt feature is used when it has not been determined whether the linkage is through the alpha- or gamma-carboxyl groupCROSSLNK Glutamyl lysine isopeptide (Lys-Gln) (interchain with Q-...)this UniProt feature is used when it has not been determined whether the linkage is through the alpha- or gamma-carboxyl groupCROSSLNK Glutamyl lysine isopeptide (Lys-Glu) (interchain with E-...)this UniProt feature is used when it has not been determined whether the linkage is through the alpha- or gamma-carboxyl groupAA012531-Mar-199531-Mar-199530-Sep-2011N6-(glycyl)-L-lysineN6-glycyllysine(2S)-2-amino-6-[(aminoacetyl)amino]hexanoic acidCAS:191-22-6ChEBI:21885C 8 H 14 N 3 O 2184.22184.108602C 0 H -2 N 0 O -1-18.02-18.010565Vierstra, R.D.Langan, S.M.Schaller, G.E.Biochemistry 25, 3105-3108, 1986Complete amino acid sequence of ubiquitin from the higher plant Avena sativa.DOI:10.1021/bi00359a006G, Kcarboxyl-terminalcross-link 2GO:0018276PSI-MOD:00134blocked carboxyl endisopeptide bondCROSSLNK Glycyl lysine isopeptide (Gly-Lys) (interchain with K-...)CROSSLNK Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter ...)AA012631-Mar-199531-Mar-199501-Mar-2013N-(L-isoaspartyl)-glycine2-amino-N4-(carboxymethyl)-butanediamic acidisoaspartyl glycineN-beta-aspartylglycineN4-(carboxymethyl)-asparagine(2S)-2-amino-4-(carboxymethyl)amino-4-oxobutanoic acidCAS:3790-52-1ChEBI:21479C 6 H 7 N 2 O 3155.13155.045667C 0 H -3 N -1 O 0-17.03-17.026549C 0 H -2 N 0 O -1-18.02-18.010565Wyss, D.F.Lahm, H.W.Manneberg, M.Labhardt, A.M.J. Antibiot. 44, 172-180, 1991Anantin -- a peptide antagonist of the atrial natriuretic factor (ANF). II. Determination of the primary sequence by NMR on the basis of proton assignments.PMID:1826288(1)H-NMR identificationKnappe, T.A.Linne, U.Zirah, S.Rebuffat, S.Xie, X.Marahiel, M.A.J. Am. Chem. Soc. 130, 11446-11454, 2008Isolation and structural characterization of capistruin, a lasso peptide predicted from the genome sequence of Burkholderia thailandensis E264.DOI:10.1021/ja802966gPMID:18671394mass spectrometric characterization and (1)H-NMR identification; gene sequence and biosynthetic studies establish that aspartic acid is activated by ATP to form the isopeptide bondFor the "lariat" or "lasso" cross-link between glycine and glutamic acid, see RESID:AA0360.capistruin synthase, beta-aspartyl-glycine cyclo-ligase CapC (EC 6.3.3.-)G, Namino-terminalcross-link 2GO:0018264PSI-MOD:00135D, Gamino-terminalcross-link 2PSI-MOD:01805blocked amino endisopeptide bondCROSSLNK Isoaspartyl glycine isopeptide (Gly-Asn)CROSSLNK Isoaspartyl glycine isopeptide (Gly-Asp)CROSSLNK Isoaspartyl glycine isopeptide (Asn-Gly)CROSSLNK Isoaspartyl glycine isopeptide (Asp-Gly)AA012731-Mar-199531-Mar-199530-Sep-2011pyruvic acid2-oxopropanoic acidCAS:127-17-3COMe:BIM000277PDBHET:PYRC 3 H 3 O 271.0671.013304C 0 H -3 N -1 O 1 S -1-33.09-33.003705C 0 H -3 N -1 O 0-17.03-17.026549C -6 H -7 N -1 O 0-93.13-93.057849Dixon, H.B.F.Fields, R.Meth. Enzymol. 25, 409-419, 1972Specific modification of NH2-terminal residues by transamination.DOI:10.1016/S0076-6879(72)25036-4chemical detection and amino terminal release using 1,2-diaminobenzeneGavaret, J.M.Cahnmann, H.J.Nunez, J.J. Biol. Chem. 254, 11218-11222, 1979The fate of the “lost side chain” during thyroid hormonogenesis.PMID:500639radiolabeling and chemical identification of pyruvate from tyrosineLi, Q.X.Dowhan, W.J. Biol. Chem. 263, 11516-11522, 1988Structural characterization of Escherichia coli phosphatidylserine decarboxylase.PMID:3042771chemical conversion to alanine using sodium cyanoborohydrideGallagher, T.Rozwarski, D.A.Ernst, S.R.Hackert, M.L.J. Mol. Biol. 230, 516-528, 1993Refined structure of the pyruvoyl-dependent histidine decarboxylase from Lactobacillus 30a.DOI:10.1006/jmbi.1993.1168PMID:8464063X-ray diffraction, 2.5 angstromsGallagher, T.Rozwarski, D.A.Ernst, S.R.Hackert, M.L.submitted to the Protein Data Bank, December 1992Refined structure of the pyruvoyl-dependent histidine decarboxylase from Lactobacillus 30a.PDB:1PYAAlbert, A.Dhanaraj, V.Genschel, U.Khan, G.Ramjee, M.K.Pulido, R.Sibanda, B.L.von Delft, F.Witty, M.Blundell, T.L.Smith, A.G.Abell, C.Nature Struct. Biol. 5, 289-293, 1998Crystal structure of aspartate decarboxylase at 2.2 A resolution provides evidence for an ester in protein self-processing.DOI:10.1038/nsb0498-289PMID:9546220X-ray diffraction, 2.20 angstroms; structure of ester intermediate formed after the N to O acyl shiftAlbert, A.Dhanaraj, V.Genschel, U.Khan, G.Ramjee, M.K.Pulido, R.Sybanda, B.L.Vondelf, F.Witty, M.Blundell, T.L.Smith, A.G.Abell, C.submitted to the Protein Data Bank, October 1997Pyruvoyl dependent aspartate decarboxylase.PDB:1AW8X-ray diffraction, 2.00 angstroms; evidence is presented for partial presence of the ester formed after the N to O acyl shiftKabisch, U.C.Graentzdoerffer, A.Schierhorn, A.Ruecknagel, K.P.Andreesen, J.R.Pich, A.J. Biol. Chem. 274, 8445-8454, 1999Identification of D-proline reductase from clostridium sticklandii as a selenoenzyme and indications for a catalytically active pyruvoyl group derived from a cysteine residue by cleavage of a proprotein.DOI:10.1074/jbc.274.13.8445PMID:10085076mass spectrometric and chemical characterizationThe pyruvic acid forming an amide bond between its 1-carboxyl group and an amino terminal residue arises from oxidative deamination of an encoded amino acid, either cysteine or serine. It is important to distinguish this modification from an exogenous pyruvic acid forming a ketimine bond with its 2-keto group and an amino terminal residue (see RESID:AA0274 and RESID:AA0275).Camino-terminalGO:0018058GO:0018387PSI-MOD:00136PSI-MOD:01154Samino-terminalGO:0018058GO:0018387PSI-MOD:00807PSI-MOD:01154Yamino-terminalPSI-MOD:01661blocked amino endMOD_RES Pyruvic acid (Cys)MOD_RES Pyruvic acid (Ser)MOD_RES Pyruvic acid (Tyr)AA012831-Mar-199531-Mar-199530-Sep-2011L-3-phenyllactic acid(2S)-2-hydroxy-3-phenylpropanoic acidCAS:20312-36-1C 9 H 9 O 2149.17149.060255C 0 H -1 N -1 O 10.980.984016Grimmelikhuijzen, C.J.P.Rinehart, K.L.Jacob, E.Graff, D.Reinscheid, R.K.Nothacker, H.P.Staley, A.L.Proc. Natl. Acad. Sci. U.S.A. 87, 5410-5414, 1990Isolation of L-3-phenyllactyl-Leu-Arg-Asn-NH2 (Antho-RNamide), a sea anemone neuropeptide containing an unusual amino-terminal blocking group.DOI:10.1073/pnas.87.14.5410PMID:1973541mass spectrometric and (1)H-NMR identification; chromatographic stereochemical characterization; chemical synthesisFamino-terminalGO:0018058GO:0018061PSI-MOD:00137blocked amino endMOD_RES 3-phenyllactic acidAA012931-Mar-199531-Mar-199525-Feb-20112-oxobutanoic acid2-ketobutyric acid2-oxobutyric acid2-oxobutanoic acidCAS:600-18-0ChEBI:30831PDBHET:2KTC 4 H 5 O 285.0885.028954C 0 H -3 N -1 O 0-17.03-17.026549Kaletta, C.Entian, K.D.Kellner, R.Jung, G.Reis, M.Sahl, H.G.Arch. Microbiol. 152, 16-19, 1989Pep5, a new lantibiotic: structural gene isolation and prepeptide sequence.DOI:10.1007/BF00447005PMID:2764678Weil, H.P.Beck-Sickinger, A.G.Metzger, J.Stevanovic, S.Jung, G.Josten, M.Sahl, H.G.Eur. J. Biochem. 194, 217-223, 1990Biosynthesis of the lantibiotic Pep5. Isolation and characterization of a prepeptide containing dehydroamino acids.DOI:10.1111/j.1432-1033.1990.tb19446.xPMID:2253617Martin, N.I.Sprules, T.Carpenter, M.R.Cotter, P.D.Hill, C.Ross, R.P.Vederas, J.C.Biochemistry 43, 3049-3056, 2004Structural characterization of lacticin 3147, a two-peptide lantibiotic with synergistic activity.DOI:10.1021/bi0362065PMID:15023056chemical method for removing the amino terminal blockTamino-terminalGO:0018058GO:0018278PSI-MOD:00138blocked amino endMOD_RES 2-oxobutanoic acidAA013031-Mar-199531-Mar-199530-Jun-2012N2-succinyl-L-tryptophan(2S)-2-amino-(6,7-dihydro-6,7-dioxo-1H-indole)-3-propanoic acid(2S)-2-(3-carboxypropanoyl)amino-3-(1H-indol-3-yl)propanoic acidCAS:514803-26-0C 15 H 15 N 2 O 4287.29287.103182C 4 H 4 N 0 O 3100.07100.016044Chan, W.C.Bycroft, B.W.Leyland, M.L.Lian, L.Y.Roberts, G.C.K.Biochem. J. 291, 23-27, 1993A novel post-translational modification of the peptide antibiotic subtilin: isolation and characterization of a natural variant from Bacillus subtilis A.T.C.C. 6633.PMID:8471040mass spectrometric, (1)H-NMR, and (13)C-NMR identification; chemical synthesisWamino-terminalGO:0018062PSI-MOD:00139blocked amino endMOD_RES N2-succinyltryptophanAA013131-Mar-199531-Mar-199530-Sep-2008S-phycocyanobilin-L-cysteine(2R,3R)-3-[(1R)-1-(((2R)-2-amino-2-carboxy)ethylsulfanyl)ethyl]-18-ethyl-1,2,3,19,21,22,24-heptahydro-2,7,13,17-tetramethyl-1,19-dioxo-(21H,22H,24H)-bilin-8,12-dipropanoic acidPCBphycobilin cysteinephycocyanobilin cysteine adduct(2R,3R)-3-[(1R)-1-(((2R)-2-amino-2-carboxy)ethylsulfanyl)ethyl]-8,12-bis(2-carboxyethyl)-18-ethyl-2,7,13,17-tetramethyl-1,2,3,19,21,22,24-heptahydrobilin-1,19(21H,22H,24H)-dioneCAS:20298-86-6ChEBI:15617COMe:BIM000148PDBHET:CYCC 36 H 43 N 5 O 7 S 1689.83689.288320C 33 H 38 N 4 O 6 S 0586.69586.279135Nagy, J.O.Bishop, J.E.Klotz, A.V.Glazer, A.N.Rapoport, H.J. Biol. Chem. 260, 4864-4868, 1985Bilin attachment sites in the alpha, beta, and gamma subunits of R-phycoerythrin. Structural studies on singly and doubly linked phycourobilins.PMID:3838747mass spectrometric and (1)H-NMR identificationMoss, G.P.Eur. J. Biochem. 178, 277-328, 1988IUPAC-IUB Joint Commission on Biochemical Nomenclature (JCBN). Nomenclature of tetrapyrroles. Recommendations 1986.DOI:10.1111/j.1432-1033.1988.tb14453.xPMID:3208761Szalontai, B.Gombos, Z.Csizmadia, V.Bagyinka, C.Lutz, M.Biochemistry 33, 11823-11832, 1994Structure and interactions of phycocyanobilin chromophores in phycocyanin and allophycocyanin from an analysis of their resonance Raman spectra.DOI:10.1021/bi00205a019PMID:7918400raman spectroscopy of covalently bound (14)N and (15)N isotopic chromophoresStec, B.Troxler, R.F.Teeter, M.M.submitted to the Protein Data Bank, June 1995Structure of phycocyanin from Cyanidium caldarium at 1.65A resolution.PDB:1PHNX-ray diffraction, 1.65 angstromsShen, G.Saunee, N.A.Williams, S.R.Gallo, E.F.Schluchter, W.M.Bryant, D.A.J. Biol. Chem. 281, 17768-17778, 2006Identification and characterization of a new nlass of bilin lyase: the cpcT gene encodes a bilin lyase responsible for attachment of phycocyanobilin to Cys-153 on the beta-subunit of phycocyanin in Synechococcus sp. PCC 7002.DOI:10.1074/jbc.M602563200PMID:16644722A second linkage, an ester between a serine and one of the propanoic acid groups, was reported at one time but was not confirmed. A second cysteine linkage has also been reported to a moiety thought to be phycocyanobilin.The phycocyanobilins transmit blue.phycocyanobilin lyase (EC 4.4.1.-)CGO:0017009GO:0018353PSI-MOD:00140chromoproteinphycocyanobilinthioether bondBINDING Phycocyanobilin chromophore (covalent; via 1 link)AA013231-Mar-199530-Jun-200530-Sep-2008S-phycoerythrobilin-L-cysteine18-ethenyl-3-[1-((2-amino-2-carboxy)ethylsulfanyl)ethyl]-2,3,15,16-tetrahydro-2,7,13,17-tetramethyl-1,19-dioxo-(21H,22H,24H)-bilin-8,12-dipropanoic acidPEBphycoerythrobilin cysteine adduct(2S,3R,16R)-18-ethenyl-3-[(1R)-1-(((2R)-2-amino-2-carboxy)ethylsulfanyl)ethyl]-8,12-bis(2-carboxyethyl)-2,7,13,17-tetramethyl-2,3,15,16-tetrahydrobilin-1,19(21H,22H,24H)-dioneCAS:18097-67-1ChEBI:15618COMe:BIM000147PDBHET:PEBC 36 H 43 N 5 O 7 S 1689.83689.288320C 33 H 38 N 4 O 6 S 0586.69586.279135Nagy, J.O.Bishop, J.E.Klotz, A.V.Glazer, A.N.Rapoport, H.J. Biol. Chem. 260, 4864-4868, 1985Bilin attachment sites in the alpha, beta, and gamma subunits of R-phycoerythrin. Structural studies on singly and doubly linked phycourobilins.PMID:3838747mass spectrometric and (1)H-NMR identificationMoss, G.P.Eur. J. Biochem. 178, 277-328, 1988IUPAC-IUB Joint Commission on Biochemical Nomenclature (JCBN). Nomenclature of tetrapyrroles. Recommendations 1986.DOI:10.1111/j.1432-1033.1988.tb14453.xPMID:3208761Chang, W.R.Jiang, T.Wan, Z.L.Zhang, J.P.Yang, Z.X.Liang, D.C.J. Mol. Biol. 262, 721-731, 1996Crystal structure of R-phycoerythrin from Polysiphonia urceolata at 2.8 angstroms resolution.DOI:10.1006/jmbi.1996.0547PMID:8876649Liang, D.C.Jiang, T.Chang, W.R.submitted to the Protein Data Bank, January 1996Crystal structure of R-phycoerythrin from Polysiphonia at 2.8 A resolution.PDB:1LIASee the comment for S-phycocyanobilin-L-cysteine (RESID:AA0131). There is an additional chiral center at C-16.The phytochromobilins and phycoerythrobilins transmit red.CGO:0017011GO:0018168PSI-MOD:00141chromoproteinphycoerythrobilinthioether bondBINDING Phycoerythrobilin chromophore (covalent; via 1 link)AA013331-Mar-199531-Mar-199531-Mar-2012S-phytochromobilin-L-cysteine18-ethenyl-3-[1-((2-amino-2-carboxy)ethylsulfanyl)ethyl]-1,2,3,19,22,24-hexahydro-2,7,13,17-tetramethyl-1,19-dioxo-21H-biline-8,12-dipropanoic acidphytochrome chromophorephytochromobilin cysteine adduct(2R,3R)-3-[(1R)-1-(((2R)-2-amino-2-carboxy)ethylsulfanyl)ethyl]-8,12-bis(2-carboxyethyl)-18-ethyl-2,7,13,17-tetramethyl-1,2,3,19,21,22,24-heptahydrobilin-1,19(21H,22H,24H)-dioneCAS:143392-71-6ChEBI:15619COMe:BIM000255C 36 H 41 N 5 O 7 S 1687.81687.272670C 33 H 36 N 4 O 6 S 0584.67584.263485Lagarias, J.C.Rapoport, H.J. Am. Chem. Soc. 102, 4821-4828, 1980Chromopeptides from phytochrome. The structure and linkage of the P(R) form of the phytochrome chromophore.DOI:10.1021/ja00534a042Ruediger, W.Thuemmler, F.Cmiel, E.Schneider, S.Proc. Natl. Acad. Sci. U.S.A. 80, 6244-6248, 1983Chromophore structure of the physiologically active form (P(fr)) of phytochrome.DOI:10.1073/pnas.80.20.6244PMID:16593380Moss, G.P.Eur. J. Biochem. 178, 277-328, 1988IUPAC-IUB Joint Commission on Biochemical Nomenclature (JCBN). Nomenclature of tetrapyrroles. Recommendations 1986.DOI:10.1111/j.1432-1033.1988.tb14453.xPMID:3208761Cornejo, J.Beale, S.I.Terry, M.J.Lagarias, J.C.J. Biol. Chem. 267, 14790-14798, 1992Phytochrome assembly. The structure and biological activity of 2(R),3(E)-phytochromobilin derived from phycobiliproteins.PMID:1634523The phytochromobilins and phycoerythrobilins transmit red.CGO:0017012GO:0018358PSI-MOD:00142chromoproteinphytochromobilinthioether bondBINDING Phytochromobilin chromophore (covalent; via 1 link)AA013431-Mar-199531-Mar-199531-Dec-2012heme-bis-L-cysteine2,4-bis[1-(S-cysteinyl)ethyl]protoporphyrin IXbiscysteinyl heme(7,12-bis[(1S)-1-([(2R)-2-amino-2-carboxyethyl]sulfanyl)ethyl]-3,8,13,17-tetramethyl-21H,23H-porphine-2,18-bis[2-carboxyethyl]-N21,N22,N23,N24)-ferrateCAS:14875-96-8ChEBI:17627COMe:BIM000241C 40 Fe 1 H 42 N 6 O 6 S 2822.78822.195663C 34 Fe 1 H 32 N 4 O 4 S 0616.50616.177293Dickerson, R.E.Takano, T.Eisenberg, D.Kallai, O.B.Samson, L.Cooper, A.Margoliash, E.J. Biol. Chem. 246, 1511-1535, 1971Ferricytochrome c. I. General features of the horse and bonito proteins at 2.8 A resolution.PMID:5545094X-ray diffraction, 2.8 angstromsGans, P.Simorre, J.P.Caffrey, M.Marion, D.Richaud, P.Vermeglio, A.J. Biochem. 119, 1131-1142, 1996Sequential 1H and 15N NMR resonance assignment and secondary structure of ferrocytochrome c2 from Rhodobacter sphaeroides.PMID:8827449(1)H-NMR and (15)N-NMR characterization; conformation of residues 22-145Allen, J.W.Tomlinson, E.J.Hong, L.Ferguson, S.J.J. Biol. Chem. 277, 33559-33563, 2002The Escherichia coli cytochrome c maturation (Ccm) system does not detectably attach heme to single cysteine variants of an apocytochrome c.DOI:10.1074/jbc.M204963200PMID:12048216evidence that a disulfide bond is transiently present in apocytochrome c prior to heme attachmentholocytochrome-c synthase (EC 4.4.1.17)C, Ccross-link 2GO:0018063GO:0018379PSI-MOD:00143chromoproteinhemeironmetalloproteinthioether bondBINDING Heme (covalent)AA013531-Mar-199531-Mar-199501-Mar-2013heme-L-cysteine4-[1-(S-cysteinyl)ethyl]protoporphyrin IXcysteinyl heme(12-ethenyl-7-[(1S)-1-([(2R)-2-amino-2-carboxyethyl]sulfanyl)ethyl]-3,8,13,17-tetramethyl-21H,23H-porphine-2,18-bis[2-carboxyethyl]-N21,N22,N23,N24)-ferrateCAS:14875-96-8ChEBI:17627C 37 Fe 1 H 37 N 5 O 5 S 1719.64719.186478C 34 Fe 1 H 32 N 4 O 4 S 0616.50616.177293Pettigrew, G.W.Leaver, J.L.Meyer, T.E.Ryle, A.P.Biochem. J. 147, 291-302, 1975Purification, properties and amino acid sequence of atypical cytochrome c from two protozoa, Euglena gracilis and Crithidia oncopelti.PMID:170910chemical and spectrographic characterization; it is uncertain whether the cysteine is linked through the 7-vinyl (as indicated) or through the 12-vinyl groupMukai, K.Yoshida, M.Toyosaki, H.Yao, Y.Wakabayashi, S.Matsubara, H.Eur. J. Biochem. 178, 649-656, 1989An atypical heme-binding structure of cytochrome c1 of Euglena gracilis mitochondrial complex III.DOI:10.1111/j.1432-1033.1989.tb14494.xPMID:2536325chemical and spectrographic characterizationMiller, M.J.Rapoport, H.J. Am. Chem. Soc. 99, 3479-3485, 1977Porphyrin-protein bond of cytochrome c558 from Euglena gracilis.DOI:10.1021/ja00452a048PMID:192772chemical characterization; the linkage is established to be through the 7-ethenyl groupYu, J.Le Brun, N.E.J. Biol. Chem. 273, 8860-8866, 1998Studies of the cytochrome subunits of menaquinone:cytochrome c reductase (bc complex) of Bacillus subtilis. Evidence for the covalent attachment of heme to the cytochrome b subunit.DOI:10.1074/jbc.273.15.8860PMID:9535866chemical characterization; demonstration of an unusual covalent heme attachment in a cytochrome bGinger, M.L.Sam, K.A.Allen, J.W.Biochem. J. 448, 253-260, 2012Probing why trypanosomes assemble atypical cytochrome c with an AxxCH haem-binding motif instead of CxxCH.DOI:10.1042/BJ20120757PMID:22928879attchment of heme to atypical AXXCH motifs in trypanosome mitochondrial cytochromesThe stereochemistry of the 7-alpha carbon has not been determined. The S form is shown.holocytochrome-c synthase (EC 4.4.1.17)CGO:0018063GO:0018378PSI-MOD:00144chromoproteinhemeironmetalloproteinthioether bondBINDING Heme (covalent; via 1 link)AA013631-Mar-199531-Mar-199501-Mar-2013tetrakis-L-cysteinyl irontetrakis(cysteinato-kappaS)-ironCOMe:BIM000027C 12 Fe 1 H 16 N 4 O 4 S 42-464.37463.941474C 0 Fe 1 H -4 N 0 O 0 S 02-51.8151.904735Watenpaugh, K.D.Siecker, L.C.Herriott, J.R.Jensen, L.H.Acta Crystallogr. B 29, 943-956, 1973Refinement of the model of a protein: rubredoxin at 1.5 angstrom resolution.DOI:10.1107/S0567740873003675X-ray diffraction, 1.5 angstromsDay, M.W.Hsu, B.T.Joshua-Tor, L.Park, J.B.Zhou, Z.H.Adams, M.W.W.Rees, D.C.Protein Sci. 1, 1494-1507, 1992X-ray crystal structures of the oxidized and reduced forms of the rubredoxin from the marine hyperthermophilic archaebacterium Pyrococcus furiosus.DOI:10.1002/pro.5560011111PMID:1303768X-ray diffraction, 1.8 angstromsDay, M.W.Hsu, B.T.Joshua-Tor, L.Park, J.B.Zhou, Z.H.Adams, M.W.W.Rees, D.C.submitted to the Protein Data Bank, May 1992X-ray crystal structures of the oxidized and reduced forms of the rubredoxin from the marine hyperthermophilic archaebacterium Pyrococcus furiosus.PDB:1CAAX-ray diffraction, 1.80 angstromsDay, M.W.Hsu, B.T.Joshua-Tor, L.Park, J.B.Zhou, Z.H.Adams, M.W.W.Rees, D.C.submitted to the Protein Data Bank, May 1992X-ray crystal structures of the oxidized and reduced forms of the rubredoxin from the marine hyperthermophilic archaebacterium Pyrococcus furiosus.PDB:1CADX-ray diffraction, 1.80 angstromsMeyer, J.Gagnon, J.Sieker, L.C.Van Dorsselaer, A.Moulis, J.M.Biochem. J. 271, 839-841, 1990Rubredoxin from Clostridium thermosaccharolyticum. Amino acid sequence, mass-spectrometric and preliminary crystallographic data.PMID:2244884mass spectrometric detectionThe stabilization of Fe(3+) by protein in tetrakis-S-cysteinyliron in the oxidized state can be regarded as a model for formation of the simplest iron-sulfur cluster. The formal charge of the reduced state, Fe(2+), is used for the mass calculation.C, C, C, Ccross-link 4GO:0018284PSI-MOD:00145ironmetalloproteinMETAL IronAA013731-Mar-199531-Mar-199501-Mar-2013tetrakis-L-cysteinyl diiron disulfidetetrakiscysteinato-1kappa(2)S,2kappa(2)S-di-mu-sulfido-diironCOMe:BIM000055PDBHET:FESC 12 Fe 2 H 16 N 4 O 4 S 62-584.34583.820553C 0 Fe 2 H -4 N 0 O 0 S 22-171.78171.783814Tsukihara, T.Fukuyama, K.Nakamura, M.Katsube, Y.Tanaka, N.Kakudo, M.Wada, K.Hase, T.Matsubara, H.J. Biochem. 90, 1763-1773, 1981X-Ray analysis of a [2Fe-2S] ferredoxin from Spirulina platensis. Main chain fold and location of side chains at 2.5 angstroms resolution.PMID:6801028X-ray diffraction, 2.5 angstroms; the spelling of "Tsukihira, T." in the PubMed citation is correctedTsukihara, T.Fukuyama, K.Mizushima, M.Harioka, T.Kusunoki, M.Katsube, Y.Hase, T.Matsubara, H.J. Mol. Biol. 216, 399-410, 1990Structure of the [2Fe-2S] ferredoxin I from the blue-green alga Aphanothece sacrum at 2.2 angstroms resolution.DOI:10.1016/S0022-2836(05)80330-4PMID:2123937X-ray diffraction, 2.2 angstromsPochapsky, T. C.Ye, X. M.Ratnaswamy, G.Lyons, T. A.submitted to the Protein Data Bank, July 1994An NMR-derived model for the solution structure of oxidized putidaredoxin, a 2-Fe, 2-S ferredoxin from Pseudomonas.PDB:1PUTNMRPetillot, Y.Golinelli, M.P.Forest, E.Meyer, J.Biochem. Biophys. Res. Commun. 210, 686-694, 1995Electrospray-ionization mass spectrometry of molecular variants of a [2Fe-2S] ferredoxin.DOI:10.1006/bbrc.1995.1714PMID:7763242Golinelli, M.P.Akin, L.A.Crouse, B.R.Johnson, M.K.Meyer, J.Biochemistry 35, 8995-9002, 1996Cysteine ligand swapping on a deletable loop of the [2Fe-2S] ferredoxin from Clostridium pasteurianum.DOI:10.1021/bi9604284PMID:8688437Frolow, F.Harel, M.Sussman, J.L.Shoham, M.submitted to the Protein Data Bank, April 19962Fe-2S Ferredoxin from Haloarcula marismortui.PDB:1DOIX-ray diffraction, 1.9 angstromsSee also RESID:AA0225.C, C, C, Ccross-link 4GO:0018285PSI-MOD:001462Fe-2Siron-sulfur proteinmetalloproteinMETAL Iron-sulfur (2Fe-2S)METAL Iron-sulfur (2Fe-2S); shared with dimeric partnerAA013831-Mar-199531-Mar-200531-May-2013hexakis-L-cysteinyl triiron trisulfidetri-mu-sulfidotris(biscysteinato-kappaS-iron)tri-mu-sulfido-hexakiscysteinato-1kappa(2)S,2kappa(2)S,3kappa(2)S-triironC 18 Fe 3 H 24 N 6 O 6 S 93-876.50875.730830C 0 Fe 3 H -6 N 0 O 0 S 33-257.67257.675721Stout, C.D.Ghosh, D.Pattabhi, V.Robbins, A.H.J. Biol. Chem. 255, 1797-1800, 1980Iron-sulfur clusters in Azotobacter ferredoxin at 2.5 A resolution.PMID:7354058George, D.G.Hunt, L.T.Yeh, L.S.Barker, W.C.J. Mol. Evol. 22, 20-31, 1985New perspectives on bacterial ferredoxin evolution.DOI:10.1007/BF02105801PMID:3932661proposal for a model of a 3Fe-3S clusterStout, C.D.J. Biol. Chem. 263, 9256-9260, 19887-Iron ferredoxin revisited.PMID:3379067the cluster is identified as being 3Fe-4SThe three-iron three-sulfur cluster is now thought not to exist except possibly as an intermediate form. See RESID:AA0139 and RESID:AA0140.C, C, C, C, C, Ccross-link 6GO:0018286PSI-MOD:00147iron-sulfur proteinmetalloproteinNot availablethis dubious modification is not currently annotated in UniProt featuresAA013931-Mar-199531-Mar-199531-May-2013tris-L-cysteinyl triiron tetrasulfidemu3-sulfido tri-mu-sulfido tris-S-L-cysteinyl triirontris-L-cysteinyl triiron tetrasulfide C3 clustertris-L-cysteinyl triiron tetrasulfide cubane formtris-L-cysteinyl triiron tetrasulfide cuboid clustertris-L-cysteinyl triiron tetrasulfide trigonal clustermu3-sulfido-tri-mu-sulfido-triscysteinato-1kappaS,2kappaS,3kappaS-triironCOMe:BIM000054PDBHET:F3SC 9 Fe 3 H 12 N 3 O 3 S 73-602.17601.698821C 0 Fe 3 H -3 N 0 O 0 S 43-292.75292.671267Howard, J.B.Lorsbach, T.W.Ghosh, D.Melis, K.Stout, C.D.J. Biol. Chem. 258, 508-522, 1983Structure of Azotobacter vinelandii 7Fe ferredoxin. Amino acid sequence and electron density maps of residues.PMID:6848518X-ray diffraction, 2 angstroms; 3Fe-4S and 4Fe-4S clustersStout, G.H.Turley, S.Sieker, L.C.Jensen, L.H.Proc. Natl. Acad. Sci. U.S.A. 85, 1020-1022, 1988Structure of ferredoxin I from Azotobacter vinelandii.DOI:10.1073/pnas.85.4.1020PMID:3422475X-ray diffraction, 2.6 angstroms; 3Fe-4S and 4Fe-4S clustersStout, C.D.submitted to the Protein Data Bank, June 1993Crystal structures of oxidized and reduced Azotobacter vinelandii ferredoxin at pH 8 and 6.PDB:1FDAX-ray diffraction, 2.10 angstromsKissinger, C.R.Sieker, L.C.Adman, E.T.Jensen, L.H.J. Mol. Biol. 219, 693-715, 1991Refined crystal structure of ferredoxin II from Desulfovibrio gigas at 1.7 A.DOI:10.1016/0022-2836(91)90665-SPMID:2056535X-ray diffraction, 1.7 angstroms; 3Fe-4S cluster, disulfide and methyl mercaptan (see RESID:AA0101)Kissinger, C.R.Sieker, L.C.Adman, E.T.Jensen, L.H.submitted to the Protein Data Bank, April 1991Refined crystal structure of ferredoxin II from Desulfovibrio gigas at 1.7 A.PDB:1FXDX-ray diffraction, 1.70 angstromsGorst, C.M.Yeh, Y.H.Teng, Q.Calzolai, L.Zhou, Z.H.Adams, M.W.W.La Mar, G.N.Biochemistry 34, 600-610, 1995[1]H NMR investigation of the paramagnetic cluster environment in Pyrococcus furiosus three-iron ferredoxin: sequence-specific assignment of ligated cysteines independent of tertiary structure.DOI:10.1021/bi00002a027PMID:7819255conformation, binding site, and disulfide bond assignments by (1)H-NMR; this ferredoxin can form a 4Fe-4S cluster but it readily converts to a stable 3Fe-4S clusterFujii, T.Hata, Y.Oozeki, M.Moriyama, H.Wakagi, T.Tanaka, N.Oshima, T.Biochemistry 36, 1505-1513, 1997The crystal structure of zinc-containing ferredoxin from the thermoacidophilic archaeon Sulfolobus sp. strain 7.DOI:10.1021/bi961966jPMID:9063899X-ray diffraction, 2.0 angstromsFujii, T.Hata, Y.Moriyama, H.Wakagi, T.Tanaka, N.Oshima, T.submitted to the Protein Data Bank, August 1996Structure of ferredoxin.PDB:1XERX-ray diffraction, 2.0 angstromsGoodfellow, B.J.Macedo, A.L.Rodrigues, P.Moura, I.Wray, V.Moura, J.J.J. Biol. Inorg. Chem. 4, 421-430, 1999The solution structure of a [3Fe-4S] ferredoxin: oxidised ferredoxin II from Desulfovibrio gigas.DOI:10.1007/s007750050328PMID:10555576Goodfellow, B.J.Macedo, A.L.Rodrigues, P.Wray, V.Moura, I.Moura, J.J.G.submitted to the Protein Data Bank, October 1998The NMR solution structure of the 3Fe ferredoxin II from Desulfovibrio gigas, 15 structures.PDB:1F2GCOSY, TOCSY, and NOESY NMR spectroscopyThe activity of some trigonal 3Fe-4S clusters has been questioned. Reconfiguration to linear 3Fe-4S clusters or to 4Fe-4S clusters may occur. See RESID:AA0140 and RESID:AA0326.Observed oxidation states for the ligated cluster are 3-, 4-, and 5-.C, C, Ccross-link 3GO:0018287PSI-MOD:001483Fe-4Siron-sulfur proteinmetalloproteinMETAL Iron-sulfur (3Fe-4S)AA014031-Mar-199531-Mar-199531-May-2013tetrakis-L-cysteinyl tetrairon tetrasulfidetetra-mu3-sulfidotetrakis(S-cysteinyliron)tetra-mu3-sulfido-tetrakis(cysteinato)-1kappaS,2kappaS,3kappaS,4kappaS-tetrahedro-tetraironCOMe:BIM000008PDBHET:SF4C 12 Fe 4 H 16 N 4 O 4 S 82-760.15759.634570C 0 Fe 4 H -4 N 0 O 0 S 42-347.59347.597831Adman, E.T.Sieker, L.C.Jensen, L.H.J. Biol. Chem. 251, 3801-3806, 1976Structure of Peptococcus aerogenes ferredoxin. Refinement at 2 angstroms resolution.PMID:932007X-ray diffraction, 2.0 angstroms; monomer with two 4Fe-4S clusters; the spelling of "Siefker, L.C." in the PubMed citation is correctedBackes, G.Mino, Y.Loehr, T.M.Meyer, T.E.Cusanovich, M.A.Sweeney, W.V.Adman, E.T.Sanders-Loehr, J.J. Am. Chem. Soc. 113, 2055-2064, 1991The environment of Fe4S4 clusters in ferredoxins and high-potential iron proteins. New information from x-ray crystallography and resonance Raman spectroscopy.DOI:10.1021/ja00006a027X-ray diffraction, 2.0 angstroms; Raman spectroscopy; monomer with two 4Fe-4S clusters compared with HiPIP typeHuber, J.G.Gaillard, J.Moulis, J.M.Biochemistry 34, 194-205, 1995NMR of Chromatium vinosum ferredoxin: evidence for structural inequivalence and impeded electron transfer between the two [4Fe-4S] clusters.DOI:10.1021/bi00001a024PMID:7819196conformation by (1)H-NMR and (13)C-NMR; monomer with two 4Fe-4S clustersSery, A.Housset, D.Serre, L.Bonicel, J.Hatchikian, C.Frey, M.Roth, M.Biochemistry 33, 15408-15417, 1994Crystal structure of the ferredoxin I from Desulfovibrio africanus at 2.3 angstrom resolution.DOI:10.1021/bi00255a022PMID:7803404X-ray diffraction, 2.3 angstroms; single 4Fe-4S clusterFukuyama, K.Nagahara, Y.Tsukihara, T.Katsube, Y.Hase, T.Matsubara, H.J. Mol. Biol. 199, 183-193, 1988Tertiary structure of Bacillus thermoproteolyticus [4Fe-4S] ferredoxin. Evolutionary implications for bacterial ferredoxins.DOI:10.1016/0022-2836(88)90388-9PMID:3351918X-ray diffraction, 2.3 angstroms; single 4Fe-4S clusterSeveral different types of 4Fe-4S cluster are observed. Typically two 4Fe-4S clusters are shared in a single domain. Also observed are: one 4Fe-4S cluster and one 3Fe-4S cluster (see RESID:AA0139) in a single domain, a single 4Fe-4S cluster, one 4Fe-4S cluster shared between dimeric partners, and two 4Fe-4S clusters shared between two different chains.Three cysteine ligands may denote that the fourth iron is labile or that it binds another prosthetic group.The oxidation states usually observed for the ligated cluster are 2- and 3-.C, C, C, Ccross-link 4GO:0018288PSI-MOD:001494Fe-4Siron-sulfur proteinmetalloproteinMETAL Iron-sulfur (4Fe-4S)METAL Iron-sulfur (4Fe-4S); shared with dimeric partnerAA014131-Mar-199531-Dec-201101-Mar-2013L-cysteinyl-L-histidino-homocitryl molybdenum heptairon nonasulfide carbidenitrogenase iron-molybdenum cofactorcysteinato-8kappaS-histidino-1kappaN(tau)-[(2R)-4-carboxy-2-(carboxymethyl)-2-oxidobutanoate-1kappaO(1),1kappaO(2)]-mu6-carbido-2:3:4:5:6:7kappa(6)C-hexa-mu3-sulfido-1:2:3kappa(3)S;1:2:4kappa(3)S;1:3:4kappa(3)S;5:6:8kappa(3)S;5:7:8kappa(3)S;6:7:8kappa(3)S-tri-mu2-sulfido-2:5kappa(2)S;3:6kappa(2)S;4:7kappa(2)S molybdenum heptaironCOMe:BIM000057PDBHET:CFMPDBHET:CFNPDBHET:HCAC 17 Fe 7 H 18 Mo 1 N 4 O 9 S 101229.821231.278059C 8 Fe 7 H 6 Mo 1 N 0 O 7 S 9989.53991.209962Kim, J.Rees, D.C.Science 257, 1677-1682, 1992Structural models for the metal centers in the nitrogenase molybdenum-iron protein.DOI:10.1126/science.1529354PMID:1529354Kim, J.Rees, D.C.Nature 360, 553-560, 1992Crystallographic structure and functional implications of the nitrogenase molybdenum-iron protein from Azotobacter vinelandii.DOI:10.1038/360553a0Ma, L.Gavini, N.Liu, H.I.Hedman, B.Hodgson, K.O.Burgess, B.K.J. Biol. Chem. 269, 18007-18015, 1994Large scale isolation and characterization of the molybdenum-iron cluster from nitrogenase.PMID:8027059EPR and X-ray absorption spectrographic analysisMayer, S.M.Lawson, D.M.Gormal, C.A.Roe, S.M.Smith, B.E.J. Mol. Biol. 292, 871-891, 1999New insights into structure-function relationships in nitrogenase: A 1.6 Angstom resolution X-ray crystallographic study of Klebsiella pneumoniae MoFe-protein.DOI:10.1006/jmbi.1999.3107PMID:10525412X-ray diffraction, 1.6 angstromsMayer, S.M.Lawson, D.M.Gormal, C.A.Roe, S.M.Smith, B.E.submitted to the Protein Data Bank, May 1999Nitrogenase Mo-Fe protein from Klebsiella pneumoniae, dithionite-reduced state.PDB:1QGUX-ray diffraction, 1.6 angstroms, reduced formEinsle, O.Tezcan, F.A.Andrade, S.L.A.Schmid, B.Yoshida, M.Howard, J.B.Rees, D.C.Science 297, 1696-1700, 2002Nitrogenase MoFe-protein at 1.16 A resolution: a central ligand in the FeMo-cofactor.DOI:10.1126/science.1073877PMID:12215645X-ray diffraction, 1.16 angstromsEinsle, O.Tezcan, F.A.Andrade, S.L.A.Schmid, B.Yoshida, M.Howard, J.B.Rees, D.C.submitted to the Protein Data Bank, June 2002Nitrogenase MoFe protein from Azotobacter vinelandii.PDB:1M1NX-ray diffraction, 1.16 angstromsLee, H.I.Benton, P.M.C.Laryukhin, M.Igarashi, R.Y.Dean, D.R.Seefeldt, L.C.Hoffman, B.M.J. Am. Chem. Soc. 125, 5604-5605, 2003The interstitial atom of the nitrogenase FeMo-Cofactor: ENDOR and ESEEM show it is not an exchangeable nitrogen.DOI:10.1021/ja034383nPMID:12733878electron-nuclear double resonance (ENDOR) spectroscopic analysis, and electron spin-echo envelope modulation (ESEEM) spectroscopic analysisLancaster, K.M.Roemelt, M.Ettenhuber, P.Hu, Y.Ribbe, M.W.Neese, F.Bergmann, U.DeBeer, S.Science 334, 974-977, 2011X-ray emission spectroscopy evidences a central carbon in the nitrogenase iron-molybdenum cofactor.DOI:10.1126/science.1206445PMID:22096198X-ray emission spectroscopy indicates that the central atom is a C(4-) ionSpatzal, T.Aksoyoglu, M.Zhang, L.Andrade, S.L.Schleicher, E.Weber, S.Rees, D.C.Einsle, O.Science 334, 940, 2011Evidence for interstitial carbon in nitrogenase FeMo cofactor.DOI:10.1126/science.1214025PMID:22096190X-ray diffraction, 1.00 angstroms, and electron spin-echo envelope modulation (ESEEM) spectroscopic analysis with (13)C labeled cofactorSpatzal, T.Einsle, O.submitted to the Protein Data Bank, October 2011A. vinelandii nitrogenase MoFe protein at atomic resolution.PDB:3U7QX-ray diffraction, 1.00 angstromsWiig, J.A.Hu, Y.Lee, C.C.Ribbe, M.W.Science 337, 1672-1675, 2012Radical SAM-dependent carbon insertion into the nitrogenase M-cluster.DOI:10.1126/science.1224603PMID:23019652the nitrogenase synthase NifB protein is a radical SAM that helps assemble 4Fe-4S clusters and provides the central carbide atom from a SAM with at least one free radical hydrogen abstractionCysteine binds one iron of a 4Fe-3S cluster; the other three irons are connected by three mu(2)-sulfides and one mu(6)-carbon to three irons of a Mo-3Fe-3S cluster; the molybdenum is further bound by the 2-oxide and 2-carboxylate of homocitrate (2-hydroxy-1,2,4-butanetricarboxylic acid) and the pros-N of histidine.C, Hcross-link 2incidental to RESID:AA0300GO:0018290PSI-MOD:00150iron-sulfur proteinmetalloproteinmolybdenumMETAL Molybdenum-iron-sulfur (7Fe-Mo-9S-X-homocitryl)these UniProt features have not been revisedMETAL Molybdenum-iron-sulfur (7Fe-Mo-9S-X-homocitryl); via pros nitrogenthese UniProt features have not been revisedAA014231-Mar-199527-Feb-199831-May-2013L-cysteinyl molybdopterincysteinyl Mo-molybdopterincysteinyl Mo-pterinmolybdoenzyme molybdenum cofactor(4R,5aR,11aR)-8-amino-2-[(2R)-2-amino-2-carboxyethyl]sulfanyl-4,5a,6,9,10,11,11a-heptahydro-4-(phosphoric acid)methyl-2,2,10-trioxo-pteridino[6,7-5,6]pyrano[3,4-4,3][1,2,5]molybdadithioleneCAS:73508-07-3PDBHET:MOPDBHET:MPNPDBHET:MSSPDBHET:MTEPDBHET:MTQPDBHET:MTVC 13 H 16 Mo 1 N 6 O 9 P 1 S 3623.41624.893259C 10 H 11 Mo 1 N 5 O 8 P 1 S 2520.27521.884074Chan, M.K.Mukund, S.Kletzin, A.Adams, M.W.W.Rees, D.C.Science 267, 1463-1469, 1995Structure of a hyperthermophilic tungstopterin enzyme, aldehyde ferredoxin oxidoreductase.DOI:10.1126/science.7878465PMID:7878465Kisker, C.Schindelin, H.Pacheco, A.Wehbi, W.A.Garrett, R.M.Rajagopalan, K.V.Enemark, J.H.Rees, D.C.Cell 91, 973-983, 1997Molecular basis of sulfite oxidase deficiency from the structure of sulfite oxidase.DOI:10.1016/S0092-8674(00)80488-2PMID:9428520Schrader, N.Fischer, K.Theis, K.Mendel, R.R.Schwarz, G.Kisker, C.Structure 11, 1251-1263, 2003The crystal structure of plant sulfite oxidase provides insights into sulfite oxidation in plants and animals.DOI:10.1016/j.str.2003.09.001PMID:14527393X-ray diffraction, 2.6 angstromsSchrader, N.Fischer, K.Theis, K.Mendel, R.R.Schwarz, G.Kisker, C.submitted to the Protein Data Bank, May 2003The crystal structure of plant sulfite oxidase provides insight into sulfite oxidation in plants and animals.PDB:1OGPX-ray diffraction, 2.6 angstromsA hydrogenated (+4H) structure is shown. The fully oxidized form would be the corresponding 4,9,10-trihydro form.CGO:0018292PSI-MOD:00151metalloproteinmolybdenummolybdopterinphosphoproteinMETAL Molybdenum-pterinAA014301-Sep-199501-Sep-199531-May-2013S-(8alpha-FAD)-L-cysteine8alpha-(S-cysteinyl)FAD(2R)-2-amino-3-[8alpha-riboflavin 5'-(trihydrogen diphosphate) 5'->5'-ester with adenosine]sulfanylpropanoic acidCOMe:BIM000201PDBHET:FADC 30 H 36 N 10 O 16 P 2 S 1886.68886.150669C 27 H 31 N 9 O 15 P 2 S 0783.54783.141485Wagner, M.A.Khanna, P.Jorns, M.S.Biochemistry 38, 5588-5595, 1999Structure of the flavocoenzyme of two homologous amine oxidases: monomeric sarcosine oxidase and N-methyltryptophan oxidase.DOI:10.1021/bi982955oPMID:10220347mass spectrometric and chemical characterizationTrickey, P.Wagner, M.A.Jorns, M.S.Mathews, F.S.Structure 7, 331-345, 1999Monomeric sarcosine oxidase: structure of a covalently flavinylated amine oxidizing enzyme.DOI:10.1016/S0969-2126(99)80043-4PMID:10368302X-ray diffraction, 1.80 angstromsWagner, M.A.Trickey, P.Chen, Z.-W.Mathews, F.S.Jorns, M.S.submitted to the Protein Data Bank, March 2000Complex of monomeric sarcosine oxidase with the inhibitor dimethylglycine.PDB:1EL5X-ray diffraction, 1.80 angstromsThe arrangement of the attachment has not been completely established in some cases.The keyword "phosphoprotein" is not used with flavin modifications linked through the flavin.autocatalyticCGO:0018294PSI-MOD:00152*phosphoproteinFADflavoproteinthioether bondMOD_RES S-8alpha-FAD cysteineAA014431-Mar-199501-Sep-199531-Mar-20123'-(8alpha-FAD)-L-histidine8alpha-(N(delta)-histidyl)FAD8alpha-(N3'-histidyl)FAD8alpha-N1-histidyl FAD [misnomer]N(pi)-(8alpha-FAD)-histidinepros-(8alpha-FAD)-histidine(2S)-2-amino-3-(3-[8alpha-riboflavin 5'-(trihydrogen diphosphate) 5'->5'-ester with adenosine]imidazol-4-yl)propanoic acidCOMe:BIM000202PDBHET:FADC 33 H 38 N 12 O 16 P 2920.68920.200396C 27 H 31 N 9 O 15 P 2783.54783.141485Edmondson, D.E.Kenney, W.C.Singer, T.P.Biochemistry 15, 2937-2945, 1976Structural elucidation and properties of 8alpha-(N1-histidyl)riboflavin: the flavin component of thiamine dehydrogenase and beta-cyclopiazonate oxidocyclase.DOI:10.1021/bi00659a001PMID:8076chemical and spectrographic characterization; the authors use biochemical rather than IUPAC numberingMalito, E.Coda, A.Bilyeu, K.D.Fraaije, M.W.Mattevi, A.J. Mol. Biol. 341, 1237-1249, 2004Structures of Michaelis and product complexes of plant cytokinin dehydrogenase: implications for flavoenzyme catalysis.DOI:10.1016/j.jmb.2004.06.083PMID:15321719X-ray diffraction, 1.7 angstromsMalito, E.Mattevi, A.submitted to the Protein Data Bank, June 2004Native cytokinin dehydrogenase.PDB:1W1OX-ray diffraction, 1.7 angstromsThe arrangement of the attachment has not been completely established in some cases.The keyword "phosphoprotein" is not used with flavin modifications linked through the flavin.autocatalyticHGO:0018295PSI-MOD:00153*phosphoproteinFADflavoproteinMOD_RES Pros-8alpha-FAD histidineAA014501-Sep-199501-Sep-199531-Mar-2012O4'-(8alpha-FAD)-L-tyrosine8alpha-(O4'-tyrosyl)FAD(2S)-2-amino-3-(4-[8alpha-riboflavin 5'-(trihydrogen diphosphate) 5'->5'-ester with adenosine]oxyphenyl)propanoic acidCOMe:BIM000196PDBHET:FADC 36 H 40 N 10 O 17 P 2946.72946.204813C 27 H 31 N 9 O 15 P 2783.54783.141485McIntire, W.Edmondson, D.E.Singer, T.P.Hopper, D.J.J. Biol. Chem. 255, 6553-6555, 19808alpha-O-tyrosyl-FAD: a new form of covalently bound flavin from p-cresol methylhydroxylase.PMID:7391034chemical and spectrographic characterizationMathews, F.S.Chen, Z.W.Bellamy, H.D.McIntire, W.S.Biochemistry 30, 238-247, 1991Three-dimensional structure of p-cresol methylhydroxylase (flavocytochrome c) from Pseudomonas putida at 3.0-A resolution.DOI:10.1021/bi00215a034PMID:1846290Cunane, L.M.Chen, Z.W.Shamala, N.Mathews, F.S.Cronin, C.N.McIntire, W.S.submitted to the Protein Data Bank, November 1999Crystal structure of p-cresol methylhydroxylase at 2.5 A resolution.PDB:1DIIX-ray diffraction, 2.50 angstromsThe keyword "phosphoprotein" is not used with flavin modifications linked through the flavin.autocatalyticYGO:0018296PSI-MOD:00154*phosphoproteinFADflavoproteinMOD_RES O-8alpha-FAD tyrosineAA014631-Mar-199531-Mar-199531-Mar-2012L-3',4'-dihydroxyphenylalanineL-3'-hydroxytyrosineL-DOPAlevodopa(2S)-2-amino-3-(3,4-dihydroxyphenyl)propanoic acidCAS:59-92-7PDBHET:DAHC 9 H 9 N 1 O 3179.18179.058243C 0 H 0 N 0 O 116.0015.994915Waite, J.H.J. Comp. Physiol. B, Biochem. Syst. Environ. Physiol. 156, 491-496, 1986Mussel glue from Mytilus californianus Conrad: a comparative study.DOI:10.1007/BF00691034PMID:3734192Waite, J.H.Jensen, R.A.Morse, D.E.Biochemistry 31, 5733-5738, 1992Cement precursor proteins of the reef-building polychaete Phragmatopoma californica (Fewkes).DOI:10.1021/bi00140a007PMID:1610822Waite, J.H.Anal. Biochem. 192, 429-433, 1991Detection of peptidyl-3,4-dihydroxyphenylalanine by amino acid analysis and microsequencing techniques.DOI:10.1016/0003-2697(91)90560-GPMID:1903612chromatographic identification; PTH derivativeYincidental to RESID:AA0368GO:0018067PSI-MOD:00155hydroxylationMOD_RES 3',4'-dihydroxyphenylalanineAA014731-Mar-199531-Mar-199531-May-2018L-2',4',5'-topaquinone2,4,5-trihydroxyphenylalanine quinone5-(2-carboxy-2-aminoethyl)-2-hydroxy-1,4-benzoquinoneL-2,4,5-TOPAquinoneTPQ(2S)-2-amino-3-(5-hydroxy-2,5-cyclohexadien-1,4-dion-2-yl)propanoic acidChEBI:21187COMe:BIM000264PDBHET:TPQC 9 H 7 N 1 O 4193.16193.037508C 0 H -2 N 0 O 229.9829.974179Janes, S.M.Mu, D.Wemmer, D.Smith, A.J.Kaur, S.Maltby, D.Burlingame, A.L.Klinman, J.P.Science 248, 981-987, 1990A new redox cofactor in eukaryotic enzymes: 6-hydroxydopa at the active site of bovine serum amine oxidase.DOI:10.1126/science.2111581PMID:2111581Mu, D.Janes, S.M.Smith, A.J.Brown, D.E.Dooley, D.M.Klinman, J.P.J. Biol. Chem. 267, 7979-7982, 1992Tyrosine codon corresponds to topa quinone at the active site of copper amine oxidases.PMID:1569055Janes, S.M.Palcic, M.M.Scaman, C.H.Smith, A.J.Brown, D.E.Dooley, D.M.Mure, M.Klinman, J.P.Biochemistry 31, 12147-12154, 1992Identification of topaquinone and its consensus sequence in copper amine oxidases.DOI:10.1021/bi00163a025PMID:1457410Murray, J.M.Saysell, C.G.Wilmot, C.M.Tambyrajah, W.S.Jaeger, J.Knowles, P.F.Phillips, S.E.McPherson, M.J.Biochemistry 38, 8217-8227, 1999The active site base controls cofactor reactivity in Escherichia coli amine oxidase: x-ray crystallographic studies with mutational variants.DOI:10.1021/bi9900469PMID:10387067this modification forms active site Schiff base intermediates with amine substratesautocatalyticYGO:0018068PSI-MOD:00156quinoproteintopaquinoneMOD_RES 2',4',5'-topaquinoneAA014831-Mar-199531-Mar-199530-Jun-2012L-tryptophyl quinone2-amino-3-(6,7-dioxo-6,7-dihydro-1H-indol-3-yl)-propionic acid3-[(2S)-2-amino-2-carboxyethyl]-6,7-indolinedioneN-(3-carboxy-1-oxopropyl)-L-tryptophan(2S)-2-amino-3-(6,7-dioxo-1H-indol-3-yl)propanoic acidCAS:73205-73-9PDBHET:TRQC 11 H 8 N 2 O 3216.20216.053492C 0 H -2 N 0 O 229.9829.974179McIntire, W.S.Wemmer, D.E.Chistoserdov, A.Lidstrom, M.E.Science 252, 817-824, 1991A new cofactor in a prokaryotic enzyme: tryptophan tryptophylquinone as the redox prosthetic group in methylamine dehydrogenase.DOI:10.1126/science.2028257PMID:2028257Wincidental to RESID:AA0149incidental to RESID:AA0313secondary to RESID:AA0521GO:0019926PSI-MOD:00157quinoproteinMOD_RES TryptophylquinoneAA014931-Mar-199531-Mar-199531-Dec-20104-(L-tryptophan-2-yl)-L-tryptophyl quinone2-amino-3-[2-[2-amino-3-(2-carboxyethyl)-6,7-dioxo-1H-indol-4-yl]-1H-indol-3-yl]propanoic acid4'-tryptophan-tryptophylquinone4-(2'-tryptophyl)tryptophan-6,7-dionealpha,alpha'-diamino-6',7'-dihydro-6',7'-dioxo-(2,4'-bi-1H-indole)-3,3'-dipropanoic acidTTQ3-[(2S)-2-amino-2-carboxyethyl]-4-(3-[(2S)-2-amino-2-carboxyethyl]-1H-indol-2-yl)-6,7-indolinedioneCAS:134645-25-3ChEBI:20251COMe:BIM000262C 22 H 16 N 4 O 4400.39400.117155C 0 H -4 N 0 O 227.9727.958529McIntire, W.S.Wemmer, D.E.Chistoserdov, A.Lidstrom, M.E.Science 252, 817-824, 1991A new cofactor in a prokaryotic enzyme: tryptophan tryptophylquinone as the redox prosthetic group in methylamine dehydrogenase.DOI:10.1126/science.2028257PMID:2028257Jensen, L.M.Sanishvili, R.Davidson, V.L.Wilmot, C.M.Science 327, 1392-1394, 2010In crystallo posttranslational modification within a MauG/pre-methylamine dehydrogenase complex.DOI:10.1126/science.1182492PMID:20223990X-ray diffraction, 2.1 angstroms; complex of methylamine dehydrogenase with the enzyme forming the modificationmethylamine dehydrogenase activase MauG (EC 6.-.-.-)W, Wcross-link 2secondary to RESID:AA0148GO:0018069PSI-MOD:00158quinoproteinCROSSLNK Tryptophan tryptophylquinone (Trp-Trp)AA015031-Mar-199531-Mar-199531-May-2018O-phosphopantetheine-L-serine(2R)-2-hydroxy-3,3-dimethyl-4-[(2S)-2-amino-2-carboxyethyl]phosphonato-N-(3-oxo-3-[(2-sulfanylethyl)amino]propyl)butanamideChEBI:64891PDBHET:PNSC 14 H 26 N 3 O 8 P 1 S 1427.41427.117822C 11 H 21 N 2 O 6 P 1 S 1340.33340.085794Majerus, P.W.Alberts, A.W.Vagelos, P.R.J. Biol. Chem. 240, 4723-4726, 1965Acyl carrier protein. VII. The primary structure of the substrate-binding site.PMID:5321310chemical characterizationPugh, E.L.Wakil, S.J.J. Biol. Chem. 240, 4727-4733, 1965Studies on the mechanism of fatty acid synthesis. XIV. The prosthetic group of acyl carrier protein and the mode of its attachment to the protein.PMID:5321311chemical characterizationRoncari, D.A.Bradshaw, R.A.Vagelos, P.R.J. Biol. Chem. 247, 6234-6242, 1972Acyl carrier protein. XIX. Amino acid sequence of liver fatty acid synthetase peptides containing 4'-phosphopantetheine.PMID:4568609radioisotope labelingEhmann, D.E.Gehring, A.M.Walsh, C.T.Biochemistry 38, 6171-6177, 1999Lysine biosynthesis in Saccharomyces cerevisiae: mechanism of alpha-aminoadipate reductase (Lys2) involves posttranslational phosphopantetheinylation by Lys5.DOI:10.1021/bi9829940PMID:10320345Parris, K.D.Lin, L.Tam, A.Mathew, R.Hixon, J.Stahl, M.Fritz, C.C.Seehra, J.Somers, W.S.Structure 8, 883-895, 2000Crystal structures of substrate binding to Bacillus subtilis holo-(acyl carrier protein) synthase reveal a novel trimeric arrangement of molecules resulting in three active sites.DOI:10.1016/S0969-2126(00)00178-7PMID:10997907X-ray diffraction, 2.3 angstromsParris, K.D.Lin, L.Tam, A.Mathew, R.Hixon, J.Stahl, M.Fritz, C.C.Seehra, J.Somers, W.S.submitted to the Protein Data Bank, June 2000Holo-(acyl carrier protein) synthase in complex with holo-(acyl carrier protein).PDB:1F80X-ray diffraction, 2.3 angstromsRoujeinikova, A.Baldock, C.Simon, W.J.Gilroy, J.Baker, P.J.Stuitje, A.R.Rice, D.W.Slabas, A.R.Rafferty, J.B.Structure 10, 825-835, 2002X-ray crystallographic studies on butyryl-ACP reveal flexibility of the structure around a putative acyl chain binding site.DOI:10.1016/S0969-2126(02)00775-XPMID:12057197X-ray diffraction, 1.2 angstromsRoujeinikova, A.Baldock, C.Simon, W.J.Gilroy, J.Baker, P.J.Stuitje, A.R.Rice, D.W.Slabas, A.R.Rafferty, J.B.submitted to the Protein Data Bank, February 2002Crystal structure of butyryl-ACP I62M mutant.PDB:1L0IX-ray diffraction, 1.2 angstromsRaychaudhuri, S.Rajasekharan, R.J. Biol. Chem. 278, 37648-37657, 2003Nonorganellar acyl carrier protein from oleaginous yeast is a homologue of ribosomal protein P2.DOI:10.1074/jbc.M305052200PMID:12869567radioisotope labeling and mass spectrometric identification; this protein does not have homology with acyl carrier protein, and many homologs of this protein are not modified by phosphopantetheineDorrestein, P.C.Bumpus, S.B.Calderone, C.T.Garneau-Tsodikova, S.Aron, Z.D.Straight, P.D.Kolter, R.Walsh, C.T.Kelleher, N.L.Biochemistry 45, 12756-12766, 2006Facile detection of acyl and peptidyl intermediates on thiotemplate carrier domains via phosphopantetheinyl elimination reactions during tandem mass spectrometry.DOI:10.1021/bi061169dPMID:17042494mass spectrometric analysis with detection with detection of phosphoserine after secondary neutral loss of pantetheineholo-[acyl-carrier-protein] synthase (EC 2.7.8.7)SGO:0018070PSI-MOD:00159phosphopantetheinephosphoproteinMOD_RES O-(pantetheine 4'-phosphoryl)serineAA015131-Mar-199526-May-200631-May-2018N4-(N-acetylamino)glucosyl-L-asparagineN4-(2-acetamido-2-deoxy-beta-D-glucopyranosyl)-L-asparagineN4-(2-acetylamino-2-deoxy-beta-D-glucopyranosyl)-L-asparagineN4-(N-acetylglucosaminyl)asparagineN4-asparagine-beta-N-acetylglucosaminideN4-glycosyl-L-asparagineN4-glycosylasparagine(2S)-2-amino-4-(2-acetamido-2-deoxy-beta-D-glucopyranosyl)amino-4-oxobutanoic acidCAS:10036-64-3CAS:2776-93-4ChEBI:132248PDBHET:NAGPDBHET:NDGC 12 H 19 N 3 O 7 +317.30 +317.122300 +C 8 H 13 N 1 O 5 +203.19 +203.079373 +Baker, J.R.Cifonelli, J.A.Rodén, L.Biochem. J. 115, 11P, 1969The linkage of corneal keratosulphate to protein.PMID:4242854chemical characterization of keratan sulfate linkage to proteinHunt, L.T.Dayhoff, M.O.Biochem. Biophys. Res. Commun. 39, 757-765, 1970The occurrence in proteins of the tripeptides Asn-X-Ser and Asn-X-Thr and of bound carbohydrate.DOI:10.1016/0006-291X(70)90270-6PMID:5490222recognition of glycosylation motifBergman, L.W.Kuehl, W.M.Biochemistry 16, 4490-4497, 1977Addition of glucosamine and mannose to nascent immunoglobulin heavy chains.DOI:10.1021/bi00639a025PMID:410438demonstration that in mammals N-glycosylation is a co-translational process; modification can begin before peptide release from the ribosomeKehry, M.Sibley, C.Fuhrman, J.Schilling, J.Hood, L.E.Proc. Natl. Acad. Sci. U.S.A. 76, 2932-2936, 1979Amino acid sequence of a mouse immunoglobulin mu chain.DOI:10.1073/pnas.76.6.2932PMID:111247glycosylation at an N-G-G-T siteMiletich, J.P.Broze Jr., G.J.J. Biol. Chem. 265, 11397-11404, 1990Beta protein C is not glycosylated at asparagine 329. The rate of translation may influence the frequency of usage at asparagine-X-cysteine sites.PMID:1694179partial glycosylation at an N-X-C siteLizak, C.Gerber, S.Numao, S.Aebi, M.Locher, K.P.Nature 474, 350-355, 2011X-ray structure of a bacterial oligosaccharyltransferase.DOI:10.1038/nature10151PMID:21677752X-ray diffraction, 3.40 angstroms; detail of sequon interaction with active siteLizak, C.Gerber, S.Numao, S.Aebi, M.Locher, K.P.submitted to the Protein Data Bank, March 2011Bacterial oligosaccharyltransferase PglB.PDB:3RCEX-ray diffraction, 3.40 angstromsMatczuk, A.K.Kunec, D.Veit, M.J. Biol. Chem. 288, 35396-35405, 2013Co-translational processing of glycoprotein 3 from equine arteritis virus: N-glycosylation adjacent to the signal peptide prevents cleavage.DOI:10.1074/jbc.M113.505420PMID:24142700the sequence NNTT can be efficiently glycosylated on both asparagines, and N-glycosylation can block signal peptide processingThis modification typically occurs in extracellar peptides with an NX[ST] motif. Partial modification has been observed to occur with cysteine, rather than serine or threonine, in the third position. Secondary structure features are important, and proline in the second or fourth positions inhibits modification.See also RESID:AA0420 and RESID:AA0421 for other N4-glycosylated asparagines.The PDB has some entries with asparagine apparently alpha-glycosylated with N-acetylglucosamine, those with PDBHET:NDG. These are low resolution structures and appear to be erroneous.dolichyl-diphosphooligosaccharide-protein glycotransferase (EC 2.4.1.119)protein N-acetylglucosaminyltransferase (EC 2.4.1.94)NGO:0006487GO:0018279PSI-MOD:00831glycoproteinCARBOHYD N-linked (GlcNAc) asparagineCARBOHYD N-linked (GlcNAc or GlcNAc...) asparagineCARBOHYD N-linked (GlcNAc...) asparagineCARBOHYD N-linked (GlcNAc...) (keratan sulfate) asparagineCARBOHYD N-linked (GlcNAc...) (polylactosaminoglycan) asparagineAA015231-Mar-199502-Dec-200531-May-2018S-glucosyl-L-cysteineS-(beta-D-glucopyranosyl)cysteineS-glycosyl-cysteine(2R)-2-amino-3-[(beta-D-glucopyranosyl)sulfanyl]propanoic acidC 9 H 15 N 1 O 6 S 1 +265.28 +265.062008 +C 6 H 10 N 0 O 5 S 0 +162.14 +162.052823 +Weiss, J.B.Lote, C.J.Bobinski, H.Nature New Biol. 234, 25-26, 1971New low molecular weight glycopeptide containing triglucosylcysteine in human erythrocyte membrane.DOI:10.1038/newbio234025a0PMID:5286858chromatographic detection and chemical characterization; S-triglucosylcysteine peptide; the peptide was not isolated or characterized in subsequent work, and the reported peptide sequence has not been found in the human proteomeElsayed, S.Bennich, H.Scand. J. Immunol. 4, 203-208, 1975The primary structure of allergen M from cod.DOI:10.1111/j.1365-3083.1975.tb02618.xPMID:1145128chromatographic detection and chemical characterization; S-glucosylcysteineOlsen, E.H.Rahbek-Nielsen, H.Thogersen, I.B.Roepstorff, P.Enghild, J.J.Biochemistry 37, 408-416, 1998Posttranslational modifications of human inter-alpha-inhibitor: identification of glycans and disulfide bridges in heavy chains 1 and 2.DOI:10.1021/bi971137dPMID:9425062mass spectrometric detection; the dihexosylation modification is not chemically characterizedOman, T.J.Boettcher, J.M.Wang, H.Okalibe, X.N.van der Donk, W.A.Nature Chem. Biol. 7, 78-80, 2011Sublancin is not a lantibiotic but an S-linked glycopeptide.DOI:10.1038/nchembio.509PMID:21196935chromatographic, mass spectrometric, (1)H-NMR, and (13)C-NMR identification; chemical characterization; biosynthesisThe beta anomeric form is shown.See also RESID:AA0392 and RESID:AA0560 for other S-glycosylated cysteines.CGO:0018240PSI-MOD:00161glycoproteinthioether bondCARBOHYD S-linked (Glc) cysteineCARBOHYD S-linked (Glc...) cysteineCARBOHYD S-linked (Hex...) cysteineAA015331-Mar-199530-Sep-200531-May-2018O5-glucosylgalactosyl-L-hydroxylysine5-(2-O-alpha-D-glucopyranosyl-beta-D-galactopyranosyl)oxy-L-lysine(2S,5R)-2,6-diamino-5-[2-O-(alpha-D-glucopyranosyl)-beta-D-galactopyranosyloxy]hexanoic acidCAS:32448-35-4ChEBI:138659C 18 H 32 N 2 O 12468.46468.195524C 12 H 20 N 0 O 11340.28340.100561Butler, W.T.Cunningham, L.W.J. Biol. Chem. 241, 3882-3888, 1966Evidence for the linkage of a disaccharide to hydroxylysine in tropocollagen.PMID:4288358Morgan, P.H.Jacobs, H.G.Segrest, J.P.Cunningham, L.W.J. Biol. Chem. 245, 5042-5048, 1970Comparative study of glycopeptides derived from selected vertebrate collagens. A possible role of the carbohydrate in fibril formation.PMID:4319110attachment of 2-O-alpha-D-glucosyl-O-beta-D-galactose to 5-hydroxylysineAllevi, P.Anastasia, M.Paroni, R.Ragusa, A.Bioorg. Med. Chem. Lett. 14, 3319-3321, 2004The first synthesis of glucosylgalactosyl hydroxylysine (Glu-Gal-Hyl), an important biological indicator of collagen turnover.DOI:10.1016/j.bmcl.2004.03.068PMID:15149698chemical synthesisMyllylä, R.Wang, C.Heikkinen, J.Juffer, A.Lampela, O.Risteli, M.Ruotsalainen, H.Salo, A.Sipilä, L.J. Cell. Physiol. 212, 323-329, 2007Expanding the lysyl hydroxylase toolbox: new insights into the localization and activities of lysyl hydroxylase 3 (LH3).DOI:10.1002/jcp.21036PMID:17516569lysyl hydroxylase 3 (LH3) also possesses galactosyl transferase and glucosyl transferase activitiesVitorino, R.Alves, R.Barros, A.Caseiro, A.Ferreira, R.Lobo, M.C.Bastos, A.Duarte, J.Carvalho, D.Santos, L.L.Amado, F.L.Proteomics 10, 3732-3742, 2010Finding new posttranslational modifications in salivary proline-rich proteins.DOI:10.1002/pmic.201000261PMID:20879038mass spectrometric detectionPerdivara, I.Perera, L.Sricholpech, M.Terajima, M.Pleshko, N.Yamauchi, M.Tomer, K.B.J. Am. Soc. Mass Spectrom. 24, 1072-1081, 2013Unusual fragmentation pathways in collagen glycopeptides.DOI:10.1007/s13361-013-0624-yPMID:23633013mass spectrometric analysis of CID fragmentation patternsSome forms of lysyl hydroxylase (EC 1.14.11.4) are multifunctional and possess both transferase activities.procollagen galactosyltransferase (EC 2.4.1.50)procollagen glucosyltransferase (EC 2.4.1.66)Ksecondary to RESID:AA0028GO:0006493GO:0018241PSI-MOD:00162glycoproteinCARBOHYD O-linked (Gal...) hydroxylysineAA015431-Mar-199531-Mar-200631-May-2018O-(N-acetylamino)galactosyl-L-serinemucin type O-glycosylserineO3-(N-acetylgalactosaminyl)serine(2S)-2-amino-3-(2-acetamido-2-deoxy-alpha-D-galactopyranosyloxy)propanoic acidChEBI:53604ChEBI:87078C 11 H 18 N 2 O 7 +290.27 +290.111401 +C 8 H 13 N 1 O 5 +203.19 +203.079373 +Robinson, E.A.Appella, E.J. Biol. Chem. 254, 11418-11430, 1979Amino acid sequence of a mouse myeloma immunoglobin heavy chain (MOPC 47 A) with a 100-residue deletion.PMID:115869O-glycosylation by N-acetylgalactosamine onlyWang, Y.Agrwal, N.Eckhardt, A.E.Stevens, R.D.Hill, R.L.J. Biol. Chem. 268, 22979-22983, 1993The acceptor substrate specificity of porcine submaxillary UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferase is dependent on the amino acid sequences adjacent to serine and threonine residues.PMID:8226812N-acetylgalactosaminyltransferase transfers to either serine or threonineHansen, J.E.Lund, O.Engelbrecht, J.Bohr, H.Nielsen, J.O.Hansen, J.E.S.Brunak, S.Biochem. J. 308, 801-813, 1995Prediction of O-glycosylation of mammalian proteins: specificity patterns of UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferase.PMID:8948436prediction using neural network; the omission of author "Brunak, S." in the PubMed citation is correctedGerken, T.A.Owens, C.L.Pasumarthy, M.J. Biol. Chem. 272, 9709-9719, 1997Determination of the site-specific O-glycosylation pattern of the porcine submaxillary mucin tandem repeat glycopeptide. Model proposed for the polypeptide:galnac transferase peptide binding site.DOI:10.1074/jbc.272.15.9709PMID:9092502Hang, H.C.Bertozzi, C.R.Bioorg. Med. Chem. 13, 5021-5034, 2005The chemistry and biology of mucin-type O-linked glycosylation.DOI:10.1016/j.bmc.2005.04.085PMID:16005634See also RESID:AA0208, RESID:AA0209, RESID:AA0210, RESID:AA0291, RESID:AA0296, RESID:AA0297, RESID:AA0397, RESID:AA0398, RESID:AA0400, RESID:AA0402, RESID:AA0404, RESID:AA0406, and RESID:AA0422 for other O-glycosylated serines.polypeptide N-acetylgalactosaminyltransferase (EC 2.4.1.41)SGO:0006493GO:0018242PSI-MOD:00163glycoproteinCARBOHYD O-linked (GalNAc) serineCARBOHYD O-linked (GalNAc...) serineCARBOHYD O-linked (HexNAc...) serinethis UniProt feature is used when the identity of the sugar has not been determinedAA015531-Mar-199531-Mar-200631-May-2018O-(N-acetylamino)galactosyl-L-threoninemucin type O-glycosylthreonineO3-(N-acetylgalactosaminyl)threonine(2S,3R)-2-amino-3-(2-acetamido-2-deoxy-alpha-D-galactopyranosyloxy)butanoic acidChEBI:87075PDBHET:GTHC 12 H 20 N 2 O 7 +304.30 +304.127051 +C 8 H 13 N 1 O 5 +203.19 +203.079373 +Talbo, G.Højrup, P.Rahbek-Nielsen, H.Andersen, S.O.Roepstorff, P.Eur. J. Biochem. 195, 495-504, 1991Determination of the covalent structure of an N- and C-terminally blocked glycoprotein from endocuticle of Locusta migratoria. Combined use of plasma desorption mass spectrometry and Edman degradation to study post-translationally modified proteins.DOI:10.1111/j.1432-1033.1991.tb15730.xPMID:1997327O-glycosylation by N-acetylgalactosamine onlyWang, Y.Agrwal, N.Eckhardt, A.E.Stevens, R.D.Hill, R.L.J. Biol. Chem. 268, 22979-22983, 1993The acceptor substrate specificity of porcine submaxillary UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferase is dependent on the amino acid sequences adjacent to serine and threonine residues.PMID:8226812N-acetylgalactosaminyltransferase transfers to either serine or threonineHansen, J.E.Lund, O.Engelbrecht, J.Bohr, H.Nielsen, J.O.Hansen, J.E.S.Brunak, S.Biochem. J. 308, 801-813, 1995Prediction of O-glycosylation of mammalian proteins: specificity patterns of UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferase.PMID:8948436prediction using neural network; the omission of author "Brunak, S." in the PubMed citation is correctedGerken, T.A.Owens, C.L.Pasumarthy, M.J. Biol. Chem. 272, 9709-9719, 1997Determination of the site-specific O-glycosylation pattern of the porcine submaxillary mucin tandem repeat glycopeptide. Model proposed for the polypeptide:galnac transferase peptide binding site.DOI:10.1074/jbc.272.15.9709PMID:9092502Hang, H.C.Bertozzi, C.R.Bioorg. Med. Chem. 13, 5021-5034, 2005The chemistry and biology of mucin-type O-linked glycosylation.DOI:10.1016/j.bmc.2005.04.085PMID:16005634See also RESID:AA0247, RESID:AA0399, RESID:AA0401, RESID:AA0403, RESID:AA0405, and RESID:AA0515 for other O-glycosylated threonines.polypeptide N-acetylgalactosaminyltransferase (EC 2.4.1.41)TGO:0006493GO:0018243PSI-MOD:00164glycoproteinCARBOHYD O-linked (GalNAc) threonineCARBOHYD O-linked (GalNAc...) threonineCARBOHYD O-linked (HexNAc) threoninethis UniProt feature is used when the identity of the sugar has not been determinedCARBOHYD O-linked (HexNAc...) threoninethis UniProt feature is used when the identity of the sugar has not been determinedAA015631-Mar-199531-Mar-200631-May-20181'-mannosyl-L-tryptophan1'-glycosyl-L-tryptophanN-mannosyl-tryptophanN1-mannosyl-tryptophan(2S)-2-amino-3-(1-D-mannopyranosyloxy-1H-indol-3-yl)propanoic acidC 17 H 20 N 2 O 6348.36348.132136C 6 H 10 N 0 O 5162.14162.052823Gäde, G.Kellner, R.Rinehart, K.L.Proefke, M.L.Biochem. Biophys. Res. Commun. 189, 1303-1309, 1992A tryptophan-substituted member of the AKH/RPCH family isolated from a stick insect corpus cardiacum.DOI:10.1016/0006-291X(92)90215-7PMID:1482345proposed, without evidence, to be 1'- or N-linkedGäde, G.Ann. N. Y. Acad. Sci. 839, 101-104, 1998The adipokinetic hormone/red pigment-concentrating hormone family. New structure, unique post-translational modifications and a unique new physiological role.DOI:10.1111/j.1749-6632.1998.tb10739.xidentified as a mannosyltryptophan, it was assumed to be 2'- or C-linked rather than 1'- or N-linkedSchnabel, M.Römpp, B.Ruckdeschel, D.Unverzagt, C.Tetrahedron Lett. 45, 295-297, 2004Synthesis of tryptophan N-glucoside.DOI:10.1016/j.tetlet.2003.10.190synthesis of 1'-glycosyltryptophan compoundsLi, J.S.Cui, L.Rock, D.L.Li, J.J. Biol. Chem. 280, 38513-38521, 2005Novel glycosidic linkage in Aedes aegypti chorion peroxidase: N-mannosyl tryptophan.DOI:10.1074/jbc.M508449200PMID:16150691evidence that the 1'-mannosyltryptophan modification occurs in arthropods In 1992, the hexose was not identified and it was proposed, but not established, that this modification had an N-linked glycosidic bond. After C-linked 2'-mannosyltryptophan was found in vertebrate proteins, it was generally assumed that the tryptophan N-glycoside structure was wrong. See RESID:AA0217 for 2'-mannosyltryptophan.The alpha anomeric form is shown.WGO:0006487GO:0018244PSI-MOD:00165glycoproteinCARBOHYD N-linked (Man) tryptophanAA015731-Mar-199531-Mar-199531-May-2018O4'-glucosyl-L-tyrosineO4'-glycosyl-L-tyrosine(2S)-2-amino-3-(4-alpha-D-glucopyranosyloxy)phenylpropanoic acidC 15 H 19 N 1 O 7 +325.32 +325.116152 +C 6 H 10 N 0 O 5 +162.14 +162.052823 +Smythe, C.Caudwell, F.B.Ferguson, M.Cohen, P.EMBO J. 7, 2681-2686, 1988Isolation and structural analysis of a peptide containing the novel tyrosyl-glucose linkage in glycogenin.PMID:3181138mass spectrometric and linkage analysisThe carbohydrate is glucose, the origin for glycogen. One to eleven alpha-1,4-linked glucose units may be auto-catalytically attached.See also RESID:AA0577 for other O-glycosylated tyrosines.glycogenin glucosyltransferase (EC 2.4.1.186)YGO:0006493GO:0018245PSI-MOD:00166glycoproteinCARBOHYD O-linked (Glc...) tyrosineAA015831-Mar-199531-Mar-199530-Apr-2010N-asparaginyl-glycosylphosphatidylinositolethanolamineC 6 H 13 N 3 O 6 P 1 +254.16 +254.054197 +C 2 H 6 N 1 O 3 P 1 +123.05 +123.008530 +Nuoffer, C.Jenoe, P.Conzelmann, A.Riezman, H.Mol. Cell. Biol. 11, 27-37, 1991Determinants for glycophospholipid anchoring of the Saccharomyces cerevisiae GAS1 protein to the plasma membrane.PMID:1824714Sugita, Y.Nakano, Y.Oda, E.Noda, K.Tobe, T.Miura, N.H.Tomita, M.J. Biochem. 114, 473-477, 1993Determination of carboxyl-terminal residue and disulfide bonds of MACIF(CD59), a glycosyl-phosphatidylinositol-anchored membrane protein.PMID:8276756A representative glycan core structure is shown.Cleavage of a carboxyl terminal propeptide accompanies transamidation.Ncarboxyl-terminalGO:0018265GO:0042050PSI-MOD:00167blocked carboxyl endglycoproteinlipoproteinphosphatidylinositol linkagephosphoproteinLIPID GPI-anchor amidated asparagineAA015931-Mar-199531-Mar-199530-Apr-2010N-aspartyl-glycosylphosphatidylinositolethanolamineC 6 H 12 N 2 O 7 P 1 +255.14 +255.038212 +C 2 H 6 N 1 O 3 P 1 +123.05 +123.008530 +Allen, G.Gurnett, L.P.Cross, G.A.M.J. Mol. Biol. 157, 527-546, 1982Complete amino acid sequence of a variant surface glycoprotein (VSG 117) from Trypanosoma brucei.DOI:10.1016/0022-2836(82)90474-0PMID:7120400A representative glycan core structure is shown.Cleavage of a carboxyl terminal propeptide accompanies transamidation.Dcarboxyl-terminalGO:0018266GO:0042050PSI-MOD:00168blocked carboxyl endglycoproteinlipoproteinphosphatidylinositol linkagephosphoproteinLIPID GPI-anchor amidated aspartateAA016031-Mar-199531-Mar-199530-Apr-2010N-cysteinyl-glycosylphosphatidylinositolethanolamineC 5 H 12 N 2 O 5 P 1 S 1 +243.19 +243.020454 +C 2 H 6 N 1 O 3 P 1 S 0 +123.05 +123.008530 +Homans, S.W.Ferguson, M.A.J.Dwek, R.A.Rademacher, T.W.Anand, R.Williams, A.F.Nature 333, 269-272, 1988Complete structure of the glycosyl phosphatidylinositol membrane anchor of rat brain Thy-1 glycoprotein.DOI:10.1038/333269a0PMID:2897081A representative glycan core structure is shown.Cleavage of a carboxyl terminal propeptide accompanies transamidation.Ccarboxyl-terminalGO:0018267GO:0042050PSI-MOD:00169blocked carboxyl endglycoproteinlipoproteinphosphatidylinositol linkagephosphoproteinLIPID GPI-anchor amidated cysteineAA016131-Mar-199531-Mar-199530-Apr-2010N-glycyl-glycosylphosphatidylinositolethanolamineC 4 H 10 N 2 O 5 P 1 +197.11 +197.032733 +C 2 H 6 N 1 O 3 P 1 +123.05 +123.008530 +Hefta, S.A.Paxton, R.J.Shively, J.E.J. Biol. Chem. 265, 8618-8626, 1990Sequence and glycosylation site identity of two distinct glycoforms of nonspecific cross-reacting antigen as demonstrated by sequence analysis and fast atom bombardment mass spectrometry.PMID:2341397A representative glycan core structure is shown.Cleavage of a carboxyl terminal propeptide accompanies transamidation.Gcarboxyl-terminalGO:0018268GO:0042050PSI-MOD:00170blocked carboxyl endglycoproteinlipoproteinphosphatidylinositol linkagephosphoproteinLIPID GPI-anchor amidated glycineAA016231-Mar-199531-Mar-199530-Apr-2010N-seryl-glycosylphosphatidylinositolethanolamineC 5 H 12 N 2 O 6 P 1 +227.13 +227.043298 +C 2 H 6 N 1 O 3 P 1 +123.05 +123.008530 +Zhu, X.L.Sly, W.S.J. Biol. Chem. 265, 8795-8801, 1990Carbonic anhydrase IV from human lung. Purification, characterization, and comparison with membrane carbonic anhydrase from human kidney.PMID:2111324evidence for glycosyl phosphatidylinositol anchorStahl, N.Baldwin, M.A.Teplow, D.B.Hood, L.Gibson, B.W.Burlingame, A.L.Prusiner, S.B.Biochemistry 32, 1991-2002, 1993Structural studies of the scrapie prion protein using mass spectrometry and amino acid sequencing.DOI:10.1021/bi00059a016PMID:8448158mass spectrometric and chemical characterizationA representative glycan core structure is shown.Cleavage of a carboxyl terminal propeptide accompanies transamidation.Scarboxyl-terminalGO:0018269GO:0042050PSI-MOD:00171blocked carboxyl endglycoproteinlipoproteinphosphatidylinositol linkagephosphoproteinLIPID GPI-anchor amidated serineAA016328-Jan-200028-Jan-200030-Apr-2010N-alanyl-glycosylphosphatidylinositolethanolamineC 5 H 12 N 2 O 5 P 1 +211.13 +211.048383 +C 2 H 6 N 1 O 3 P 1 +123.05 +123.008530 +Moy, P.Lobb, R.Tizard, R.Olson, D.Hession, C.J. Biol. Chem. 268, 8835-8841, 1993Cloning of an inflammation-specific phosphatidyl inositol-linked form of murine vascular cell adhesion molecule-1.PMID:7682556predicted cleavage siteVergas Romero, C.Neudorfer, I.Mann, K.Schäfer, D.Eur. J. Biochem. 229, 262-269, 1995Purification and amino acid sequence of aminopeptidase P from pig kidney.DOI:10.1111/j.1432-1033.1995.0262l.xPMID:7744038enzymatic and sequence evidenceA representative glycan core structure is shown.Cleavage of a carboxyl terminal propeptide accompanies transamidation.Acarboxyl-terminalGO:0018270GO:0042050PSI-MOD:00172blocked carboxyl endglycoproteinlipoproteinphosphatidylinositol linkagephosphoproteinLIPID GPI-anchor amidated alanineAA016430-Sep-200330-Sep-200330-Apr-2010N-threonyl-glycosylphosphatidylinositolethanolamineC 6 H 14 N 2 O 6 P 1 +241.16 +241.058948 +C 2 H 6 N 1 O 3 P 1 +123.05 +123.008530 +This modification is predicted for proteins with sequence characteristics for the GPI-anchor modification, and with threonine at the cleavage and anchor attachment site.A representative glycan core structure is shown.Cleavage of a carboxyl terminal propeptide accompanies transamidation.Tcarboxyl-terminalGO:0050493PSI-MOD:00173blocked carboxyl endglycoproteinlipoproteinphosphatidylinositol linkagephosphoproteinLIPID GPI-anchor amidated threonineAA016530-Sep-200330-Sep-200330-Apr-2010N-glycyl-glycosylsphingolipidinositolethanolamineC 4 H 10 N 2 O 5 P 1 +197.11 +197.032733 +C 2 H 6 N 1 O 3 P 1 +123.05 +123.008530 +Haynes, P.A.Gooley, A.A.Ferguson, M.A.Redmond, J.W.Williams, K.L.Eur. J. Biochem. 216, 729-737, 1993Post-translational modifications of the Dictyostelium discoideum glycoprotein PsA. Glycosylphosphatidylinositol membrane anchor and composition of O-linked oligosaccharides.DOI:10.1111/j.1432-1033.1993.tb18192.xPMID:8404891despite identifying the lipid as monoacylated phosphoceramide inositol, which does not contain glycerol, the authors repeatedly refer to it incorrectly as a phosphatidyl inositol, which would contain glycerolFontaine, T.Magnin, T.Melhert, A.Lamont, D.Latge, J.P.Ferguson, M.A.Glycobiology 13, 169-177, 2003Structures of the glycosylphosphatidylinositol membrane anchors from Aspergillus fumigatus membrane proteins.DOI:10.1093/glycob/cwg004PMID:12626404A representative glycan core structure is shown.Cleavage of a carboxyl terminal propeptide accompanies transamidation.Gcarboxyl-terminalGO:0050494PSI-MOD:00174blocked carboxyl endglycoproteinlipoproteinphosphoproteinsphingolipidinositol linkageLIPID GPI-like-anchor amidated glycineAA016609-Aug-199509-Aug-199530-Apr-2010N-seryl-glycosylsphingolipidinositolethanolamineC 5 H 12 N 2 O 6 P 1 +227.13 +227.043298 +C 2 H 6 N 1 O 3 P 1 +123.05 +123.008530 +Stadler, J.Keenan, T.W.Bauer, G.Gerisch, G.EMBO J. 8, 371-377, 1989The contact site A glycoprotein of Dictyostelium discoideum carries a phospholipid anchor of a novel type.PMID:2721485partial chemical characterizationSaito, T.Ochiai, H.Eur. J. Biochem. 218, 623-628, 1993Evidence for a glycolipid anchor of gp64, a putative cell-cell adhesion protein of Polysphondylium pallidum.DOI:10.1111/j.1432-1033.1993.tb18415.xPMID:8269952mass spectrometric and chemical characterizationFontaine, T.Magnin, T.Melhert, A.Lamont, D.Latge, J.P.Ferguson, M.A.Glycobiology 13, 169-177, 2003Structures of the glycosylphosphatidylinositol membrane anchors from Aspergillus fumigatus membrane proteins.DOI:10.1093/glycob/cwg004PMID:12626404A representative glycan core structure is shown.Cleavage of a carboxyl terminal propeptide accompanies transamidation.Scarboxyl-terminalGO:0018281GO:0042050PSI-MOD:00175blocked carboxyl endglycoproteinlipoproteinphosphoproteinsphingolipidinositol linkageLIPID GPI-like-anchor amidated serineAA016731-Mar-199531-Mar-199530-Sep-2011O-(phosphoribosyl dephospho-coenzyme A)-L-serineO3-(phosphate-5-ribosyl-alpha-2-adenosine-5-diphosphate pantetheine)-L-serineO3-(phosphoribosyl dephospho-coenzyme A)-L-serineO3-2'-(5''-phosphoribosyl-3'-dephosphocoenzyme A)-L-serineC 29 H 47 N 8 O 21 P 3 S 1968.71968.178931C 26 H 42 N 7 O 19 P 3 S 1881.63881.146903Dimroth, P.Eur. J. Biochem. 64, 269-281, 1976The prosthetic group of citrate-lyase acyl-carrier protein.DOI:10.1111/j.1432-1033.1976.00269.pp.xPMID:179809chemical characterizationRobinson Jr., J.B.Singh, M.Srere, P.A.Proc. Natl. Acad. Sci. U.S.A. 73, 1872-1876, 1976Structure of the prosthetic group of Klebsiella aerogenes citrate (pro-3S)-lyase.DOI:10.1073/pnas.73.6.1872PMID:180526chemical characterizationOppenheimer, N.J.Singh, M.Sweeley, C.C.Sung, S.J.Srere, P.A.J. Biol. Chem. 254, 1000-1002, 1979The configuration and location of the ribosidic linkage in the prosthetic group of citrate lyase (Klebsiella aerogenes).PMID:368065NMR and mass spectrometry of permethylation derivatives establish that phosphoribosyl glycosidic linkage is alpha 1->2Schneider, K.Dimroth, P.Bott, M.Biochemistry 39, 9438-9450, 2000Biosynthesis of the prosthetic group of citrate lyase.DOI:10.1021/bi000401rPMID:10924139Hoenke, S.Wild, M.R.Dimroth, P.Biochemistry 39, 13223-13232, 2000Biosynthesis of triphosphoribosyl-dephospho-coenzyme A, the precursor of the prosthetic group of malonate decarboxylase.DOI:10.1021/bi0011532PMID:11052675holo-ACP synthase (EC 2.7.7.61)SGO:0018247PSI-MOD:00176coenzyme AphosphoproteinMOD_RES O-(phosphoribosyl dephospho-coenzyme A)serineAA016831-Mar-199531-Mar-199531-May-2018N(omega)-(ADP-ribosyl)-L-arginineN(omega)-alpha-D-ribofuranosyl-L-arginine 5'->5'-ester with adenosine 5'-(trihydrogen diphosphate)N(omega)-[alpha-D-ribofuranoside 5'->5'-ester with adenosine 5'-(trihydrogen diphosphate)]-L-arginine(S)-2-amino-5-([imino([adenosine 5'-(trihydrogen diphosphate) 5'->5'-ester with alpha-D-ribofuranosyl]amino)methyl]amino)pentanoic acidCAS:71388-78-8C 21 H 33 N 9 O 14 P 2697.49697.162220C 15 H 21 N 5 O 13 P 2541.30541.061109Oppenheimer, N.J.J. Biol. Chem. 253, 4907-4910, 1978Structural determination and stereospecificity of the choleragen-catalyzed reaction of NAD+ with guanidines.PMID:209022mass spectrometric and (1)H-NMR characterization; chemical synthesisVan Dop, C.Tsubokawa, M.Bourne, H.R.Ramachandran, J.J. Biol. Chem. 259, 696-698, 1984Amino acid sequence of retinal transducin at the site ADP-ribosylated by cholera toxin.PMID:6582062mass spectrometric analysisPope, M.R.Murrell, S.A.Ludden, P.W.Proc. Natl. Acad. Sci. U.S.A. 82, 3173-3177, 1985Covalent modification of the iron protein of nitrogenase from Rhodospirillum rubrum by adenosine diphosphoribosylation of a specific arginine residue.DOI:10.1073/pnas.82.10.3173PMID:3923473mass spectrometric, (1)H-NMR and (31)P-NMR identificationPope, M.R.Saari, L.L.Ludden, P.W.J. Biol. Chem. 261, 10104-10111, 1986N-glycohydrolysis of adenosine diphosphoribosyl arginine linkages by dinitrogenase reductase activating glycohydrolase (activating enzyme) from Rhodospirillum rubrum.PMID:3090031stereochemical characterization; ADP-ribosyl-nitrogenase hydrolase (EC 3.2.2.24) appears to remove only the alpha anomeric formOsago, H.Yamada, K.Shibata, T.Yoshino, K.-I.Hara, N.Tsuchiya, M.Anal. Biochem. 393, 248-254, 2009Precursor ion scanning and sequencing of arginine-ADP-ribosylated peptide by mass spectrometry.DOI:10.1016/j.ab.2009.06.028PMID:19560435detection of N-(ADP-ribosyl)-carbodiimide as a marker ion for ADP-ribosylation in MS/MS analysisMatic, I.Ahel, I.Hay, R.T.Nature Methods 9, 771-772, 2012Reanalysis of phosphoproteomics data uncovers ADP-ribosylation sites.DOI:10.1038/nmeth.2106PMID:22847107mass spectrometric detection in reanalysis of phosphoproteomics dataCholera toxin appears to catalyze formation of the alpha form which subsequently anomerizes to approximately equal concentrations of the alpha and beta forms. The alpha form is presented.The keyword "phosphoprotein" is not used with toxin modification.NAD(P)+--arginine ADP-ribosyltransferase (EC 2.4.2.31)NAD+--nitrogenase ADP-D-ribosyltransferase (EC 2.4.2.37)RGO:0006471GO:0018120PSI-MOD:00177*phosphoproteinMOD_RES ADP-ribosylarginineAA016931-Mar-199531-Mar-199530-Sep-2008S-(ADP-ribosyl)-L-cysteineS-alpha-D-ribofuranosyl-L-cysteine 5'->5'-ester with adenosine 5'-(trihydrogen diphosphate)S-L-cysteine alpha-D-ribofuranoside 5'->5'-ester with adenosine 5'-(trihydrogen diphosphate)(R)-2-amino-3-([adenosine 5'-(trihydrogen diphosphate) 5'->5'-ester with alpha-D-ribofuranosyl]sulfanyl)propanoic acidC 18 H 26 N 6 O 14 P 2 S 1644.44644.070294C 15 H 21 N 5 O 13 P 2 S 0541.30541.061109West Jr., R.E.Moss, J.Vaughan, M.Liu, T.Liu, T.Y.J. Biol. Chem. 260, 14428-14430, 1985Pertussis toxin-catalyzed ADP-ribosylation of transducin. Cysteine 347 is the ADP-ribose acceptor site.PMID:3863818radioisotope labeling; chromatographic separationThe anomeric form of the pertussis toxin product has not been characterized; the alpha form is presented.The keywords "phosphoprotein" and "thioether bond" are not used with toxin modification.NAD(P)+--cysteine ADP-ribosyltransferase (EC 2.4.2.-)CGO:0006471GO:0018123PSI-MOD:00178*phosphoprotein*thioether bondMOD_RES ADP-ribosylcysteineAA017031-Mar-199531-Mar-199520-Nov-20095-L-glutamyl glycerylphosphorylethanolamineL-glutamyl 5-glycerophosphoethanolamineL-glutamyl 5-glycerophosphorylethanolamineL-glutamyl 5-glycerylphosphorylethanolamine(S)-2-amino-5-[2-([([2,3-dihydroxypropyl]oxy)(hydroxy)phosphoryl]oxy)ethyl]amino-5-oxopentanoic acidCAS:1190-00-7C 10 H 19 N 2 O 8 P 1326.24326.087902C 5 H 12 N 1 O 5 P 1197.13197.045309Dever, T.E.Costello, C.E.Owens, C.L.Rosenberry, T.L.Merrick, W.C.J. Biol. Chem. 264, 20518-20525, 1989Location of seven post-translational modifications in rabbit elongation factor 1alpha including dimethyllysine, trimethyllysine, and glycerylphosphorylethanolamine.PMID:2511205mass spectrometric and chemical characterizationWhiteheart, S.W.Shenbagamurthi, P.Chen, L.Cotter, R.J.Hart, G.W.J. Biol. Chem. 264, 14334-14341, 1989Murine elongation factor 1alpha (EF-1alpha) is posttranslationally modified by novel amide-linked ethanolamine-phosphoglycerol moieties. Addition of ethanolamine-phosphoglycerol to specific glutamic acid residues on EF-1alpha.PMID:2569467mass spectrometric and chemical characterizationRansom, W.D.Lao, P.-C.Gage, D.A.Boss, W.F.Plant Physiol. 117, 949-960, 1998Phosphoglycerylethanolamine posttranslational modification of plant eukaryotic elongation factor 1alpha.DOI:10.1104/pp.117.3.949PMID:9662537mass spectrometric detection; isotope labeling; possible secondary modification by long chain fatty acylation; the punctuation of "Lao, P.C." in the PubMed citation is correctedSignorell, A.Jelk, J.Rauch, M.Bütikofer, P.J. Biol. Chem. 283, 20320-20329, 2008Phosphatidylethanolamine is the precursor of the ethanolamine phosphoglycerol moiety bound to eukaryotic elongation factor 1A.DOI:10.1074/jbc.M802430200PMID:18499667mass spectrometric detection and linkage analysis5-Glutamyl glycerylphosphorylethanolamine appears to occur uniquely in translation elongation factor eEF-1 alpha chains. It is known to be a modification of glutamic acid. The stereochemistry of the glycerol phosphate has not been determined. The sn-3 form is shown.It has been established that is possible for the glycerol group to be secondarily modified by conjugation with long chain fatty acids, but probably not with inositol-containing lipids or glycolipids. The predominant soluble form is not lipidated, and the modified protein does not appear to be membrane associated.EGO:0018072PSI-MOD:00179phosphoproteinMOD_RES 5-glutamyl glycerylphosphorylethanolamineAA017131-Mar-199531-Mar-199531-Dec-2012S-sulfo-L-cysteine2-amino-3-(sulfothio)propanoic acid3-(sulfosulfanyl)-L-alaninecysteine sulfate thioestercysteine-S-sulfonic acidS-sulfocysteine(2R)-2-amino-3-(sulfosulfanyl)propanoic acidCAS:1637-71-4ChEBI:27891PDBHET:CSUC 3 H 5 N 1 O 4 S 2183.20182.966000C 0 H 0 N 0 O 3 S 180.0679.956815Ploegman, J.H.Drent, G.Kalk, K.H.Hol, W.G.J.Heinrikson, R.L.Keim, P.Weng, L.Russell, J.Nature 273, 124-129, 1978The covalent and tertiary structure of bovine liver rhodanese.DOI:10.1038/273124a0PMID:643076X-ray diffraction, 2.9 angstromsLim, A.Prokaeva, T.McComb, M.E.Connors, L.H.Skinner, M.Costello, C.E.Protein Sci. 12, 1775-1785, 2003Identification of S-sulfonation and S-thiolation of a novel transthyretin Phe33Cys variant from a patient diagnosed with familial transthyretin amyloidosis.DOI:10.1110/ps.0349703PMID:12876326mass spectrometric detection of S-sulfocysteine in a mutant proteinGales, L.Saraiva, M.J.Damas, A.M.Biochim. Biophys. Acta 1774, 59-64, 2007Structural basis for the protective role of sulfite against transthyretin amyloid formation.DOI:10.1016/j.bbapap.2006.10.015PMID:17175208X-ray diffraction, 1.45 angstromsGales, L.Damas, A.M.submitted to the Protein Data Bank, May 2006Crystal structure of Cys10 sulfonated transthyretin.PDB:2H4EX-ray diffraction, 1.45 angstromsCGO:0018248PSI-MOD:00180sulfoproteinACT_SITEAA017231-Mar-199531-Mar-199531-May-2018O4'-sulfo-L-tyrosine2-amino-3-(4-hydroxyphenyl)propanoic acid 4'-sulfateO4-sulfotyrosinetyrosine sulfatetyrosine-O-sulfonic acidtyrosine-O-sulphonic acid(S)-2-amino-3-(4-sulfooxyphenyl)propanoic acidCAS:956-46-7ChEBI:65316PDBHET:TYSC 9 H 9 N 1 O 5 S 1243.23243.020143C 0 H 0 N 0 O 3 S 180.0679.956815Nachman, R.J.Holman, G.M.Cook, B.J.Haddon, W.F.Ling, N.Biochem. Biophys. Res. Commun. 140, 357-364, 1986Leucosulfakinin-II, a blocked sulfated insect neuropeptide with homology to cholecystokinin and gastrin.DOI:10.1016/0006-291X(86)91098-3PMID:3778455chromatographic detection; mass spectrometric identification; chemical synthesisHortin, G.Folz, R.Gordon, J.I.Strauss, A.W.Biochem. Biophys. Res. Commun. 141, 326-333, 1986Characterization of sites of tyrosine sulfation in proteins and criteria for predicting their occurrence.DOI:10.1016/S0006-291X(86)80372-2PMID:3801003Johnsen, A.H.Rehfeld, J.F.J. Biol. Chem. 265, 3054-3058, 1990Cionin: a disulfotyrosyl hybrid of cholecystokinin and gastrin from the neural ganglion of the protochordate Ciona intestinalis.PMID:2303439sulfotyrosyl-sulfotyrosyl sequence confirmed by enzymatic analysis and synthesisWolfender, J.L.Chu, F.Ball, H.Wolfender, F.Fainzilber, M.Baldwin, M.A.Burlingame, A.L.J. Mass Spectrom. 34, 447-454, 1999Identification of tyrosine sulfation in Conus pennaceus conotoxins alpha-PnIA and alpha-PnIB: further investigation of labile sulfo- and phosphopeptides by electrospray, matrix-assisted laser desorption/ionization (MALDI) and atmospheric pressure MALDI mass spectrometry.DOI:10.1002/(SICI)1096-9888(199904)34:4<447::AID-JMS801>3.3.CO;2-TPMID:10226369attempt to distinguish between the essentially isobaric protonated forms of phosphotyrosine (see RESID:AA0039) and sulfotyrosine by negative ion mode MALDIprotein-tyrosine sulfotransferase (EC 2.8.2.20)YGO:0006478PSI-MOD:00181sulfoproteinMOD_RES SulfotyrosineAA017331-Mar-199531-Mar-199530-Sep-2008L-bromohistidineBr 1 C 6 H 6 N 3 O 1216.04214.969424Br 1 C 0 H -1 N 0 O 078.9077.910512Takao, T.Yoshino, K.Suzuki, N.Shimonishi, Y.Biomed. Environ. Mass Spectrom. 19, 705-712, 1990Analysis of post-translational modifications of proteins by accurate mass measurement in fast atom bombardment mass spectrometry.DOI:10.1002/bms.1200191109PMID:2076468mass spectrometric identificationThe position of the bromine substitution is uncertain. The 2'-bromohistidine is shown.HGO:0018074PSI-MOD:00182bromineMOD_RES BromohistidineAA017431-Mar-199531-Mar-199530-Sep-2008L-2'-bromophenylalanineo-bromophenylalanineortho-bromophenylalanine(S)-2-amino-3-(2-bromophenyl)propanoic acidCAS:42538-40-9Br 1 C 9 H 8 N 1 O 1226.07224.978926Br 1 C 0 H -1 N 0 O 078.9077.910512Yoshino, K.Takao, T.Suhara, M.Kitai, T.Hori, H.Nomura, K.Yamaguchi, M.Shimonishi, Y.Suzuki, N.Biochemistry 30, 6203-6209, 1991Identification of a novel amino acid, o-bromo-L-phenylalanine, in egg-associated peptides that activate spermatozoa.DOI:10.1021/bi00239a018PMID:2059627Takao, T.Yoshino, K.Suzuki, N.Shimonishi, Y.Biomed. Environ. Mass Spectrom. 19, 705-712, 1990Analysis of post-translational modifications of proteins by accurate mass measurement in fast atom bombardment mass spectrometry.DOI:10.1002/bms.1200191109PMID:2076468chromatographic and mass spectrometric identification; chemical synthesisFGO:0018075GO:0018397PSI-MOD:00183bromineNot availablethis modification is not annotated in UniProt featuresAA017531-Mar-199531-Mar-199530-Sep-2008L-3'-bromophenylalaninem-bromophenylalaninemeta-bromophenylalanine(S)-2-amino-3-(3-bromophenyl)propanoic acidCAS:82311-69-1Br 1 C 9 H 8 N 1 O 1226.07224.978926Br 1 C 0 H -1 N 0 O 078.9077.910512Takao, T.Yoshino, K.Suzuki, N.Shimonishi, Y.Biomed. Environ. Mass Spectrom. 19, 705-712, 1990Analysis of post-translational modifications of proteins by accurate mass measurement in fast atom bombardment mass spectrometry.DOI:10.1002/bms.1200191109PMID:2076468chemical synthesisFGO:0018075GO:0018398PSI-MOD:00184bromineNot availablethis modification is not annotated in UniProt featuresAA017631-Mar-199531-Mar-199531-Dec-2012L-4'-bromophenylalaninep-bromophenylalaninepara-bromophenylalanine(2S)-2-amino-3-(4-bromophenyl)propanoic acidCAS:24250-84-8PDBHET:4BFBr 1 C 9 H 8 N 1 O 1226.07224.978926Br 1 C 0 H -1 N 0 O 078.9077.910512Takao, T.Yoshino, K.Suzuki, N.Shimonishi, Y.Biomed. Environ. Mass Spectrom. 19, 705-712, 1990Analysis of post-translational modifications of proteins by accurate mass measurement in fast atom bombardment mass spectrometry.DOI:10.1002/bms.1200191109PMID:2076468chemical synthesisFGO:0018075GO:0018399PSI-MOD:00185bromineNot availablethis modification is not annotated in UniProt featuresAA017731-Mar-199531-Mar-199531-May-20183',3'',5'-triiodo-L-thyronine3,3',5-triiodo-L-thyronine3,5,3'-triiodo-L-thyronine4-(4-hydroxy-3-iodophenoxy)-3,5-diiodo-L-phenylalanineliothyronineO-(4-hydroxy-3-iodophenyl)-3,5-diiodo-L-tyrosineT3(S)-2-amino-3-[4-(4-hydroxy-3-iodophenoxy)-3,5-diiodophenyl]propanoic acidCAS:6893-02-3ChEBI:90874PDBHET:T3C 15 H 10 I 3 N 1 O 3632.96632.779486C 6 H 1 I 3 N 0 O 1469.79469.716158Marriq, C.Rolland, M.Lissitzky, S.Biochem. Biophys. Res. Commun. 112, 206-213, 1983Amino acid sequence of the unique 3,5,3'-triiodothyronine-containing sequence from porcine thyroglobulin.DOI:10.1016/0006-291X(83)91817-X PMID:6838607Salek, M.Lehmann, W.D.Proteomics 5, 351-353, 2005Analysis of thyroglobulin iodination by tandem mass spectrometry using immonium ions of monoiodo- and diiodo-tyrosine.DOI:10.1002/pmic.200400949PMID:15627961YGO:0018078GO:0018407PSI-MOD:00186iodineMOD_RES TriiodothyronineAA017831-Mar-199531-Mar-199531-May-2018L-thyroxine3',3'',5',5''-tetraiodo-L-thyronine3,3',5,5'-tetraiodo-L-thyronine3,5,3',5'-tetraiodo-L-thyronine4-(4-hydroxy-3,5-diiodophenoxy)-3,5-diiodo-L-phenylalanineO-(4-hydroxy-3,5-diiodophenyl)-3,5-diiodo-L-tyrosineT4(S)-2-amino-3-[4-(4-hydroxy-3,5-diiodophenoxy)-3,5-diiodophenyl]propanoic acidCAS:51-48-9ChEBI:90872PDBHET:T44C 15 H 9 I 4 N 1 O 3758.86758.676134C 6 H 0 I 4 N 0 O 1595.68595.612805Rawitch, A.B.Litwer, M.R.Gregg, J.Turner, C.D.Rouse, J.B.Hamilton, J.W.Biochem. Biophys. Res. Commun. 118, 423-429, 1984The isolation of identical thyroxine containing amino acid sequences from bovine, ovine and porcine thyroglobulins.DOI:10.1016/0006-291X(84)91320-2PMID:6704086YGO:0018078GO:0018408PSI-MOD:00187iodineMOD_RES ThyroxineAA017928-Feb-199728-Feb-199731-Dec-20116'-bromo-L-tryptophan(2S)-2-amino-3-(6-bromo-1H-indol-3-yl)propanoic acidCAS:52448-17-6ChEBI:61899PDBHET:BTRBr 1 C 11 H 9 N 2 O 1265.11263.989825Br 1 C 0 H -1 N 0 O 078.9077.910512Jimenez, E.C.Craig, A.G.Watkins, M.Hillyard, D.R.Gray, W.R.Gulyas, J.Rivier, J.E.Cruz, L.J.Olivera, B.M.Biochemistry 36, 989-994, 1997Bromocontryphan: post-translational bromination of tryptophan.DOI:10.1021/bi962840pPMID:9033387mass spectrometric detection; chromatographic characterization; chemical synthesisCraig, A.G.Jimenez, E.C.Dykert, J.Nielsen, D.B.Gulyas, J.Abogadie, F.C.Porter, J.Rivier, J.E.Cruz, L.J.Olivera, B.M.McIntosh, J.M.J. Biol. Chem. 272, 4689-4698, 1997A novel post-translational modification involving bromination of tryptophan. Identification of the residue, L-6-bromotryptophan, in peptides from Conus imperialis and Conus radiatus venom.DOI:10.1074/jbc.272.8.4689PMID:9030520mass spectrometric detection; chromatographic characterization; chemical synthesisTaylor, S.W.Kammerer, B.Nicholson, G.J.Pusecker, K.Walk, T.Bayer, E.Scippa, S.de Vincentiis, M.Arch. Biochem. Biophys. 348, 278-288, 1997Morulin Pm: a modified polypeptide containing TOPA and 6-bromotryptophan from the morula cells of the ascidian, Phallusia mammillata.DOI:10.1006/abbi.1997.0371PMID:9434739(1)H-NMR and (13)C-NMR characterizationRigby, A.C.Lucas-Meunier, E.Kalume, D.E.Czerwiec, E.Hambe, B.Dahlqvist, I.Fossier, P.Baux, G.Roepstorff, P.Baleja, J.D.Furie, B.C.Furie, B.Stenflo, J.Proc. Natl. Acad. Sci. U.S.A. 96, 5758-5763, 1999A conotoxin from Conus textile with unusual posttranslational modifications reduces presynaptic Ca2+ influx.DOI:10.1073/pnas.96.10.5758PMID:10318957mass spectrometric and (1)H-NMR identificationRigby, A.C.Hambe, B.Czerwiec, E.Baleja, J.D.Furie, B.C.Furie, B.Stenflo, J.submitted to the Protein Data Bank, June 1999A novel conotoxin from Conus textile with unusual post-translational modifications reduces presynaptic calcium influx, NMR, 1 structure, glycosylated protein.PDB:1WCTconformation by (1)H-NMRFujii, R.Yoshida, H.Fukusumi, S.Habata, Y.Hosoya, M.Kawamata, Y.Yano, T.Hinuma, S.Kitada, C.Asami, T.Mori, M.Fujisawa, Y.Fujino, M.J. Biol. Chem. 277, 34010-34016, 2002Identification of a neuropeptide modified with bromine as an endogenous ligand for GPR7.DOI:10.1074/jbc.M205883200PMID:12118011identification of an edogenous ligand for an "orphan" G protein-coupled receptorWGO:0018080PSI-MOD:00188bromineMOD_RES 6'-bromotryptophanAA018031-Dec-200631-Dec-200631-Dec-20126'-chloro-L-tryptophan(2S)-2-amino-3-(6-chloro-1H-indol-3-yl)propanoic acidCAS:17808-35-4PDBHET:6CWC 11 Cl 1 H 9 N 2 O 1220.66220.040341C 0 Cl 1 H -1 N 0 O 034.4433.961028Lazzarini, A.Gastaldo, L.Candiani, G.Ciciliato, I.Losi, D.Marinelli, F.Selva, E.Parenti, F.submitted to the European Patent Office, 17 February 2005Antibiotic 107891, its factors A1 and A2, pharmaceutically acceptable salts and compositions, and use thereof.EPO:EP1646646WIPO:WO2005014628mass spectrometric and (1)H-NMR identificationWPSI-MOD:00886chlorineMOD_RES 6'-chlorotryptophanAA018131-Mar-199531-Mar-199513-Sep-2013dehydroalanine2,3-didehydroalanine2-aminoacrylic acid4-methylidene-imidazole-5-one (MIO) active siteanhydroserineDha2-aminopropenoic acidCAS:1948-56-7ChEBI:17123PDBHET:DHAPDBHET:MDOC 3 H 3 N 1 O 169.0669.021464C 0 H -2 N 0 O 0 S -1-34.08-33.987721C 0 H -2 N 0 O 0 Se -1-80.99-81.932171C 0 H -2 N 0 O -1-18.02-18.010565C -6 H -6 N 0 O -1-94.11-94.041865Marriq, C.Lejeune, P.J.Venot, N.Vinet, L.FEBS Lett. 242, 414-418, 1989Hormone synthesis in human thyroglobulin: possible cleavage of the polypeptide chain at the tyrosine donor site.DOI:10.1016/0014-5793(89)80513-7PMID:2914619formation of thyroxine and dehydroalanine by tyrosine ring donationBartone, N.A.Bentley, J.D.Maclaren, J.A.J. Protein Chem. 10, 603-607, 1991Determination of dehydroalanine residues in proteins and peptides: an improved method.DOI:10.1007/BF01025712PMID:1815586conversion with 4-pyridoethanethiol to 4-pyridoethyl cysteineChan, W.C.Bycroft, B.W.Leyland, M.L.Lian, L.Y.Yang, J.C.Roberts, G.C.K.FEBS Lett. 300, 56-62, 1992Sequence-specific resonance assignment and conformational analysis of subtilin by 2D NMR.DOI:10.1016/0014-5793(92)80163-BPMID:1547888(1)H-NMR identificationHernandez, D.Stroh, J.G.Phillips, A.T.Arch. Biochem. Biophys. 307, 126-132, 1993Identification of Ser(143) as the site of modification in the active site of histidine ammonia-lyase.DOI:10.1006/abbi.1993.1570PMID:8239649mass spectrometric and UV spectrographic characterizationLanger, M.Lieber, A.Retey, J.Biochemistry 33, 14034-14038, 1994Histidine ammonia-lyase mutant S143C is posttranslationally converted into fully active wild-type enzyme. Evidence for serine 143 to be the precursor of active site dehydroalanine.DOI:10.1021/bi00251a011PMID:7947813mutational analysis; no chemical characterizationSchwede, T.F.Retey, J.Schulz, G.E.Biochemistry 38, 5355-5361, 1999Crystal structure of histidine ammonia-lyase revealing a novel polypeptide modification as the catalytic electrophile.DOI:10.1021/bi982929qPMID:10220322X-ray diffraction, 2.1 angstromsMa, S.Caprioli, R.M.Hill, K.E.Burk, R.F.J. Am. Soc. Mass Spectrom. 14, 593-600, 2003Loss of selenium from selenoproteins: conversion of selenocysteine to dehydroalanine in vitro.DOI:10.1016/S1044-0305(03)00141-7PMID:12781460observation of artifactual conversion of seleocysteine to dehydroalanine Claesen, J.Bibb, M.Proc. Natl. Acad. Sci. U.S.A. 107, 16297-16302, 2010Genome mining and genetic analysis of cypemycin biosynthesis reveal an unusual class of posttranslationally modified peptides.DOI:10.1073/pnas.1008608107PMID:20805503gene sequence for the encoded peptide, biosynthesis as an intermediate from cysteineChatterjee, A.Abeydeera, N.D.Bale, S.Pai, P.J.Dorrestein, P.C.Russell, D.H.Ealick, S.E.Begley, T.P.Nature 478, 542-546, 2011Saccharomyces cerevisiae THI4p is a suicide thiamine thiazole synthase.DOI:10.1038/nature10503PMID:22031445X-ray diffraction, 1.82 angstroms; one protein molecule is shown to synthesize a thiazole for thiamine from NAD by donating a sulfur from a peptide cysteine and forming dehydroalanineBale, S.Chatterjee, A.Dorrestein, P.C.Begley, T.P.Ealick, S.E.submitted to the Protein Data Bank, January 2009Saccharomyces cerevisiae THI4p is a suicide thiamin thiazole synthase.PDB:3FPZX-ray diffraction, 1.82 angstromsWang, S.K.Weaver, J.D.Zhang, S.Lei, X.G.Free Radic. Biol. Med. 51, 197-204, 2011Knockout of SOD1 promotes conversion of selenocysteine to dehydroalanine in murine hepatic GPX1 protein.DOI:10.1016/j.freeradbiomed.2011.03.018PMID:21420488deselenation of seleocysteine to dehydroalanine in glutathione peroxidase-1 caused by superoxide radical accumulating in the absence of superoxide dismutaseThe modification of serine to dehydroalanine coupled with the formation of 5-imidazolinone by the two neighboring residues produces the 4-methylidene-imidazole-5-one (MIO) active site of some amino acid ammonia-lyases that differs by UV and mass spectrometric evidence from other known dehydroalanine containing peptides not containing the second modification.The formation of iodinated thyronine, O-(4-hydroxyphenyl)-tyrosine, by phenoxy radical transfer from tyrosine in thyroglobulin produces dehydroalanine as a by-product. See RESID:AA0177 and RESID:AA0178.The formation of S-(2-aminovinyl)-L-cysteine, see RESID:AA0548, requires that an interior cysteine first undergoes oxidative dethiolation to form dehydroalanine. This reaction is normally followed by formation of an L-lanthionine through reformation of an L-cysteine in a thioether bond with the C-terminal cysteine. The C-terminal cysteine is subsequently decarboxylated. Because the intermediate dehydroalanine formed from cysteine is not normally observed, it is not annotated as a feature in UniProt.Either free or in a peptide chain, dehydroalanine is unstable, undergoing hydrolysis with formation of 2-hydroxyalanine which can, like 2-hydroxyglycine (see RESID:AA0434), decompose by deamination breaking the peptide backbone to form a peptide amide and a pyruvoyl peptide (see RESID:AA0127). A 2,3-didehydro amino acid blocks Edman degradation.protein-cysteine dethiolase (EC 4.4.1.-)autocatalyticprotein-serine dehydratase (EC 4.2.1.-)CPSI-MOD:00793PSI-MOD:01168UPSI-MOD:01954Sincidental to RESID:AA0187incidental to RESID:AA0188PSI-MOD:00189PSI-MOD:01168Yincidental to RESID:AA0178GO:0018250PSI-MOD:00824PSI-MOD:01168MOD_RES 2,3-didehydroalanine (Ser)MOD_RES 2,3-didehydroalanine (Cys)AA018231-Mar-199531-Mar-199513-Sep-2013(Z)-dehydrobutyrine(Z)-2-amino-2-butenoic acid(Z)-2-aminobutenoic acid2,3-didehydrobutyrine3-methyldehydroalaninealpha,beta-dehydroaminobutyric acidanhydrothreonineDhbmethyl-dehydroalanine(2Z)-2-aminobut-2-enoic acidCAS:71018-10-5PDBHET:DBUC 4 H 5 N 1 O 183.0983.037114C 0 H -2 N 0 O -1-18.02-18.010565Allgaier, H.Jung, G.Werner, R.G.Schneider, U.Zaehner, H.Eur. J. Biochem. 160, 9-22, 1986Epidermin: sequencing of a heterodet tetracyclic 21-peptide amide antibiotic.DOI:10.1111/j.1432-1033.1986.tb09933.xPMID:3769923(1)H-NMR and (13)C-NMR identificationChan, W.C.Bycroft, B.W.Leyland, M.L.Lian, L.Y.Yang, J.C.Roberts, G.C.K.FEBS Lett. 300, 56-62, 1992Sequence-specific resonance assignment and conformational analysis of subtilin by 2D NMR.DOI:10.1016/0014-5793(92)80163-BPMID:1547888(1)H-NMR identificationPiard, J.C.Kuipers, O.P.Rollema, H.S.Desmazeaud, M.J.de Vos, W.M.J. Biol. Chem. 268, 16361-16368, 1993Structure, organization, and expression of the lct gene for lacticin 481, a novel lantibiotic produced by Lactococcus lactis.PMID:8344922the (E)- and (Z)-isomers are distinguished by (1)H-NOE NMRLi, H.Xu, H.Zhou, Y.Zhang, J.Long, C.Li, S.Chen, S.Zhou, J.M.Shao, F.Science 315, 1000-1003, 2007The phosphothreonine lyase activity of a bacterial type III effector family.DOI:10.1126/science.1138960PMID:17303758mass spectrometric identificationShenkarev, Z.O.Finkina, E.I.Nurmukhamedova, E.K.Balandin, S.V.Mineev, K.S.Nadezhdin, K.D.Yakimenko, Z.A.Tagaev, A.A.Temirov, Y.V.Arseniev, A.S.Ovchinnikova, T.V.Biochemistry 49, 6462-6472, 2010Isolation, structure elucidation, and synergistic antibacterial activity of a novel two-component lantibiotic lichenicidin from Bacillus licheniformis VK21.DOI:10.1021/bi100871bPMID:20578714the (E)- and (Z)- isomers are distinguished by (1)H-NOE NMRIn some cases it has not been firmly established whether the natural form is the Z or the E isomer. For the E isomer, see RESID:AA0547.A 2,3-didehydro amino acid blocks Edman degradation.protein-threonine dehydratase (EC 4.2.1.-)phosphothreonine lyase (EC 4.3.2.-)TGO:0018082PSI-MOD:00190PSI-MOD:01471MOD_RES (Z)-2,3-didehydrobutyrineMOD_RES 2,3-didehydrobutyrinethis UniProt feature is used when the stereochemistry has not been determinedAA018331-Mar-199531-Mar-199531-Dec-2011(Z)-2,3-didehydrotyrosineamino-(para-hydroxybenzylidenyl)acetic acidcis-dehydrotyrosinegreen fluorescent protein chromophorepara-hydroxybenzylidene-imidazolidinone chromophorered fluorescent protein chromophore(2Z)-2-amino-3-(4-hydroxyphenyl)prop-2-enoic acidPDBHET:CH6PDBHET:CROPDBHET:CRQC 9 H 7 N 1 O 2161.16161.047678C 0 H -2 N 0 O 0-2.02-2.015650Prasher, D.C.Eckenrode, V.K.Ward, W.W.Prendergast, F.G.Cormier, M.J.Gene 111, 229-233, 1992Primary structure of the Aequorea victoria green-fluorescent protein.DOI:10.1016/0378-1119(92)90691-HPMID:1347277Yang, F.Moss, L.G.Phillips Jr., G.N.submitted to the Protein Data Bank, August 1996Structure of green fluorescent protein.PDB:1GFLX-ray diffraction, 1.9 angstromsYang, F.Moss, L.G.Phillips Jr., G.N.Nature Biotechnol. 14, 1246-1251, 1996The molecular structure of green fluorescent protein.DOI:10.1038/nbt1096-1246PMID:9631087X-ray diffraction, 1.9 angstromsYincidental to RESID:AA0184incidental to RESID:AA0187incidental to RESID:AA0188incidental to RESID:AA0189incidental to RESID:AA0378incidental to RESID:AA0379incidental to RESID:AA0380incidental to RESID:AA0381GO:0018251GO:0030921PSI-MOD:00191MOD_RES (Z)-2,3-didehydrotyrosineMOD_RES 2,3-didehydrotyrosinethis UniProt feature is used when the isomeric structure has not been determinedAA018431-Mar-199502-Nov-199913-Sep-2013L-serine 5-imidazolinone glycine2-[1-amino-2-hydroxyethyl]-1-carboxymethyl-1-imidazolin-5-one4-methylidene-imidazole-5-one (MIO) active sitegreen fluorescent protein chromophorepara-hydroxybenzylidene-imidazolidinone chromophoreseryl-5-imidazolinone glycine(2-[(1R)-1-amino-2-hydroxyethyl]-5-oxo-4,5-dihydro-1H-imidazol-1-yl)acetic acidPDBHET:GYSC 5 H 6 N 2 O 2126.11126.042927C 0 H -2 N 0 O -1-18.02-18.010565Prasher, D.C.Eckenrode, V.K.Ward, W.W.Prendergast, F.G.Cormier, M.J.Gene 111, 229-233, 1992Primary structure of the Aequorea victoria green-fluorescent protein.DOI:10.1016/0378-1119(92)90691-HPMID:1347277Yang, F.Moss, L.G.Phillips Jr., G.N.submitted to the Protein Data Bank, August 1996Structure of green fluorescent protein.PDB:1GFLX-ray diffraction, 1.9 angstromsYang, F.Moss, L.G.Phillips Jr., G.N.Nature Biotechnol. 14, 1246-1251, 1996The molecular structure of green fluorescent protein.DOI:10.1038/nbt1096-1246PMID:9631087X-ray diffraction, 1.9 angstromsThis entry represents the cross-link of the peptide backbone from the alpha-carboxyl carbon of residue N, a serine, to the alpha-amino nitrogen of residue N+2, a glycine, coupled with the formation of a double bond to the alpha-amino nitrogen of residue N+1 which loses one hydrogen, and the loss of a molecule of water.This cross-link is accompanied by modification of residue N+1. The modified residue N+1 is presented in a separate entry and is not included in the mass accounting of this entry. The backbone atoms of residue N+1 are shown in gray in the diagram.The chirality of residue N is (R) rather then (S) because of the reversed order of precedence with respect to the beta-carbon methoxy group of the 5-imidazolinone group replacing the carboxyl group.The modification of serine to dehydroalanine coupled with the formation of 5-imidazolinone by the two neighboring residues produces the 4-methylidene-imidazole-5-one (MIO) active site of some amino acid ammonia-lyases that differs by UV and mass spectrometric evidence from other known dehydroalanine containing peptides not containing the second modification.autocatalyticG, Scarboxamidinecross-link 1incidental to RESID:AA0183incidental to RESID:AA0365GO:0018252GO:0018253PSI-MOD:00192chromoproteinimidazolinone/oxazolinone ringCROSSLNK 5-imidazolinone (Ser-Gly)AA018526-Oct-199526-Oct-199531-May-2018L-3-oxoalanine2-amino-3-oxopropionic acidC(alpha)-formylglycine [misnomer]L-amino-malonic acid semialdehydeL-aminomalonaldehydic acidL-serinesemialdehyde [misnomer](S)-2-amino-3-oxopropanoic acidCAS:5735-66-0ChEBI:85621PDBHET:FGLC 3 H 3 N 1 O 285.0685.016378C 0 H -2 N 0 O 1 S -1-18.08-17.992806C 0 H -2 N 0 O 0-2.02-2.015650Schmidt, B.Selmer, T.Ingendoh, A.von Figura, K.Cell 82, 271-278, 1995A novel amino acid modification in sulfatases that is defective in multiple sulfatase deficiency.DOI:10.1016/0092-8674(95)90314-3PMID:7628016mass spectrometric detectionSelmer, T.Hallmann, A.Schmidt, B.Sumper, M.von Figura, K.Eur. J. Biochem. 238, 341-345, 1996The evolutionary conservation of a novel protein modification, the conversion of cysteine to serinesemialdehyde in arylsulfatase from Volvox carteri.DOI:10.1111/j.1432-1033.1996.0341z.xPMID:8681943mass spectrometric and chemical characterizationMiech, C.Dierks, T.Selmer, T.von Figura, K.Schmidt, B.J. Biol. Chem. 273, 4835-4837, 1998Arylsulfatase from Klebsiella pneumoniae carries a formylglycine generated from a serine.DOI:10.1074/jbc.273.9.4835PMID:9478923mass spectrometric and chemical characterization; radioisotope labeling; modification of serine is demonstratedLandgrebe, J.Dierks, T.Schmidt, B.von Figura, K.Gene 316, 47-56, 2003The human SUMF1 gene, required for posttranslational sulfatase modification, defines a new gene family which is conserved from pro- to eukaryotes.DOI:10.1016/S0378-1119(03)00746-7PMID:14563551Peng, J.Schmidt, B.von Figura, K.Dierks, T.J. Mass Spectrom. 38, 80-86, 2003Identification of formylglycine in sulfatases by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry.DOI:10.1002/jms.404PMID:12526009mass spectrometric detectionBenjdia, A.Subramanian, S.Leprince, J.Vaudry, H.Johnson, M.K.Berteau, O.J. Biol. Chem. 283, 17815-17826, 2008Anaerobic sulfatase-maturating enzymes, first dual substrate radical S-adenosylmethionine enzymes.DOI:10.1074/jbc.M710074200PMID:18408004one bacterial "radical-SAM" enzyme uses S-adenosylmethionine to convert both serine and cysteine at sulfatase active sitesThe modified cysteine is found in sulfatases at the second position in the sequence motif [L/V]C[A/C/S/T]PSR.In at least one case, the oxidation acceptor or cofactor for the generating enzyme is known to be S-adenosylmethionine. The generating enzyme activity acting on serine would be EC 1.1.99.-, and acting on cysteine would be EC 1.8.99.-.This modification should not be confused with N-formylglycine (see RESID:AA0057). The use of the misleading, non-standard name "C-alpha-formyl glycine" should be avoided.This active site residue occurs in the hydrated form, 2-amino-3,3-dihydroxypropanoic acid, as observed in crystallographic structures. See RESID:AA0492.The PDB Hetgroup FGL was originally designated as the "C(alpha)-formyl glycine" active site residue L-3-oxoalanine observed in its hydrated form. That structure, a gem-diol with an sp(3) carbon, was misinterpreted as a carboxyl with an sp(2) carbon, and assigned to aminomalonic acid (see RESID:AA0458) instead.sulfatase maturing enzyme (sulfatase modifying factor, C-alpha-formylglycine-generating enzyme) (EC 1.1.99.-)sulfatase maturing enzyme (sulfatase modifying factor, C-alpha-formylglycine-generating enzyme) (EC 1.8.99.-)CGO:0018083PSI-MOD:00193PSI-MOD:01169SGO:0018083PSI-MOD:00835PSI-MOD:01169MOD_RES 3-oxoalanine (Cys)MOD_RES 3-oxoalanine (Ser)AA018623-Jan-199831-Dec-201131-Dec-2011lactic acid2-hydroxypropionic acidalpha-hydroxypropionic acid(2R)-2-hydroxypropanoic acidCAS:10326-41-7ChEBI:42111PDBHET:LACC 3 H 5 O 273.0773.028954C 0 H -1 N -1 O 0-15.02-15.010899van de Kamp, M.van den Hooven, H.W.Konings, R.N.H.Bierbaum, G.Sahl, H.G.Kuipers, O.P.Siezen, R.J.de Vos, W.M.Hilbers, C.W.van de Ven, F.J.M.Eur. J. Biochem. 230, 587-600, 1995Elucidation of the primary structure of the lantibiotic epilancin K7 from Staphylococcus epidermidis K7. Cloning and characterisation of the epilancin-K7-encoding gene and NMR analysis of mature epilancin K7.DOI:10.1111/j.1432-1033.1995.tb20600.xPMID:7607233(1)H-NMR and (13)C-NMR identification; the stereochemistry was not determinedVelásquez, J.E.Zhang, X.van der Donk, W.A.Chem. Biol. 18, 857-867, 2011Biosynthesis of the antimicrobial peptide epilancin 15X and its N-terminal lactate.DOI:10.1016/j.chembiol.2011.05.007PMID:21802007the lactoyl group of epilancin 15X is shown to be the D- stereoisomer by enzymatic analysisThe stereochemistry has not been determined in all the peptides with this modification.protein-serine dehydratase ElxB (EC 4.2.1.-)D-lactoyl-protein dehydrogenase ElxO (EC 1.1.1.-)Samino-terminalGO:0018084PSI-MOD:00194blocked amino endMOD_RES Lactic acidAA018714-May-199902-Nov-200130-Sep-2011L-alanine 5-imidazolinone glycine2-[1-aminoethyl]-1-carboxymethyl-1-imidazolin-5-one4-methylidene-imidazole-5-one active sitealanyl-5-imidazolinone glycinepara-hydroxybenzylidene-imidazolidinone chromophore(2-[(1S)-1-aminoethyl]-5-oxo-4,5-dihydro-1H-imidazol-1-yl)acetic acidPDBHET:AYGPDBHET:MDOPDBHET:X9QC 5 H 6 N 2 O 1110.12110.048013C 0 H -2 N 0 O -1-18.02-18.010565Schwede, T.F.Retey, J.Schulz, G.E.Biochemistry 38, 5355-5361, 1999Crystal structure of histidine ammonia-lyase revealing a novel polypeptide modification as the catalytic electrophile.DOI:10.1021/bi982929qPMID:10220322X-ray diffraction, 2.1 angstromsBaedeker, M.Schulz, G.E.Eur. J. Biochem. 269, 1790-1797, 2002Structures of two histidine ammonia-lyase modifications and implications for the catalytic mechanism.DOI:10.1046/j.1432-1327.2002.02827.xPMID:11895450X-ray diffraction, 1.7 angstromsBaedeker, M.Schulz, G.E.submitted to the Protein Data Bank, August 2001Histidine ammonia-lyase (HAL) from Pseudomonas putida inhibited with L-cysteine.PDB:1GKMX-ray diffraction, 1.00 angstromsThis entry represents the cross-link of the peptide backbone from the alpha-carboxyl carbon of residue N, an alanine, to the alpha-amino nitrogen of residue N+2, a glycine, coupled with the formation of a double bond to the alpha-amino nitrogen of residue N+1 which loses one hydrogen, and the loss of a molecule of water.This cross-link is accompanied by modification of residue N+1. The modified residue N+1 is presented in a separate entry and is not included in the mass accounting of this entry. The backbone atoms of residue N+1 are shown in gray in the diagram.A, Gcarboxamidinecross-link 1incidental to RESID:AA0181incidental to RESID:AA0183incidental to RESID:AA0365GO:0018253GO:0018313PSI-MOD:00195chromoproteinimidazolinone/oxazolinone ringCROSSLNK 5-imidazolinone (Ala-Gly)AA018824-Nov-199924-Nov-199913-Sep-2013L-cysteine 5-imidazolinone glycine2-[1-amino-2-sulfanylethyl]-1-carboxymethyl-1-imidazolin-5-one4-methylidene-imidazole-5-one (MIO) active sitecysteinyl-5-imidazolinone glycinepara-hydroxybenzylidene-imidazolidinone chromophore(2-[(1R)-1-amino-2-sulfanylethyl]-5-oxo-4,5-dihydro-1H-imidazol-1-yl)acetic acidPDBHET:GYCC 5 H 6 N 2 O 1 S 1142.18142.020084C 0 H -2 N 0 O -1 S 0-18.02-18.010565Wu, P.C.Kroening, T.A.White, P.J.Kendrick, K.E.J. Bacteriol. 174, 1647-1655, 1992Purification of histidase from Streptomyces griseus and nucleotide sequence of the hutH structural gene.PMID:1537807prediction of dehydroalanine active siteThis entry represents the cross-link of the peptide backbone from the alpha-carboxyl carbon of residue N, a cysteine, to the alpha-amino nitrogen of residue N+2, a glycine, coupled with the formation of a double bond to the alpha-amino nitrogen of residue N+1 which loses one hydrogen, and the loss of a molecule of water.This cross-link is accompanied by modification of residue N+1.The modification of serine to dehydroalanine coupled with the formation of 5-imidazolinone by the two neighboring residues produces the 4-methylidene-imidazole-5-one (MIO) active site of some amino acid ammonia-lyases that differs by UV and mass spectrometric evidence from other known dehydroalanine containing peptides not containing the second modification.C, Gcarboxamidinecross-link 1incidental to RESID:AA0181incidental to RESID:AA0183incidental to RESID:AA0365GO:0018253GO:0050745PSI-MOD:00196chromoproteinimidazolinone/oxazolinone ringCROSSLNK 5-imidazolinone (Cys-Gly)AA018902-Nov-200102-Nov-200120-May-20112-imino-glutamine 5-imidazolinone glycine2,N-didehydroglutaminyl-5-imidazolinone glycine2-(3-carbamoyl-1-imino-propyl)-1-carboxymethyl-1-imidazolin-5-onefluorescent protein FP583 chromophorepara-hydroxybenzylidene-imidazolidinone chromophorered fluorescent protein chromophore[2-(3-carbamoyl-1-imino-propyl)-5-oxo-4,5-dihydro-imidazol-1-yl]-acetic acid[2-(4-amino-4-oxobutanimidoyl)-5-oxo-4,5-dihydro-1H-imidazol-1-yl]acetic acidPDBHET:CRQPDBHET:QLGC 7 H 7 N 3 O 2165.15165.053826C 0 H -4 N 0 O -1-20.03-20.026215Gross, L.A.Baird, G.S.Hoffman, R.C.Baldridge, K.K.Tsien, R.Y.Proc. Natl. Acad. Sci. U.S.A. 97, 11990-11995, 2000The structure of the chromophore within DsRed, a red fluorescent protein from coral.DOI:10.1073/pnas.97.22.11990PMID:11050230Yarbrough, D.Wachter, R.M.Kallio, K.Matz, M.V.Remington, S.J.submitted to the Protein Data Bank, December 2000Crystal structure of DsRed, a red fluorescent protein from Discosoma sp. red.PDB:1G7KX-ray diffraction, 2.00 angstromsYarbrough, D.Wachter, R.M.Kallio, K.Matz, M.V.Remington, S.J.Proc. Natl. Acad. Sci. U.S.A. 98, 462-467, 2001Refined crystal structure of DsRed, a red fluorescent protein from coral, at 2.0-A resolution.DOI:10.1073/pnas.98.2.462PMID:11209050This entry represents the cross-link of the peptide backbone from the alpha-carboxyl carbon of residue N, a glutamine, to the alpha-amino nitrogen of residue N+2, a glycine, coupled with the formation of a double bond to the alpha-amino nitrogen of residue N, and the loss of a molecule of water.This cross-link is accompanied by modification of residue N+1. The modified residue N+1 is presented in a separate entry and is not included in the mass accounting of this entry. The backbone atoms of residue N+1 are shown in gray in the diagram.autocatalyticG, Qcarboxamidinecross-link 1incidental to RESID:AA0183incidental to RESID:AA0365GO:0019729PSI-MOD:00197chromoproteinimidazolinone/oxazolinone ringCROSSLNK 2-iminomethyl-5-imidazolinone (Gln-Gly)AA019030-Jun-201230-Jun-201230-Jun-2012D-aspartic acid2-azanylbutanedioic acidaminosuccinic acid(2R)-2-aminobutanedioic acidCAS:1783-96-6ChEBI:48094PDBHET:DASC 4 H 5 N 1 O 3115.09115.026943C 0 H 0 N 0 O 00.000.000000C 0 H -1 N -1 O 10.980.984016Di Marco, S.Priestle, J.P.Structure 5, 1465-1474, 1997Structure of the complex of leech-derived tryptase inhibitor (LDTI) with trypsin and modeling of the LDTI-tryptase system.PMID:9384562X-ray diffraction, 2.03 angstroms; porcine trypsin in complex with leech-derived tryptase inhibitor can apparently crystallize only after the spontaneous conversion of Asn-115 to D-Asp via a succinimde intermediateDi Marco, S.Priestle, J.P.submitted to the Protein Data Bank, June 1997Leech-derived tryptase inhibitor/trypsin complex.PDB:1AN1X-ray diffraction, 2.03 angstromsThe stereoisomeric conversion of L-aspartic acid or L-asparagine to D-aspartic acid is probably mediated by the spontaneous cyclization and deamidation to a 2-aminosuccinimidyl group (see RESID:AA0441).DPSI-MOD:01921NPSI-MOD:01930D-amino acidNot availablethis modification is not annotated in UniProt featuresAA019131-Mar-199531-Mar-199525-Feb-2011D-alanine(R)-2-aminopropanoic acidCAS:338-69-2ChEBI:29949PDBHET:DALC 3 H 5 N 1 O 171.0871.037114C 0 H 0 N 0 O 00.000.000000C 0 H 0 N 0 O -1-16.00-15.994915Montecucchi, P.C.de Castiglione, R.Erspamer, V.Int. J. Pept. Protein Res. 17, 316-321, 1981Identification of dermorphin and Hyp(6)-dermorphin in skin extracts of the Brazilian frog Phyllomedusa rhodei.PMID:7287302Skaugen, M.Nissen-Meyer, J.Jung, G.Stevanovic, S.Sletten, K.Abildgaard, C.I.M.Nes, I.F.J. Biol. Chem. 269, 27183-27185, 1994In vivo conversion of L-serine to D-alanine in a ribosomally synthesized polypeptide.PMID:7961627the spelling of "C.I.M. Abildgaard" in the PubMed citation is corrected, and the name "C. Inger" is removedMartin, N.I.Sprules, T.Carpenter, M.R.Cotter, P.D.Hill, C.Ross, R.P.Vederas, J.C.Biochemistry 43, 3049-3056, 2004Structural characterization of lacticin 3147, a two-peptide lantibiotic with synergistic activity.DOI:10.1021/bi0362065PMID:15023056protein-alanine epimerase (EC 5.1.1.-)AGO:0019122GO:0019916PSI-MOD:00198PSI-MOD:00862SGO:0019122GO:0019917PSI-MOD:00858PSI-MOD:00862D-amino acidMOD_RES D-alanine (Ala)MOD_RES D-alanine (Ser)AA019231-Mar-199531-Mar-199525-Feb-2011D-allo-isoleucine2-azanyl-3-methylpentanoic acid3-methyl-norvalineallo-D-isoleucinealpha-amino-beta-methylvaleric acidD-threo-isoleucine(2R,3S)-2-amino-3-methylpentanoic acidCAS:1509-35-9ChEBI:30007PDBHET:DILC 6 H 11 N 1 O 1113.16113.084064C 0 H 0 N 0 O 00.000.000000Mignogna, G.Simmaco, M.Kreil, G.Barra, D.EMBO J. 12, 4829-4832, 1993Antibacterial and haemolytic peptides containing D-alloisoleucine from the skin of Bombina variegata.PMID:8223491chromatographic separationprotein-isoleucine 2-epimerase (EC 5.1.1.-)IGO:0019124PSI-MOD:00199D-amino acidMOD_RES D-allo-isoleucineAA019331-Mar-199531-Mar-199530-Sep-2011D-methionine2-amino-4-(methylthio)butanoic acid2-amino-4-(methylthio)butyric acid(2R)-2-amino-4-(methylsulfanyl)butanoic acidCAS:348-67-4ChEBI:29984PDBHET:MEDC 5 H 9 N 1 O 1 S 1131.19131.040485C 0 H 0 N 0 O 0 S 00.000.000000Kreil, G.Barra, D.Simmaco, M.Erspamer, V.Erspamer, G.F.Negri, L.Severini, C.Corsi, R.Melchiorri, P.Eur. J. Pharmacol. 162, 123-128, 1989Deltorphin, a novel amphibian skin peptide with high selectivity and affinity for delta opioid receptors.DOI:10.1016/0014-2999(89)90611-0PMID:2542051Torres, A.M.Tsampazi, C.Geraghty, D.P.Bansal, P.S.Alewood, P.F.Kuchel, P.W.Biochem. J. 391, 215-220, 2005D-amino acid residue in a defensin-like peptide from platypus venom: effect on structure and chromatographic properties.DOI:10.1042/BJ20050900PMID:16033333protein-methionine epimerase (EC 5.1.1.-)MGO:0019123PSI-MOD:00200D-amino acidMOD_RES D-methionineAA019431-Mar-199531-Mar-199520-May-2011D-phenylalanine(R)-2-amino-3-phenylpropanoic acidCAS:673-06-3ChEBI:29996PDBHET:DPNC 9 H 9 N 1 O 1147.18147.068414C 0 H 0 N 0 O 00.000.000000Kamatani, Y.Minakata, H.Kenny, P.T.M.Iwashita, T.Watanabe, K.Funase, K.Sun, X.P.Yongsiri, A.Kim, K.H.Novales-Li, P.Novales, E.T.Kanapi, C.G.Takeuchi, H.Nomoto, K.Biochem. Biophys. Res. Commun. 160, 1015-1020, 1989Achatin-I, an endogenous neuroexcitatory tetrapeptide from Achatina fulica Férussac containing a D-amino acid residue.DOI:10.1016/S0006-291X(89)80103-2PMID:2597281(1)H-NMR identification; chemical synthesis confirmation of stereochemistry; the truncated list of authors in the PubMed citation is correctedIshida, T.In, Y.Inoue, M.Yasuda-Kamatani, Y.Minakata, H.Iwashita, T.Nomoto, K.FEBS Lett. 307, 253-256, 1992Effect of the D-Phe(2) residue on molecular conformation of an endogenous neuropeptide achatin-I. Comparison of X-ray crystal structures of achatin-I (H-Gly-D-Phe-Ala-Asp-OH) and achatin-II (H-Gly-Phe-Ala-Asp-OH).DOI:10.1016/0014-5793(92)80689-EPMID:1644179X-ray diffraction, 0.85 angstromsMatsuyama, T.Kaneda, K.Nakagawa, Y.Isa, K.Hara-Hotta, H.Yano, I.J. Bacteriol. 174, 1769-1776, 1992A novel extracellular cyclic lipopeptide which promotes flagellum-dependent and -independent spreading growth of Serratia marcescens.PMID:1548227mass spectrometric and (1)H-NMR characterizationprotein-phenylalanine epimerase (EC 5.1.1.-)FGO:0019125PSI-MOD:00201D-amino acidMOD_RES D-phenylalanineAA019531-Mar-199531-Mar-199520-May-2011D-serine(R)-2-amino-3-hydroxypropanoic acidCAS:312-84-5ChEBI:29998PDBHET:DSNC 3 H 5 N 1 O 287.0887.032028C 0 H 0 N 0 O 00.000.000000C 0 H 0 N 0 O 1 S -1-16.06-15.977156Faulstich, H.Buku, A.Bodenmüller, H.Wieland, T.Biochemistry 19, 3334-3343, 1980Virotoxins: actin-binding cyclic peptides of Amanita virosa mushrooms.DOI:10.1021/bi00555a036PMID:6893271Heck, S.D.Siok, C.J.Krapcho, K.J.Kelbaugh, P.R.Thadeio, P.F.Welch, M.J.Williams, R.D.Ganong, A.H.Kelly, M.E.Lanzetti, A.J.Gray, W.R.Phillips, D.Parks, T.N.Jackson, H.Ahlijanian, M.K.Saccomano, N.A.Volkmann, R.A.Science 266, 1065-1068, 1994Functional consequences of posttranslational isomerization of Ser(46) in a calcium channel toxin.DOI:10.1126/science.7973665PMID:7973665identification of enzymatically racemized serine; the truncated list of authors in the PubMed citation is correctedShikata, Y.Watanabe, T.Teramoto, T.Inoue, A.Kawakami, Y.Nishizawa, Y.Katayama, K.Kuwada, M.J. Biol. Chem. 270, 16719-16723, 1995Isolation and characterization of a peptide isomerase from funnel web spider venom.DOI:10.1074/jbc.270.28.16719PMID:7622482Hallen, H.E.Luo, H.Scott-Craig, J.S.Walton, J.D.Proc. Natl. Acad. Sci. U.S.A. 104, 19097-19101, 2007Gene family encoding the major toxins of lethal Amanita mushrooms.DOI:10.1073/pnas.0707340104PMID:18025465protein-serine epimerase (EC 5.1.1.16)SGO:0019126PSI-MOD:00202PSI-MOD:00891CPSI-MOD:00891PSI-MOD:00892D-amino acidMOD_RES D-serine (Ser)MOD_RES D-serine (Cys)AA019630-Jun-199522-Nov-199625-Feb-2011D-asparagineD-alpha-aminosuccinamic acidD-aspartic acid beta-amide(R)-2-amino-4-butanediamic acidCAS:2058-58-4ChEBI:29957PDBHET:DSGC 4 H 6 N 2 O 2114.10114.042927C 0 H 0 N 0 O 00.000.000000Ohta, N.Kubota, I.Takao, T.Shimonishi, Y.Yasuda-Kamatani, Y.Minakata, H.Nomoto, K.Muneoka, Y.Kobayashi, M.Biochem. Biophys. Res. Commun. 178, 486-493, 1991Fulicin, a novel neuropeptide containing a D-amino acid residue isolated from the ganglia of Achatina fulica.DOI:10.1016/0006-291X(91)90133-RPMID:1859408chromatographic spectrographic identification; stereochemical determination; chemical synthesisprotein-asparagine epimerase (EC 5.1.1.-)NGO:0018091PSI-MOD:00203D-amino acidMOD_RES D-asparagineAA019722-Nov-199622-Nov-199620-May-2011D-leucinealpha-aminoisocaproic acid(2R)-2-amino-4-methylpentanoic acidCAS:328-38-1ChEBI:30005PDBHET:DLEC 6 H 11 N 1 O 1113.16113.084064C 0 H 0 N 0 O 00.000.000000Fujisawa, Y.Ikeda, T.Nomoto, K.Yasuda-Kamatani, Y.Minakata, H.Kenny, P.T.M.Kubota, I.Muneoka, Y.Comp. Biochem. Physiol. C, Comp. Pharmacol. Toxicol. 102, 91-95, 1992The FMRFamide-related decapeptide of Mytilus contains a D-amino acid residue.DOI:10.1016/0742-8413(92)90049-DPMID:1358533chromatographic detection; chemical synthesisMatsuyama, T.Kaneda, K.Nakagawa, Y.Isa, K.Hara-Hotta, H.Yano, I.J. Bacteriol. 174, 1769-1776, 1992A novel extracellular cyclic lipopeptide which promotes flagellum-dependent and -independent spreading growth of Serratia marcescens.PMID:1548227mass spectrometric and (1)H-NMR characterizationJacobsen, R.B.Jimenez, E.C.De la Cruz, R.G.Gray, W.R.Cruz, L.J.Olivera, B.M.J. Pept. Res. 54, 93-99, 1999A novel D-leucine-containing Conus peptide: diverse conformational dynamics in the contryphan family.DOI:10.1034/j.1399-3011.1999.00093.xPMID:10461743Torres, A.M.Menz, I.Alewood, P.F.Bansal, P.Lahnstein, J.Gallagher, C.H.Kuchel, P.W.FEBS Lett. 524, 172-176, 2002D-Amino acid residue in the C-type natriuretic peptide from the venom of the mammal, Ornithorhynchus anatinus, the Australian platypus.DOI:10.1016/S0014-5793(02)03050-8PMID:12135762protein-leucine epimerase (EC 5.1.1.-)LGO:0019129PSI-MOD:00204D-amino acidMOD_RES D-leucineAA019822-Nov-199622-Nov-199631-Mar-2011D-tryptophanalpha-amino-beta-(3-indolyl)propionoic acid(R)-2-amino-3-(1H-indol-3-yl)propanoic acidCAS:153-94-6ChEBI:29955PDBHET:DTRC 11 H 10 N 2 O 1186.21186.079313C 0 H 0 N 0 O 00.000.000000Jimenez, E.C.Olivera, B.M.Gray, W.R.Cruz, L.J.J. Biol. Chem. 271, 28002-28005, 1996Contryphan is a D-tryptophan-containing Conus peptide.DOI:10.1074/jbc.271.45.28002PMID:8910408chromatographic detection; chemical synthesisYano, K.Toki, S.Nakanishi, S.Ochiai, K.Ando, K.Yoshida, M.Matsuda, Y.Yamasaki, M.Bioorg. Med. Chem. 4, 115-120, 1996MS-271, a novel inhibitor of calmodulin-activated myosin light chain kinase from Streptomyces sp.--I. Isolation, structural determination and biological properties of MS-271.DOI:10.1016/0968-0896(95)00175-1PMID:8689231Pallaghy, P.K.He, W.Jimenez, E.C.Olivera, B.M.Norton, R.S.Biochemistry 39, 12845-12852, 2000Structures of the contryphan family of cyclic peptides. Role of electrostatic interactions in cis-trans isomerism.DOI:10.1021/bi0010930PMID:11041849Pallaghy, P.K.He, W.Jimenez, E.C.Olivera, B.M.Norton, R.S.submitted to the Protein Data Bank, November 1999NMR structure of contryphan-SM cyclic peptide (major form - cis).PDB:1DFYconformation by (1)H-NMRprotein-tryptophan epimerase (EC 5.1.1.-)WGO:0019128PSI-MOD:00205D-amino acidMOD_RES D-tryptophanAA019931-Dec-200731-Dec-200725-Feb-2011D-threonine(2R,3R)-2-amino-3-hydroxybutanoic acidCAS:632-20-2ChEBI:32826PDBHET:DTHC 4 H 7 N 1 O 2101.10101.047678C 0 H 0 N 0 O 00.000.000000Faulstich, H.Buku, A.Bodenmüller, H.Wieland, T.Biochemistry 19, 3334-3343, 1980Virotoxins: actin-binding cyclic peptides of Amanita virosa mushrooms.DOI:10.1021/bi00555a036PMID:6893271it is not clear from the report whether D-threonine or D-allo-threonine was found; D-threonine is shownHallen, H.E.Luo, H.Scott-Craig, J.S.Walton, J.D.Proc. Natl. Acad. Sci. U.S.A. 104, 19097-19101, 2007Gene family encoding the major toxins of lethal Amanita mushrooms.DOI:10.1073/pnas.0707340104PMID:18025465protein-threonine 2-epimerase (EC 5.1.1.-)TPSI-MOD:00863D-amino acidMOD_RES D-threonineAA020028-Oct-200528-Oct-200525-Feb-2011D-valinealpha-amino-beta-methylbutyric acidalpha-aminoisovaleric acid(R)-2-amino-3-methylbutanoic acidCAS:640-68-6ChEBI:30016PDBHET:DVAC 5 H 9 N 1 O 199.1399.068414C 0 H 0 N 0 O 00.000.000000Pisarewicz, K.Mora, D.Pflueger, F.C.Fields, G.B.Mari, F.J. Am. Chem. Soc. 127, 6207-6215, 2005Polypeptide chains containing D-gamma-hydroxyvaline.DOI:10.1021/ja050088mPMID:15853325mass spectrographic, and 1D- and 2D-TOCSY NMR analysisprotein-valine epimerase (EC 5.1.1.-)VPSI-MOD:00705D-amino acidMOD_RES D-valineAA020131-Mar-199531-Mar-199520-Nov-2009L-isoglutamyl-polyglycinegamma-glutamylpolyglycineChEBI:21343C 7 H 10 N 2 O 4 +186.17 +186.064057 +C 2 H 3 N 1 O 1 +57.05 +57.021464 +Redeker, V.Levilliers, N.Schmitter, J.M.Le Caer, J.P.Rossier, J.Adoutte, A.Bre, M.H.Science 266, 1688-1691, 1994Polyglycylation of tubulin: a posttranslational modification in axonemal microtubules.DOI:10.1126/science.7992051PMID:7992051mass spectrometric identification; the polyglycine is composed of 3 to 34 residuesVinh, J.Langridge, J.I.Bre, M.H.Levilliers, N.Redeker, V.Loyaux, D.Rossier, J.Biochemistry 38, 3133-3139, 1999Structural characterization by tandem mass spectrometry of the posttranslational polyglycylation of tubulin.DOI:10.1021/bi982304sPMID:10074368mass spectrometric characterization; multiple sites are identifiedLalle, M.Salzano, A.M.Crescenzi, M.Pozio, E.J. Biol. Chem. 281, 5137-5148, 2006The Giardia duodenalis 14-3-3 protein is post-translationally modified by phosphorylation and polyglycylation of the C-terminal tail.DOI:10.1074/jbc.M509673200PMID:16368691Rogowski, K.Juge, F.van Dijk, J.Wloga, D.Strub, J.M.Levilliers, N.Thomas, D.Bré, M.H.Van Dorsselaer, A.Gaertig, J.Janke, C.Cell 137, 1076-1087, 2009Evolutionary divergence of enzymatic mechanisms for posttranslational polyglycylation.DOI:10.1016/j.cell.2009.05.020PMID:19524510glycine:protein-glutamate gamma-ligase (ADP-forming) (EC 6.3.2.-)glycine:protein-glutamyl(gamma-polyglycine) N-ligase (ADP-forming) (EC 6.3.2.-)EGO:0018094PSI-MOD:00206MOD_RES 5-glutamyl polyglycineAA020231-Mar-199531-Mar-199513-Sep-2013L-isoglutamyl-polyglutamic acidgamma-glutamylpolyglutamic acidC 10 H 14 N 2 O 6 +258.23 +258.085186 +C 5 H 7 N 1 O 3 +129.12 +129.042593 +Edde, B.Rossier, J.Le Caer, J.P.Berwald-Netter, Y.Koulakoff, A.Gros, F.Denoulet, P.J. Cell. Biochem. 46, 134-142, 1991A combination of posttranslational modifications is responsible for the production of neuronal alpha-tubulin heterogeneity.DOI:10.1002/jcb.240460207PMID:1680872the polyglutamate is composed of 3 to 6 residuesRegnard, C.Desbruyeres, E.Huet, J.C.Beauvallet, C.Pernollet, J.C.Edde, B.J. Biol. Chem. 275, 15969-15976, 2000Polyglutamylation of nucleosome assembly proteins.DOI:10.1074/jbc.M000045200PMID:10747868monoclonal antibody detection of modification in proteins other than tubulinXiao, H.El Bissati, K.Verdier-Pinard, P.Burd, B.Zhang, H.Kim, K.Fiser, A.Angeletti, R.H.Weiss, L.M.J. Proteome Res. 9, 359-372, 2010Post-translational modifications to Toxoplasma gondii α- and β-tubulins include novel C-terminal methylation.DOI:10.1021/pr900699aPMID:19886702detection of multiple glutamylations by mass-spectrometry in reflector modeThis entry is for L-isoglutamyl-polyglutamic acid where there are 2 to 6 alpha-peptide linked glutamic acid residues attached to a peptide glutamyl residue by an isopeptide bond. For a single glutamic acid attached to a peptide glutamyl residue by an isopeptide bond, see 5-glutamyl glutamic acid, RESID:AA0612.EGO:0018095PSI-MOD:00207Not availablethis modification is not annotated in UniProt featuresAA020331-Mar-199531-Mar-199531-May-2018O4'-(phospho-5'-adenosine)-L-tyrosine5'-adenylic-O-tyrosinehydrogen 5'-adenylate tyrosine esterO-adenyl-L-tyrosineO4'-L-tyrosine 5'-adenosine phosphodiester(2S)-2-amino-3-[4-(5'-adenosine phosphonoxy)phenyl]propanoic acidCAS:93957-03-0ChEBI:83625PDBHET:AMPC 19 H 21 N 6 O 8 P 1492.38492.115848C 10 H 12 N 5 O 6 P 1329.21329.052520Heinrikson, R.L.Kingdon, H.S.J. Biol. Chem. 246, 1099-1106, 1971Primary structure of Escherichia coli glutamine synthetase. II. The complete amino acid sequence of a tryptic heneicosapeptide containing covalently bound adenylic acid.PMID:5543675chemical characterizationMüller, M.P.Peters, H.Blümer, J.Blankenfeldt, W.Goody, R.S.Itzen, A.Science 329, 946-949, 2010The Legionella effector protein DrrA AMPylates the membrane traffic regulator Rab1b.DOI:10.1126/science.1192276PMID:20651120X-ray diffraction, 1.70 angstromsMuller, M.P.Peters, H.Blumer, J.Blankenfeldt, W.Goody, R.S.Itzen, A.submitted to the Protein Data Bank, June 2010Crystal structure of RAB1B covalently modified with AMP at Y77.PDB:3NKVX-ray diffraction, 1.70 angstromsLi, Y.Al-Eryani, R.Yarbrough, M.L.Orth, K.Ball, H.L.J. Am. Soc. Mass Spectrom. 22, 752-761, 2011Characterization of AMPylation on Threonine, Serine, and Tyrosine Using Mass Spectrometry.DOI:10.1007/s13361-011-0084-1PMID:21472612mass spectrometric detection and characterization of tandem-MS fragmentationYGO:0018254PSI-MOD:00208phosphoproteinMOD_RES O-AMP-tyrosineAA020430-Jun-199530-Jun-199520-May-2011S-(2-aminovinyl)-D-cysteine(S,Z)-S-(2-aminovinyl)cysteine(2S)-2-amino-3-([(Z)-2-aminoethenyl]sulfanyl)propanoic acidC 5 H 7 N 2 O 1 S 1143.18143.027909C -1 H -4 N 0 O -2 S -1-80.10-79.993200C -1 H -4 N 0 O -3 S 0-64.04-64.016044Allgaier, H.Jung, G.Werner, R.G.Schneider, U.Zaehner, H.Eur. J. Biochem. 160, 9-22, 1986Epidermin: sequencing of a heterodet tetracyclic 21-peptide amide antibiotic.DOI:10.1111/j.1432-1033.1986.tb09933.xPMID:3769923mass spectrometric, (1)H-NMR, and (13)C-NMR identification; stereochemical determinationKellner, R.Jung, G.Hoerner, T.Zaehner, H.Schnell, N.Entian, K.D.Goetz, F.Eur. J. Biochem. 177, 53-59, 1988Gallidermin: a new lanthionine-containing polypeptide antibiotic.DOI:10.1111/j.1432-1033.1988.tb14344.xPMID:3181159mass spectrometric identificationMinami, Y.Yoshida, K.Azuma, R.Urakawa, A.Kawauchi, T.Otani, T.Komiyama, K.Omura, S.Tetrahedron Lett. 35, 8001-8004, 1994Structure of cypemycin, a new peptide antibiotic.DOI:10.1016/0040-4039(94)80033-2mass spectrometric, (1)H-NMR, and (13)C-NMR identificationLi, B.Sher, D.Kelly, L.Shi, Y.Huang, K.Knerr, P.J.Joewono, I.Rusch, D.Chisholm, S.W.van der Donk, W.A.Proc. Natl. Acad. Sci. U.S.A. 107, 10430-10435, 2010Catalytic promiscuity in the biosynthesis of cyclic peptide secondary metabolites in planktonic marine cyanobacteria.DOI:10.1073/pnas.0913677107PMID:20479271Claesen, J.Bibb, M.Proc. Natl. Acad. Sci. U.S.A. 107, 16297-16302, 2010Genome mining and genetic analysis of cypemycin biosynthesis reveal an unusual class of posttranslationally modified peptides.DOI:10.1073/pnas.1008608107PMID:20805503gene sequence for the encoded peptide, biosynthesis; the authors did not have enough material to determine the stereochemistry and assume that it was the D stereoisomer [private communication]This cross-link arises from the decarboxylation of the carboxyl-terminal portion of a lanthionine, either L-lanthionine (see RESID:AA0110) or meso-lanthionine (see RESID:AA0111).This residue is acid labile. It may be identified as (2-aminoethyl)-D-cysteine (D-4-thialysine) after hydrogenation with palladium/charcoal catalyst.For the L stereoisomer, see RESID:AA0548. The stereochemistry of the (2-aminovinyl)-cysteine derived from two L-cysteine residues in cypemycin has not been determined.peptidyl-cysteine dethiolase (EC 4.4.1.-)peptidyl-phosphoserine/phosphothreonine dehydratase (EC 4.2.1.-)peptidyl-cysteine dehydroalanine/dehydrobutyrine ligase (EC 6.2.-.-)C, Ccarboxyl-terminalcross-link 2PSI-MOD:01849C, Scarboxyl-terminalcross-link 2GO:0018096PSI-MOD:00209blocked carboxyl endlanthioninethioether bondCROSSLNK S-(2-aminovinyl)-D-cysteine (Cys-Cys)CROSSLNK S-(2-aminovinyl)-D-cysteine (Ser-Cys)AA020530-Jun-199530-Jun-199531-Dec-2011L-cysteine sulfenic acid(2R)-2-amino-3-(oxido-lambda(4)-sulfanyl)propanoic acid [tautomer]2-amino-2-carboxyethanesulfenic acid2-amino-3-sulfinylpropanoic acid [tautomer]3-sulfenoalaninecysteine S-oxide [tautomer]cysteine sulfoxide [tautomer]cysteine sulphenic acidS-hydroxycysteineS-oxocysteine [tautomer]S-oxycysteine [tautomer](2R)-2-amino-3-(hydroxysulfanyl)propanoic acidCAS:5722-80-5CAS:73243-12-6ChEBI:61962ChEBI:61973PDBHET:CSOPDBHET:CSXC 3 H 5 N 1 O 2 S 1119.14119.004099C 0 H 0 N 0 O 1 S 016.0015.994915Poole, L.B.Claiborne, A.J. Biol. Chem. 264, 12330-12338, 1989The non-flavin redox center of the streptococcal NADH peroxidase. II. Evidence for a stabilized cysteine-sulfenic acid.PMID:2501303mass spectrometric and chemical characterizationYeh, J.I.Claiborne, A.Hol, W.G.J.Biochemistry 35, 9951-9957, 1996Structure of the native cysteine-sulfenic acid redox center of enterococcal NADH peroxidase refined at 2.8 Angstroms resolution.DOI:10.1021/bi961037sPMID:8756456X-ray diffraction, 2.8 angstroms, active cysteine sulfenic acid formCrane 3rd, E.J.Vervoort, J.Claiborne, A.Biochemistry 36, 8611-8618, 199713C NMR analysis of the cysteine-sulfenic acid redox center of enterococcal NADH peroxidase.DOI:10.1021/bi9707990PMID:9214307(13)C-NMR characterizationChoi, H.J.Kang, S.W.Yang, C.H.Rhee, S.G.Ryu, S.E.Nature Struct. Biol. 5, 400-406, 1998Crystal structure of a novel human peroxidase enzyme at 2.0 angstroms resolution.DOI:10.1038/nsb0598-400PMID:9587003X-ray diffraction, 2.0 angstromsNagashima, S.Nakasako, M.Dohmae, N.Tsujimura, M.Takio, K.Odaka, M.Yohda, M.Kamiya, N.Endo, I.Nature Struct. Biol. 5, 347-351, 1998Novel non-heme iron center of nitrile hydratase with a claw setting of oxygen atoms.DOI:10.1038/nsb0598-347PMID:9586994X-ray diffraction, 1.7 angstroms; mass spectroscopic identificationBoschi-Muller, S.Azza, S.Sanglier-Cianferani, S.Talfournier, F.Van Dorsselaer, A.Branlant, G.J. Biol. Chem. 275, 35908-35913, 2000A sulfenic acid enzyme intermediate is involved in the catalytic mechanism of peptide methionine sulfoxide reductase from Escherichia coli.DOI:10.1074/jbc.M006137200PMID:10964927sulfenic acid intermediate; the spelling of "Van Dorsselear" in the journal and in the PubMed citation is correctedThis reactive residue must be stabilized by the protein structure. As a active site it may be reduced to cysteine or cysteine anion and reoxidized during the reaction cycle.The "active site" feature is used if the stable form is the reduced cysteine; the "modified site" feature is used if the stable form is the oxidized cysteine sulfenic acid.CGO:0018171GO:0018324PSI-MOD:00210ACT_SITE Cysteine sulfenic acid (-SOH) intermediateACT_SITE Redox-activeMOD_RES Cysteine sulfenic acid (-SOH)AA020630-Jun-199530-Jun-199531-May-2018S-(glycyl)-L-cysteine1-(cystein-S-yl)-glycinateglycine cysteine thioesterS-(2-amino-1-oxoethyl)cysteine(2R)-2-amino-3-[(aminoacetyl)sulfanyl]propanoic acidChEBI:22050C 5 H 7 N 2 O 2 S 1159.18159.022823C 5 H 9 N 2 O 3 S 1177.20177.033388C 0 H -2 N 0 O -1 S 0-18.02-18.010565C 3 H 5 N 1 O 1 S 1103.14103.009185Jentsch, S.McGrath, J.P.Varshavsky, A.Nature 329, 131-134, 1987The yeast DNA repair gene RAD6 encodes a ubiquitin-conjugating enzyme.DOI:10.1038/329131a0PMID:3306404Mossessova, E.Lima, C.D.Mol. Cell 5, 865-876, 2000Ulp1-SUMO crystal structure and genetic analysis reveal conserved interactions and a regulatory element essential for cell growth in yeast.PMID:10882122X-ray diffraction, 1.60 angstromsMossessova, E.Lima, C.D.submitted to the Protein Data Bank, April 2000X-ray structure of the C-terminal Ulp1 protease domain in complex with Smt3, the yeast ortholog of SUMO.PDB:1EUVX-ray diffraction, 1.60 angstromsCarvalho, A.F.Pinto, M.P.Grou, C.P.Alencastre, I.S.Fransen, M.Sá-Miranda, C.Azevedo, J.E.J. Biol. Chem. 282, 31267-31272, 2007Ubiquitination of mammalian Pex5p, the peroxisomal import receptor.DOI:10.1074/jbc.M706325200PMID:17726030chemical and directed mutation analysis; thioester formed with a target protein, not an intermediateGrou, C.P.Carvalho, A.F.Pinto, M.P.Wiese, S.Piechura, H.Meyer, H.E.Warscheid, B.Sá-Miranda, C.Azevedo, J.E.J. Biol. Chem. 283, 14190-14197, 2008Members of the E2D (UbcH5) family mediate the ubiquitination of the conserved cysteine of Pex5p, the peroxisomal import receptor.DOI:10.1074/jbc.M800402200PMID:18359941Ågren, D.Schnell, R.Oehlmann, W.Singh, M.Schneider, G.J. Biol. Chem. 283, 31567-31574, 2008Cysteine synthase (CysM) of Mycobacterium tuberculosis is an O-phosphoserine sulfhydrylase: evidence for an alternative cysteine biosynthesis pathway in mycobacteria.DOI:10.1074/jbc.M804877200PMID:18799456the encoding of an author's name in the PubMed citation is corrected to UTF8Jurgenson, C.T.Burns, K.E.Begley, T.P.Ealick, S.E.Biochemistry 47, 10354-10364, 2008Crystal structure of a sulfur carrier protein complex found in the cysteine biosynthetic pathway of Mycobacterium tuberculosis.DOI:10.1021/bi800915jPMID:18771296O'Leary, S.E.Jurgenson, C.T.Ealick, S.E.Begley, T.P.Biochemistry 47, 11606-11615, 2008O-phospho-L-serine and the thiocarboxylated sulfur carrier protein CysO-COSH are substrates for CysM, a cysteine synthase from Mycobacterium tuberculosis.DOI:10.1021/bi8013664PMID:18842002cysteine thioester linked to a carboxyl terminal glycine is formed by condensation of a carboxyl terminal thioglycine with free phosphoserineThe formula and records labeled "GCX" refers to a carboxyl end glycine residue thioester cross-linked to a peptidyl cysteine residue.The formula and records labeled "GLY" refers to a carboxyl end glycine residue thioester bonded to a free cysteine. A carboxyl end thioglycine residue (see RESID:AA0265) is converted to this S-(glycyl)-L-cysteine. It then transamidates, transiently forming a peptide bond to a free cysteine (see RESID:AA0529) before the cysteine is released by a peptidase activity.C, Gcarboxyl-terminalcross-link 2GO:0018255PSI-MOD:00211Gcarboxyl-terminalPSI-MOD:01777blocked carboxyl endthioester bondACT_SITE Glycyl thioester intermediateCROSSLNK Glycyl cysteine thioester (Cys-Gly) (interchain with G-Cter ...)MOD_RES CysO-cysteine adductAA020730-Jun-199530-Jun-199531-Mar-2012S-4-hydroxycinnamyl-L-cysteinecinnamate cysteine thioesterS-para-coumaryl-L-cysteine(2R)-2-amino-3-([(2E)-3-(4-hydroxyphenyl)prop-2-enoyl]sulfanyl)propanoic acidCOMe:BIM000151PDBHET:HC4C 12 H 11 N 1 O 3 S 1249.28249.045964C 9 H 6 N 0 O 2 S 0146.14146.036779Hoff, W.D.Duex, P.Haard, K.Devreese, B.Nugteren-Roodzant, I.M.Crielaard, W.Boelens, R.Kaptein, R.Van Beeumen, J.Hellingwerf, K.J.Biochemistry 33, 13959-13962, 1994Thiol ester-linked p-coumaric acid as a new photoactive prosthetic group in a protein with rhodopsin-like photochemistry.DOI:10.1021/bi00251a001PMID:7947803spectrographic characterization; (1)H-NMR and (13)C-NMR identification; the capitalization of "van Beeumen" in the PubMed citation is correctedBaca, M.Borgstahl, G.E.O.Boissinot, M.Burke, P.M.Williams, D.R.Slater, K.A.Getzoff, E.D.Biochemistry 33, 14369-14377, 1994Complete chemical structure of photoactive yellow protein: novel thioester-linked 4-hydroxycinnamyl chromophore and photocycle chemistry.DOI:10.1021/bi00252a001PMID:7981196mass spectrometric and chemical characterization; X-ray diffraction, 1.4 angstromsCGO:0018097PSI-MOD:00212chromoproteinhydroxylationphotoreceptorthioester bondMOD_RES S-(4-hydroxycinnamyl)cysteineAA020830-Jun-199530-Jun-199531-May-2018chondroitin sulfate D-glucuronosyl-D-galactosyl-D-galactosyl-D-xylosyl-L-serinechondroitin 4-sulfate (chondroitin sulfate A)chondroitin 6-sulfate (chondroitin sulfate C)poly[beta-1,4-D-glucopyranuronosyl-beta-1,3-(2-acetamido-2-deoxy-4-sulfate-D-galactosyl)]-beta-1,4-D-glucopyranuronosyl-beta-1,3-D-galactosyl-beta-1,3-D-galactosyl-beta-1,4-D-xylosyl-beta-1,3-L-serine; poly[beta-1,4-D-glucopyranuronosyl-beta-1,3-(2-acetamido-2-deoxy-6-sulfate D-galactosyl)]-beta-1,4-D-glucopyranuronosyl-beta-1,3-D-galactosyl-beta-1,3-D-galactosyl-beta-1,4-D-xylosyl-beta-1,3-L-serineCAS:24967-93-9CAS:25322-46-7CAS:9007-28-7C 3 H 4 N 1 O 2 +86.07 +86.024203 +C 0 H -1 N 0 O 0 +-1.01 +-1.007825 +Bourdon, M.A.Krusius, T.Campbell, S.Schwartz, N.B.Ruoslahti, E.Proc. Natl. Acad. Sci. U.S.A. 84, 3194-3198, 1987Identification and synthesis of a recognition signal for the attachment of glycosaminoglycans to proteins.DOI:10.1073/pnas.84.10.3194PMID:3472204Enghild, J.J.Salvesen, G.Hefta, S.A.Thogersen, I.B.Rutherfurd, S.Pizzo, S.V.J. Biol. Chem. 266, 747-751, 1991Chondroitin 4-sulfate covalently cross-links the chains of the human blood protein pre-alpha-inhibitor.PMID:1898736Chirat, F.Balduyck, M.Mizon, C.Laroui, S.Sautiere, P.Mizon, J.Int. J. Biochem. 23, 1201-1203, 1991A chondroitin-sulfate chain is located on serine-10 of the urinary trypsin inhibitor.DOI:10.1016/0020-711X(91)90216-APMID:1794445The attachment polysaccharide has not been characterized for all forms of the chondroitin sulfate proteoglycans.Chondroitin 4-sulfate, chondroitin sulfate A, is shown.See also RESID:AA0154, RESID:AA0209, RESID:AA0210, RESID:AA0291, RESID:AA0296, RESID:AA0297, RESID:AA0397, RESID:AA0398, RESID:AA0400, RESID:AA0402, RESID:AA0404, RESID:AA0406, and RESID:AA0422 for other O-glycosylated serines.protein xylosyltransferase (EC 2.4.2.26)xylosylprotein 4-beta-galactosyltransferase (EC 2.4.1.133)galactosylxylosylprotein 3-beta-galactosyltransferase (EC 2.4.1.134)galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase (EC 2.4.1.135)glucuronylgalactosylproteoglycan beta-1,4-N-acetylgalactosaminyltransferase (EC 2.4.1.174)chondroitin 4-sulfotransferase (EC 2.8.2.5)chondroitin 6-sulfotransferase (EC 2.8.2.17)SGO:0018402PSI-MOD:00213chondroitin sulfate proteoglycanglycoproteinCARBOHYD O-linked (Xyl...) (chondroitin sulfate) serineCARBOHYD O-linked (Xyl...) (glycosaminoglycan) serineAA020930-Jun-199530-Jun-199531-May-2018dermatan 4-sulfate D-glucuronosyl-D-galactosyl-D-galactosyl-D-xylosyl-L-serinebeta-heparinchondroitin sulfate Bpoly[beta-1,4-L-idopyranuronosyl-alpha-1,3-(2-acetamido-2-deoxy-4-sulfate D-galactosyl)]-beta-1,4-D-glucopyranuronosyl-beta-1,3-D-galactosyl-beta-1,3-D-galactosyl-beta-1,4-D-xylosyl-beta-1,3-L-serineCAS:24967-94-0C 3 H 4 N 1 O 2 +86.07 +86.024203 +C 0 H -1 N 0 O 0 +-1.01 +-1.007825 +Bourdon, M.A.Krusius, T.Campbell, S.Schwartz, N.B.Ruoslahti, E.Proc. Natl. Acad. Sci. U.S.A. 84, 3194-3198, 1987Identification and synthesis of a recognition signal for the attachment of glycosaminoglycans to proteins.DOI:10.1073/pnas.84.10.3194PMID:3472204Choi, H.U.Johnson, T.L.Pal, S.Tang, L.H.Rosenberg, L.Neame, P.J.J. Biol. Chem. 264, 2876-2884, 1989Characterization of the dermatan sulfate proteoglycans, DS-PGI and DS-PGII, from bovine articular cartilage and skin isolated by octyl-sepharose chromatography.PMID:2914936The attachment polysaccharide has not been characterized for all forms of the chondroitin sulfate proteoglycans.See also RESID:AA0154, RESID:AA0208, RESID:AA0210, RESID:AA0291, RESID:AA0296, RESID:AA0297, RESID:AA0397, RESID:AA0398, RESID:AA0400, RESID:AA0402, RESID:AA0404, RESID:AA0406, and RESID:AA0422 for other O-glycosylated serines.protein xylosyltransferase (EC 2.4.2.26)xylosylprotein 4-beta-galactosyltransferase (EC 2.4.1.133)galactosylxylosylprotein 3-beta-galactosyltransferase (EC 2.4.1.134)galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase (EC 2.4.1.135)glucuronylgalactosylproteoglycan beta-1,4-N-acetylgalactosaminyltransferase (EC 2.4.1.174)chondroitin 4-sulfotransferase (EC 2.8.2.5)chondroitin 6-sulfotransferase (EC 2.8.2.17)SGO:0018403PSI-MOD:00214chondroitin sulfate proteoglycandermatan sulfateglycoproteinCARBOHYD O-linked (Xyl...) (dermatan sulfate) serineCARBOHYD O-linked (Xyl...) (glycosaminoglycan) serineAA021030-Jun-199530-Jun-199531-May-2018heparan sulfate D-glucuronosyl-D-galactosyl-D-galactosyl-D-xylosyl-L-serineheparinheparitin sulfatepoly[alpha-1,4-(2-sulfate D-glucopyranuronosyl)-beta-1,4-(2-sulfamino-2-deoxy-6-sulfate D-glucosyl)]-beta-1,4-D-glucopyranuronosyl-beta-1,3-D-galactosyl-beta-1,3-D-galactosyl-beta-1,4-D-xylosyl-beta-1,3-L-serineCAS:9005-49-6C 3 H 4 N 1 O 2 +86.07 +86.024203 +C 0 H -1 N 0 O 0 +-1.01 +-1.007825 +Bourdon, M.A.Krusius, T.Campbell, S.Schwartz, N.B.Ruoslahti, E.Proc. Natl. Acad. Sci. U.S.A. 84, 3194-3198, 1987Identification and synthesis of a recognition signal for the attachment of glycosaminoglycans to proteins.DOI:10.1073/pnas.84.10.3194PMID:3472204The attachment polysaccharide has not been characterized for all forms of the chondroitin sulfate proteoglycans.The glucosamine 2-amino groups are to some extent acetylated rather than sulfated.See also RESID:AA0154, RESID:AA0208, RESID:AA0209, RESID:AA0291, RESID:AA0296, RESID:AA0297, RESID:AA0397, RESID:AA0398, RESID:AA0400, RESID:AA0402, RESID:AA0404, RESID:AA0406, and RESID:AA0422 for other O-glycosylated serines.protein xylosyltransferase (EC 2.4.2.26)xylosylprotein 4-beta-galactosyltransferase (EC 2.4.1.133)galactosylxylosylprotein 3-beta-galactosyltransferase (EC 2.4.1.134)galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase (EC 2.4.1.135)glucuronylgalactosylproteoglycan beta-1,4-N-acetylgalactosaminyltransferase (EC 2.4.1.174)chondroitin 4-sulfotransferase (EC 2.8.2.5)chondroitin 6-sulfotransferase (EC 2.8.2.17)SGO:0015012GO:0018404PSI-MOD:00215chondroitin sulfate proteoglycanglycoproteinheparan sulfateCARBOHYD O-linked (Xyl...) (heparan sulfate) serineCARBOHYD O-linked (Xyl...) (glycosaminoglycan) serineAA021109-Aug-199509-Aug-199531-May-2018N6-formyl-L-lysineepsilon-formyllysineN(zeta)-formyllysine(2S)-2-amino-6-(formylamino)hexanoic acidCAS:1190-48-3C 7 H 12 N 2 O 2156.19156.089878C 1 H 0 N 0 O 128.0127.994915Doonan, S.Garman, A.J.Hanson, J.M.Loudon, A.G.Vernon, C.A.J. Chem. Soc. Perkin Trans. I 1978, 1157-1160, 1978Identification by mass spectrometry of N(epsilon)-formyl-lysine residues in a peptide from bee venom.DOI:10.1039/P19780001157mass spectrometric identificationJiang, T.Zhou, X.Taghizadeh, K.Dong, M.Dedon, P.C.Proc. Natl. Acad. Sci. U.S.A. 104, 60-65, 2007N-formylation of lysine in histone proteins as a secondary modification arising from oxidative DNA damage.DOI:10.1073/pnas.0606775103PMID:17190813N6-formyllysine in histone is formed as an artifact of oxidative DNA damageWiśniewski, J.R.Zougman, A.Mann, M.Nucleic Acids Res. 36, 570-577, 2008N(epsilon)-formylation of lysine is a widespread post-translational modification of nuclear proteins occurring at residues involved in regulation of chromatin function.DOI:10.1093/nar/gkm1057PMID:18056081mass spectrometric identification; distinguishes from nominally isobaric N6,N6-dimethyllysine (see RESID:AA0075); care was taken not to expose the sample to either formic acid or formaldehyde, however oxidation of N6-methyllysine was not precluded; the encoding of an author's name in the PubMed citation is corrected to UTF8KGO:0018257PSI-MOD:00216formylationMOD_RES N6-formyllysineAA021218-Aug-199528-Oct-200531-May-2018O4-arabinosyl-L-hydroxyproline4-(beta-L-arabinofuranosyloxy)prolinebeta-arabinofuranosyl-4-hydroxyprolineO4-glycosyl-hydroxyproline(2S,4R)-4-(beta-L-arabinofuranosyloxy)pyrrolidine-2-carboxylic acidChEBI:131610C 10 H 15 N 1 O 6 +245.23 +245.089937 +C 5 H 8 N 0 O 5 +148.11 +148.037173 +Allen, A.K.Desai, N.N.Neuberger, A.Creeth, J.M.Biochem. J. 171, 665-674, 1978Properties of potato lectin and the nature of its glycoprotein linkages.PMID:666730the modification is identified as beta-L-arabinofuranosyloxy-4-prolineKieliszewski, M.J.O'Neill, M.Leykam, J.Orlando, R.J. Biol. Chem. 270, 2541-2549, 1995Tandem mass spectrometry and structural elucidation of glycopeptides from a hydroxyproline-rich plant cell wall glycoprotein indicate that contiguous hydroxyproline residues are the major sites of hydroxyproline O-arabinosylation.DOI:10.1074/jbc.270.6.2541PMID:7852316mass spectrometric detection; the glycan in plant hydroxyproline-rich cell wall glycoprotein typically consists of 1 to 5 arabinose units 1-2 alpha-linkedOgawa-Ohnishi, M.Matsushita, W.Matsubayashi, Y.Nature Chem. Biol. 9, 726-730, 2013Identification of three hydroxyproline O-arabinosyltransferases in Arabidopsis thaliana.DOI:10.1038/nchembio.1351PMID:24036508biosynthesisSee also RESID:AA0389 and RESID:AA0390 for other O4-glycosylated 4-hydroxyprolines.hydroxyproline O-arabinosyltransferaseUDP-β-L-arabinofuranose:[protein]-trans-4-hydroxy-L-proline L-arabinofuranosyl transferase (configuration-retaining) (EC 2.4.2.58)Psecondary to RESID:AA0030GO:0006493GO:0018258PSI-MOD:00217glycoproteinhydroxylationCARBOHYD O-linked (Ara...) hydroxyprolineAA021318-Aug-199528-Feb-199720-May-2011O-(phospho-5'-RNA)-L-serineO3-(phospho-5'-RNA)-L-serineO3-L-serine 5'-RNA phosphodiester(S)-2-amino-3-(5'-ribonucleic acid phosphonoxy)propanoic acidC 3 H 5 N 1 O 5 P 1 +166.05 +165.990534 +C 0 H 0 N 0 O 3 P 1 +78.97 +78.958505 +Samad, A.Carroll, R.B.Mol. Cell. Biol. 11, 1598-1606, 1991The tumor suppressor p53 is bound to RNA by a stable covalent linkage.DOI:10.1128/MCB.11.3.1598PMID:1705009chromatographic detection; chemical characterizationOlspert, A.Peil, L.Hébrard, E.Fargette, D.Truve, E.J. Gen. Virol. 92, 445-452, 2011Protein-RNA linkage and post-translational modifications of two sobemovirus VPgs.DOI:10.1099/vir.0.026476-0PMID:21068217mass spectrometric identification; for the genome-linked protein (VPg) of rice yellow mottle virus, the 5'-end is adenosine and pAp was identified attached to Ser-1SGO:0018259PSI-MOD:00218genome-linked proteinphosphoproteinMOD_RES O-(5'-phospho-RNA)-serineAA021425-Aug-199525-Aug-199531-Dec-2013L-citrulline2-amino-5-(aminocarbonyl)aminopentanoic acidalpha-amino-delta-ureidovaleric aciddelta-ureidonorvalineN5-(aminocarbonyl)ornithineN5-carbamoylornithineN5-carbamylornithine(S)-2-amino-5-(carbamoylamino)pentanoic acidCAS:372-75-8PDBHET:CIRC 6 H 11 N 3 O 2157.17157.085127C 0 H -1 N -1 O 10.980.984016Wood, D.D.Moscarello, M.A.J. Biol. Chem. 264, 5121-5127, 1989The isolation, characterization, and lipid-aggregating properties of a citrulline containing myelin basic protein.PMID:2466844chromatographic identification; the mechanism for non-specific formation of citrulline from arginine in myelin is not known, but is probably artifactualLoos, T.Mortier, A.Gouwy, M.Ronsse, I.Put, W.Lenaerts, J.P.Van Damme, J.Proost, P.Blood 112, 2648-2656, 2008Citrullination of CXCL10 and CXCL11 by peptidylarginine deiminase: a naturally occurring posttranslational modification of chemokines and new dimension of immunoregulation.DOI:10.1182/blood-2008-04-149039PMID:18645041the deimination of a specific arginine in a protein by peptidylarginine deiminase is establishedprotein-arginine deiminase (EC 3.5.3.15)RGO:0018101PSI-MOD:00219citrullineMOD_RES CitrullineAA021503-Nov-199503-Nov-199531-Jul-20094-hydroxy-L-arginine2-amino-5-(carbamimidamido)-4-hydroxypentanoic acid [tautomer]2-amino-5-guanidino-4-hydroxypentanoic acid2-amino-5-[(aminoiminomethyl)amino]-4-hydroxypentanoic acid [tautomer]C(gamma)-hydroxyargininegamma-hydroxyarginine(2S,4Xi)-2-amino-5-[(diaminomethylidene)amino]-4-hydroxypentanoic acidCAS:2524-31-4CAS:61370-10-3PDBHET:AROC 6 H 12 N 4 O 2172.19172.096026C 0 H 0 N 0 O 116.0015.994915Papov, V.V.Diamond, T.V.Biemann, K.Waite, J.H.J. Biol. Chem. 270, 20183-20192, 1995Hydroxyarginine-containing polyphenolic proteins in the adhesive plaques of the marine mussel Mytilus edulis.DOI:10.1074/jbc.270.34.20183PMID:7650037chromatographic detection; mass spectrometric and chemical characterizationHaenzelmann, P.Dobbek, H.Gremer, L.Huber, R.Meyer, O.J. Mol. Biol. 301, 1221-1235, 2000The effect of intracellular molybdenum in Hydrogenophaga pseudoflava on the crystallographic structure of the seleno-molybdo-iron-sulfur flavoenzyme carbon monoxide dehydrogenase.DOI:10.1006/jmbi.2000.4023PMID:10966817X-ray diffraction, 2.25 angstroms; an arginine residue involved in binding molybdopterin appears to be modified to (2S,4R)-4-hydroxyarginineHaenzelmann, P.Dobbek, H.Gremer, L.Huber, R.Meyer, O.submitted to the Protein Data Bank, September 2000Carbon monoxide dehydrogenase from Hydrogenophaga pseudoflava.PDB:1FFVX-ray diffraction, 2.25 angstromsThe stereochemistry for the second chiral center has not been resolved. The (2S,4R) diastereomer is shown.RGO:0018102PSI-MOD:00220hydroxylationMOD_RES 4-hydroxyarginineAA021601-Sep-199501-Sep-199520-Nov-2009N-(L-isoaspartyl)-L-cysteine2-(3-amino-3-carboxypropanoyl)amino-3-mercaptopropanoic acid2-amino-N4-(1-carboxy-2-mercaptoethyl)butanediamic acidN-beta-aspartylcysteineN-isoaspartyl cysteine(S)-2-amino-4-((R)-1-carboxy-2-sulfanylethyl)amino-4-oxobutanoic acidC 7 H 9 N 2 O 3 S 1201.22201.033388C 0 H -3 N -1 O 0 S 0-17.03-17.026549Frechet, D.Guitton, J.D.Herman, F.Faucher, D.Helynck, G.Monegier du Sorbier, B.Ridoux, J.P.James-Surcouf, E.Vuilhorgne, M.Biochemistry 33, 42-50, 1994Solution structure of RP 71955, a new 21 amino acid tricyclic peptide active against HIV-1 virus.DOI:10.1021/bi00167a006PMID:8286361Frechet, D.Guitton, J.D.Herman, F.Faucher, D.Helynck, G.Monegier du Sorbier, B.Ridoux, J.P.James-Surcouf, E.Vuilhorgne, M.submitted to the Protein Data Bank, August 1993Solution structure of RP 71955, a new 21 amino acid tricyclic peptide active against HIV-1 virus.PDB:1RPBconformation by (1)H-NMRC, Namino-terminalcross-link 2GO:0018263PSI-MOD:00221blocked amino endisopeptide bondCROSSLNK Isoaspartyl cysteine isopeptide (Cys-Asn)AA021701-Sep-199524-Jul-199720-Apr-20122'-mannosyl-L-tryptophan2'-tryptophan C-mannoside(2S)-2-amino-3-(2-beta-D-mannopyranosyl-1H-indol-3-yl)propanoic acidPDBHET:BMAC 17 H 20 N 2 O 6348.36348.132136C 6 H 10 N 0 O 5162.14162.052823Hofsteenge, J.Mueller, D.R.de Beer, T.Loeffler, A.Richter, W.J.Vliegenthart, J.F.G.Biochemistry 33, 13524-13530, 1994New type of linkage between a carbohydrate and a protein: C-glycosylation of a specific tryptophan residue in human RNase U-s.DOI:10.1021/bi00250a003PMID:7947762mass spectrometric, (1)H-NMR, and (13)C-NMR identificationde Beer, T.Vliegenthart, J.F.Loffler, A.Hofsteenge, J.Biochemistry 34, 11785-11789, 1995The hexopyranosyl residue that is C-glycosidically linked to the side chain of tryptophan-7 in human RNase Us is alpha-mannopyranose.DOI:10.1021/bi00037a016PMID:7547911(1)H-NMR and (13)C-NMR identificationLovelace, L.L.Cooper, C.L.Sodetz, J.M.Lebioda, L.J. Biol. Chem. 286, 17585-17592, 2011Structure of human C8 protein provides mechanistic insight into membrane pore formation by complement.DOI:10.1074/jbc.M111.219766PMID:21454577X-ray diffraction, 2.51 angstroms; the authors note that the multiple sites of mannosylated tryptophan are fit better by the beta anomeric structureLovelace, L.L.Cooper, C.L.Sodetz, J.M.Lebioda, L.submitted to the Protein Data Bank, August 2010Crystal structure of human complement component C8.PDB:3OJYX-ray diffraction, 2.51 angstromsThe carbohydrate, identified as mannose, is linked to tryptophan by an unusual C-glycosidic linkage.The structures determined in NMR and X-ray diffraction studies differ in assigning the glycosylation as being alpha or beta, respectively. The beta anomeric form is shown.WGO:0018103GO:0018406PSI-MOD:00222glycoproteinCARBOHYD C-linked (Man)CARBOHYD C-linked (Hex)this UniProt feature is used when the identity of the sugar has not been determinedAA021801-Sep-199501-Sep-199530-Apr-2010N6-mureinyl-L-lysineN6-[(2R,6S)-2-(N-(N-mureinyl-(R)-alanyl)-(S)-glutamyl)amino-6-amino-6-carboxy-1-oxohex-1-yl]lysineC 6 H 11 N 2 O 1 +127.17 +127.087138 +C 0 H -1 N 0 O 0 +-1.01 +-1.007825 +Braun, V.Bosch, V.Eur. J. Biochem. 28, 51-69, 1972Sequence of the murein-lipoprotein and the attachment site of the lipid.DOI:10.1111/j.1432-1033.1972.tb01883.xPMID:4261992chemical characterizationThe epsilon-amino group of lysine is covalently linked to bacterial cell wall murein by a peptide-like L-alanyl-D-glutamyl-2,6-diaminopimelic acid linkage.KGO:0019121PSI-MOD:00223peptidoglycanMOD_RES N6-murein peptidoglycan lysineAA021919-May-200019-May-200031-Mar-20091-chondroitin sulfate-L-aspartic acid ester1-aspartic acid ester with 6-chondroitin 4-sulfatepoly[beta-1,4-D-glucopyranuronosyl-beta-1,3-(2-acetamido-2-deoxy-4-sulfate D-galactosyl)]beta-1,4-D-glucopyranuronosyl-beta-1,3-(2-acetamido-2-deoxy-4-sulfate-6-(1-L-aspartyl)-D-galactose)protein-glycosaminoglycan-protein cross-linkC 18 H 25 N 2 O 17 S 1 +573.45 +573.087393 +C 14 H 19 N 1 O 13 S 1 +441.36 +441.057711 +Enghild, J.J.Salvesen, G.Hefta, S.A.Thogersen, I.B.Rutherfurd, S.Pizzo, S.V.J. Biol. Chem. 266, 747-751, 1991Chondroitin 4-sulfate covalently cross-links the chains of the human blood protein pre-alpha-inhibitor.PMID:1898736Dcarboxyl-terminalGO:0019800PSI-MOD:00224blocked carboxyl endchondroitin sulfate proteoglycanglycoproteinMOD_RES Aspartate 1-(chondroitin 4-sulfate)-esterAA022001-Sep-199501-Sep-199530-Apr-2010S-(6-FMN)-L-cysteine6-[S-cysteinyl]flavin mononucleotide6-[S-cysteinyl]FMN(R)-2-amino-3-[6-riboflavin 5'-dihydrogen phosphate]sulfanylpropanoic acidCOMe:BIM000137PDBHET:FMNC 20 H 24 N 5 O 10 P 1 S 1557.47557.098150C 17 H 19 N 4 O 9 P 1 S 0454.33454.088965Kenney, W.C.McIntire, W.Steenkamp, D.J.Benisek, W.F.FEBS Lett. 85, 137-140, 1978Amino acid sequence of a cofactor peptide from trimethylamine dehydrogenase.DOI:10.1016/0014-5793(78)81265-4PMID:620783Barber, M.J.Neame, P.J.Lim, L.W.White, S.Matthews, F.S.J. Biol. Chem. 267, 6611-6619, 1992Correlation of X-ray deduced and experimental amino acid sequences of trimethylamine dehydrogenase.PMID:1551870X-ray diffraction, 2.4 angstromsMathews, F.S.Lim, L.W.White, S.submitted to the Protein Data Bank, October 1993Correlation of X-ray deduced and experimental amino acid sequences of trimethylamine dehydrogenase.PDB:2TMDX-ray diffraction, 2.4 angstromsTrickey, P.Basran, J.Lian, L.Y.Chen, Z.Barton, J.D.Sutcliffe, M.J.Scrutton, N.S.Mathews, F.S.Biochemistry 39, 7678-7688, 2000Structural and biochemical characterization of recombinant wild type and a C30A mutant of trimethylamine dehydrogenase from methylophilus methylotrophus (sp. W(3)A(1)).DOI:10.1021/bi9927181PMID:10869173X-ray diffraction, 2.2 angstromsThe keyword "phosphoprotein" is not used with flavin modifications linked through the flavin.autocatalyticCGO:0018310PSI-MOD:00225*phosphoproteinflavoproteinFMNthioether bondMOD_RES S-6-FMN cysteineAA022101-Sep-199501-Sep-199531-Mar-20121'-(8alpha-FAD)-L-histidine8alpha-(N(epsilon)-histidyl)FAD8alpha-(N1'-histidyl)FAD8alpha-N3-histidyl FAD [misnomer]N(tau)-(8alpha-FAD)-histidinetele-(8alpha-FAD)-histidine(S)-2-amino-3-(1-[8alpha riboflavin 5'-(trihydrogen diphosphate) 5'->5'-ester with adenosine]imidazol-4-yl)propanoic acidCOMe:BIM000138PDBHET:FADC 33 H 38 N 12 O 16 P 2920.68920.200396C 27 H 31 N 9 O 15 P 2783.54783.141485Walker, W.H.Singer, T.P.Ghisla, S.Hemmerich, P.Eur. J. Biochem. 26, 279-289, 1972Studies on succinate dehydrogenase. 8alpha-Histidyl-FAD as the active center of succinate dehydrogenase.DOI:10.1111/j.1432-1033.1972.tb01766.xPMID:4339951Pinto, J.T.Frisell, W.R.Arch. Biochem. Biophys. 169, 483-491, 1975Characterization of the peptide-bound flavin of a bacterial sarcosine dehydrogenase.DOI:10.1016/0003-9861(75)90191-5PMID:241294chemical and spectrographic characterization; the authors use biochemical rather than IUPAC numberingde Jong, E.van Berkel, W.J.van der Zwan, R.P.de Bont, J.A.Eur. J. Biochem. 208, 651-657, 1992Purification and characterization of vanillyl-alcohol oxidase from Penicillium simplicissimum. A novel aromatic alcohol oxidase containing covalently bound FAD.DOI:10.1111/j.1432-1033.1992.tb17231.xPMID:1396672Mattevi, A.Fraaije, M.W.Mozzarelli, A.Olivi, L.Coda, A.van Berkel, W.J.Structure 5, 907-920, 1997Crystal structures and inhibitor binding in the octameric flavoenzyme vanillyl-alcohol oxidase: the shape of the active-site cavity controls substrate specificity.DOI:10.1016/S0969-2126(97)00245-1PMID:9261083Mattevi, A.submitted to the Protein Data Bank, April 1997Structure of the octameric flavoenzyme vanillyl-alcohol oxidase.PDB:1VAOX-ray diffraction, 2.50 angstromsFraaije, M.W.van den Heuvel, R.H.van Berkel, W.J.Mattevi, A.J. Biol. Chem. 274, 35514-35520, 1999Covalent flavinylation is essential for efficient redox catalysis in vanillyl-alcohol oxidase.DOI:10.1074/jbc.274.50.35514PMID:10585424Hao, H.X.Khalimonchuk, O.Schraders, M.Dephoure, N.Bayley, J.P.Kunst, H.Devilee, P.Cremers, C.W.Schiffman, J.D.Bentz, B.G.Gygi, S.P.Winge, D.R.Kremer, H.Rutter, J.Science 325, 1139-1142, 2009SDH5, a gene required for flavination of succinate dehydrogenase, is mutated in paraganglioma.DOI:10.1126/science.1175689PMID:19628817genetic, mutant and interaction analysis in yeast and human; directed mutagenesis in yeastThe arrangement of the attachment has not been completely established in some cases.The keyword "phosphoprotein" is not used with flavin modifications linked through the flavin.apo mitochondrial succinate dehydrogenase [ubiquinone] flavoprotein subunit---FAD ligase sdh5 (EC 6.3.4.-)HGO:0018297PSI-MOD:00226*phosphoproteinFADflavoproteinMOD_RES Tele-8alpha-FAD histidineAA022210-Nov-199510-Nov-199531-Jul-2009omega-N-phospho-L-arginine(2S)-2-amino-5-(N'-phosphonocarbamimidamido)pentanoic acidalpha-amino-delta-phosphonoguanidinovaleric acidN(gamma)-phosphoarginineN(omega)-phosphono-L-arginineN5-[imino(phosphonoamino)methyl]-L-ornithinephosphoarginine(2S)-2-amino-5-([amino(phosphonoamino)methylidene]amino)pentanoic acidCAS:1189-11-3C 6 H 13 N 4 O 4 P 1236.17236.067442C 0 H 1 N 0 O 3 P 179.9879.966331Wakim, B.T.Aswad, G.D.J. Biol. Chem. 269, 2722-2727, 1994Ca(2+)-calmodulin-dependent phosphorylation of arginine in histone 3 by a nuclear kinase from mouse leukemia cells.PMID:8300603chemical characterizationFuhrmann, J.Schmidt, A.Spiess, S.Lehner, A.Turgay, K.Mechtler, K.Charpentier, E.Clausen, T.Science 324, 1323-1327, 2009McsB is a protein arginine kinase that phosphorylates and inhibits the heat-shock regulator CtsR.DOI:10.1126/science.1170088PMID:19498169mass spectrometric and (31)P-NMR identification; in Bacillus stearothermophilus McsB is identified as a protein-arginine kinase acting on CtsRhistone-arginine kinase (EC 2.7.3.-)protein-arginine kinase (EC 2.7.3.-)RGO:0018109PSI-MOD:00227phosphoproteinMOD_RES PhosphoarginineAA022305-Jan-199605-Jan-199631-Mar-2012S-(diphytanylglyceryl)-L-cysteineS-archaeol cysteineS-[2',3'-bis(phytanyloxy)propyl]cysteine(2R)-2-amino-3-([(2S)-2,3-bis(3,7,11,15-tetramethylhexadecanyloxy)propyl]sulfanyl)propanoic acidC 46 H 91 N 1 O 3 S 1738.30737.671967C 43 H 86 N 0 O 2 S 0635.16634.662782Mattar, S.Scharf, B.Kent, S.B.H.Rodewald, K.Oesterhelt, D.Engelhard, M.J. Biol. Chem. 269, 14939-14945, 1994The primary structure of halocyanin, an archaeal blue copper protein, predicts a lipid anchor for membrane fixation.PMID:8195126Sagami, H.Kikuchi, A.Ogura, K.J. Biol. Chem. 270, 14851-14854, 1995A novel type of protein modification by isoprenoid-derived materials. Diphytanylglycerylated proteins in Halobacteria.DOI:10.1074/jbc.270.25.14851PMID:7797461chromatographic, mass spectrometric and (1)H-NMR identificationThe stereochemistry of the glycerol has not been determined. The S form is shown.Cincidental to RESID:AA0043GO:0018115GO:0042050PSI-MOD:00228PSI-MOD:00897lipoproteinthioether bondLIPID S-archaeol cysteineAA022426-Jan-199626-Jan-199630-Apr-2010alpha-1-microglobulin-Ig alpha complex chromophoreC 6 H 8 N 2 O 2 S 2 +204.26 +204.002720 +C 0 H -2 N 0 O 0 S 0 +-2.02 +-2.015650 +Calero, M.Escribano, J.Grubb, A.Méndez, E.J. Biol. Chem. 269, 384-389, 1994Location of a novel type of interpolypeptide chain linkage in the human protein HC-IgA complex (HC-IgA) and identification of a heterogeneous chromophore associated with the complex.PMID:7506257Åkerström, B.Bratt, T.Enghild, J.J.FEBS Lett. 362, 50-54, 1995Formation of the α1-microglobulin chromophore in mammalian and insect cells: a novel post-translational mechanism?DOI:10.1016/0014-5793(95)00206-OPMID:7535251Åkerström, B.Lögdberg, L.Berggård, T.Osmark, P.Lindqvist, A.Biochim. Biophys. Acta 1482, 172-184, 2000α1-Microglobulin: a yellow-brown lipocalin.DOI:10.1016/S0167-4838(00)00157-6PMID:11058759Allhorn, M.Berggård, T.Nordberg, J.Olsson, M.L.Åkerström, B.Blood 99, 1894-1901, 2002Processing of the lipocalin α1-microglobulin by hemoglobin induces heme-binding and heme-degradation properties.DOI:10.1182/blood.V99.6.1894PMID:11877257The structure of the chromophore is not known. It is probably heterogeneous, and involves two cysteines in thioether bonds.C, Ccross-link 2GO:0019923PSI-MOD:00229chromoproteinthioether bondBINDING Multimeric 3-hydroxykynurenine chromophore (covalent)AA022508-Mar-199616-Jul-199820-Apr-2012bis-L-cysteinyl bis-L-histidino diiron disulfideRieske iron-sulfur cofactordi-mu-sulfido(bis-S-cysteinyliron)(bis-N3'-histidinoiron)COMe:BIM000056PDBHET:FESC 18 Fe 2 H 20 N 8 O 4 S 42-652.34651.920007C 0 Fe 2 H -4 N 0 O 0 S 22-171.78171.783814Rieske, J.S.MacLennan, D.H.Coleman, R.Biochem. Biophys. Res. Commun. 15, 338-344, 1964Isolation and properties of an iron-protein from the (reduced coenzyme Q)-cytochrome C reductase complex of the respiratory chain.DOI:10.1016/0006-291X(64)90171-8elemental analysis; EPR spectrometryGurbiel, R.J.Batie, C.J.Sivaraja, M.True, A.E.Fee, J.A.Hoffman, B.M.Ballou, D.P.Biochemistry 28, 4861-4871, 1989Electron-nuclear double resonance spectroscopy of (15)N-enriched phthalate dioxygenase from Pseudomonas cepacia proves that two histidines are coordinated to the [2Fe-2S] Rieske-type clusters.DOI:10.1021/bi00437a051PMID:2765515(15)N-NMR characterizationIwata, S.Saynovits, M.Link, T.A.Michel, H.submitted to the Protein Data Bank, February 1996Structure of a water soluble fragment of the Rieske iron-sulfur protein of the bovine heart mitochondrial cytochrome bc1-complex.PDB:1RIEX-ray diffraction, 1.5 angstromsIwata, S.Lee, J.W.Okada, K.Lee, J.K.Iwata, M.Rasmussen, B.Link, T.A.Ramaswamy, S.Jap, B.K.Science 281, 64-71, 1998Complete structure of the 11-subunit bovine mitochondrial cytochrome bc1 complex.DOI:10.1126/science.281.5373.64PMID:9651245X-ray diffraction, 4.0 angstromsC, C, H, Hcross-link 4GO:0018299PSI-MOD:002302Fe-2SmetalloproteinRieske iron-sulfur proteinMETAL Iron-sulfur (2Fe-2S)METAL Iron-sulfur (2Fe-2S); via pros nitrogenAA022608-Mar-199608-Mar-199601-Mar-2013hexakis-L-cysteinyl hexairon hexasulfidehexa-mu3-sulfido-hexakis(S-cysteinyliron)prismane iron-sulfur cofactorhexa-mu3-sulfido-hexakis(cysteinato-kappaS)-hexaironC 18 Fe 6 H 24 N 6 O 6 S 121-1140.221139.450758C 0 Fe 6 H -6 N 0 O 0 S 61-521.38521.395649Moura, I.Tavares, P.Moura, J.J.Ravi, N.Huynh, B.H.Liu, M.Y.LeGall, J.J. Biol. Chem. 267, 4489-4496, 1992Direct spectroscopic evidence for the presence of a 6Fe cluster in an iron-sulfur protein isolated from Desulfovibrio desulfuricans (ATCC 27774).PMID:1311311EPR and Moessbauer spectrographic analysisPierik, A.J.Hagen, W.R.Dunham, W.R.Sands, R.H.Eur. J. Biochem. 206, 705-719, 1992Multi-frequency EPR and high-resolution Mössbauer spectroscopy of a putative [6Fe-6S] prismane-cluster-containing protein from Desulfovibrio vulgaris (Hildenborough).DOI:10.1111/j.1432-1033.1992.tb16977.xPMID:1318833EPR and Moessbauer spectrographic analysisThe prismane 6Fe-6S cluster is now thought not to exist. The structure determined by X-ray consists of a 4Fe-4S cluster, see RESID:AA0140, and a four iron cluster with mixed ligands, see RESID:AA0268.The formal charge for the hypothetical "as-isolated" ligated cluster was 1-.C, C, C, C, C, Ccross-link 6GO:0018300PSI-MOD:00231iron-sulfur proteinmetalloproteinNot availablethis dubious modification is not currently annotated in UniProt featuresAA022717-May-199617-May-199631-Dec-2013N6-(phospho-5'-adenosine)-L-lysine5'-adenylic-N6-L-lysineepsilon-5'-adenylic-L-lysineL-lysine monoanhydride with 5'-adenylic acidN(zeta)-5'-adenylic-L-lysineN6-L-lysine 5'-adenosine phosphoramidester(2S)-2-amino-6-(5'-adenosine phosphonamino)hexanoic acidCAS:35985-27-4PDBHET:AMPPDBHET:APKC 16 H 24 N 7 O 7 P 1457.38457.147483C 10 H 12 N 5 O 6 P 1329.21329.052520Gumport, R.I.Lehman, I.R.Proc. Natl. Acad. Sci. U.S.A. 68, 2559-2563, 1971Structure of the DNA ligase-adenylate intermediate: lysine (epsilon-amino)-linked adenosine monophosphoramidate.DOI:10.1073/pnas.68.10.2559PMID:4944632chemical characterizationThogersen, H.C.Morris, H.R.Rand, K.N.Gait, M.J.Eur. J. Biochem. 147, 325-329, 1985Location of the adenylylation site in T4 RNA ligase.DOI:10.1111/j.1432-1033.1985.tb08753.xPMID:3882425mass spectrometric characterizationCotner-Gohara, E.Kim, I.-K.Hammel, M.Tainer, J.A.Tomkinson, A.E.Ellenberger, T.Biochemistry 49, 6165-6176, 2010Human DNA ligase III recognizes DNA ends by dynamic switching between two DNA-bound states.DOI:10.1021/bi100503wPMID:20518483X-ray diffraction, 3.00 angstroms; authors' initials in the PubMed citation are correctedCotner-Gohara, E.Kim, I.-K.Hammel, M.Tainer, J.A.Tomkinson, A.E.Ellenberger, T.submitted to the Protein Data Bank, December 2009Human DNA ligase III recognizes DNA ends by dynamic switching between two DNA bound states.PDB:3L2PX-ray diffraction, 3.00 angstromsHansen, T.Albers, M.Hedberg, C.Sickmann, A.Proteomics 13, 955-963, 2013Adenylylation, MS, and proteomics --- Introducing a "new" modification to bottom-up proteomics.DOI:10.1002/pmic.201200344PMID:23335384mass spectrometric detection; analysis comparison; confirms that phosphodiester modifications, such as adenylylation, can be incorrectly identified as phosphorylations in some experimentsKGO:0018116GO:0018329PSI-MOD:00232phosphoproteinACT_SITE N6-AMP-lysine intermediateAA022817-May-199617-May-199631-May-2018N6-(phospho-5'-guanosine)-L-lysine5'-guanylic-N6-L-lysineepsilon-5'-guanylic-L-lysineL-lysine monoanhydride with 5'-guanylic acidlysine guanosine-5'-monophosphateN(zeta)-5'-guanylic-lysineN6-(5'-guanylyl)-lysine N6-L-lysine 5'-guanosine phosphoramidester(2S)-2-amino-6-(5'-guanosine phosphonamino)hexanoic acidChEBI:138294PDBHET:GPLC 16 H 24 N 7 O 8 P 1473.38473.142397C 10 H 12 N 5 O 7 P 1345.21345.047434Shuman, S.Hurwitz, J.Proc. Natl. Acad. Sci. U.S.A. 78, 187-191, 1981Mechanism of mRNA capping by vaccinia virus guanylyltransferase: characterization of an enzyme-guanylate intermediate.DOI:10.1073/pnas.78.1.187PMID:6264433chemical characterizationRoth, M.J.Hurwitz, J.J. Biol. Chem. 259, 13488-13494, 1984RNA capping by the vaccinia virus guanylyltransferase. Structure of enzyme-guanylate intermediate.PMID:6092377chemical characterizationKGO:0018261GO:0018330PSI-MOD:00233phosphoproteinACT_SITE N6-GMP-lysine intermediateAA022917-May-199617-May-199613-Sep-2013L-cysteine glutathione disulfidecysteinyl glutathioneL-gamma-glutamyl-L-cysteinyl-glycine (2-1')-disulfide with L-cysteineN-(N-gamma-glutamyl-cystinyl)-glycine(2S)-2-amino-3-((2S)-2-((4R)-4-amino-4-carboxyl-1-oxobutyl)amino-3-(carboxylmethyl)amino-3-oxo-propyl)dithio-propanoic acidCAS:13081-14-6ChEBI:21264PDBHET:GSHC 13 H 20 N 4 O 7 S 2408.44408.077341C 10 H 15 N 3 O 6 S 1305.30305.068156Bergenhem, N.Carlsson, U.Strid, L.Biochim. Biophys. Acta 871, 55-60, 1986The existence of glutathione and cysteine disulfide-linked to erythrocyte carbonic anhydrase from tiger shark.DOI:10.1016/0167-4838(86)90132-9PMID:3083866chemical characterizationDörmann, P.Börchers, T.Korf, U.Højrup, P.Roepstorff, P.Spener, F.J. Biol. Chem. 268, 16286-16292, 1993Amino acid exchange and covalent modification by cysteine and glutathione explain isoforms of fatty acid-binding protein occurring in bovine liver.PMID:8344916chemical characterizationDisulfide formation with free glutatione extracellularly is probably not enzymatically catalyzed.CGO:0018118PSI-MOD:00234disulfide bondglutathioneMOD_RES S-glutathionyl cysteineAA023017-May-199617-May-199601-Mar-2013S-nitrosyl-L-cysteineL-cysteine nitrite esterS-nitrosocysteine(2R)-2-amino-3-nitrososulfanyl-propanoic acidCAS:51209-75-7PDBHET:NOPDBHET:SNCC 3 H 4 N 2 O 2 S 1132.14131.999348C 0 H -1 N 1 O 1 S 029.0028.990164Jia, L.Bonaventura, C.Bonaventura, J.Stamler, J.S.Nature 380, 221-226, 1996S-Nitrosohaemoglobin: a dynamic activity of blood involved in vascular control.DOI:10.1038/380221a0PMID:8637569evidence is presented for the binding of nitrosonium to form S-nitrosocysteineMohr, S.Stamler, J.S.Bruene, B.J. Biol. Chem. 271, 4209-4214, 1996Posttranslational modification of glyceraldehyde-3-phosphate dehydrogenase by S-nitrosylation and subsequent NADH attachment.DOI:10.1074/jbc.271.8.4209PMID:8626764chemical characterizationChan, N.L.Rogers, P.H.Arnone, A.Biochemistry 37, 16459-16464, 1998Crystal structure of the S-nitroso form of liganded human hemoglobin.DOI:10.1021/bi9816711PMID:9843411X-ray diffraction, 1.8 angstromsSun, J.H.Xin, C.L.Eu, J.P.Stamler, J.S.Meissner, G.Proc. Natl. Acad. Sci. U.S.A. 98, 11158-11162, 2001Cysteine-3635 is responsible for skeletal muscle ryanodine receptor modulation by NO.DOI:10.1073/pnas.201289098PMID:11562475Doulias, P.T.Greene, J.L.Greco, T.M.Tenopoulou, M.Seeholzer, S.H.Dunbrack, R.L.Ischiropoulos, H.Proc. Natl. Acad. Sci. U.S.A. 107, 16958-16963, 2010Structural profiling of endogenous S-nitrosocysteine residues reveals unique features that accommodate diverse mechanisms for protein S-nitrosylation.DOI:10.1073/pnas.1008036107PMID:20837516Kornberg, M.D.Sen, N.Hara, M.R.Juluri, K.R.Nguyen, J.V.Snowman, A.M.Law, L.Hester, L.D.Snyder, S.H.Nature Cell Biol. 12, 1094-1100, 2010GAPDH mediates nitrosylation of nuclear proteins.DOI:10.1038/ncb2114PMID:20972425S-nitrosylated glyceraldehyde-3-phosphate dehydrogenase can transfer the nitrosyl group to cysteine residues of other proteins, acting as a carrier proteinThe reaction of nitrosonium (NO+) with cysteine residues may not be enzymatically catalyzed; the reaction of a cysteine residue with, or the reductive production of, nitric oxide (NO) has not been clarified.autocatalyticpeptidyl-cysteine S-nitrosyltransferase (EC 2.6.99.-)CGO:0018119PSI-MOD:00235MOD_RES S-nitrosocysteineAA023124-May-199624-May-199630-Sep-2008N4-(ADP-ribosyl)-L-asparagineN4-alpha-D-ribofuranosyl-L-asparagine 5'->5'-ester with adenosine 5'-(trihydrogen diphosphate)N4-[alpha-D-ribofuranoside 5'->5'-ester with adenosine 5'-(trihydrogen diphosphate)]-L-asparagine(S)-2-amino-4-([adenosine 5'-(trihydrogen diphosphate) 5'->5'-ester with alpha-D-ribofuranosyl]amino)-4-oxobutanoic acidC 19 H 27 N 7 O 15 P 2655.41655.104036C 15 H 21 N 5 O 13 P 2541.30541.061109Sekine, A.Fujiwara, M.Narumiya, S.J. Biol. Chem. 264, 8602-8605, 1989Asparagine residue in the rho gene product is the modification site for botulinum ADP-ribosyltransferase.PMID:2498316identification of ADP-ribosylation siteIt is not known whether botulinum exoenzyme C3 catalyzes formation of the alpha or beta isomer. The alpha form is presented.The keyword "phosphoprotein" is not used with toxin modification.NAD(P)+--asparagine ADP-ribosyltransferase (EC 2.4.2.-)NGO:0006471GO:0018122PSI-MOD:00236*phosphoproteinMOD_RES ADP-ribosylasparagineAA023216-Aug-199630-Sep-200931-May-20183-(methylthio)-L-aspartic acid3-carboxy-S-methyl-cysteine3-methylthio-aspartic acidbeta-methylthio-aspartic acid(2R,3Xi)-2-amino-3-(methylsulfanyl)butanedioic acidCAS:180420-54-6ChEBI:73619PDBHET:OTDC 5 H 7 N 1 O 3 S 1161.18161.014664C 1 H 2 N 0 O 0 S 146.0945.987721Kowalak, J.A.Walsh, K.A.Protein Sci. 5, 1625-1632, 1996beta-Methylthio-aspartic acid: Identification of a novel posttranslational modification in ribosomal protein S12 from Escherichia coli.DOI:10.1002/pro.5560050816PMID:8844851mass spectrometric identification; chemical characterizationStrader, M.B.VerBerkmoes, N.C.Tabb, D.L.Connelly, H.M.Barton, J.W.Bruce, B.D.Pelletier, D.A.Davison, B.H.Hettich, R.L.Larimer, F.W.Hurst, G.B.J. Proteome Res. 3, 965-978, 2004Characterization of the 70S Ribosome from Rhodopseudomonas palustris Using an Integrated "Top-Down" and "Bottom-Up" Mass Spectrometric Approach.DOI:10.1021/pr049940zPMID:15473684the capitalization of "Verberkmoes" in the PubMed citation is correctedAnton, B.P.Saleh, L.Benner, J.S.Raleigh, E.A.Kasif, S.Roberts, R.J.Proc. Natl. Acad. Sci. U.S.A. 105, 1826-1831, 2008RimO, a MiaB-like enzyme, methylthiolates the universally conserved Asp88 residue of ribosomal protein S12 in Escherichia coli.DOI:10.1073/pnas.0708608105PMID:18252828Demirci, H.Murphy IV, F.Murphy, E.Gregory, S.T.Dahlberg, A.E.Jogl, G.Nature Commun. 4, 1355, 2013A structural basis for streptomycin-induced misreading of the genetic code.DOI:10.1038/ncomms2346PMID:23322043X-ray diffraction, 3.60 angstroms; a structure was built incorporating the (2R,3S) model; the suffix of F. Murphy IV in the PubMed citation is correctedDemirci, H.Murphy IV, F.Murphy, E.Gregory, S.T.Dahlberg, A.E.Jogl, G.submitted to the Protein Data Bank, February 2012Crystal structure of the apo 30s ribosomal subunit from Thermus thermophilus (HB8).PDB:4DR1X-ray diffraction, 3.60 angstromsArragain, S.Garcia-Serres, R.Blondin, G.Douki, T.Clemancey, M.Latour, J.M.Forouhar, F.Neely, H.Montelione, G.T.Hunt, J.F.Mulliez, E.Fontecave, M.Atta, M.J. Biol. Chem. 285, 5792-5801, 2010Post-translational modification of ribosomal proteins: structural and functional characterization of RimO from Thermotoga maritima, a radical S-adenosylmethionine methylthiotransferase.DOI:10.1074/jbc.M109.065516PMID:20007320the modification enzyme contains a [4Fe-4S-AdoMet] radical-SAM cluster and an additional [4Fe-4S] cluster with 3 cysteine ligands; double modification can occur with the model substrateForouhar, F.Arragain, S.Atta, M.Gambarelli, S.Mouesca, J.M.Hussain, M.Xiao, R.Kieffer-Jaquinod, S.Seetharaman, J.Acton, T.B.Montelione, G.T.Mulliez, E.Hunt, J.F.Fontecave, M.Nature Chem. Biol. 9, 333-338, 2013Two Fe-S clusters catalyze sulfur insertion by radical-SAM methylthiotransferases.DOI:10.1038/nchembio.1229PMID:23542644enzymatic mechanism of modification; the enzyme contains 3 to 5 additional exogenous sulfur atoms connecting the iron-sulfur clusters; evidence that first a hydrogen radical is abstracted, a sulfur atom is inserted, then a methyl radical is transferred; double modification can occur with a model substrateThe stereochemistry for the second chiral center has not been resolved. The (2R,3S) form is shown.beta-Methylthioaspartic acid probably occurs uniquely in ribosomal protein S12. Althouh the aspartic acid is invariant, the modification is not required for activity.ribosomal protein S12 methylthiotransferase RimO (EC 2.-.-.-)DGO:0018339PSI-MOD:00237thioether bondMOD_RES 3-methylthioaspartic acidAA023306-Sep-199606-Sep-199631-Jul-20092'-(L-lys-N6-yl)-L-4',5'-topaquinone2'-(L-lysine)-L-tyrosyl-4',5'-quinoneLTQlysyl oxidase cofactor1-[(S)-5-amino-5-carboxypentyl]amino-2-[(S)-2-amino-2-carboxyethyl]-2,6-cyclohexadien-4,5-dioneCOMe:BIM000263C 15 H 17 N 3 O 4303.32303.121906C 0 H -4 N 0 O 111.9711.963614Wang, S.X.Mure, M.Medzihradszky, K.F.Burlingame, A.L.Brown, D.E.Dooley, D.M.Smith, A.J.Kagan, H.M.Klinman, J.P.Science 273, 1078-1084, 1996A crosslinked cofactor in lysyl oxidase: redox function for amino acid side chains.DOI:10.1126/science.273.5278.1078PMID:8688089mass spectrometric, raman spectrographic, visible/UV spectrographic, and chemical characterization; phenylhydrazine derivativeThe linkage between the two components has not been established with certainty. The relation of this cofactor to the copper binding site has not been established.K, Ycross-link 2secondary to RESID:AA0147GO:0018124PSI-MOD:00238quinoproteinCROSSLNK Lysine tyrosylquinone (Lys-Tyr)CROSSLNK Lysine tyrosylquinone (Tyr-Lys)AA023406-Sep-199606-Sep-199631-May-2018S-methyl-L-cysteineL-3-(methylthio)alanine(R)-2-amino-3-(methylsulfanyl)propanoic acidCAS:1187-84-4ChEBI:82612PDBHET:SMCC 4 H 7 N 1 O 1 S 1117.17117.024835C 1 H 2 N 0 O 0 S 014.0314.015650Gonzalez, J.C.Banerjee, R.V.Huang, S.Sumner, J.S.Matthews, R.G.Biochemistry 31, 6045-6056, 1992Comparison of cobalamin-independent and cobalamin-dependent methionine synthases from Escherichia coli: two solutions to the same chemical problem.DOI:10.1021/bi00141a013PMID:1339288radioisotope labelingSelmer, T.Kahnt, J.Goubeaud, M.Shima, S.Grabarse, W.Ermler, U.Thauer, R.K.J. Biol. Chem. 275, 3755-3760, 2000The biosynthesis of methylated amino acids in the active site region of methyl-coenzyme M reductase.DOI:10.1074/jbc.275.6.3755PMID:10660523mass spectrometric characterization; in methyl-coenzyme M reductase the biosynthetic origin of the methyl group is S-adenosyl methionine, not methyl-coenzyme MTaylor, T.C.Backlund, A.Bjorhall, K.Spreitzer, R.J.Andersson, I.J. Biol. Chem. 276, 48159-48164, 2001First crystal structure of Rubisco from a green alga, Chlamydomonas reinhardtii.DOI:10.1074/jbc.M107765200PMID:11641402X-ray diffraction, 1.40 angstromsTaylor, T.C.Spreitzer, R.J.Andersson, I.submitted to the Protein Data Bank, August 2001Rubisco from Chlamydomonas reinhardtii.PDB:1GK8X-ray diffraction, 1.40 angstromsGrove, T.L.Benner, J.S.Radle, M.I.Ahlum, J.H.Landgraf, B.J.Krebs, C.Booker, S.J.Science 332, 604-607, 2011A radically different mechanism for S-adenosylmethionine-dependent methyltransferases.DOI:10.1126/science.1200877PMID:21415317isotope labeling mass spectrometric detectionBoal, A.K.Grove, T.L.McLaughlin, M.I.Yennawar, N.H.Booker, S.J.Rosenzweig, A.C.Science 332, 1089-1092, 2011Structural basis for methyl transfer by a radical SAM enzyme.DOI:10.1126/science.1205358PMID:21527678X-ray diffraction, 2.05 angstroms; an S-methylcysteine is generated in the enzyme, converted to a radical, and transfered as a methyl radicalBoal, A.K.Grove, T.L.McLaughlin, M.I.Yennawar, N.H.Booker, S.J.Rosenzweig, A.C.submitted to the Protein Data Bank, April 2005X-ray structure of RlmN from Escherichia coli in complex with S-adenosylmethionine.PDB:3RFAX-ray diffraction, 2.05 angstroms; trapped S-methyl-cysteine intermediateFor methylated--DNA--[protein]-cysteine S-methyltransferase (EC 2.2.1.63), the Enzyme Commission acknowledges that "This enzyme catalyses only one turnover and therefore is not strictly catalytic."autocatalyticmethylated--DNA--[protein]-cysteine S-methyltransferase (EC 2.2.1.63)protein-cysteine methyltransferase, NleE (EC 2.2.1.-)CGO:0018125GO:0018320PSI-MOD:00239methylated amino acidthioether bondACT_SITE S-methylcysteine intermediateMOD_RES S-methylcysteineAA023508-Nov-199608-Nov-199631-May-20184-hydroxy-L-lysinealpha,epsilon-diamino-gamma-hydroxycaproic acidL-threo-gamma-hydroxylysine(2S,4R)-2,6-diamino-4-hydroxyhexanoic acidCAS:60594-62-9ChEBI:86271C 6 H 12 N 2 O 2144.17144.089878C 0 H 0 N 0 O 116.0015.994915Sidler, W.Kumpf, B.Suter, F.Morisset, W.Wehrmeyer, W.Zuber, H.Biol. Chem. Hoppe-Seyler 366, 233-244, 1985Structural studies on cryptomonad biliprotein subunits. Two different alpha-subunits in Chroomonas phycocyanin-645 and Cryptomonas phycoerythrin-545.PMID:4005040chromatographic evidence with no comparison to 5-hydroxylysine; the stereochemistry was not establishedFeng, T.Yamamoto, A.Wilkins, S.E.Sokolova, E.Yates, L.A.Münzel, M.Singh, P.Hopkinson, R.J.Fischer, R.Cockman, M.E.Shelley, J.Trudgian, D.C.Schödel, J.McCullagh, J.S.Ge, W.Kessler, B.M.Gilbert, R.J.Frolova, L.Y.Alkalaeva, E.Ratcliffe, P.J.Schofield, C.J.Coleman, M.L.Mol. Cell 53, 645-654, 2014Optimal translational termination requires C4 lysyl hydroxylation of eRF1.DOI:10.1016/j.molcel.2013.12.028PMID:24486019chromatographic and mass spectrometric identification5-Hydroxy-L-lysine (see RESID:AA0028) was found at a homologous position in the closely related species Rhodomonas CS24. See also RESID:AA0370.The (2S,4R) diastereomer is shown.[protein]-lysine 4-dioxygenase, Jmjd4 (EC 1.14.11.-)KGO:0018396PSI-MOD:00240hydroxylationNot availablethis modification is not currently annotated in UniProt featuresAA023608-Nov-199622-Nov-199630-Sep-2013N4-hydroxymethyl-L-asparagine2-amino-N4-hydroxymethylbutanediamic acidbeta-hydroxymethylasparagineN(gamma)-hydroxymethylasparagineN4-hydroxymethylasparagine(2S)-2-amino-4-[(hydroxymethyl)amino]-4-oxobutanoic acidC 5 H 8 N 2 O 3144.13144.053492C 1 H 2 N 0 O 130.0330.010565Minami, Y.Yamada, F.Hase, T.Matsubara, H.Murakami, A.Fujita, Y.Takao, T.Shimonishi, Y.FEBS Lett. 191, 216-220, 1985Amino acid sequences of allophycocyanin alpha- and beta-subunits isolated from Anabaena cylindrica.DOI:10.1016/0014-5793(85)80011-9chromatographic and mass spectrometric characterizationN4-methyl-L-asparagine (see RESID:AA0070) was found at a homologous position in the closely related species Anabaena variabilis. Since the peptide containing this modification was obtained by enzymatic cleavage, not cyanogen bromide cleavage, it could have experienced oxidation of the following methionine residue, leading to the erroneous attribution of a mass of 29 for the modification rather than 14.NGO:0018311PSI-MOD:00241hydroxylationmethylated amino acidNot availablethis dubious modification is not currently annotated in UniProt featuresAA023722-Nov-199622-Nov-199630-Sep-2008O-(ADP-ribosyl)-L-serineO3-(ADP-ribosyl)-L-serineO3-alpha-D-ribofuranosyl-L-serine 5'->5'-ester with adenosine 5'-(trihydrogen diphosphate)O3-[alpha-D-ribofuranoside 5'->5'-ester with adenosine 5'-(trihydrogen diphosphate)]-L-serine(S)-2-amino-3-([adenosine 5'-(trihydrogen diphosphate) 5'->5'-ester with alpha-D-ribofuranosyl]oxy)-propanoic acidC 18 H 26 N 6 O 15 P 2628.38628.093137C 15 H 21 N 5 O 13 P 2541.30541.061109Bokoch, G.M.Parkos, C.A.Mumby, S.M.J. Biol. Chem. 263, 16744-16749, 1988Purification and characterization of the 22,000-Dalton GTP-binding protein substrate for ADP-ribosylation by botulinum toxin, G-22K.PMID:3141412ADP-ribosylation detected; neither the residue nor the location is determinedIt is not known whether botulinum exoenzyme C3 catalyzes formation of the alpha or beta isomer. The alpha form is presented.The keyword "phosphoprotein" is not used with toxin modification.NAD(P)+--serine ADP-ribosyltransferase (EC 2.4.2.-)SGO:0006471GO:0018312PSI-MOD:00242*phosphoproteinMOD_RES ADP-ribosylserineAA023806-Dec-199606-Dec-199625-Feb-2011L-cysteine oxazole-4-carboxylic acid2-(1-azanyl-2-sulfanylethyl)-4-oxazolecarboxylic acid2-[(1R)-1-amino-2-sulfanylethyl]-1,3-oxazole-4-carboxylic acidC 6 H 6 N 2 O 2 S 1170.19170.014998C 0 H -4 N 0 O -1 S 0-20.03-20.026215Li, Y.M.Milne, J.C.Madison, L.L.Kolter, R.Walsh, C.T.Science 274, 1188-1193, 1996From peptide precursors to oxazole and thiazole-containing peptide antibiotics: microcin B17 synthase.DOI:10.1126/science.274.5290.1188PMID:8895467mass spectrometric identification of peptides and biosynthetic intermediatesYorgey, P.Lee, J.Koerdel, J.Vivas, E.Warner, P.Jebaratnam, D.Kolter, R.Proc. Natl. Acad. Sci. U.S.A. 91, 4519-4523, 1994Posttranslational modifications in microcin B17 define an additional class of DNA gyrase inhibitor.DOI:10.1073/pnas.91.10.4519PMID:8183941(1)H-NMR identificationFormed by the condensation of a serine hydroxyl with the carbonyl of the preceding residue and alpha-beta dehydrogenation.peptidyl-serine cyclase (EC 4.2.1.-)peptidyl-oxazoline dehydrogenase (EC 1.3.-.-)C, Scross-link 1GO:0018132PSI-MOD:00243oxazole/thiazole ringCROSSLNK Oxazole-4-carboxylic acid (Cys-Ser)AA023906-Dec-199606-Dec-199625-Feb-2011L-cysteine oxazoline-4-carboxylic acid2-[1-azanyl-2-sulfanylethyl]-4,5-dihydro-1,3-oxazole-4-carboxylic acid(4S)-2-[(1R)-1-amino-2-sulfanylethyl]-4,5-dihydro-1,3-oxazole-4-carboxylic acidC 6 H 8 N 2 O 2 S 1172.20172.030649C 0 H -2 N 0 O -1 S 0-18.02-18.010565Kettenring, J.Colombo, L.Ferrari, P.Tavecchia, P.Nebuloni, M.Vekey, K.Gallo, G.G.Selva, E.J. Antibiot. 44, 702-715, 1991Antibiotic GE2270 A: a novel inhibitor of bacterial protein synthesis. II. Structure elucidation.PMID:1880060mass spectrometric, (1)H-NMR, (13)C-NMR, and IR identificationTavecchia, P.Gentili, P.Kurz, M.Sottani, C.Bonfichi, R.Lociuro, S.Selva, E.J. Antibiot. 47, 1564-1567, 1994Revised structure of the antibiotic GE 2270A.PMID:7844053Heffron, S.E.Jurnak, F.Biochemistry 39, 37-45, 2000Structure of an EF-Tu complex with a thiazolyl peptide antibiotic determined at 2.35 A resolution: atomic basis for GE2270A inhibition of EF-Tu.DOI:10.1021/bi9913597PMID:10625477Heffron, S.E.Jurnak, F.submitted to the Protein Data Bank, October 1999Crystal structure of elongation factor, Tu (EF-Tu-MGGDP) complexed with GE2270A, a thiazolyl peptide antibiotic.PDB:1D8TX-ray diffraction, 2.35 angstromsFormed by the condensation of a serine hydroxyl with the carbonyl of the preceding residue.peptidyl-serine cyclase (EC 4.2.1.-)C, Scross-link 1GO:0018133PSI-MOD:00244oxazole/thiazole ringCROSSLNK Oxazoline-4-carboxylic acid (Cys-Ser)AA024006-Dec-199606-Dec-199625-Feb-2011glycine oxazole-4-carboxylic acid2-azanylmethyl-1,3-oxazole-4-carboxylic acid2-aminomethyl-1,3-oxazole-4-carboxylic acidC 5 H 4 N 2 O 2124.10124.027277C 0 H -4 N 0 O -1-20.03-20.026215Li, Y.M.Milne, J.C.Madison, L.L.Kolter, R.Walsh, C.T.Science 274, 1188-1193, 1996From peptide precursors to oxazole and thiazole-containing peptide antibiotics: microcin B17 synthase.DOI:10.1126/science.274.5290.1188PMID:8895467mass spectrometric identification of peptides and biosynthetic intermediatesYorgey, P.Lee, J.Koerdel, J.Vivas, E.Warner, P.Jebaratnam, D.Kolter, R.Proc. Natl. Acad. Sci. U.S.A. 91, 4519-4523, 1994Posttranslational modifications in microcin B17 define an additional class of DNA gyrase inhibitor.DOI:10.1073/pnas.91.10.4519PMID:8183941(1)H-NMR identificationFormed by the condensation of a serine hydroxyl with the carbonyl of the preceding residue and alpha-beta dehydrogenation.peptidyl-serine cyclase (EC 4.2.1.-)peptidyl-oxazoline dehydrogenase (EC 1.3.-.-)G, Scross-link 1GO:0018134PSI-MOD:00245oxazole/thiazole ringCROSSLNK Oxazole-4-carboxylic acid (Gly-Ser)AA024106-Dec-199606-Dec-199630-Sep-2011glycine thiazole-4-carboxylic acid2-(azanylmethyl)-1,3-thiazole-4-carboxylic acid2-(aminomethyl)-1,3-thiazole-4-carboxylic acidCAS:25438-22-6ChEBI:21276PDBHET:BB9C 5 H 4 N 2 O 1 S 1140.16140.004434C 0 H -4 N 0 O -1 S 0-20.03-20.026215Li, Y.M.Milne, J.C.Madison, L.L.Kolter, R.Walsh, C.T.Science 274, 1188-1193, 1996From peptide precursors to oxazole and thiazole-containing peptide antibiotics: microcin B17 synthase.DOI:10.1126/science.274.5290.1188PMID:8895467mass spectrometric identification of peptides and biosynthetic intermediatesYorgey, P.Lee, J.Koerdel, J.Vivas, E.Warner, P.Jebaratnam, D.Kolter, R.Proc. Natl. Acad. Sci. U.S.A. 91, 4519-4523, 1994Posttranslational modifications in microcin B17 define an additional class of DNA gyrase inhibitor.DOI:10.1073/pnas.91.10.4519PMID:8183941(1)H-NMR identificationFormed by the condensation of a cysteine thiol with the carbonyl of the preceding residue and alpha-beta dehydrogenation.peptidyl-cysteine cyclase (EC 4.2.1.-)peptidyl-thiazoline dehydrogenase (EC 1.3.-.-)C, Gcross-link 1GO:0018137PSI-MOD:00246oxazole/thiazole ringthioether bondCROSSLNK Thiazole-4-carboxylic acid (Gly-Cys)AA024206-Dec-199606-Dec-199630-Sep-2011L-serine thiazole-4-carboxylic acid2-[1-azanyl-2-hydroxyethyl]-1,3-thiazole-4-carboxylic acid2-[(1S)-1-amino-2-hydroxyethyl]-1,3-thiazole-4-carboxylic acidPDBHET:BB9C 6 H 6 N 2 O 2 S 1170.19170.014998C 0 H -4 N 0 O -1 S 0-20.03-20.026215Li, Y.M.Milne, J.C.Madison, L.L.Kolter, R.Walsh, C.T.Science 274, 1188-1193, 1996From peptide precursors to oxazole and thiazole-containing peptide antibiotics: microcin B17 synthase.DOI:10.1126/science.274.5290.1188PMID:8895467mass spectrometric identification of peptides and biosynthetic intermediatesYorgey, P.Lee, J.Koerdel, J.Vivas, E.Warner, P.Jebaratnam, D.Kolter, R.Proc. Natl. Acad. Sci. U.S.A. 91, 4519-4523, 1994Posttranslational modifications in microcin B17 define an additional class of DNA gyrase inhibitor.DOI:10.1073/pnas.91.10.4519PMID:8183941(1)H-NMR identificationFormed by the condensation of a cysteine thiol with the carbonyl of the preceding residue and alpha-beta dehydrogenation.peptidyl-cysteine cyclase (EC 4.2.1.-)peptidyl-thiazoline dehydrogenase (EC 1.3.-.-)C, Scross-link 1GO:0018138PSI-MOD:00247oxazole/thiazole ringthioether bondCROSSLNK Thiazole-4-carboxylic acid (Ser-Cys)AA024306-Dec-199606-Dec-199630-Sep-2011L-phenylalanine thiazole-4-carboxylic acid2-[1-azanyl-2-phenylethyl]-1,3-thiazole-4-carboxylic acid2-[(1S)-1-amino-2-phenylethyl]-1,3-thiazole-4-carboxylic acidPDBHET:BB9C 12 H 10 N 2 O 1 S 1230.29230.051384C 0 H -4 N 0 O -1 S 0-20.03-20.026215Kettenring, J.Colombo, L.Ferrari, P.Tavecchia, P.Nebuloni, M.Vekey, K.Gallo, G.G.Selva, E.J. Antibiot. 44, 702-715, 1991Antibiotic GE2270 A: a novel inhibitor of bacterial protein synthesis. II. Structure elucidation.PMID:1880060mass spectrometric, (1)H-NMR, (13)C-NMR, and IR identificationTavecchia, P.Gentili, P.Kurz, M.Sottani, C.Bonfichi, R.Lociuro, S.Selva, E.J. Antibiot. 47, 1564-1567, 1994Revised structure of the antibiotic GE 2270A.PMID:7844053Heffron, S.E.Jurnak, F.Biochemistry 39, 37-45, 2000Structure of an EF-Tu complex with a thiazolyl peptide antibiotic determined at 2.35 A resolution: atomic basis for GE2270A inhibition of EF-Tu.DOI:10.1021/bi9913597PMID:10625477Heffron, S.E.Jurnak, F.submitted to the Protein Data Bank, October 1999Crystal structure of elongation factor, Tu (EF-Tu-MGGDP) complexed with GE2270A, a thiazolyl peptide antibiotic.PDB:1D8TX-ray diffraction, 2.35 angstromsFormed by the condensation of a cysteine thiol with the carbonyl of the preceding residue and alpha-beta dehydrogenation.peptidyl-cysteine cyclase (EC 4.2.1.-)peptidyl-thiazoline dehydrogenase (EC 1.3.-.-)C, Fcross-link 1GO:0018139PSI-MOD:00248oxazole/thiazole ringthioether bondCROSSLNK Thiazole-4-carboxylic acid (Phe-Cys)AA024406-Dec-199606-Dec-199630-Sep-2011L-cysteine thiazole-4-carboxylic acid2-[1-azanyl-2-sulfanylethyl]-1,3-thiazole-4-carboxylic acid2-[(1S)-1-amino-2-sulfanylethyl]-1,3-thiazole-4-carboxylic acidPDBHET:BB9C 6 H 6 N 2 O 1 S 2186.25185.992155C 0 H -4 N 0 O -1 S 0-20.03-20.026215Kettenring, J.Colombo, L.Ferrari, P.Tavecchia, P.Nebuloni, M.Vekey, K.Gallo, G.G.Selva, E.J. Antibiot. 44, 702-715, 1991Antibiotic GE2270 A: a novel inhibitor of bacterial protein synthesis. II. Structure elucidation.PMID:1880060mass spectrometric, (1)H-NMR, (13)C-NMR, and IR identificationTavecchia, P.Gentili, P.Kurz, M.Sottani, C.Bonfichi, R.Lociuro, S.Selva, E.J. Antibiot. 47, 1564-1567, 1994Revised structure of the antibiotic GE 2270A.PMID:7844053Heffron, S.E.Jurnak, F.Biochemistry 39, 37-45, 2000Structure of an EF-Tu complex with a thiazolyl peptide antibiotic determined at 2.35 A resolution: atomic basis for GE2270A inhibition of EF-Tu.DOI:10.1021/bi9913597PMID:10625477Heffron, S.E.Jurnak, F.submitted to the Protein Data Bank, October 1999Crystal structure of elongation factor, Tu (EF-Tu-MGGDP) complexed with GE2270A, a thiazolyl peptide antibiotic.PDB:1D8TX-ray diffraction, 2.35 angstromsFormed by the condensation of a cysteine thiol with the carbonyl of the preceding residue and alpha-beta dehydrogenation.The first cysteine may be condensed on the carbonyl of the residue preceding it, forming a 2,4'-bithiazole structure.peptidyl-cysteine cyclase (EC 4.2.1.-)peptidyl-thiazoline dehydrogenase (EC 1.3.-.-)C, Ccross-link 1GO:0018140PSI-MOD:00249oxazole/thiazole ringthioether bondCROSSLNK Thiazole-4-carboxylic acid (Cys-Cys)AA024506-Dec-199606-Dec-199625-Feb-2011L-lysine thiazole-4-carboxylic acid2-[1,5-bis(azanyl)pentyl]-1,3-thiazole-4-carboxylic acid2-[(1S)-1,5-diaminopentyl]-1,3-thiazole-4-carboxylic acidC 9 H 13 N 3 O 1 S 1211.28211.077933C 0 H -4 N 0 O -1 S 0-20.03-20.026215Kettenring, J.Colombo, L.Ferrari, P.Tavecchia, P.Nebuloni, M.Vekey, K.Gallo, G.G.Selva, E.J. Antibiot. 44, 702-715, 1991Antibiotic GE2270 A: a novel inhibitor of bacterial protein synthesis. II. Structure elucidation.PMID:1880060mass spectrometric, (1)H-NMR, (13)C-NMR, and IR identificationLysine is now thought not to be encoded in the peptide sequence modified to produce GE2270. See RESID:AA0470.C, Kcross-link 1GO:0018141PSI-MOD:00250oxazole/thiazole ringthioether bondNot availablethis dubious modification is not currently annotated in UniProt featuresAA024628-Feb-199728-Feb-199730-Apr-2010O-(phospho-5'-DNA)-L-serineO3-(phospho-5'-DNA)-L-serineO3-L-serine 5'-DNA phosphodiester(S)-2-amino-3-(5'-deoxyribonucleic acid phosphonoxy)propanoic acidC 3 H 5 N 1 O 5 P 1 +166.05 +165.990534 +C 0 H 0 N 0 O 3 P 1 +78.97 +78.958505 +Desiderio, S.V.Kelly Jr., T.J.J. Mol. Biol. 145, 319-337, 1981Structure of the linkage between adenovirus DNA and the 55,000 molecular weight terminal protein.DOI:10.1016/0022-2836(81)90208-4PMID:7265205chromatographic detection; chemical characterizationSmart, J.E.Stillman, B.W.J. Biol. Chem. 257, 13499-13506, 1982Adenovirus terminal protein precursor. Partial amino acid sequence and the site of covalent linkage to virus DNA.PMID:7142163chromatographic detection; chemical characterizationThe keyword "phosphoprotein" is not used with polynucleotide-linked intermediate modifications.SGO:0018145PSI-MOD:00251*phosphoproteingenome-linked proteinACT_SITE O-(5'-phospho-DNA)-serine intermediateMOD_RES O-(5'-phospho-DNA)-serineAA024721-Mar-199721-Mar-199731-May-2018keratan sulfate D-glucuronosyl-D-galactosyl-D-galactosyl-D-xylosyl-L-threoninekeratosulfatepoly[beta-1,4-(2-acetamido-2-deoxy-6-sulfate D-glucosyl)-beta-1,3-D-galactosyl]-beta-1,4-D-glucopyranuronosyl-beta-1,3-D-galactosyl-beta-1,3-D-galactosyl-beta-1,4-D-xylosyl-beta-1,3-L-threonineC 4 H 6 N 1 O 2 +100.10 +100.039853 +C 0 H -1 N 0 O 0 +-1.01 +-1.007825 +Bourdon, M.A.Krusius, T.Campbell, S.Schwartz, N.B.Ruoslahti, E.Proc. Natl. Acad. Sci. U.S.A. 84, 3194-3198, 1987Identification and synthesis of a recognition signal for the attachment of glycosaminoglycans to proteins.DOI:10.1073/pnas.84.10.3194PMID:3472204Barry, F.P.Gaw, J.U.Young, C.N.Neame, P.J.Biochem. J. 286, 761-769, 1992Hyaluronan-binding region of aggrecan from pig laryngeal cartilage. Amino acid sequence, analysis of N-linked oligosaccharides and location of the keratan sulphate.PMID:1417734antibody detection during sequencingThe attachment polysaccharide has not been characterized for all forms of the chondroitin sulfate proteoglycans.See also RESID:AA0155, RESID:AA0399, RESID:AA0401, RESID:AA0403, RESID:AA0405, and RESID:AA0515 for other O-glycosylated threonines.protein xylosyltransferase (EC 2.4.2.26)xylosylprotein 4-beta-galactosyltransferase (EC 2.4.1.133)galactosylxylosylprotein 3-beta-galactosyltransferase (EC 2.4.1.134)galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase (EC 2.4.1.135)glucuronylgalactosylproteoglycan beta-1,4-N-acetylgalactosaminyltransferase (EC 2.4.1.174)chondroitin 4-sulfotransferase (EC 2.8.2.5)chondroitin 6-sulfotransferase (EC 2.8.2.17)TGO:0018146GO:0018405PSI-MOD:00252chondroitin sulfate proteoglycanglycoproteinkeratan sulfateCARBOHYD O-linked (Xyl...) (keratan sulfate) threonineAA024812-Sep-199707-Sep-200131-Mar-2013L-selenocysteinyl molybdenum bis(molybdopterin guanine dinucleotide)2-amino-5,6-dimercapto-7-methyl-3,7,8a,9-tetrahydro-8-oxa-1,3,9,10-tetraazaanthracen-4-one guanosine dinucleotideformate dehydrogenase selenocysteine molybdenum cofactorbis[8-amino-1a,2,4a,5,6,7,10-heptahydro-2-(trihydrogen diphosphate 5'-ester with guanosine)methyl-6-oxo-3,4-disulfanyl-pteridino[6,7-5,6]pyranoato-S3,S4]-selenocysteinyl-Se-molybdenumPDBHET:MGDPDBHET:MOC 43 H 52 Mo 1 N 21 O 27 P 4 S 4 Se 11722.071723.939410C 40 H 47 Mo 1 N 20 O 26 P 4 S 3 Se 11618.931620.930226C 40 H 47 Mo 1 N 20 O 26 P 4 S 4 Se 01572.021572.985775Axley, M.J.Grahame, D.A.Stadtman, T.C.J. Biol. Chem. 265, 18213-18218, 1990Escherichia coli formate-hydrogen lyase. Purification and properties of the selenium-dependent formate dehydrogenase component.PMID:2211698Gladyshev, V.N.Khangulov, S.V.Axley, M.J.Stadtman, T.C.Proc. Natl. Acad. Sci. U.S.A. 91, 7708-7711, 1994Coordination of selenium to molybdenum in formate dehydrogenase H from Escherichia coli.DOI:10.1073/pnas.91.16.7708PMID:8052647selenium coordination of cofactor by EPRSun, P.D.Boyington, J.C.submitted to the Protein Data Bank, January 1997Reduced form of formate dehydrogenase H from E. coli.PDB:1AA6X-ray diffraction, 2.3 angstroms, reduced formSun, P.D.Boyington, J.C.submitted to the Protein Data Bank, January 1997Oxidized form of Formate Dehydrogenase H from E. coli.PDB:1FDOX-ray diffraction, 2.8 angstroms, oxidized formBoyington, J.C.Gladyshev, V.N.Khangulov, S.V.Stadtman, T.C.Sun, P.D.Science 275, 1305-1308, 1997Crystal structure of formate dehydrogenase H: catalysis involving Mo, molybdopterin, selenocysteine, and an Fe4S4 cluster.DOI:10.1126/science.275.5304.1305PMID:9036855X-ray diffractionOne possible structure of a reduced form (+4H) is shown. The fully reduced form would be 1a,2,3,4,4a,5,6,7,10-nonahydro. The fully oxidized form would be 2,6,7-trihydro.Csecondary to RESID:AA0022GO:0018147PSI-MOD:01468UPSI-MOD:00253metalloproteinmolybdenummolybdopterinphosphoproteinseleniumselenocysteineMETAL Molybdenumthis UniProt feature has a structural misrepresentationAA024912-Sep-199712-Sep-199720-May-2011O4'-(phospho-5'-RNA)-L-tyrosineO4'-L-tyrosine 5'-RNA phosphodiester(S)-2-amino-3-[4-(5'-ribonucleic acid phosphonoxy)phenyl]propanoic acidC 9 H 10 N 1 O 5 P 1 +243.15 +243.029659 +C 0 H 1 N 0 O 3 P 1 +79.98 +79.966331 +Ambros, V.Baltimore, D.J. Biol. Chem. 253, 5263-5266, 1978Protein is linked to the 5' end of poliovirus RNA by a phosphodiester linkage to tyrosine.PMID:209034Rothberg, P.G.Harris, T.J.Nomoto, A.Wimmer, E.Proc. Natl. Acad. Sci. U.S.A. 75, 4868-4872, 1978O4-(5'-Uridylyl)tyrosine is the bond between the genome-linked protein and the RNA of poliovirus.DOI:10.1038/291547a0PMID:217003chemical characterizationKitamura, N.Semler, B.L.Rothberg, P.G.Larsen, G.R.Adler, C.J.Dorner, A.J.Emini, E.A.Hanecak, R.Lee, J.J.van der Werf, S.Anderson, C.W.Wimmer, E.Nature 291, 547-553, 1981Primary structure, gene organization and polypeptide expression of poliovirus RNA.DOI:10.1038/291547a0PMID:6264310protein sequenceMurphy, J.F.Rychlik, W.Rhoads, R.E.Hunt, A.G.Shaw, J.G.J. Virol. 65, 511-513, 1991A tyrosine residue in the small nuclear inclusion protein of tobacco vein mottling virus links the VPg to the viral RNA.PMID:1702164chemical characterizationOlspert, A.Peil, L.Hébrard, E.Fargette, D.Truve, E.J. Gen. Virol. 92, 445-452, 2011Protein-RNA linkage and post-translational modifications of two sobemovirus VPgs.DOI:10.1099/vir.0.026476-0PMID:21068217mass spectrometric identification; for the genome-linked protein (VPg) of cocksfoot mottle virus, the 5'-end is guanosine and pGp was identified attached to Tyr-5YGO:0018148PSI-MOD:00254genome-linked proteinphosphoproteinMOD_RES O-(5'-phospho-RNA)-tyrosineAA025021-Nov-199721-Nov-199731-Mar-20113-(3'-L-histidyl)-L-tyrosine3-(N3'-histidyl)tyrosine3-(pi-histidyl)tyrosine3-(pros-histidyl)tyrosinebeta-(N(delta)-histidyl)tyrosinebeta-(N3'-histidyl)tyrosine(2S,3R)-2-amino-3-(5-[(2S)-2-amino-2-carboxyethyl]-1H-imidazol-1-yl)-3-(4-hydroxyphenyl)propanoic acidC 15 H 14 N 4 O 3298.30298.106590C 0 H -2 N 0 O 0-2.02-2.015650Bravo, J.Fita, I.Ferrer, J.C.Ens, W.Hillar, A.Switala, J.Loewen, P.C.Protein Sci. 6, 1016-1023, 1997Identification of a novel bond between a histidine and the essential tyrosine in catalase HPII of Escherichia coli.DOI:10.1002/pro.5560060507PMID:9144772X-ray diffraction identification, 1.9 angstroms; mass spectrometric detectionMelik-Adamyan, W.R.Bravo, J.Carpena, X.Switala, J.Mate, M.J.Fita, I.Loewen, P.C.submitted to the Protein Data Bank, August 2000Crystal structure of catalase HPII from Escherichia coli, native structure at 1.9 A resolution.PDB:1GGEX-ray diffraction, 1.89 angstromsThe chirality of tyrosine C-3 is not specified; from the model it appears to be 3R.This modification is different from the modification 3'-(1'-L-histidyl)-L-tyrosine, see RESID:AA0270.H, Ycross-link 2GO:0018150PSI-MOD:00255CROSSLNK 3'-histidyl-3-tyrosine (His-Tyr)AA025121-Nov-199721-Nov-199731-Mar-2012L-methionine sulfoneL-methionine S,S-dioxideS,S-dioxymethionine(2S)-2-amino-4-(methylsulfonyl)butanoic acidCAS:7314-32-1PDBHET:OMTC 5 H 9 N 1 O 3 S 1163.19163.030314C 0 H 0 N 0 O 2 S 032.0031.989829Buzy, A.Bracchi, V.Sterjiades, R.Chroboczek, J.Thibault, P.Gagnon, J.Jouve, H.M.Hudry-Clergeon, G.J. Protein Chem. 14, 59-72, 1995Complete amino acid sequence of Proteus mirabilis PR catalase. Occurrence of a methionine sulfone in the close proximity of the active site.DOI:10.1007/BF01888363PMID:7786407mass spectrometric detectionGouet, P.Jouve, H.M.Dideberg, O.J. Mol. Biol. 249, 933-954, 1995Crystal structure of Proteus mirabilis PR catalase with and without bound NADPH.DOI:10.1006/jmbi.1995.0350PMID:7791219X-ray diffraction, 2.2 angstromsGouet, P.Jouve, H.M.Dideberg, O.submitted to the Protein Data Bank, July 1996Structure of Proteus mirabilis PR catalase for the native form (E-Fe(III)) complexed with NADPH.PDB:2CAHX-ray diffraction, 2.7 angstromsMGO:0018159PSI-MOD:00256MOD_RES Methionine sulfoneAA025212-Dec-199718-May-200131-Mar-2012dipyrrolylmethanemethyl-L-cysteine3-[5-(3-acetic acid-4-propanoic acid-1-pyrrol-2-yl)methyl-3-acetic acid-4-propanoic acid-1-pyrrol-2-yl]methylthio-2-aminopropanoic aciddipyrrole cofactordipyrrolylmethyl-L-cysteinedipyrromethane cofactorpyrromethane cofactor(2S)-3-[5-[4-(2-carboxy)ethyl-3-carboxymethyl-1-pyrrol-2-yl]methyl-4-(2-carboxy)ethyl-3-carboxymethyl-1-pyrrol-2-yl]methylthio-2-aminopropanoic acidCAS:29261-13-0ChEBI:23842PDBHET:DPMC 23 H 27 N 3 O 9 S 1521.54521.146800C 20 H 22 N 2 O 8 S 0418.40418.137616Jordan, P.M.Warren, M.J.Williams, H.J.Stolowich, N.J.Roessner, C.A.Grant, S.K.Scott, A.I.FEBS Lett. 235, 189-193, 1988Identification of a cysteine residue as the binding site for the dipyrromethane cofactor at the active site of Escherichia coli porphobilinogen deaminase.DOI:10.1016/0014-5793(88)81260-2PMID:3042456radioisotope labeling; (13)C-NMR characterizationHart, G.J.Miller, A.D.Battersby, A.R.Biochem. J. 252, 909-912, 1988Evidence that the pyrromethane cofactor of hydroxymethylbilane synthase (porphobilinogen deaminase) is bound through the sulphur atom of a cysteine residue.PMID:3421931chemical characterization; (13)C-NMR identificationMiller, A.D.Hart, G.J.Packman, L.C.Battersby, A.R.Biochem. J. 254, 915-918, 1988Evidence that the pyrromethane cofactor of hydroxymethylbilane synthase (porphobilinogen deaminase) is bound to the protein through the sulphur atom of cysteine-242.PMID:3196304chemical characterizationLouie, G.V.Brownlie, P.D.Lambert, R.Cooper, J.B.Blundell, T.L.Wood, S.P.Malashkevich, V.N.Haedener, A.Warren, M.J.Shoolingin-Jordan, P.M.Proteins 25, 48-78, 1996The three-dimensional structure of Escherichia coli porphobilinogen deaminase at 1.76-angstroms resolution.DOI:10.1002/(SICI)1097-0134(199605)25:1<48::AID-PROT5>3.0.CO;2-GPMID:8727319X-ray diffraction, 1.76 angstromsLouie, G.V.Brownlie, P.D.Lambert, R.Cooper, J.B.Blundell, T.L.Wood, S.P.Warren, M.J.Woodcock, S.C.Jordan, P.M.submitted to the Protein Data Bank, November 1992Structure of porphobilinogen deaminase reveals a flexible multidomain polymerase with a single catalytic site.PDB:1PDAX-ray diffraction, 1.76 angstromsThe pyrromethane cofactor is synthesized on the enzyme autocatalytically by condensation of two porphobilinogen molecules.CGO:0018160PSI-MOD:00257thioether bondMOD_RES S-(dipyrrolylmethanemethyl)cysteineAA025323-Jan-199823-Jan-199830-Sep-2011S-(2-aminovinyl)-3-methyl-D-cysteine2-amino-3-[(2-aminovinyl)sulfanyl]butanoic aciddecarboxylated methyllanthionine(2S,3S)-2-amino-3-[((Z)-2-aminoethenyl)sulfanyl]butanoic acidPDBHET:ABAPDBHET:DBBPDBHET:DHLPDBHET:TEEC 6 H 9 N 2 O 1 S 1157.21157.043559C -1 H -4 N 0 O -3 S 0-64.04-64.016044Prasch, T.Naumann, T.Markert, R.L.M.Sattler, M.Schubert, W.Schaal, S.Bauch, M.Kogler, H.Griesinger, C.Eur. J. Biochem. 244, 501-512, 1997Constitution and solution conformation of the antibiotic mersacidin determined by NMR and molecular dynamics.DOI:10.1111/j.1432-1033.1997.00501.xPMID:9119018identification by (1)H- and (13)C-NMRSchneider, T.R.Kärcher, J.Pohl, E.Lubini, P.Sheldrick, G.M.Acta Crystallogr. D Biol. Crystallogr. 56, 705-713, 2000Ab initio structure determination of the lantibiotic mersacidin.DOI:10.1107/S0907444900003711PMID:10818347X-ray diffraction, 1.06 angstromsSchneider, T.R.Kärcher, J.Sheldrick, G.M.submitted to the Protein Data Bank, November 1999Ab initio structure determination of the lantibiotic mersacidin.PDB:1QOWX-ray diffraction, 1.06 angstromsLi, B.Sher, D.Kelly, L.Shi, Y.Huang, K.Knerr, P.J.Joewono, I.Rusch, D.Chisholm, S.W.van der Donk, W.A.Proc. Natl. Acad. Sci. U.S.A. 107, 10430-10435, 2010Catalytic promiscuity in the biosynthesis of cyclic peptide secondary metabolites in planktonic marine cyanobacteria.DOI:10.1073/pnas.0913677107PMID:20479271This cross-link arises from the decarboxylation of the carboxyl-terminal portion of 3-methyllanthionine.peptidyl-phosphoserine/phosphothreonine dehydratase (EC 4.2.1.-)peptidyl-cysteine dehydroalanine/dehydrobutyrine ligase (EC 6.2.-.-)C, Tcarboxyl-terminalcross-link 2GO:0018162PSI-MOD:00258blocked carboxyl endlanthioninethioether bondCROSSLNK S-(2-aminovinyl)-3-methyl-D-cysteine (Thr-Cys)AA025429-May-199829-May-199830-Apr-2010O4'-(phospho-5'-DNA)-L-tyrosineO4'-L-tyrosine 5'-DNA phosphodiester(S)-2-amino-3-[4-(5'-deoxyribonucleic acid phosphonoxy)phenyl]propanoic acidC 9 H 10 N 1 O 5 P 1 +243.15 +243.029659 +C 0 H 1 N 0 O 3 P 1 +79.98 +79.966331 +van Mansfeld, A.D.M.van Teeffelen, H.A.A.M.Baas, P.D.Jansz, H.S.Nucleic Acids Res. 14, 4229-4238, 1986Two juxtaposed tyrosyl-OH groups participate in phi X174 gene A protein catalysed cleavage and ligation of DNA.DOI:10.1093/nar/14.10.4229PMID:2940511isotope labelingHsieh, J.C.Jung, G.H.Leavitt, M.C.Ito, J.Nucleic Acids Res. 15, 8999-9009, 1987Primary structure of the DNA terminal protein of bacteriophage PRD1.DOI:10.1093/nar/15.21.8999PMID:3684578structure predictionShiue, S.Y.Hsieh, J.C.Ito, J.Nucleic Acids Res. 19, 3805-3810, 1991Mapping of the DNA linking tyrosine residue of the PRD1 terminal protein.DOI:10.1093/nar/19.14.3805PMID:1861973directed mutation analysisThe keyword "phosphoprotein" is not used with polynucleotide-linked intermediate modifications.YGO:0018163PSI-MOD:00259*phosphoproteingenome-linked proteinACT_SITE O-(5'-phospho-DNA)-tyrosine intermediateMOD_RES O-(5'-phospho-DNA)-tyrosineAA025505-Jun-199805-Jun-199830-Apr-2010O-(phospho-5'-DNA)-L-threonineO3-(phospho-5'-DNA)-L-threonineO3-L-threonine 5'-DNA phosphodiester(S)-2-amino-3-(5'-deoxyribonucleic acid phosphonoxy)butanoic acidC 4 H 7 N 1 O 5 P 1 +180.08 +180.006184 +C 0 H 0 N 0 O 3 P 1 +78.97 +78.958505 +Garcia, P.Hermoso, J.M.Garcia, J.A.Garcia, E.Lopez, R.Salas, M.J. Virol. 58, 31-35, 1986Formation of a covalent complex between the terminal protein of pneumococcal bacteriophage Cp-1 and 5'-dAMP.PMID:3081736chemical characterizationTGO:0018164PSI-MOD:00260genome-linked proteinphosphoproteinNot availablethis modification is not annotated in UniProt featuresAA025611-Sep-199811-Sep-199830-Sep-2008O4'-(phospho-5'-uridine)-L-tyrosine5'-uridylic-O-tyrosinehydrogen 5'-uridylate tyrosine esterO4'-L-tyrosine 5'-uridine phosphodiester(S)-2-amino-3-[4-(5'-uridine phosphonoxy)phenyl]propanoic acidC 18 H 20 N 3 O 10 P 1469.34469.088630C 9 H 11 N 2 O 8 P 1306.17306.025302Son, H.S.Rhee, S.G.J. Biol. Chem. 262, 8690-8695, 1987Cascade control of Escherichia coli glutamine synthetase: purification and properties of P-II protein and nucleotide sequence of its structural gene.PMID:2885322chemical detection and spectrographic characterizationuridylyltransferase (EC 2.7.7.59)YGO:0018165PSI-MOD:00261phosphoproteinMOD_RES O-UMP-tyrosineAA025711-Sep-199831-Dec-201231-Dec-2012L-glutamyl L-tyrosineN-(L-glutamyl)-L-tyrosine(S,S)-2-(2-aminopentanedio-1-yl)amino-3-(4-hydoxyphenyl)propanoic acidChEBI:21477C 14 H 17 N 2 O 6309.30309.108661C 9 H 9 N 1 O 2163.18163.063329Flavin, M.Murofushi, H.Meth. Enzymol. 106, 223-237, 1984Tyrosine incorporation in tubulin.DOI:10.1016/0076-6879(84)06024-9PMID:6387372Ersfeld, K.Wehland, J.Plessmann, U.Dodemont, H.Gerke, V.Weber, K.J. Cell Biol. 120, 725-732, 1993Characterization of the tubulin-tyrosine ligase.DOI:10.1083/jcb.120.3.725PMID:8093886biosynthesisXiao, H.El Bissati, K.Verdier-Pinard, P.Burd, B.Zhang, H.Kim, K.Fiser, A.Angeletti, R.H.Weiss, L.M.J. Proteome Res. 9, 359-372, 2010Post-translational modifications to Toxoplasma gondii α- and β-tubulins include novel C-terminal methylation.DOI:10.1021/pr900699aPMID:19886702detection by mass-spectrometry in reflector modetubulin--tyrosine ligase (EC 6.3.2.25)Ecarboxyl-terminalGO:0018166PSI-MOD:00262SITE Involved in polymerizationAA025830-Sep-199930-Sep-199929-Oct-2010S-phycoviolobilin-L-cysteinecryptobiliviolincryptoviolincryptoviolobilinPBVPVBPXBS-phycobiliviolin-L-cysteine(4S)-3-[(1R)-1-(((2R)-2-amino-2-carboxy)ethylsulfanyl)ethyl]-8,12-bis(2-carboxyethyl)-18-ethyl-4,5-dihydro-2,7,13,17-tetramethyl-(21H,22H,24H)-biladiene-bc-1,19-dioneCAS:124861-40-1COMe:BIM000254PDBHET:PVNC 36 H 43 N 5 O 7 S 1689.83689.288320C 33 H 38 N 4 O 6 S 0586.69586.279135Bishop, J.E.Rapoport, H.Klotz, A.V.Chan, C.F.Glazer, A.N.Fueglistaller, P.Zuber, H.J. Am. Chem. Soc. 109, 875-881, 1987Chromopeptides from phycoerythrocyanin. Structure and linkage of the three bilin groups.DOI:10.1021/ja00237a039spectrographic characterization; mass spectrometric and (1)H-NMR identification; peptide linkageMoss, G.P.Eur. J. Biochem. 178, 277-328, 1988IUPAC-IUB Joint Commission on Biochemical Nomenclature (JCBN). Nomenclature of tetrapyrroles. Recommendations 1986.DOI:10.1111/j.1432-1033.1988.tb14453.xPMID:3208761Duerring, M.Huber, R.Bode, W.Ruembeli, R.Zuber, H.J. Mol. Biol. 211, 633-644, 1990Refined three-dimensional structure of phycoerythrocyanin from the cyanobacterium Mastigocladus laminosus at 2.7 A.DOI:10.1016/0022-2836(90)90270-VPMID:2106585X-ray diffraction, 2.7 angstromsZhao, K.H.Deng, M.G.Zheng, M.Zhou, M.Parbel, A.Storf, M.Meyer, M.Strohmann, B.Scheer, H.FEBS Lett. 469, 9-13, 2000Novel activity of a phycobiliprotein lyase: both the attachment of phycocyanobilin and the isomerization to phycoviolobilin are catalyzed by the proteins PecE and PecF encoded by the phycoerythrocyanin operon.DOI:10.1016/S0014-5793(00)01245-XPMID:10708746The phycoviolobilins transmit violet.It has not been established whether the chromophores that have been referred to as cryptoviolins have the same structure as phycoviolobilin.CGO:0017008GO:0018356PSI-MOD:00263chromoproteinphycoviolobilinthioether bondBINDING Phycoviolobilin chromophore (covalent; via 1 link)AA025930-Sep-199930-Sep-199930-Sep-2008phycoerythrobilin-bis-L-cysteine3,18-bis-[1-((2-amino-2-carboxy)ethylsulfanyl)ethyl]-2,3,15,16-tetrahydro-2,7,13,17-tetramethyl-1,19-dioxo-(21H,22H,24H)-biladiene-ab-8,12-dipropanoic acidPEBphycoerythrobilin biscysteine adduct(2S,3R,16R)-3,18-bis-[(R)-1-(((2R)-2-amino-2-carboxy)ethylsulfanyl)ethyl]-8,12-bis(2-carboxyethyl)-2,7,13,17-tetramethyl-2,3,15,16-tetrahydrobilin-1,19(21H,22H,24H)-dioneCAS:18097-67-1COMe:BIM000150C 39 H 48 N 6 O 8 S 2792.97792.297505C 33 H 38 N 4 O 6 S 0586.69586.279135Nagy, J.O.Bishop, J.E.Klotz, A.V.Glazer, A.N.Rapoport, H.J. Biol. Chem. 260, 4864-4868, 1985Bilin attachment sites in the alpha, beta, and gamma subunits of R-phycoerythrin. Structural studies on singly and doubly linked phycourobilins.PMID:3838747mass spectrometric and (1)H-NMR identificationMoss, G.P.Eur. J. Biochem. 178, 277-328, 1988IUPAC-IUB Joint Commission on Biochemical Nomenclature (JCBN). Nomenclature of tetrapyrroles. Recommendations 1986.DOI:10.1111/j.1432-1033.1988.tb14453.xPMID:3208761There are additional chiral centers at C-2, C-3, and C-16.The phytochromobilins and phycoerythrobilins transmit red.C, Ccross-link 2GO:0017011GO:0018167PSI-MOD:00264chromoproteinphycoerythrobilinthioether bondBINDING Phycoerythrobilin chromophore (covalent; via 2 links)AA026030-Sep-199908-Jun-200120-May-2011phycourobilin-bis-L-cysteine3,18-bis(1-[(R)-2-amino-2-carboxyethyl]sulfanylethyl)-2,7,13,17-tetramethyl-1,19-dioxo-4,5,15,16-tetrahydro-(21H,22H,24H)-bilene-b-8,12-dipropanoic acidphycourobilin biscysteine adductPUB3,18-bis(1-[(R)-2-amino-2-carboxyethyl]sulfanylethyl)-8,12-bis(2-carboxyethyl)-2,7,13,17-tetramethyl-4,5,15,16-tetrahydro-(21H,22H,24H)-bilene-b-1,19(4H,16H)-dioneCAS:61932-71-6COMe:BIM000146PDBHET:PUBC 39 H 48 N 6 O 8 S 2792.97792.297505C 33 H 38 N 4 O 6 S 0586.69586.279135Nagy, J.O.Bishop, J.E.Klotz, A.V.Glazer, A.N.Rapoport, H.J. Biol. Chem. 260, 4864-4868, 1985Bilin attachment sites in the alpha, beta, and gamma subunits of R-phycoerythrin. Structural studies on singly and doubly linked phycourobilins.PMID:3838747mass spectrometric and (1)H-NMR identificationKillilea, S.D.O'Carra, P.Biochem. J. 226, 723-731, 1985Structure and apoprotein linkages of phycourobilin.PMID:3838665Moss, G.P.Eur. J. Biochem. 178, 277-328, 1988IUPAC-IUB Joint Commission on Biochemical Nomenclature (JCBN). Nomenclature of tetrapyrroles. Recommendations 1986.DOI:10.1111/j.1432-1033.1988.tb14453.xPMID:3208761Chang, W.R.Jiang, T.Wan, Z.L.Zhang, J.P.Yang, Z.X.Liang, D.C.J. Mol. Biol. 262, 721-731, 1996Crystal structure of R-phycoerythrin from Polysiphonia urceolata at 2.8 angstroms resolution.DOI:10.1006/jmbi.1996.0547PMID:8876649Liang, D.C.Jiang, T.Chang, W.R.submitted to the Protein Data Bank, January 1996Crystal structure of R-phycoerythrin from Polysiphonia at 2.8 A resolution.PDB:1LIAThere are additional chiral centers at C-3alpha, C-4, C-16 and C-18alpha.C, Ccross-link 2GO:0017010GO:0018357PSI-MOD:00265chromoproteinphycourobilinthioether bondBINDING Phycourobilin chromophore (covalent; via 2 links)AA026111-Sep-199831-Dec-201231-Dec-2012N-(L-glutamyl)-poly-L-glutamic acidC 10 H 15 N 2 O 7 +275.24 +275.087926 +C 5 H 7 N 1 O 3 +129.12 +129.042593 +Hitz, H.Schäfer, D.Wittmann-Liebold, B.Eur. J. Biochem. 75, 497-512, 1977Determination of the complete amino-acid sequence of protein S6 from the wild-type and a mutant of Escherichia coli.DOI:10.1111/j.1432-1033.1977.00497.pp.xPMID:328274five forms of the protein, which differ only in the number of carboxyl-terminal glutamic acid residues, were isolated and sequencedKang, W.K.Icho, T.Isono, S.Kitakawa, M.Isono, K.Mol. Gen. Genet. 217, 281-288, 1989Characterization of the gene rimK responsible for the addition of glutamic acid residues to the C-terminus of ribosomal protein S6 in Escherichia coli K12.DOI:10.1007/BF02464894PMID:2570347ribosomal S6--glutamic acid ligase (EC 6.3.2.-)Ecarboxyl-terminalGO:0018170PSI-MOD:00266CHAIN 30S ribosomal protein S6, fully modified isoformthis is not annotated as a modification in UniProt featuresAA026230-Sep-199930-Sep-199931-May-2018L-cysteine sulfinic acid2-amino-2-carboxyethanesulfinic acid2-amino-3-(dioxido-lambda(6)-sulfanyl)propanoic acid [tautomer]2-amino-3-sulfonylpropanoic acid [tautomer]3-sulfinoalanine3-sulphinoalaninecysteine sulphinic acidcysteine-S,S-dioxide [tautomer]S-cysteinesulfinic acidS-hydroxy-S-oxo-L-cysteine residue S-sulfinocysteine(2R)-2-amino-3-sulfinopropanoic acidCAS:1115-65-7CAS:2381-08-0ChEBI:61964ChEBI:61967PDBHET:CSDPDBHET:CSWC 3 H 5 N 1 O 3 S 1135.14134.999014C 0 H 0 N 0 O 2 S 032.0031.989829Nagashima, S.Nakasako, M.Dohmae, N.Tsujimura, M.Takio, K.Odaka, M.Yohda, M.Kamiya, N.Endo, I.Nature Struct. Biol. 5, 347-351, 1998Novel non-heme iron center of nitrile hydratase with a claw setting of oxygen atoms.DOI:10.1038/nsb0598-347PMID:9586994X-ray diffraction, 1.7 angstroms; mass spectroscopic identificationCGO:0018171GO:0018323PSI-MOD:00267ACT_SITE Redox-activeMOD_RES Cysteine sulfinic acid (-SO2H)AA026330-Sep-199930-Sep-199924-Oct-2008L-3',4',5'-trihydroxyphenylalanineL-3,4,5-TOPA(S)-2-amino-3-(3,4,5-trihydroxyphenyl)propanoic acidC 9 H 9 N 1 O 4195.17195.053158C 0 H 0 N 0 O 232.0031.989829Taylor, S.W.Ross, M.M.Waite, J.H.Arch. Biochem. Biophys. 324, 228-240, 1995Novel 3,4-di- and 3,4,5-trihydroxyphenylalanine-containing polypeptides from the blood cells of the ascidians Ascidia ceratodes and Molgula manhattensis.DOI:10.1006/abbi.1995.0035PMID:8554314chromatographic and mass spectrometric detection; (1)H-NMR identificationTaylor, S.W.Kammerer, B.Nicholson, G.J.Pusecker, K.Walk, T.Bayer, E.Scippa, S.de Vincentiis, M.Arch. Biochem. Biophys. 348, 278-288, 1997Morulin Pm: a modified polypeptide containing TOPA and 6-bromotryptophan from the morula cells of the ascidian, Phallusia mammillata.DOI:10.1006/abbi.1997.0371PMID:9434739(1)H-NMR and (13)C-NMR characterizationYGO:0018172PSI-MOD:00268hydroxylationNot availablethis modification is not annotated in UniProt featuresAA026404-Dec-199804-Dec-199831-Mar-2011O-(sn-1-glycerophosphoryl)-L-serinealpha-glycerophosphoryl serineglycerophosphoserineO3-(sn-1-glycerophosphoryl)-L-serineO3-2,3-dihydroxypropyl hydrogen phosphate-L-serine esterO3-L-serine glyceryl-1-phosphodiester(2S)-2-amino-3-[(2Xi)-2,3-dihydroxypropyl]phosphonoxypropanoic acidCAS:26289-09-8PDBHET:OPEC 6 H 12 N 1 O 7 P 1241.14241.035138C 3 H 7 N 0 O 5 P 1154.06154.003110Stimson, E.Virji, M.Barker, S.Panico, M.Blench, I.Saunders, J.Payne, G.Moxon, E.R.Dell, A.Morris, H.R.Biochem. J. 316, 29-33, 1996Discovery of a novel protein modification: alpha-glycerophosphate is a substituent of meningococcal pilin.PMID:8645220mass spectrometric identificationForest, K.T.Dunham, S.A.Koomey, M.Tainer, J.A.Mol. Microbiol. 31, 743-752, 1999Crystallographic structure reveals phosphorylated pilin from Neisseria: phosphoserine sites modify type IV pilus surface chemistry and fibre morphology.DOI:10.1046/J.1365-2958.1999.01184.XPMID:10048019X-ray diffraction, 2.60 angstroms; density was observed at the predicted position of the phosphoryl group, but was too low to model due to low occupancy or disorderChamot-Rooke, J.Mikaty, G.Malosse, C.Soyer, M.Dumont, A.Gault, J.Imhaus, A.F.Martin, P.Trellet, M.Clary, G.Chafey, P.Camoin, L.Nilges, M.Nassif, X.Duménil, G.Science 331, 778-782, 2011Posttranslational modification of pili upon cell contact triggers N. meningitidis dissemination.DOI:10.1126/science.1200729PMID:21311024mass spectrometric detection; directed mutation analysisThe stereochemistry of the glycerol phosphate has not been determined. The sn-1 form is assumed.SGO:0018340PSI-MOD:00269phosphoproteinMOD_RES O-(sn-1-glycerophosphoryl)serineAA026530-Apr-199930-Apr-199931-May-20181-thioglycine2-amino-1-sulfanylethanoneaminoethanethioic O-acidaminoethanethioic S-acidaminoethanethiolic acidaminoethanethionic acidaminothioacetic acidaminoethanethioic acidCAS:758-10-1PDBHET:GL3C 2 H 3 N 1 O 0 S 173.1172.998620C 2 H 4 N 1 O 1 S 190.1290.001360C 0 H 0 N 0 O -1 S 116.0615.977156C 0 H 0 N 0 O -1 S 116.0615.977156Ermler, U.Grabarse, W.Shima, S.Goubeaud, M.Thauer, R.K.Science 278, 1457-1462, 1997Crystal structure of methyl-coenzyme M reductase: the key enzyme of biological methane formation.DOI:10.1126/science.278.5342.1457PMID:9367957X-ray diffraction, 1.45 angstromsLeimkuehler, S.Wuebbens, M.M.Rajagopalan, K.V.J. Biol. Chem. 276, 34695-34701, 2001Characterization of Escherichia coli MoeB and its involvement in the activation of molybdopterin synthase for the biosynthesis of the molybdenum cofactor.DOI:10.1074/jbc.M102787200PMID:11463785Leidel, S.Pedrioli, P.G.Bucher, T.Brost, R.Costanzo, M.Schmidt, A.Aebersold, R.Boone, C.Hofmann, K.Peter, M.Nature 458, 228-232, 2009Ubiquitin-related modifier Urm1 acts as a sulphur carrier in thiolation of eukaryotic transfer RNA.DOI:10.1038/nature07643PMID:19145231As a peptide this may exist predominantly in the iminyl-thiol [-C(SH)=N-] tautomeric form.See also RESID:AA0206.The formula and records labeled "INT" refers to thioglycine occurring as an internal residue with a thioamide peptide bond.The formula and records labeled "CTER" refers to thioglycine occurring as a carboxyl end residue.GGO:0018173GO:0019920PSI-MOD:00270Gcarboxyl-terminalGO:0018173GO:0019921PSI-MOD:01623thiopeptide bondMOD_RES 1-thioglycineAA026630-Apr-199931-Dec-200931-Dec-2013heme P460-bis-L-cysteine-L-tyrosinebis(S-cysteinyl)-(tyros-3'-yl)-heme(10S,11S)-[7,12-bis((S)-1-[((R)-2-amino-2-carboxy)ethylsulfanyl]ethyl)-10-(2-hydroxy-5-[(S)-2-amino-2-carboxy]ethylphenyl)-3,8,13,17-tetramethyl-21H,23H-10,11-dihydroporphine-2,18-bis(2-carboxyethyl)-N21,N22,N23,N24]-ferrateCOMe:BIM000242PDBHET:HECC 49 Fe 1 H 51 N 7 O 8 S 2985.95985.258991C 34 Fe 1 H 32 N 4 O 4 S 0616.50616.177293Arciero, D.M.Hooper, A.B.J. Biol. Chem. 268, 14645-14654, 1993Hydroxylamine oxidoreductase from Nitrosomonas europaea is a multimer of an octa-heme subunit.PMID:8325841Tanaka, N.Igarashi, N.Moriyama, H.submitted to the Protein Data Bank, March 1997X-Ray structure of hydroxylamine oxidoreductase.PDB:1FGJX-ray diffraction, 2.8 angstromsIgarashi, N.Moriyama, H.Fujiwara, T.Fukumori, Y.Tanaka, N.Nature Struct. Biol. 4, 276-284, 1997The 2.8 A structure of hydroxylamine oxidoreductase from a nitrifying chemoautotrophic bacterium, Nitrosomonas europaea.DOI:10.1038/nsb0497-276PMID:9095195X-ray diffraction, 2.8 angstromsPearson, A.R.Elmore, B.O.Yang, C.Ferrara, J.D.Hooper, A.B.Wilmot, C.M.Biochemistry 46, 8340-8349, 2007The crystal structure of cytochrome P460 of Nitrosomonas europaea reveals a novel cytochrome fold and heme-protein cross-link.DOI:10.1021/bi700086rPMID:17583915an alternative structure is proposed for the tyrosyl-heme linkage based on the higher resolution structure obtained for a lysyl-heme linkageThe diagram has been corrected for reduction of the protoporphyrin C10-C11 bond. A corrected model is not available.A mechanism for free radical reductive addition is not provided by the authors of the proposed structure, and the alternative structure with a tyrosyl-O linkage seems more plausible. See RESID:AA0271.The heavy atom coordinates of the model are assigned according to the coordinates in PDB:1FDJ and the instructions for transformation given by the authors.C, C, Ycross-link 3GO:0018174GO:0018359PSI-MOD:00271chromoproteinhemeironmetalloproteinthioether bondBINDING Heme (covalent; via 3 links)AA026730-Apr-199930-Apr-199931-May-2018O-(phospho-5'-adenosine)-L-threonine5'-adenylic-O3-L-threoninebeta-5'-adenylic-L-threonineL-threonine monoanhydride with 5'-adenylic acidO(gamma)-5'-adenylic-L-threonineO3-(phospho-5'-adenosine)-L-threonineO3-L-threonine 5'-adenosine phosphodiester(2S,3R)-2-amino-3-(5'-adenosine phosphonoxy)butanoic acidChEBI:138113C 14 H 19 N 6 O 8 P 1430.31430.100198C 10 H 12 N 5 O 6 P 1329.21329.052520Culp, J.S.Blytt, H.J.Hermodson, M.Butler, L.G.J. Biol. Chem. 260, 8320-8324, 1985Amino acid sequence of the active site peptide of bovine intestinal 5'-nucleotide phosphodiesterase and identification of the active site residue as threonine.PMID:2989287radioisotope labelingStefan, C.Stalmans, W.Bollen, M.Eur. J. Biochem. 241, 338-342, 1996Threonine autophosphorylation and nucleotidylation of the hepatic membrane protein PC-1.DOI:10.1111/j.1432-1033.1996.00338.xPMID:8917428radioisotope labeling; linkage analysisYarbrough, M.L.Li, Y.Kinch, L.N.Grishin, N.V.Ball, H.L.Orth, K.Science 323, 269-272, 2009AMPylation of Rho GTPases by Vibrio VopS disrupts effector binding and downstream signaling.DOI:10.1126/science.1166382PMID:19039103Kinch, L.N.Yarbrough, M.L.Orth, K.Grishin, N.V.PLoS One 4, e5818, 2009Fido, a novel AMPylation domain common to fic, doc, and AvrB.DOI:10.1371/journal.pone.0005818PMID:19503829Li, Y.Al-Eryani, R.Yarbrough, M.L.Orth, K.Ball, H.L.J. Am. Soc. Mass Spectrom. 22, 752-761, 2011Characterization of AMPylation on Threonine, Serine, and Tyrosine Using Mass Spectrometry.DOI:10.1007/s13361-011-0084-1PMID:21472612mass spectrometric detection and characterization of tandem-MS fragmentationTGO:0018178GO:0018332PSI-MOD:00272phosphoproteinACT_SITE AMP-threonine intermediateMOD_RES O-AMP-threonineAA026807-May-199907-May-199931-Dec-2009tris-L-cysteinyl L-cysteine persulfido bis-L-glutamato L-histidino tetrairon disulfide trioxide4Fe-2S-3O clusterhybrid four iron cluster 2prismane iron-sulfur cofactor [misnomer]mu-1:2kappaO-oxido-mu-1:3kappaO-oxido-mu-2:4kappaO-oxido-mu-3:4kappaS-sulfido-mu3-2:3:4kappaS-sulfido-S-cysteinyl-N1'-histidino-O5-glutamato 1-iron-S5-cysteine persulfido-O5-glutamato 2-iron-3,4-bis-(S-cysteinyl iron)COMe:BIM000058C 28 Fe 4 H 34 N 9 O 14 S 71168.431167.766769C 0 Fe 4 H -7 N 0 O 3 S 3360.50360.585932Arendsen, A.F.Hadden, J.Card, G.McAlpine, A.S.Bailey, S.Zaitsev, V.Duke, E.H.M.Lindley, P.F.Kroeckel, M.Trautwein, A.X.Feiters, M.C.Charnock, J.M.Garner, C.D.Marritt, S.J.Thomson, A.J.Kooter, I.M.Johnson, M.K.van den Berg, W.A.M.van Dongen, W.M.A.M.Hagen, W.R.J. Biol. Inorg. Chem. 3, 81-95, 1998The "prismane" protein resolved: X-ray structure at 1.7 angstroms and multiple spectroscopy of two novel 4Fe clusters.DOI:10.1007/s007750050210oxidized form; X-ray diffraction, 1.7 angstroms; EPR, Moessbauer, and MCD spectrographic analysisAragao, D.Macedo, S.Mitchell, E.P.Romao, C.V.Liu, M.Y.Frazao, C.Saraiva, L.M.Xavier, A.V.LeGall, J.van Dongen, W.M.A.M.Hagen, W.R.Teixeira, M.Carrondo, M.A.Lindley, P.J. Biol. Inorg. Chem. 8, 540-548, 2003Reduced hybrid cluster proteins (HCP) from Desulfovibrio desulfuricans ATCC 27774 and Desulfovibrio vulgaris (Hildenborough): X-ray structures at high resolution using synchrotron radiation.DOI:10.1007/s00775-003-0443-xPMID:12764602X-ray diffraction, 1.25 angstroms; structure after reduction by dithionite; it is not demonstrated that the oxidized structure can be recovered after reduction by dithioniteThe name "prismane" for this hybrid cluster is a now known to be a misnomer. The structure determined by X-ray consists of a four iron cluster with mixed ligands. One of the oxygen ligands, designated here as the mu-1:3-oxido, is actually partially occupied by an unidentified atom and is probably the reactive center.Because of the uncertainty in the structure, a formal charge cannot be calculated.C, C, C, C, E, E, Hcross-link 7secondary to RESID:AA0269GO:0018301PSI-MOD:002734Fe-2S-3Oiron-sulfur proteinmetalloproteinMETAL Iron-oxo-sulfur (4Fe-2O-2S)METAL Iron-oxo-sulfur (4Fe-2O-2S); via tele nitrogenMETAL Iron-oxo-sulfur (4Fe-2O-2S); via persulfide groupAA026914-May-199914-May-199931-Dec-2011L-cysteine persulfide2-amino-3-disulfanylpropanoic acid2-amino-3-hydrodisulfidopropanoic acid2-amino-3-hydropersulfidopropanoic acid2-amino-3-persulfhydrylpropanoic acid3-(thiosulfeno)-alanine3-disulfanylalanineS-mercaptocysteineS-sulfanylcysteinethiocysteine(R)-2-amino-3-disulfanylpropanoic acidCAS:5652-32-4ChEBI:61963PDBHET:CSSC 3 H 5 N 1 O 1 S 2135.20134.981256C 0 H 0 N 0 O 0 S 132.0631.972071Branzoli, U.Massey, V.J. Biol. Chem. 249, 4346-4349, 1974Evidence for an active site persulfide residue in rabbit liver aldehyde oxidase.PMID:4276457investigation of persulfide group chemistryZheng, L.White, R.H.Cash, V.L.Dean, D.R.Biochemistry 33, 4714-4720, 1994Mechanism for the desulfurization of L-cysteine catalyzed by the nifS gene product.DOI:10.1021/bi00181a031PMID:8161529chemical detection of persulfide groupArendsen, A.F.Hadden, J.Card, G.McAlpine, A.S.Bailey, S.Zaitsev, V.Duke, E.H.M.Lindley, P.F.Kroeckel, M.Trautwein, A.X.Feiters, M.C.Charnock, J.M.Garner, C.D.Marritt, S.J.Thomson, A.J.Kooter, I.M.Johnson, M.K.van den Berg, W.A.M.van Dongen, W.M.A.M.Hagen, W.R.J. Biol. Inorg. Chem. 3, 81-95, 1998The "prismane" protein resolved: X-ray structure at 1.7 angstroms and multiple spectroscopy of two novel 4Fe clusters.DOI:10.1007/s007750050210X-ray diffraction, 1.7 angstroms; EPR, Moessbauer, and MCD spectrographic analysisde Beus, M.D.Chung, J.Colon, W.Protein Sci. 13, 1347-1355, 2004Modification of cysteine 111 in Cu/Zn superoxide dismutase results in altered spectroscopic and biophysical properties.DOI:10.1110/ps.03576904PMID:15096637spectrographic, and mass spectrometric detection; chemical characterizationUrich, T.Gomes, C.M.Kletzin, A.Frazão, C.Science 311, 996-1000, 2006X-ray Structure of a self-compartmentalizing sulfur cycle metalloenzyme.DOI:10.1126/science.1120306PMID:16484493X-ray diffraction, 1.70 angstromsUrich, T.Gomes, C.M.Kletzin, A.Frazao, C.submitted to the Protein Data Bank, December 2005Sulfur oxygenase reductase from Acidianus ambivalens.PDB:2CB2X-ray diffraction, 1.70 angstromsMustafa, A.K.Gadalla, M.M.Sen, N.Kim, S.Mu, W.Gazi, S.K.Barrow, R.K.Yang, G.Wang, R.Snyder, S.H.Science Signal. 2, ra72, 2009H2S signals through protein S-sulfhydration.DOI:10.1126/scisignal.2000464PMID:19903941In desulfurization, the sulfur is donated by free cysteine to peptidyl-cysteine producing free alanine and peptidyl-cysteine persulfide. See also RESID:AA0101 and RESID:AA0268.CGO:0018179GO:0018192PSI-MOD:00274ACT_SITEACT_SITE Cysteine persulfide intermediateMOD_RES Cysteine persulfideAA027014-May-199914-May-199931-Dec-20103'-(1'-L-histidyl)-L-tyrosine3'-(N(epsilon)-histidyl)tyrosine3'-(N1'-histidyl)tyrosine3'-(tau-histidyl)tyrosine3'-(tele-histidyl)tyrosine(2S)-2-amino-3-[1-(5-[(2S)-2-amino-2-carboxyethyl]-2-hydroxyphenyl)-1H-imidazol-4-yl]propanoic acidChEBI:19837COMe:BIM000381C 15 H 14 N 4 O 3298.30298.106590C 0 H -2 N 0 O 0-2.02-2.015650Buse, G.Soulimane, T.Dewor, M.Meyer, H.E.Blueggel, M.Protein Sci. 8, 985-990, 1999Evidence for a copper-coordinated histidine-tyrosine cross-link in the active site of cytochrome oxidase.DOI:10.1110/ps.8.5.985PMID:10338009mass spectrometric and chemical characterizationHemp, J.Robinson, D.E.Ganesan, K.B.Martinez, T.J.Kelleher, N.L.Gennis, R.B.Biochemistry 45, 15405-15410, 2006Evolutionary migration of a post-translationally modified active-site residue in the proton-pumping heme-copper oxygen reductases.DOI:10.1021/bi062026uPMID:17176062mass spectrometric detectionThis modification is different from the modification 3-(3'-L-histidyl)-L-tyrosine, see RESID:AA0250.H, Ycross-link 2GO:0018152PSI-MOD:00275CROSSLNK 1'-histidyl-3'-tyrosine (His-Tyr)AA027130-Sep-199931-Dec-200931-Dec-2009heme P460-bis-L-cysteine-L-lysinebis(S-cysteinyl)-N6-lysino-heme(19S,20S)-[7,12-bis((S)-1-[((R)-2-amino-2-carboxy)ethylsulfanyl]ethyl)-20-([(S)-5-amino-5-carboxypentyl]amino)-3,8,13,17-tetramethyl-21H,23H-19,20-dihydroporphine-2,18-bis(2-carboxyethyl)-N21,N22,N23,N24]-ferratePDBHET:HECC 46 Fe 1 H 54 N 8 O 7 S 2950.95950.290626C 34 Fe 1 H 32 N 4 O 4 S 0616.50616.177293Arciero, D.M.Hooper, A.B.FEBS Lett. 410, 457-460, 1997Evidence for a crosslink between c-heme and a lysine residue in cytochrome P460 of Nitrosomonas europaea.DOI:10.1016/S0014-5793(97)00635-2PMID:9237682spectrographic characterization; chemical characterizationBergmann, D.J.Hooper, A.B.Eur. J. Biochem. 270, 1935-1941, 2003Cytochrome P460 of Nitrosomonas europaea. Formation of the heme-lysine cross-link in a heterologous host and mutagenic conversion to a non-cross-linked cytochrome c'.DOI:10.1046/j.1432-1033.2003.03550.xPMID:12709052mutagenic analysis; catalytic characterizationPearson, A.R.Elmore, B.O.Yang, C.Ferrara, J.D.Hooper, A.B.Wilmot, C.M.Biochemistry 46, 8340-8349, 2007The crystal structure of cytochrome P460 of Nitrosomonas europaea reveals a novel cytochrome fold and heme-protein cross-link.DOI:10.1021/bi700086rPMID:17583915X-ray diffraction, 1.8 angstromsPearson, A.R.Elmore, B.O.Yang, C.Ferrara, J.D.Hooper, A.B.Wilmot, C.M.submitted to the Protein Data Bank, January 2007Cytochrome P460 from Nitrosomonas europaea - probable physiological form.PDB:2JE3X-ray diffraction, 1.8 angstromsThe heme-lysine cross-link is probably produced auto-catalytically. See RESID:AA0266.C, C, Kcross-link 3GO:0018174GO:0018360PSI-MOD:00276chromoproteinhemeironmetalloproteinthioether bondBINDING Heme (covalent; via 3 links)AA027230-Sep-199930-Sep-199930-Sep-20085-methyl-L-arginine2-amino-5-guanidinohexanoic acid4-methylarginine [misnomer]delta-methylarginine(2S,5S)-2-amino-5-carbamimidamidohexanoic acidPDBHET:AGMC 7 H 14 N 4 O 1170.22170.116761C 1 H 2 N 0 O 014.0314.015650Ermler, U.Grabarse, W.Shima, S.Goubeaud, M.Thauer, R.K.Science 278, 1457-1462, 1997Crystal structure of methyl-coenzyme M reductase: the key enzyme of biological methane formation.DOI:10.1126/science.278.5342.1457PMID:9367957X-ray diffraction, 1.45 angstromsSelmer, T.Kahnt, J.Goubeaud, M.Shima, S.Grabarse, W.Ermler, U.Thauer, R.K.J. Biol. Chem. 275, 3755-3760, 2000The biosynthesis of methylated amino acids in the active site region of methyl-coenzyme M reductase.DOI:10.1074/jbc.275.6.3755PMID:10660523mass spectrometric characterization; the biosynthetic origin of the methyl group is S-adenosyl methionine, not methyl-coenzyme MThis modification should not be confused with N5-methylarginine (see RESID:AA0305).In methyl-coenzyme M reductase the arginine 5-methyl group is derived from S-adenosyl-methionine and is not produced as a side reaction of the enzyme.RGO:0018181PSI-MOD:00277methylated amino acidMOD_RES 5-methylarginineAA027330-Sep-199930-Sep-199930-Sep-20082-methyl-L-glutamine2-methylglutaminealpha-methylglutamine(S)-2-amino-2-methylpentanediamic acidCAS:4247-16-9PDBHET:MGNC 6 H 10 N 2 O 2142.16142.074228C 1 H 2 N 0 O 014.0314.015650Ermler, U.Grabarse, W.Shima, S.Goubeaud, M.Thauer, R.K.Science 278, 1457-1462, 1997Crystal structure of methyl-coenzyme M reductase: the key enzyme of biological methane formation.DOI:10.1126/science.278.5342.1457PMID:9367957X-ray diffraction, 1.45 angstromsSelmer, T.Kahnt, J.Goubeaud, M.Shima, S.Grabarse, W.Ermler, U.Thauer, R.K.J. Biol. Chem. 275, 3755-3760, 2000The biosynthesis of methylated amino acids in the active site region of methyl-coenzyme M reductase.DOI:10.1074/jbc.275.6.3755PMID:10660523mass spectrometric characterization; the biosynthetic origin of the methyl group is S-adenosyl methionine, not methyl-coenzyme MQGO:0018361PSI-MOD:00278methylated amino acidMOD_RES 2-methylglutamineAA027430-Sep-199930-Sep-199930-Sep-2008N-pyruvic acid 2-iminyl-L-cysteine(R)-2-(1-carboxy-2-sulfanylethanimino)propanoic acidC 6 H 8 N 1 O 3 S 1174.19174.022489C 3 H 2 N 0 O 2 S 070.0570.005479Rose, K.Simona, M.G.Savoy, L.A.Regamey, P.O.Green, B.N.Clore, G.M.Gronenborn, A.M.Wingfield, P.T.J. Biol. Chem. 267, 19101-19106, 1992Pyruvic acid is attached through its central carbon atom to the amino terminus of the recombinant DNA-derived DNA-binding protein Ner of bacteriophage Mu.PMID:1388164mass spectrometric and chemical characterization; (1)H-NMR identification; 2,4-dinitrophenylhydrazine used for detectionThe cysteine sulfhydryl may cyclize with the imine to form 2-methyl-thiazolidine-2,4-dicarboxylic acid [CAS:152574-58-8].Camino-terminalGO:0018386PSI-MOD:00279blocked amino endMOD_RES N-pyruvate 2-iminyl-cysteineAA027530-Sep-199930-Sep-199930-Sep-2008N-pyruvic acid 2-iminyl-L-valine(S)-2-(1-carboxy-2-methylpropanimino)propanoic acidC 8 H 12 N 1 O 3170.19170.081718C 3 H 2 N 0 O 270.0570.005479Prome, D.Blouquit, Y.Ponthus, C.Prome, J.C.Rosa, J.J. Biol. Chem. 266, 13050-13054, 1991Structure of the human adult hemoglobin minor fraction A-1b by electrospray and secondary ion mass spectrometry. Pyruvic acid as amino-terminal blocking group.PMID:2071591Vamino-terminalGO:0018388PSI-MOD:00280blocked amino endMOD_RES N-pyruvate 2-iminyl-valineAA027630-Sep-199931-Dec-200213-Sep-20133'-heme-L-histidine2-[1-(N3'-histidyl)ethyl]protoporphyrin IXN(delta)-histidyl hemeN(pi)-histidyl hemeN3'-histidyl hemepros-histidyl heme[7-ethenyl-12-((S)-1-[((R)-2-amino-2-carboxyethyl)-3H-imidazol-3-yl]ethyl)-3,8,13,17-tetramethyl-21H,23H-porphine-2,18-bis(2-carboxyethyl)-N21,N22,N23,N24]-ferrateC 40 Fe 1 H 39 N 7 O 5753.64753.236205C 34 Fe 1 H 32 N 4 O 4616.50616.177293Schulz, H.Hennecke, H.Thoeny-Meyer, L.Science 281, 1197-1200, 1998Prototype of a heme chaperone essential for cytochrome c maturation.DOI:10.1126/science.281.5380.1197PMID:9712585mass spectrometric identificationDaltrop, O.Stevens, J.M.Higham, C.W.Ferguson, S.J.Proc. Natl. Acad. Sci. U.S.A. 99, 9703-9708, 2002The CcmE protein of the c-type cytochrome biogenesis system: Unusual in vitro heme incorporation into apo-CcmE and transfer from holo-CcmE to apocytochrome.DOI:10.1073/pnas.152120699PMID:12119398Enggist, E.Thoeny-Meyer, L.Guentert, P.Pervushin, K.Structure 10, 1551-1557, 2002NMR structure of the heme chaperone CcmE reveals a novel functional motif.DOI:10.1016/S0969-2126(02)00885-7PMID:12429096Enggist, E.Schneider, M.J.Schulz, H.Thoeny-Meyer, L.J. Bacteriol. 185, 175-183, 2003Biochemical and mutational characterization of the heme chaperone CcmE reveals a heme binding site.DOI:10.1128/JB.185.1.175-183.2003PMID:12486054directed mutation analysis; spectrographic characterizationEnggist, E.Thony-Meyer, L.Guntert, P.Pervushin, K.submitted to the Protein Data Bank, March 2004Solution structure of the heme chaperone CcmE of Escherichia coli.PDB:1SR3conformation by NMR; these models do not include the hemeThe NMR model structure and the spectrographic characterization suggest, but do not establish, that the heme is attached to the pros-nitrogen.HGO:0018182PSI-MOD:00281chromoproteinhemeironmetalloproteinBINDING Heme (covalent; via pros nitrogen)AA027724-Nov-199924-Nov-199924-Aug-2012S-selanyl-L-cysteine2-amino-3-hydroselenosulfidopropanoic acid2-amino-3-hydroselenylsulfidopropanoic acid2-amino-3-hydroselenylthiopropanoic acidcysteine perselenide [misnomer]S-selanylcysteineS-selenylcysteine(R)-2-amino-3-(selanylsulfanyl)propanoic acidPDBHET:CSZC 3 H 5 N 1 O 1 S 1 Se 1182.11182.925706C 0 H 0 N 0 O 0 S 0 Se 178.9779.916521Dobbek, H.Gremer, L.Meyer, O.Huber, R.Proc. Natl. Acad. Sci. U.S.A. 96, 8884-8889, 1999Crystal structure and mechanism of CO dehydrogenase, a molybdo iron-sulfur flavoprotein containing S-selanylcysteine.DOI:10.1073/pnas.96.16.8884PMID:10430865X-ray diffraction, 2.2 angstroms; this structure has been revised with a metal cluster that does not contain selenium, see RESID:AA0355Haenzelmann, P.Dobbek, H.Gremer, L.Huber, R.Meyer, O.J. Mol. Biol. 301, 1221-1235, 2000The effect of intracellular molybdenum in Hydrogenophaga pseudoflava on the crystallographic structure of the seleno-molybdo-iron-sulfur flavoenzyme carbon monoxide dehydrogenase.DOI:10.1006/jmbi.2000.4023PMID:10966817X-ray diffraction, 2.25 angstroms; this structure may not be correct, see RESID:AA0355Haenzelmann, P.Dobbek, H.Gremer, L.Huber, R.Meyer, O.submitted to the Protein Data Bank, September 2000Carbon monoxide dehydrogenase from Hydrogenophaga pseudoflava.PDB:1FFVX-ray diffraction, 2.25 angstroms; this structure may not be correct, see RESID:AA0355Lima, C.D.J. Mol. Biol. 315, 1199-1208, 2002Analysis of the E. coli NifS CsdB protein at 2.0 A reveals the structural basis for perselenide and persulfide intermediate formation.DOI:10.1006/jmbi.2001.5308PMID:11827487X-ray diffraction, 2.2 angstromsLima, C.D.Burley, S.K.submitted to the Protein Data Bank, December 2001E. coli NifS/CsdB protein at 2.20 A with the cysteine perselenide intermediate (residue CSZ).PDB:1KMKX-ray diffraction, 2.20 angstromsWolfe, M.D.Ahmed, F.Lacourciere, G.M.Lauhon, C.T.Stadtman, T.C.Larson, T.J.J. Biol. Chem. 279, 1801-1809, 2004Functional diversity of the rhodanese homology domain: the Escherichia coli ybbB gene encodes a selenophosphate-dependent tRNA 2-selenouridine synthase.DOI:10.1074/jbc.M310442200PMID:14594807evidence for a potential active site S-selanylcysteine intermediate in 2-selenouridine synthetaseCGO:0018183PSI-MOD:00282seleniumACT_SITE S-selanylcysteine intermediateMOD_RES S-selanylcysteineAA027824-Nov-199906-Feb-200430-Jun-2012N6-propylamino-poly(propylmethylamino)-propyldimethylamine-L-lysinelysine derivative Lys(x)N6-[3-([(omega)-(dimethyl)aminopropyl-poly(3-[methylamino]propyl)]amino)propyl]lysinesilaffin polycationic lysine derivative(alpha)- ([([(5S)-5-amino-5-carboxypentyl]amino)propyl][(methyl)amino])-(omega)-methyl poly[propane-1,3-diyl(methylimino)]C 30 H 66 N 8 O 1 +554.91 +554.535959 +C 24 H 54 N 6 O 0 +426.74 +426.440996 +Kroeger, N.Deutzmann, R.Sumper, M.Science 286, 1129-1132, 1999Polycationic peptides from diatom biosilica that direct silica nanosphere formation.DOI:10.1126/science.286.5442.1129PMID:10550045chromatographic, mass spectrometric and (1)H-NMR identificationKroeger, N.Deutzmann, R.Sumper, M.J. Biol. Chem. 276, 26066-26070, 2001Silica-precipitating peptides from diatoms. The chemical structure of silaffin-A from Cylindrotheca fusiformis.DOI:10.1074/jbc.M102093200PMID:11349130chromatographic and mass spectrometric identificationIn silaffin from the diatom Cylindrotheca fusiformis there are five to eleven N-methyl-propylamine monomeric units on each lysine. Six are shown.KGO:0018185PSI-MOD:00283methylated amino acidMOD_RES N6-poly(methylaminopropyl)lysineAA027924-Nov-199924-Nov-199924-Oct-2008dihydroxyheme-L-aspartate ester-L-glutamate ester1,5-bishydroxymethyl protoporphyrin IX 1-glutamate ester 5-aspartate esterperoxidase heme cofactor[13-[(S)-(4-amino-4-carboxy)butanoyloxymethyl]-3-[(S)-(3-amino-3-carboxy)propanoyloxymethyl]-7,12-diethenyl-8,17-dimethyl-21H,23H-porphine-2,18-bis(2-carboxyethyl)-N21,N22,N23,N24]-ferrateCOMe:BIM000243C 43 Fe 1 H 40 N 6 O 10856.67856.215529C 34 Fe 1 H 28 N 4 O 4612.47612.145993Kooter, I.M.Moguilevsky, N.Bollen, A.Sijtsema, N.M.Otto, C.Dekker, H.L.Wever, R.Eur. J. Biochem. 264, 211-217, 1999Characterization of the Asp94 and Glu242 mutants in myeloperoxidase, the residues linking the heme group via ester bonds.DOI:10.1046/j.1432-1327.1999.00606.xPMID:10447690directed mutation analysis; activity comparisonFor structural studies of the myeloperoxidase heme cofactor, see RESID:AA0280.D, Ecross-link 2GO:0018186GO:0018362PSI-MOD:00284chromoproteinhemehydroxylationironmetalloproteinBINDING Heme (covalent; via 2 links)AA028024-Nov-199924-Nov-199931-Dec-2009dihydroxyheme-L-aspartate ester-L-glutamate ester-L-methionine sulfonium1,5-bishydroxymethyl protoporphyrin IX 1-glutamate ester 5-aspartate ester 2-methionine sulfoniummyeloperoxidase heme cofactor[13-[(S)-(4-amino-4-carboxy)butanoyloxymethyl]-3-[(S)-(3-amino-3-carboxy)propanoyloxymethyl]-12-[(S)-(3-amino-3-carboxy)propylsulfoniumethyl]-7-ethenyl-8,17-dimethyl-21H,23H-porphine-2,18-bis(2-carboxyethyl)-N21,N22,N23,N24]-ferrateCOMe:BIM000245PDBHET:HEMC 48 Fe 1 H 50 N 7 O 11 S 11+988.87988.263290C 34 Fe 1 H 29 N 4 O 4 S 01+613.47613.153269Kooter, I.M.Moguilevsky, N.Bollen, A.van der Veen, L.A.Otto, C.Dekker, H.L.Wever, R.J. Biol. Chem. 274, 26794-26802, 1999The sulfonium ion linkage in myeloperoxidase. Direct spectroscopic detection by and effect of mutation.DOI:10.1074/jbc.274.38.26794PMID:10480885radioisotope labeling; spectrographic characterizationKooter, I.M.Moguilevsky, N.Bollen, A.Sijtsema, N.M.Otto, C.Dekker, H.L.Wever, R.Eur. J. Biochem. 264, 211-217, 1999Characterization of the Asp94 and Glu242 mutants in myeloperoxidase, the residues linking the heme group via ester bonds.DOI:10.1046/j.1432-1327.1999.00606.xPMID:10447690directed mutation analysisFenna, R.E.Zeng, J.Davey, C.submitted to the Protein Data Bank, June 1995Crystal structure of human myeloperoxidase isoform C crystallized in space group P2(1) at pH 5.5 and 20 deg C.PDB:1MHLX-ray diffraction, 2.25 angstromsFenna, R.Zeng, J.Davey, C.Arch. Biochem. Biophys. 316, 653-656, 1995Structure of the green heme in myeloperoxidase.DOI:10.1006/abbi.1995.1086PMID:7840679X-ray diffraction, 2.25 angstromsFenna, R.E.Zeng, J.submitted to the Protein Data Bank, April 1992X-ray crystal structure of canine myeloperoxidase at 3 A resolution.PDB:1MYPX-ray diffraction, 3.0 angstromsZeng, J.Fenna, R.E.J. Mol. Biol. 226, 185-207, 1992X-ray crystal structure of canine myeloperoxidase at 3 Angstroms resolution.DOI:10.1016/0022-2836(92)90133-5PMID:1320128X-ray diffraction, 3.0 angstromsD, E, Mcross-link 3GO:0018186GO:0018363PSI-MOD:00285chromoproteinhemehydroxylationironmetalloproteinBINDING Heme (covalent; via 3 links)AA028103-Dec-199907-Sep-200131-Mar-2013L-cysteinyl molybdenum bis(molybdopterin guanine dinucleotide)2-amino-5,6-dimercapto-7-methyl-3,7,8a,9-tetrahydro-8-oxa-1,3,9,10-tetraazaanthracen-4-one guanosine dinucleotidebis[8-amino-1a,2,4a,5,6,7,10-heptahydro-2-(trihydrogen diphosphate 5'-ester with guanosine)methyl-6-oxo-3,4-disulfanyl-pteridino[6,7-5,6]pyranoato-S3,S4]-cystein-S-yl-molybdenumCAS:128007-95-4PDBHET:MGDPDBHET:MOC 43 H 52 Mo 1 N 21 O 27 P 4 S 51675.151675.994960C 40 H 47 Mo 1 N 20 O 26 P 4 S 41572.021572.985775Arnoux, P.Sabaty, M.Alric, J.Frangioni, B.Guigliarelli, B.Adriano, J.M.Pignol, D.Nature Struct. Biol. 10, 928-934, 2003Structural and redox plasticity in the heterodimeric periplasmic nitrate reductase.DOI:10.1038/nsb994PMID:14528294X-ray diffraction, 3.20 angstromsArnoux, P.Sabaty, M.Alric, J.Frangioni, B.Guigliarelli, B.Adriano, J.M.Pignol, D.submitted to the Protein Data Bank, May 2003Crystal structure of the heterodimeric nitrate reductase from Rhodobacter sphaeroides.PDB:1OGYX-ray diffraction, 3.20 angstromsOne possible structure of a reduced form (+4H) is shown. The fully reduced form would be 1a,2,3,4,4a,5,6,7,10-nonahydro. The fully oxidized form would be 2,6,7-trihydro.This modification occurs in enzymes homologous to formate dehydrogenase in organisms where the position corresponding to selenocysteine instead encodes cysteine (see RESID:AA0248).CGO:0018187PSI-MOD:00286metalloproteinmolybdenummolybdopterinphosphoproteinNot availablethis modification is not annotated in UniProt featuresAA028228-Jan-200028-Jan-200031-Mar-2009(2S,3R,4S)-3,4-dihydroxyproline2,3-trans-3,4-cis-3,4-dihydroxy-L-proline2-alpha-3-beta-4-beta-3,4-dihydroxyprolinetrans-2,3-cis-3,4-dihydroxy-L-proline(2S,3R,4S)-3,4-dihydroxypyrrolidine-2-carboxylic acidCAS:95341-64-3C 5 H 7 N 1 O 3129.12129.042593C 0 H 0 N 0 O 232.0031.989829Taylor, S.W.Waite, J.H.Ross, M.M.Shabanowitz, J.Hunt, D.F.J. Am. Chem. Soc. 116, 10803-10804, 1994trans-2,3-cis-3,4-Dihydroxyproline, a new naturally occurring amino acid, is the sixth residue in the tandemly repeated consensus decapeptides of an adhesive protein from Mytilus edulis.DOI:10.1021/ja00102a063chromatographic detection; mass spectrometric and (1)H-NMR identificationPGO:0018188PSI-MOD:00287hydroxylationMOD_RES (3R,4S)-3,4-dihydroxyprolineAA028318-Feb-200018-Feb-200030-Sep-2013pyrroloquinoline quinone2,4,6-tricarboxylic-pyrrolo[2,3-5,6]quinoline 8,9-quinone2,7,9-tricarboxy-1H-pyrrolo(2,3-f)quinoline-4,5-dionecoenzyme PQQmethoxatin4,5-dihydro-4,5-dioxo-1H-pyrrolo[2,3-5,6]quinoline-2,7,9-tricarboxylic acidCAS:72909-34-3ChEBI:18315PDBHET:PQQC 14 H 6 N 2 O 8330.21330.012415C 0 H -10 N 0 O 337.9237.906494Salisbury, S.A.Forrest, H.S.Cruse, W.B.Kennard, O.Nature 280, 843-844, 1979A novel coenzyme from bacterial primary alcohol dehydrogenases.PMID:471057X-ray diffractionDuine, J.A.Frank Jzn., J.Verwiel, P.E.J.Eur. J. Biochem. 108, 187-192, 1980Structure and Activity of the Prosthetic Group of Methanol Dehydrogenase.DOI:10.1111/j.1432-1033.1980.tb04711.xchemical characterization; mass spectrometric and (1)H-NMR identificationGoosen, N.Huinen, R.G.van de Putte, P.J. Bacteriol. 174, 1426-1427, 1992A 24-amino-acid polypeptide is essential for the biosynthesis of the coenzyme pyrrolo-quinoline-quinone.PMID:1310505mutagenic evidence that specific glutamic acid and tyrosine residues of the pqqA protein were utilizedVelterop, J.S.Sellink, E.Meulenberg, J.J.David, S.Bulder, I.Postma, P.W.J. Bacteriol. 177, 5088-5098, 1995Synthesis of pyrroloquinoline quinone in vivo and in vitro and detection of an intermediate in the biosynthetic pathway.PMID:7665488evidence that the pqqA protein was the origin of pyrroloquinoline quinoneIn some prokaryotes, the pqqA protein is the origin of pyrroloquinoline quinone. In other organisms the endogenous source, if there is one, has not been established.E, Ycross-link 2GO:0018189PSI-MOD:00288quinoproteinCROSSLNK Pyrroloquinoline quinone (Glu-Tyr)AA028417-Mar-200017-Mar-200025-Feb-2011tris-L-cysteinyl L-N1'-histidino tetrairon tetrasulfidetetra-mu3-sulfidotris(S-cysteinyliron)(N1'-histidinoiron)COMe:BIM000059PDBHET:SF4C 15 Fe 4 H 18 N 6 O 4 S 72-794.15793.684297C 0 Fe 4 H -4 N 0 O 0 S 42-347.59347.597831Peters, J.W.Lanzilotta, W.N.Lemon, B.J.Seefeldt, L.C.Science 282, 1853-1858, 1998X-ray crystal structure of the Fe-only hydrogenase (CpI) from Clostridium pasteurianum to 1.8 angstrom resolution.DOI:10.1126/science.282.5395.1853PMID:9836629X-ray diffraction, 1.8 angstromsC, C, C, Hcross-link 4GO:0018302PSI-MOD:002894Fe-4Siron-sulfur proteinmetalloproteinMETAL Iron-sulfur (4Fe-4S)METAL Iron-sulfur (4Fe-4S); via tele nitrogenAA028517-Mar-200017-Mar-200025-Feb-2011tris-L-cysteinyl L-N3'-histidino tetrairon tetrasulfidetetra-mu3-sulfidotris(S-cysteinyliron)(N3'-histidinoiron)COMe:BIM000060PDBHET:SF4C 15 Fe 4 H 18 N 6 O 4 S 72-794.15793.684297C 0 Fe 4 H -4 N 0 O 0 S 42-347.59347.597831Volbeda, A.Charon, M.H.Piras, C.Hatchikian, E.C.Frey, M.Fontecilla-Camps, J.C.Nature 373, 580-587, 1995Crystal structure of the nickel-iron hydrogenase from Desulfovibrio gigas.DOI:10.1038/373580a0PMID:7854413X-ray diffraction, 2.85 angstromsVolbeda, A.Frey, M.Fontecilla-Camps, J.C.submitted to the Protein Data Bank, March 1996Crystal structure of the oxidized form of Ni-Fe hydrogenase.PDB:1FRVannotation; X-ray diffraction, 2.85 angstromsC, C, C, Hcross-link 4GO:0018303PSI-MOD:002904Fe-4Siron-sulfur proteinmetalloproteinMETAL Iron-sulfur (4Fe-4S)METAL Iron-sulfur (4Fe-4S); via pros nitrogenAA028617-Mar-200017-Mar-200025-Feb-2011tris-L-cysteinyl L-aspartato tetrairon tetrasulfidetetra-mu3-sulfidotris(S-cysteinyliron)(O4-aspartatoiron)COMe:BIM000061PDBHET:SF4C 13 Fe 4 H 16 N 4 O 6 S 72-772.09771.652328C 0 Fe 4 H -4 N 0 O 0 S 42-347.59347.597831Gorst, C.M.Yeh, Y.H.Teng, Q.Calzolai, L.Zhou, Z.H.Adams, M.W.W.La Mar, G.N.Biochemistry 34, 600-610, 1995[1]H NMR investigation of the paramagnetic cluster environment in Pyrococcus furiosus three-iron ferredoxin: sequence-specific assignment of ligated cysteines independent of tertiary structure.DOI:10.1021/bi00002a027PMID:7819255conformation, binding site, and disulfide bond assignments by (1)H-NMRZhou, Z.H.Adams, M.W.W.Biochemistry 36, 10892-10900, 1997Site-directed mutations of the 4Fe-ferredoxin from the hyperthermophilic archaeon Pyrococcus furiosus: role of the cluster-coordinating aspartate in physiological electron transfer reactions.DOI:10.1021/bi9708141PMID:9283079demonstration of aspartate bindingC, C, C, Dcross-link 4GO:0018304PSI-MOD:002914Fe-4Siron-sulfur proteinmetalloproteinMETAL Iron-sulfur (4Fe-4S)AA028717-Mar-200017-Mar-200030-Jun-2012N6-pyruvic acid 2-iminyl-L-lysine(2S)-2-amino-6-([1-carboxyethylidene]amino)hexanoic acidPDBHET:KPIPDBHET:PYRC 9 H 14 N 2 O 3198.22198.100442C 3 H 2 N 0 O 270.0570.005479Laber, B.Gomis-Rueth, F.X.Romao, M.J.Huber, R.Biochem. J. 288, 691-695, 1992Escherichia coli dihydrodipicolinate synthase. Identification of the active site and crystallization.PMID:1463470evidence for covalent intermediateMirwaldt, C.Korndoerfer, I.Huber, R.J. Mol. Biol. 246, 227-239, 1995The crystal structure of dihydrodipicolinate synthase from Escherichia coli at 2.5 angstroms resolution.DOI:10.1006/jmbi.1994.0078PMID:7853400X-ray diffraction, 2.5 angstromsMirwaldt, C.Korndoerfer, I.Huber, R.submitted to the Protein Data Bank, February 1995Dihydrodipicolinate synthase.PDB:1DHPX-ray diffraction, 2.5 angstromsLawrence, M.C.Barbosa, J.A.R.G.Smith, B.J.Hall, N.E.Pilling, P.A.Ooi, H.C.Marcuccio, S.M.submitted to the Protein Data Bank, July 1996N-Acetylneuraminate lyase in complex with hydroxypyruvate.PDB:1FDYX-ray diffraction, 2.45 angstromsLawrence, M.C.Barbosa, J.A.R.G.Smith, B.J.Hall, N.E.Pilling, P.A.Ooi, H.C.Marcuccio, S.M.J. Mol. Biol. 266, 381-399, 1997Structure and mechanism of a sub-family of enzymes related to N-acetylneuraminate lyase.DOI:10.1006/jmbi.1996.0769PMID:9047371X-ray diffraction, 2.45 angstromsKGO:0018308PSI-MOD:00292ACT_SITEACT_SITE Schiff-base intermediate with substrateAA028820-Apr-200020-Apr-200031-May-2013tris-L-cysteinyl L-serinyl tetrairon tetrasulfidetetra-mu3-sulfidotris(S-cysteinyliron)(O3-serinyliron)PDBHET:SF4C 12 Fe 4 H 16 N 4 O 5 S 72-744.08743.657414C 0 Fe 4 H -4 N 0 O 0 S 42-347.59347.597831Mansy, S.S.Xiong, Y.Hemann, C.Hille, R.Sundaralingam, M.Cowan, J.A.Biochemistry 41, 1195-1201, 2002Crystal structure and stability studies of C77S HiPIP: a serine ligated [4Fe-4S] cluster.PMID:11802718X-ray diffraction, 1.90 angstromsMansy, S.S.Xiong, Y.Hemann, C.Hille, R.Sundaralingam, M.Cowan, J.A.submitted to the Protein Data Bank, August 2001Crystal structure of C77S HIPIP: a serine ligated [4Fe-4S] cluster.PDB:1JS2X-ray diffraction, 1.90 angstromsThe occurrence of serine rather than cysteine in an otherwise strongly conserved homology domain known to bind the 4Fe-4S cluster in other proteins suggested that serine might also bind iron-sulfur clusters. The engineered replacement of a cysteine ligand to a [4Fe-4S] cluster with serine resulted in a ligand bond that was 0.11 angstroms shorter. However, the cluster was less stable because of increased sensitivity to proton mediated solvolysis.C, C, C, Scross-link 4GO:0018305PSI-MOD:002934Fe-4Siron-sulfur proteinmetalloproteinNot availablethis modification is not annotated in UniProt featuresAA028920-Apr-200020-Apr-200025-Feb-2011bis-L-cysteinyl L-N3'-histidino L-serinyl tetrairon tetrasulfidetetra-mu3-sulfidobis(S-cysteinyliron)(N3'-histidinoiron)(O3-serinyliron)PDBHET:SF4C 15 Fe 4 H 18 N 6 O 5 S 62-778.09777.707141C 0 Fe 4 H -4 N 0 O 0 S 42-347.59347.597831The occurrence of serine rather than cysteine in an otherwise strongly conserved homology domain known to bind the 4Fe-4S cluster in other proteins suggests that serine may also bind iron-sulfur clusters.C, C, H, Scross-link 4GO:0018306PSI-MOD:002944Fe-4Siron-sulfur proteinmetalloproteinMETAL Iron-sulfur (4Fe-4S)METAL Iron-sulfur (4Fe-4S); via pros nitrogenAA029016-Jun-200016-Jun-200025-Feb-2011O-octanoyl-L-serineL-serine octanoate esterO3-octanoyl-L-serine(2S)-2-amino-3-(octanoyloxy)propanoic acidC 11 H 19 N 1 O 3213.28213.136493C 8 H 14 N 0 O 1126.20126.104465Kojima, M.Hosoda, H.Date, Y.Nakazato, M.Matsuo, H.Kangawa, K.Nature 402, 656-660, 1999Ghrelin is a growth-hormone-releasing acylated peptide from stomach.DOI:10.1038/45230PMID:10604470chromatographic and mass spectrometric identification; chemical synthesisYang, J.Brown, M.S.Liang, G.Grishin, N.V.Goldstein, J.L.Cell 132, 387-396, 2008Identification of the acyltransferase that octanoylates ghrelin, an appetite-stimulating peptide hormone.DOI:10.1016/j.cell.2008.01.017PMID:18267071ghrelin O-acyltransferase, GOAT (EC 2.3.1.-)SGO:0018191GO:0042050PSI-MOD:00295lipoproteinLIPID O-octanoyl serineAA029131-Mar-200131-Mar-200131-May-2018O-D-glucuronosyl-L-serineO3-D-glucuronosyl-L-serine(2S)-2-amino-3-(beta-D-glucopyranuronosyl)propanoic acidCAS:528-16-5C 9 H 13 N 1 O 8263.20263.064116C 6 H 8 N 0 O 6176.12176.032088Jonsson, A.P.Griffiths, W.J.Bratt, P.Johansson, I.Stroemberg, N.Joernvall, H.Bergman, T.FEBS Lett. 475, 131-134, 2000A novel Ser O-glucuronidation in acidic proline-rich proteins identified by tandem mass spectrometry.DOI:10.1016/S0014-5793(00)01645-8PMID:10858503neither the identity of the hexuronic acid nor the mode of linkage is definitively establishedVitorino, R.Alves, R.Barros, A.Caseiro, A.Ferreira, R.Lobo, M.C.Bastos, A.Duarte, J.Carvalho, D.Santos, L.L.Amado, F.L.Proteomics 10, 3732-3742, 2010Finding new posttranslational modifications in salivary proline-rich proteins.DOI:10.1002/pmic.201000261PMID:20879038mass spectrometric detectionThe beta glucuronosyl form is shown.See also RESID:AA0154, RESID:AA0208, RESID:AA0209, RESID:AA0210, RESID:AA0296, RESID:AA0297, RESID:AA0397, RESID:AA0398, RESID:AA0400, RESID:AA0402, RESID:AA0404, RESID:AA0406, and RESID:AA0422 for other O-glycosylated serines.UDP-glucuronate beta-D-glucuronosyltransferase (acceptor-unspecific) (EC 2.4.1.17)SGO:0018413PSI-MOD:00296glycoproteinCARBOHYD O-linked (GlcA) serineAA029231-Mar-200131-Mar-200131-Mar-2009tris-L-cysteinyl L-cysteine persulfido bis-L-glutamato L-histidino nickel triiron disulfide trioxidecarbon monoxide dehydrogenase nickel-iron cofactorhybrid nickel-triiron clusterNi-3Fe-2S-3O clustermu-1:2kappaO-oxido-mu-1:3kappaO-oxido-mu-2:4kappaO-oxido-mu-3:4kappaS-sulfido-mu3-2:3:4kappaS-sulfido-S-cysteinyl-N1'-histidino-O5-glutamato 1-iron-S5-cysteine persulfido-O5-glutamato 2-nickel-3,4-bis-(S-cysteinyl iron)C 28 Fe 3 H 34 N 9 Ni 1 O 14 S 71171.281169.767174C 0 Fe 3 H -7 N 0 Ni 1 O 3 S 3363.35362.586337This one nickel, three iron cluster with mixed ligands is now thought not to exist. See RESID:AA0310.C, C, C, C, E, E, Hcross-link 7secondary to RESID:AA0269GO:0018415GO:0018416PSI-MOD:00297iron-sulfur proteinmetalloproteinNi-3Fe-2S-3OnickelNot availablethis dubious modification is not currently annotated in UniProt featuresAA029331-Mar-200131-Mar-200131-Mar-2009tris-L-cysteinyl L-cysteine persulfido L-glutamato L-histidino L-serinyl nickel triiron disulfide trioxidecarbon monoxide dehydrogenase nickel-iron cofactorhybrid nickel-triiron clusterNi-3Fe-2S-3O clustermu-1:2kappaO-oxido-mu-1:3kappaO-oxido-mu-2:4kappaO-oxido-mu-3:4kappaS-sulfido-mu3-2:3:4kappaS-sulfido-S-cysteinyl-N1'-histidino-O5-glutamato 1-iron-S5-cysteine persulfido-O3-serinyl 2-nickel-3,4-bis-(S-cysteinyl iron)C 26 Fe 3 H 32 N 9 Ni 1 O 13 S 71129.241127.756609C 0 Fe 3 H -7 N 0 Ni 1 O 3 S 3363.35362.586337Stephens, P.J.McKenna, M.C.Ensign, S.A.Bonam, D.Ludden, P.W.J. Biol. Chem. 264, 16347-16350, 1989Identification of a Ni- and Fe-containing cluster in Rhodospirillum rubrum carbon monoxide dehydrogenase.PMID:2550436This one nickel, three iron cluster with mixed ligands is now thought not to exist. See RESID:AA0310.C, C, C, C, E, H, Scross-link 7secondary to RESID:AA0269GO:0018417GO:0018418PSI-MOD:00298iron-sulfur proteinmetalloproteinNi-3Fe-2S-3OnickelNot availablethis dubious modification is not currently annotated in UniProt featuresAA029431-Mar-200131-Mar-200131-May-2018N6-(L-isoaspartyl)-L-lysinebeta-(N6-lysyl)aspartyl acidisoaspartyl N6-lysineN(epsilon)-(beta-aspartyl)lysine(2S)-2-amino-6-([(3S)-3-amino-3-carboxypropanoyl]amino)hexanoic acidCAS:5853-83-8ChEBI:21862C 10 H 15 N 3 O 3225.25225.111341C 0 H -3 N -1 O 0-17.03-17.026549C 0 H -2 N 0 O -1-18.02-18.010565Klostermeyer, H.Meth. Enzymol. 107, 258-261, 1984Nepsilon-(beta-Aspartyl)lysine.DOI:10.1016/0076-6879(84)07016-6PMID:6503713review; discussion of occurrence as an excretion product from an unknown metabolic or dietary sourceWikoff, W.R.Liljas, L.Duda, R.L.Tsuruta, H.Hendrix, R.W.Johnson, J.E.Science 289, 2129-2133, 2000Topologically linked protein rings in the bacteriophage HK97 capsid.DOI:10.1126/science.289.5487.2129PMID:11000116Osička, R.Procházková, K.Šulc, M.Linhartová, I.Havlíček, V.Šebo, P.J. Biol. Chem. 279, 24944-24956, 2004A novel "clip-and-link" activity of repeat in toxin (RTX) proteins from gram-negative pathogens. Covalent protein cross-linking by an Asp-Lys isopeptide bond upon calcium-dependent processing at an Asp-Pro bond.DOI:10.1074/jbc.M314013200PMID:15044436chemical characterization and mass spectrometric identification; directed mutation analysis; it was not determined whether the cross-links were through the aspartyl C1 or C4 carboxyl, and both are probably formed, see also RESID:AA0583; the encoding of an author's name in the PubMed citation is corrected to UTF8Kang, H.J.Coulibaly, F.Clow, F.Proft, T.Baker, E.N.Science 318, 1625-1628, 2007Stabilizing isopeptide bonds revealed in gram-positive bacterial pilus structure.DOI:10.1126/science.1145806PMID:18063798X-ray diffraction, 2.2 angstroms; evidence for multiple intrachain isoaspartyl lysine isopeptide cross-linksK, Ncross-link 2GO:0018420GO:0019937GO:0019938PSI-MOD:00299D, Kcross-link 2PSI-MOD:01917isopeptide bondCROSSLNK Isoaspartyl lysine isopeptide (Lys-Asn)CROSSLNK Isoaspartyl lysine isopeptide (Asn-Lys) (interchain with K-...)CROSSLNK Isoaspartyl lysine isopeptide (Lys-Asn) (interchain with N-...)CROSSLNK Isoaspartyl lysine isopeptide (Asp-Lys) (interchain with K-...)CROSSLNK Isoaspartyl lysine isopeptide (Lys-Asp) (interchain with D-...)CROSSLNK Isoaspartyl lysine isopeptide (Lys-Asp)AA029504-May-200104-May-200130-Sep-2013L-glutamyl-5-poly(ADP-ribose)L-isoglutamyl-poly(ADP-ribose)(S)-2-amino-5-poly[2'-adenosine 5'-(trihydrogen diphosphate) 5'->5'-ester with 1alpha-D-ribofuranosyl]oxy-5-oxopentanoic acidCAS:26656-46-2C 20 H 28 N 6 O 16 P 2 +670.42 +670.103702 +C 15 H 21 N 5 O 13 P 2 +541.30 +541.061109 +Smith, S.Trends Biochem. Sci. 26, 174-179, 2001The world according to PARP.DOI:10.1016/S0968-0004(00)01780-1PMID:11246023reviewLindahl, T.Satoh, M.S.Poirier, G.G.Klungland, A.Trends Biochem. Sci. 20, 405-411, 1995Post-translational modification of poly(ADP-ribose) polymerase induced by DNA strand breaks.DOI:10.1016/S0968-0004(00)89089-1PMID:8533153reviewMatic, I.Ahel, I.Hay, R.T.Nature Methods 9, 771-772, 2012Reanalysis of phosphoproteomics data uncovers ADP-ribosylation sites.DOI:10.1038/nmeth.2106PMID:22847107mass spectrometric detection of modification by mono-ADPR in reanalysis of phosphoproteomics dataThe alpha form is presented.This entry represents modification by one or more subunits of ADP-ribose.NAD+ ADP-ribosyltransferase (EC 2.4.2.30)EGO:0006471GO:0018424PSI-MOD:00300phosphoproteinpoly adenosine diphosphate riboseMOD_RES PolyADP-ribosyl glutamic acidAA029608-Jun-200108-Jun-200120-Apr-2012O-(N-acetylglucosamine-1-phosphoryl)-L-serineO-beta(N-acetyl-glucosamine-alpha1-phosphate)serineO3-(N-acetylglucosamine-1-phosphoryl)-L-serineO3-L-serine 2-(acetylamino)-2-deoxy-D-glucopyranose 1-phosphodiester(2S)-2-amino-3-[([(2-acetamido-2-deoxy-alpha-D-glucopyranosyl)oxy][hydroxy]phosphoryl)oxy]propanoic acidCAS:6866-69-9C 11 H 19 N 2 O 10 P 1370.25370.077731C 8 H 14 N 1 O 8 P 1283.17283.045703Gustafson, G.L.Milner, L.A.J. Biol. Chem. 255, 7208-7210, 1980Occurrence of N-acetylglucosamine-1-phosphate in proteinase I from Dictyostelium discoideum.PMID:6993483chemical characterizationGustafson, G.L.Gander, J.E.Meth. Enzymol. 107, 172-183, 1984O beta-(N-acetyl-alpha-glucosamine-1-phosphoryl)serine in proteinase I from Dictyostelium discoideum.DOI:10.1016/0076-6879(84)07011-7PMID:6438439Mehta, D.P.Ichikawa, M.Salimath, P.V.Etchison, J.R.Haak, R.Manzi, A.Freeze, H.H.J. Biol. Chem. 271, 10897-10903, 1996A lysosomal cysteine proteinase from Dictyostelium discoideum contains N-acetylglucosamine-1-phosphate bound to serine but not mannose-6-phosphate on N-linked oligosaccharides.DOI:10.1074/jbc.271.18.10897PMID:8631906See also RESID:AA0154, RESID:AA0208, RESID:AA0209, RESID:AA0210, RESID:AA0291, RESID:AA0297, RESID:AA0397, RESID:AA0398, RESID:AA0400, RESID:AA0402, RESID:AA0404, RESID:AA0406, and RESID:AA0422 for other O-glycosylated serines.UDP-N-acetylglucosamine:serine-protein N-acetylglucosamine-1-phosphotransferase (EC 2.7.8.-)SGO:0018425PSI-MOD:00301glycoproteinphosphoproteinNot availablethis modification is not annotated in UniProt featuresAA029708-Jun-200130-Jun-200631-May-2018O-(D-mannose-1-phosphoryl)-L-serineO-(alpha-D-mannosyl-1-phosphoryl)-L-serineO3-(D-mannose-1-phosphoryl)-L-serineO3-L-serine alpha-D-mannopyranose 1-phosphodiesterO-[alpha-D-mannopyranosyloxy(hydroxy)phosphoryl]-L-serineC 9 H 16 N 1 O 10 P 1 +329.20 +329.051182 +C 6 H 11 N 0 O 8 P 1 +242.12 +242.019154 +Moss, J.M.Reid, G.E.Mullin, K.A.Zawadzki, J.L.Simpson, R.J.McConville, M.J.J. Biol. Chem. 274, 6678-6688, 1999Characterization of a novel GDP-mannose:Serine-protein mannose-1-phosphotransferase from Leishmania mexicana.DOI:10.1074/jbc.274.10.6678PMID:10037765biosynthesisMacrae, J.I.Acosta-Serrano, A.Morrice, N.A.Mehlert, A.Ferguson, M.A.J. Biol. Chem. 280, 12201-12211, 2005Structural characterization of NETNES, a novel glycoconjugate in Trypanosoma cruzi epimastigotes.DOI:10.1074/jbc.M412939200PMID:15649890Mannose oligosaccharides and short phosphoglycan chains may be attached to the mannose 1-phosphate at the 2 position.See also RESID:AA0154, RESID:AA0208, RESID:AA0209, RESID:AA0210, RESID:AA0291, RESID:AA0296, RESID:AA0397, RESID:AA0398, RESID:AA0400, RESID:AA0402, RESID:AA0404, RESID:AA0406, and RESID:AA0422 for other O-glycosylated serines.GDP-mannose:serine-protein mannose-1-phosphotransferase (EC 2.7.8.-)SGO:0018426PSI-MOD:00302glycoproteinphosphoproteinCARBOHYD O-linked (P-Man...) serineAA029808-Jun-200108-Jun-200131-Dec-2009heptakis-L-histidino tetracopper mu4-sulfide hydroxidenitrous oxide reductase nosZ CuZ clusterpentakis-L-N1'-histidino-bis-L-N3'-histidino tetracopper sulfide hydroxidemu4-sulfido bis(bis-N1'-histidino copper)(N1'-histidino-N3'-histidino copper)(N3'-histidino hydroxide copper)COMe:BIM000109PDBHET:CUZC 42 Cu 4 H 43 N 21 O 8 S 11256.191253.050808C 0 Cu 4 H -6 N 0 O 1 S 1296.19293.638425Rasmussen, T.Berks, B.C.Sanders-Loehr, J.Dooley, D.M.Zumft, W.G.Thomson, A.J.Biochemistry 39, 12753-12756, 2000The catalytic center in nitrous oxide reductase, CuZ, is a copper-sulfide cluster.DOI:10.1021/bi001811iPMID:11041839Brown, K.Djinovic-Carugo, K.Haltia, T.Cabrito, I.Saraste, M.Moura, J.J.Moura, I.Tegoni, M.Cambillau, C.J. Biol. Chem. 275, 41133-41136, 2000Revisiting the catalytic CuZ cluster of nitrous oxide (N2O) reductase. Evidence of a bridging inorganic sulfur.DOI:10.1074/jbc.M008617200PMID:11024061Brown, K.Tegoni, M.Cambillau, C.submitted to the Protein Data Bank, October 1999Crystal structure of nitrous oxide reductase from Pseudomonas nautica, at 2.4A resolution.PDB:1QNIX-ray diffraction, 2.40 angstromsThe hydroxide is probably replaced by the nitrous oxide substrate. An undetermined number of the histidine ligands are protonated and there is, as yet, no evidence for calculation of the formal charge.H, H, H, H, H, H, Hcross-link 7GO:0018429PSI-MOD:00303coppermetalloproteinMETAL Copper Zthis UniProt feature has a structural misrepresentationAA029930-Jun-200130-Jun-200131-Dec-2013L-leucine methyl ester2-amino-4-methylpentanoic methyl esteralpha-aminoisocaproic methyl estermethyl L-leucinatemethyl (2S)-2-amino-4-methylpentanoateCAS:2666-93-5ChEBI:44075PDBHET:MLLC 7 H 14 N 1 O 2144.19144.102454C 1 H 2 N 0 O 014.0314.015650Xie, H.Clarke, S.J. Biol. Chem. 268, 13364-13371, 1993Methyl esterification of C-terminal leucine residues in cytosolic 36-kDa polypeptides of bovine brain. A novel eucaryotic protein carboxyl methylation reaction.PMID:8514774radiolabeling and enzymatic evidence for carboxyl methylation of the C-terminal leucine of an unidentified cytoplasmic proteinFavre, B.Zolnierowicz, S.Turowski, P.Hemmings, B.A.J. Biol. Chem. 269, 16311-16317, 1994The catalytic subunit of protein phosphatase 2A is carboxyl-methylated in vivo.PMID:8206937chemical and immunological characterizationBryant, J.C.Westphal, R.S.Wadzinski, B.E.Biochem. J. 339, 241-246, 1999Methylated C-terminal leucine residue of PP2A catalytic subunit is important for binding of regulatory Balpha subunit.DOI:10.1042/0264-6021:3390241PMID:10191253biochemical role of modificationCho, U.S.Xu, W.Nature 445, 53-57, 2007Crystal structure of a protein phosphatase 2A heterotrimeric holoenzyme.DOI:10.1038/nature05351PMID:17086192X-ray diffraction, 3.50 angstromsCHO, U.S.XU, W.submitted to the Protein Data Bank, September 2006Crystal structure of a protein phosphatase 2A (PP2A) holoenzyme.PDB:2IAEX-ray diffraction, 3.50 angstromsXing, Y.Li, Z.Chen, Y.Stock, J.B.Jeffrey, P.D.Shi, Y.Cell 133, 154-163, 2008Structural mechanism of demethylation and inactivation of protein phosphatase 2A.DOI:10.1016/j.cell.2008.02.041PMID:18394995the modification of serine/threonine-protein phosphatase 2A catalytic subunit beta is required for protein phosphatase 2A (PP2A) activity, and is reversed by PP2A-specific methylesterase PME-1(EC 3.1.1.89)The carboxy-terminal motif for this modification, [PAMV][DG]YFL*, is strongly conserved.[phosphatase 2A protein]-leucine-carboxy methyltransferase (EC 2.1.1.233)Lcarboxyl-terminalincidental to RESID:AA0039GO:0018439PSI-MOD:00304methylated carboxyl endMOD_RES Leucine methyl esterAA030030-Jun-200130-Jun-200131-Dec-2009hexakis-L-cysteinyl L-serinyl octairon heptasulfidenitrogenase P-clusterCOMe:BIM000067PDBHET:CLFC 21 Fe 8 H 27 N 7 O 8 S 133-1369.031368.310179C 0 Fe 8 H -8 N 0 O 0 S 73-663.12663.223042Peters, J.W.Stowell, M.H.Soltis, S.M.Finnegan, M.G.Johnson, M.K.Rees, D.C.Biochemistry 36, 1181-1187, 1997Redox-dependent structural changes in the nitrogenase P-cluster.DOI:10.1021/bi9626665PMID:9063865structural reinterpretationMayer, S.M.Lawson, D.M.Gormal, C.A.Roe, S.M.Smith, B.E.J. Mol. Biol. 292, 871-891, 1999New insights into structure-function relationships in nitrogenase: A 1.6 Angstom resolution X-ray crystallographic study of Klebsiella pneumoniae MoFe-protein.DOI:10.1006/jmbi.1999.3107PMID:10525412X-ray diffraction, 1.6 angstromsMayer, S.M.Lawson, D.M.Gormal, C.A.Roe, S.M.Smith, B.E.submitted to the Protein Data Bank, May 1999Nitrogenase Mo-Fe protein from Klebsiella pneumoniae, dithionite-reduced state.PDB:1QGUX-ray diffraction, 1.6 angstroms, reduced formMayer, S.M.Lawson, D.M.Gormal, C.A.Roe, S.M.Smith, B.E.submitted to the Protein Data Bank, May 1999Nitrogenase Mo-Fe protein from Klebsiella pneumoniae, phenosafranin oxidized state.PDB:1QH1X-ray diffraction, 1.6 angstroms, oxidized formEinsle, O.Tezcan, F.A.Andrade, S.L.A.Schmid, B.Yoshida, M.Howard, J.B.Rees, D.C.Science 297, 1696-1700, 2002Nitrogenase MoFe-protein at 1.16 A resolution: a central ligand in the FeMo-cofactor.DOI:10.1126/science.1073877PMID:12215645X-ray diffraction, 1.16 angstromsEinsle, O.Tezcan, F.A.Andrade, S.L.A.Schmid, B.Yoshida, M.Howard, J.B.Rees, D.C.submitted to the Protein Data Bank, June 2002Nitrogenase MoFe protein from Azotobacter vinelandii.PDB:1M1NX-ray diffraction, 1.16 angstromsIn the oxidized state the cluster can be described as two 4Fe-3S subclusters, one ligated by two cysteines, the other ligated by two cysteines and a serine, with the subclusters bridged by one mu-3 sulfur and two cysteine mu-2 sulfurs, one of these cysteines also being ligated through its alpha-amino group. In the reduced state, the serine and cysteine amino ligands are protonated and the bridging sulfur is mu-4 ligated.C, C, C, C, C, C, Scross-link 7incidental to RESID:AA0141GO:0018441PSI-MOD:00305iron-sulfur proteinmetalloproteinMETAL Iron-sulfur (8Fe-7S)AA030124-Aug-200124-Aug-200130-Apr-2010L-isoleucine or L-leucineC 6 H 11 N 1 O 1113.16113.084064Dixon, H.B.F.Eur. J. Biochem. 264, 607-609, 1999IUPAC-IUBMB Joint Commission on Biochemical Nomenclature (JCBN) and Nomenclature Committee of IUBMB (NC-IUBMB), newsletter 1999.PMID:10523135http://www.chem.qmul.ac.uk/iubmb/newsletter/1999/item3.htmlThis represents an uncertainty between L-isoleucine and L-leucine, sometimes encountered in mass spectrometry and NMR. The symbol and abbreviation have not officially been adopted by IUPAC or IUBMB.JXlePSI-MOD:00306AA030224-Aug-200124-Aug-200130-Jun-2012L-aspartimide2-amino-butanimidealpha-aminosuccinimideASIL-2-aminosuccinimideL-3-aminosuccinimide [misnomer]L-asparaginimide(3S)-3-amino-2,5-pyrrolidinedioneCAS:5615-80-5PDBHET:SNNC 4 H 5 N 2 O 2113.10113.035102C 0 H -2 N 0 O -1-18.02-18.010565Robson, V.M.Rae, I.D.Ng, F.Biol. Chem. Hoppe-Seyler 371, 423-431, 1990Identification of the aspartimide structure in a previously-reported peptide.PMID:2378679report of modification not in an intein, probably artifactualToney, K.Bateman, A.Gagnon, C.Bennett, H.P.J. Biol. Chem. 268, 1024-1031, 1993Aspartimide formation in the joining peptide sequence of porcine and mouse pro-opiomelanocortin.PMID:8380403mass spectrometric detection and enzymatic evidence for natural formation of aspartimide intermediateXu, M.Q.Comb, D.G.Paulus, H.Noren, C.J.Shao, Y.Perler, F.B.EMBO J. 13, 5517-5522, 1994Protein splicing: an analysis of the branched intermediate and its resolution by succinimide formation.PMID:7988548Shao, Y.Xu, M.Q.Paulus, H.Biochemistry 34, 10844-10850, 1995Protein splicing: characterization of the aminosuccinimide residue at the carboxyl terminus of the excised intervening sequence.DOI:10.1021/bi00034a017PMID:7662664Shao, Y.Paulus, H.J. Pept. Res. 50, 193-198, 1997Protein splicing: estimation of the rate of O-N and S-N acyl rearrangements, the last step of the splicing process.PMID:9309583Regni, C.A.Roush, R.F.Miller, D.J.Nourse, A.Walsh, C.T.Schulman, B.A.EMBO J. 28, 1953-1964, 2009How the MccB bacterial ancestor of ubiquitin E1 initiates biosynthesis of the microcin C7 antibiotic.DOI:10.1038/emboj.2009.146PMID:19494832this modification is produced as an intermediate by the MccB enzymeRegni, C.A.Roush, R.F.Miller, D.Nourse, A.Walsh, C.T.Schulman, B.A.submitted to the Protein Data Bank, April 2009Crystal structure of E. coli MccB + succinimide.PDB:3H5RX-ray diffraction, 2.10 angstromsThis modification is autocatalytically produced from the carboxyl-terminal asparagine of spliced inteins.This modification is produced by the MccB enzyme as an intermediate in the process of biosynthesizing (3-aminopropyl)(L-aspartyl-1-amino)phosphoryl-5'-adenosine. See RESID:AA0328.Ncarboxyl-terminalGO:0019801PSI-MOD:00307blocked carboxyl endprotein splicingsuccinimide ringNot availablethis modification is not annotated in UniProt featuresAA030324-Aug-200124-Aug-200130-Jun-2009L-glutamimide2-aminopentanimide3-amino-2,6-piperidinedionealpha-aminoglutarimide(3S)-3-aminopiperidine-2,6-dioneCAS:2353-44-8C 5 H 7 N 2 O 2127.12127.050752C 0 H -2 N 0 O -1-18.02-18.010565Amitai, G.Dassa, B.Pietrokovski, S.J. Biol. Chem. 279, 3121-3131, 2004Protein splicing of inteins with atypical glutamine and aspartate C-terminal residues.DOI:10.1074/jbc.M311343200PMID:14593103mass spectrometric identificationThis modification is autocatalytically produced from the carboxyl-terminal glutamine of spliced inteins.Qcarboxyl-terminalGO:0019802PSI-MOD:00308blocked carboxyl endprotein splicingNot availablethis modification is not annotated in UniProt featuresAA030424-Aug-200124-Aug-200130-Sep-20133-carboxy-L-aspartic acid2-amino-3-carboxybutanedioic acid3-carboxyaspartic acidbeta-carboxyaspartic acid(2S)-2-aminoethane-1,1,2-tricarboxylic acidCAS:75898-26-9C 5 H 5 N 1 O 5159.10159.016772C 1 H 0 N 0 O 244.0143.989829Hauschka, P.V.Henson, E.B.Gallop, P.M.Anal. Biochem. 108, 57-63, 1980Quantitative analysis and comparative decarboxylation of aminomalonic acid, beta-carboxyaspartic acid, and gamma-carboxyglutamic acid.DOI:10.1016/0003-2697(80)90691-0PMID:7457858Richey, B.Christy, M.R.Haltiwanger, R.C.Koch, T.H.Gill, S.J.Biochemistry 21, 4819-4823, 1982Unusual zwitterion of D,L-beta-carboxyaspartic acid: pKa and X-ray crystallographic measurements.DOI:10.1021/bi00262a046PMID:7138832X-ray diffraction; pKa determinationsKoch, T.H.Christy, M.R.Barkley, R.M.Sluski, R.Bohemier, D.Van Buskirk, J.J.Kirsch, W.M.Meth. Enzymol. 107, 563-575, 1984beta-Carboxyaspartic acid.DOI:10.1016/0076-6879(84)07040-3PMID:6390094reviewNishimoto, S.K.Zhao, J.Dass, C.Anal. Biochem. 216, 159-164, 1994Isolation and characterization of the reaction product of 4-diazobenzenesulfonic acid and gamma-carboxyglutamic acid: modification of the assay for measurement of beta-carboxyaspartic acid.DOI:10.1006/abio.1994.1020PMID:8135347colorimetric detectionThis extremely acid labile modification has been detected but not located by sequencing in proteins.DGO:0019803PSI-MOD:00309Not availablethis modification is not annotated in UniProt featuresAA030524-Aug-200124-Aug-200131-Dec-2011N5-methyl-L-argininedelta-N-methylarginineN5-carbamimidoyl-N5-methyl-L-ornithine(2S)-2-amino-5-(N-methylcarbamimidamido)pentanoic acidChEBI:21848C 7 H 14 N 4 O 1170.22170.116761C 1 H 2 N 0 O 014.0314.015650Zobel-Thropp, P.Gary, J.D.Clarke, S.J. Biol. Chem. 273, 29283-29286, 1998delta-N-methylarginine is a novel posttranslational modification of arginine residues in yeast proteins.DOI:10.1074/jbc.273.45.29283PMID:9792625Niewmierzycka, A.Clarke, S.J. Biol. Chem. 274, 814-824, 1999S-Adenosylmethionine-dependent methylation in Saccharomyces cerevisiae. Identification of a novel protein arginine methyltransferase.DOI:10.1074/jbc.274.2.814PMID:9873020Chern, M.K.Chang, K.N.Liu, L.F.Tam, T.C.Liu, Y.C.Liang, Y.L.Tam, M.F.J. Biol. Chem. 277, 15345-15353, 2002Yeast ribosomal protein L12 is a substrate of protein-arginine methyltransferase 2.DOI:10.1074/jbc.M111379200PMID:11856739This modification should not be confused with 5-methylarginine (see RESID:AA0272).protein-arginine N5-methyltransferase (EC 2.1.1.-)RGO:0019701PSI-MOD:00310methylated amino acidMOD_RES N5-methylarginineAA030624-Aug-200124-Aug-200130-Sep-2008L-cysteine coenzyme A disulfidecoenzyme A L-cysteine mixed disulfide(2R)-2-amino-3-(2-((3-(((2R)-2,4-dihydroxy-3,3-dimethyl-1-oxobutyl)amino)-1-oxopropyl)amino)ethyl)dithio-propanoic acid 4'-ester with adenosine 5'-(trihydrogen diphosphate) 3'-(dihydrogen phosphate)C 24 H 39 N 8 O 17 P 3 S 2868.66868.108744C 21 H 34 N 7 O 16 P 3 S 1765.52765.099559Thorneley, R.N.Abell, C.Ashby, G.A.Drummond, M.H.Eady, R.R.Huff, S.Macdonald, C.J.Shneier, A.Biochemistry 31, 1216-1224, 1992Posttranslational modification of Klebsiella pneumoniae flavodoxin by covalent attachment of coenzyme A, shown by 31P NMR and electrospray mass spectrometry, prevents electron transfer from the nifJ protein to nitrogenase. A possible new regulatory mechanism for biological nitrogen fixation.DOI:10.1021/bi00119a035PMID:1734967this modification, of a Klebsiella pneumoniae protein over-expressed in Escherichia coli cells, has not been demonstrated under natural conditionsCGO:0019703PSI-MOD:00311coenzyme Adisulfide bondphosphoproteinNot availablethis modification is not annotated in UniProt featuresAA030707-Sep-200107-Sep-200101-Mar-2013S-myristoyl-L-cysteinetetradecanoate cysteine thioester(R)-2-amino-3-(tetradecanoylsulfanyl)propanoic acidChEBI:22061PDBHET:MYRC 17 H 31 N 1 O 2 S 1313.50313.207550C 14 H 26 N 0 O 1 S 0210.36210.198365Armah, D.A.Mensa-Wilmot, K.J. Biol. Chem. 274, 5931-5938, 1999S-Myristoylation of a glycosylphosphatidylinositol-specific phospholipase C in Trypanosoma brucei.DOI:10.1074/jbc.274.9.5931PMID:10026218chemical characterization; chromatographic detection; radioisotope labelingArmah, D.A.Mensa-Wilmot, K.Biochem. Biophys. Res. Commun. 256, 569-572, 1999Protein S-myristoylation in Leishmania revealed with a heterologous reporter.DOI:10.1006/bbrc.1999.0376PMID:10080938chemical characterization; chromatographic detection; radioisotope labelingSteinert, P.M.Kim, S.Y.Chung, S.I.Marekov, L.N.J. Biol. Chem. 271, 26242-26250, 1996The transglutaminase 1 enzyme is variably acylated by myristate and palmitate during differentiation in epidermal keratinocytes.DOI:10.1074/jbc.271.42.26242PMID:8824274mass spectrometric identification; differential S-palmitoylation and S-myristoylation (see RESID:AA0106)Kim, Y.G.Sohn, E.J.Seo, J.Lee, K.J.Lee, H.S.Hwang, I.Whiteway, M.Sacher, M.Oh, B.H.Nature Struct. Mol. Biol. 12, 38-45, 2005Crystal structure of bet3 reveals a novel mechanism for Golgi localization of tethering factor TRAPP.DOI:10.1038/nsmb871PMID:15608655X-ray diffraction, 1.60 angstromsKim, Y.-G.Sacher, M.Oh, B.-H.submitted to the Protein Data Bank, November 2004The Crystal Structure of Truncated Mouse Bet3P.PDB:1WC9X-ray diffraction, 1.60 angstromsThe predominant palmitoyl transferase in mammalian systems appears to utilize a mixture of saturated and unsaturated fatty acids including myristoic acid. Some systems may be more specific in their incorporation of other fatty acids. See RESID:AA0106 and RESID:AA0308.protein-cysteine S-myristoyltransferase (EC 2.3.1.-)CGO:0019704GO:0042050PSI-MOD:00312lipoproteinmyristoylationthioester bondLIPID S-myristoyl cysteineAA030807-Sep-200107-Sep-200131-May-2018S-palmitoleoyl-L-cysteinecis-9-hexadecenoate cysteine thioesterS-palmitoleyl-L-cysteine [misnomer](R)-2-amino-3-((Z)-9-hexadecenoylsulfanyl)propanoic acidC 19 H 33 N 1 O 2 S 1339.54339.223200C 16 H 28 N 0 O 1 S 0236.40236.214016Casey, W.M.Gibson, K.J.Parks, L.W.J. Biol. Chem. 269, 2082-2085, 1994Covalent attachment of palmitoleic acid (C16:1 Delta 9) to proteins in Saccharomyces cerevisiae. Evidence for a third class of acylated proteins.PMID:8294460This specific modification has been detected but not located by sequencing in proteins. This modification may also arise from non-specific activity of the enzymes that produce S-palmitoyl-L-cysteine; see RESID:AA0106.protein-cysteine S-palmitoleoyltransferase (EC 2.3.1.-)CGO:0019939GO:0042050PSI-MOD:00313lipoproteinthioester bondNot availablethis modification is not annotated in UniProt featuresAA030907-Sep-200107-Sep-200129-Nov-2010glycine cholesterol estercholesteryl glycinatehedgehog lipophilic adductglycine cholest-5-en-3beta-ol esterCAS:57-88-5C 29 H 48 N 1 O 2442.71442.368505C 27 H 44 N 0 O 0368.65368.344301Porter, J.A.Young, K.E.Beachy, P.A.Science 274, 255-259, 1996Cholesterol modification of hedgehog signaling proteins in animal development.DOI:10.1126/science.274.5285.255PMID:8824192chemical characterization; chromatographic detection; radioisotope labelingMann, R.K.Beachy, P.A.Biochim. Biophys. Acta 1529, 188-202, 2000Cholesterol modification of proteins.DOI:10.1016/S1388-1981(00)00148-7PMID:11111088review articleThis modification occurs at the carboxyl end released during autolytic cleavage.Gcarboxyl-terminalincidental to RESID:AA0060GO:0019708PSI-MOD:00314blocked carboxyl endlipoproteinLIPID Cholesterol glycine esterAA031030-Sep-200130-Sep-200131-Dec-2009pentakis-L-cysteinyl L-histidino nickel tetrairon pentasulfidecarbon monoxide dehydrogenase nickel-iron cofactorNi-4Fe-5S clustermu-1:2kappaS-sulfido-mu3-1:3:5kappaS-sulfido-mu3-2:3:4kappaS-sulfido-mu3-2:4:5kappaS-sulfido-mu3-3:4:5kappaS-sulfido-N1'-histidino-S-cysteinyl-1-iron-S-cysteinyl-2-nickel-3,4,5-tris-(S-cysteinyl iron)COMe:BIM000272PDBHET:NFSC 21 Fe 4 H 26 N 8 Ni 1 O 6 S 101089.161087.593333C 0 Fe 4 H -6 N 0 Ni 1 O 0 S 5436.33435.488498Stephens, P.J.McKenna, M.C.Ensign, S.A.Bonam, D.Ludden, P.W.J. Biol. Chem. 264, 16347-16350, 1989Identification of a Ni- and Fe-containing cluster in Rhodospirillum rubrum carbon monoxide dehydrogenase.PMID:2550436Dobbek, H.Svetlitchnyi, V.Gremer, L.Huber, R.Meyer, O.Science 293, 1281-1285, 2001Crystal structure of a carbon monoxide dehydrogenase reveals a [Ni-4Fe-5S] cluster.DOI:10.1126/science.1061500PMID:11509720X-ray diffraction, 1.6 angstromsDobbek, H.Svetlitchnyi, V.Liss, J.Meyer, O.J. Am. Chem. Soc. 126, 5382-5387, 2004Carbon monoxide induced decomposition of the active site [Ni-4Fe-5S] cluster of CO dehydrogenase.DOI:10.1021/ja037776vPMID:15113209X-ray diffraction, 1.12 angstromsDobbek, H.Svetlitchnyi, V.Gremer, L.Huber, R.Meyer, O.submitted to the Protein Data Bank, May 2004Carbon monoxide dehydrogenase from Carboxydothermus hydrogenoformans - DTT reduced state.PDB:1SU7X-ray diffraction, 1.12 angstromsC, C, C, C, C, Hcross-link 6GO:0019709GO:0042075PSI-MOD:00315iron-sulfur proteinmetalloproteinNi-4Fe-5SnickelMETAL Nickel-iron-sulfur (Ni-4Fe-5S)METAL Nickel-iron-sulfur (Ni-4Fe-5S); via tele nitrogenAA031130-Sep-200130-Sep-200130-Sep-2013N4,N4-dimethyl-L-asparagine2-amino-N4,N4-dimethylbutanediamic acidbeta-dimethylasparagine [misnomer]N(gamma),N(gamma)-dimethylasparagine(2S)-2-amino-4-(dimethylamino)-4-oxobutanoic acidPDBHET:DMHC 6 H 10 N 2 O 2142.16142.074228C 2 H 4 N 0 O 028.0528.031300Ducret, A.Bruun, C.F.Bures, E.J.Marhaug, G.Husby, G.Aebersold, R.Electrophoresis 17, 866-876, 1996Characterization of human serum amyloid A protein isoforms separated by two-dimensional electrophoresis by liquid chromatography/electrospray ionization tandem mass spectrometry.DOI:10.1002/elps.1150170508PMID:8783012mass spectrometric detectionThis structure has not been confirmed.NGO:0019710PSI-MOD:00316methylated amino acidMOD_RES N4,N4-dimethylasparagineAA031231-Dec-200131-Dec-200113-Sep-2013N6-(3,4-didehydroretinylidene)-L-lysineN6-3-dehydroretinal-L-lysineN6-3-dehydroretinyl-lysine(S)-2-amino-6-[(2E,4E,6E,8E)-3,7-dimethyl-9-(2,6,6-trimethylcyclohexa-1,3-dien-1-yl)-2,4,6,8-nonatetraenylidene]aminohexanoic acidCAS:472-87-7C 26 H 36 N 2 O 1392.59392.282764C 20 H 24 N 0 O 0264.41264.187801Suzuki, T.Maeda, Y.Toh, Y.Eguchi, E.Vision Res. 28, 1061-1070, 1988Retinyl and 3-dehydroretinyl esters in the crayfish retina.DOI:10.1016/0042-6989(88)90132-0PMID:3257009identification of covalently bound 3-dehydroretinal as the visual pigment in a porphyropsinTsin, A.T.Santos, F.R.J. Exp. Zool. 235, 181-186, 1985The 3,4-didehydroretinal chromophore of goldfish porphyropsin.DOI:10.1002/jez.1402350204PMID:4056688interconversion of the all-trans and 11-cis forms in a porphyropsinThe all-trans form is shown. Light-induced interconversion with the 11-cis (4Z) form in porphyropsin and cyanopsin is utilized for light sensing in some animals.This modification has been detected but not located by sequencing in proteins. It may be substituted for retinal (see RESID:AA0120) in opsin.KGO:0019931PSI-MOD:00317chromoproteinretinalNot availablethis modification is not annotated in UniProt featuresAA031331-Dec-200131-Dec-200124-Aug-20124'-(L-cystein-S-yl)-L-tryptophyl quinone3-(2-amino-2-carboxyethyl)-4-[2-amino-2-carboxyethyl]sulfanyl-6,7-indolinedione4-(S-cysteinyl)tryptophan-6,7-dioneCTQcysteine tryptophylquinone(2R)-2-amino-3-[(3-[(2S)-2-amino-2-carboxyethyl]-6,7-dioxo-6,7-dihydro-1H-indol-4-yl)sulfanyl]propanoic acidC 14 H 11 N 3 O 4 S 1317.32317.047027C 0 H -4 N 0 O 2 S 027.9727.958529Datta, S.Mori, Y.Takagi, K.Kawaguchi, K.Chen, Z.W.Okajima, T.Kuroda, S.Ikeda, T.Kano, K.Tanizawa, K.Mathews, F.S.Proc. Natl. Acad. Sci. U.S.A. 98, 14268-14273, 2001Structure of a quinohemoprotein amine dehydrogenase with an uncommon redox cofactor and highly unusual crosslinking.DOI:10.1073/pnas.241429098PMID:11717396X-ray diffraction, 2.05 angstroms; mass spectrometric characterization; p-nitrophenylhydrazine derivative of cysteine tryptophylquinoneDatta, S.Mori, Y.Takagi, K.Kawaguchi, K.Chen, Z.W.Kano, K.Ikeda, T.Okajima, T.Kuroda, S.Tanizawa, K.Mathews, F.S.submitted to the Protein Data Bank, July 2001Structure of a quinohemoprotein amine dehydrogenase with a unique redox cofactor and highly unusual crosslinking.PDB:1JJUX-ray diffraction, 2.05 angstromsVandenberghe, I.Kim, J.K.Devreese, B.Hacisalihoglu, A.Iwabuki, H.Okajima, T.Kuroda, S.Adachi, O.Jongejan, J.A.Duine, J.A.Tanizawa, K.Van Beeumen, J.J. Biol. Chem. 276, 42923-42931, 2001The covalent structure of the small subunit from Pseudomonas putida amine dehydrogenase reveals the presence of three novel types of internal cross-linkages, all involving cysteine in a thioether bond.DOI:10.1074/jbc.M107164200PMID:11555656mass spectrometric and chemical characterizationC, Wcross-link 2secondary to RESID:AA0148GO:0019927PSI-MOD:00318quinoproteinthioether bondCROSSLNK 4'-cysteinyl-tryptophylquinone (Cys-Trp)AA031431-Dec-200131-Dec-200131-Mar-20133-(L-cystein-S-yl)-L-aspartic acid(2R,3S,6R)-2,6-diamino-3-carboxy-4-thiaheptanedioic acid3-carboxy-L-lanthionine(2R,3S)-2-amino-3-([(2R)-2-amino-2-carboxyethyl]sulfanyl)butanedioic acidC 7 H 8 N 2 O 4 S 1216.21216.020478C 0 H -2 N 0 O 0 S 0-2.02-2.015650Datta, S.Mori, Y.Takagi, K.Kawaguchi, K.Chen, Z.W.Okajima, T.Kuroda, S.Ikeda, T.Kano, K.Tanizawa, K.Mathews, F.S.Proc. Natl. Acad. Sci. U.S.A. 98, 14268-14273, 2001Structure of a quinohemoprotein amine dehydrogenase with an uncommon redox cofactor and highly unusual crosslinking.DOI:10.1073/pnas.241429098PMID:11717396X-ray diffraction, 2.05 angstroms; mass spectrometric characterizationDatta, S.Mori, Y.Takagi, K.Kawaguchi, K.Chen, Z.W.Kano, K.Ikeda, T.Okajima, T.Kuroda, S.Tanizawa, K.Mathews, F.S.submitted to the Protein Data Bank, July 2001Structure of a quinohemoprotein amine dehydrogenase with a unique redox cofactor and highly unusual crosslinking.PDB:1JJUX-ray diffraction, 2.05 angstromsVandenberghe, I.Kim, J.K.Devreese, B.Hacisalihoglu, A.Iwabuki, H.Okajima, T.Kuroda, S.Adachi, O.Jongejan, J.A.Duine, J.A.Tanizawa, K.Van Beeumen, J.J. Biol. Chem. 276, 42923-42931, 2001The covalent structure of the small subunit from Pseudomonas putida amine dehydrogenase reveals the presence of three novel types of internal cross-linkages, all involving cysteine in a thioether bond.DOI:10.1074/jbc.M107164200PMID:11555656mass spectrometric and chemical characterizationC, Dcross-link 2GO:0019928PSI-MOD:00319lanthioninethioether bondCROSSLNK 3-cysteinyl-aspartic acid (Cys-Asp)AA031531-Dec-200131-Dec-200131-Mar-20124-(L-cystein-S-yl)-L-glutamic acid(2S,3S,7R)-2,7-diamino-4-carboxy-5-thiaoctanedioic acid(2S,4S)-2-amino-4-[(R)-2-amino-2-carboxyethyl]sulfanylpentanedioic acidChEBI:20293C 8 H 10 N 2 O 4 S 1230.24230.036128C 0 H -2 N 0 O 0 S 0-2.02-2.015650Datta, S.Mori, Y.Takagi, K.Kawaguchi, K.Chen, Z.W.Okajima, T.Kuroda, S.Ikeda, T.Kano, K.Tanizawa, K.Mathews, F.S.Proc. Natl. Acad. Sci. U.S.A. 98, 14268-14273, 2001Structure of a quinohemoprotein amine dehydrogenase with an uncommon redox cofactor and highly unusual crosslinking.DOI:10.1073/pnas.241429098PMID:11717396X-ray diffraction, 2.05 angstroms; mass spectrometric characterizationDatta, S.Mori, Y.Takagi, K.Kawaguchi, K.Chen, Z.W.Kano, K.Ikeda, T.Okajima, T.Kuroda, S.Tanizawa, K.Mathews, F.S.submitted to the Protein Data Bank, July 2001Structure of a quinohemoprotein amine dehydrogenase with a unique redox cofactor and highly unusual crosslinking.PDB:1JJUX-ray diffraction, 2.05 angstromsVandenberghe, I.Kim, J.K.Devreese, B.Hacisalihoglu, A.Iwabuki, H.Okajima, T.Kuroda, S.Adachi, O.Jongejan, J.A.Duine, J.A.Tanizawa, K.Van Beeumen, J.J. Biol. Chem. 276, 42923-42931, 2001The covalent structure of the small subunit from Pseudomonas putida amine dehydrogenase reveals the presence of three novel types of internal cross-linkages, all involving cysteine in a thioether bond.DOI:10.1074/jbc.M107164200PMID:11555656mass spectrometric and chemical characterizationC, Ecross-link 2GO:0019929PSI-MOD:00320thioether bondCROSSLNK 4-cysteinyl-glutamic acid (Cys-Glu)AA031631-Dec-200131-Dec-200120-May-2011cis-14-hydroxy-10,13-dioxo-7-heptadecenoic acid L-aspartate esterbarley lipid transfer protein modification(7Z,14Xi)-14-[(S)-3-amino-3-carboxy-propanoyl]oxy-10,13-dioxo-7-heptadecenoic acidC 21 H 31 N 1 O 7409.48409.210052C 17 H 26 N 0 O 4294.39294.183109Lindorff-Larsen, K.Lerche, M.H.Poulsen, F.M.Roepstorff, P.Winther, J.R.J. Biol. Chem. 276, 33547-33553, 2001Barley lipid transfer protein, LTP1, contains a new type of lipid-like post-translational modification.DOI:10.1074/jbc.M104841200PMID:11435437mass spectrometric, (1)H-NMR, and (13)C-NMR characterizationThe stereochemistry for the second chiral center has not been resolved. The (14S) form is shown.DGO:0019930GO:0042050PSI-MOD:00321lipoproteinLIPID Cis-14-hydroxy-10,13-dioxo-7-heptadecenoic acid aspartate esterAA031718-Jan-200218-Jan-200231-May-20181'-methyl-L-histidine3-methylhistidine [misnomer]4-methyl-histidine [misnomer]N(epsilon)-methylhistidineN(tau)-methylhistidinetele-methylhistidine(S)-2-amino-3-(1-methyl-1H-imidazol-4-yl)propanoic acidCAS:332-80-9ChEBI:16367PDBHET:HICC 7 H 9 N 3 O 1151.17151.074562C 1 H 2 N 0 O 014.0314.015650Asatoor, A.M.Armstrong, M.D.Biochem. Biophys. Res. Commun. 26, 168-174, 19673-methyl histidine, a component of actin.DOI:10.1016/0006-291X(67)90229-XPMID:6067661identified as 1'-methylhistidine (tele-) and distinguished from 3'-methylhistidine (pros-) by ion exchange chromatographyEdmondson, D.E.Kenney, W.C.Singer, T.P.Biochemistry 15, 2937-2945, 1976Structural elucidation and properties of 8alpha-(N1-histidyl)riboflavin: the flavin component of thiamine dehydrogenase and beta-cyclopiazonate oxidocyclase.DOI:10.1021/bi00659a001PMID:8076chemical and spectrographic characterization of both 1'- and 3'-methylhistidine; the authors use biochemical rather than IUPAC numberingIUPAC-IUB Joint Commission on Biochemical Nomenclature (JCBN)Eur. J. Biochem. 138, 9-37, 1984Nomenclature and symbolism for amino acids and peptides. Recommendations 1983.DOI:10.1111/j.1432-1033.1984.tb07877.xPMID:6692818tele-, tau-, and pros-, pi-, nomenclatureRaftery, M.J.Harrison, C.A.Alewood, P.Jones, A.Geczy, C.L.Biochem. J. 316, 285-293, 1996Isolation of the murine S100 protein MRP14 (14 kDa migration-inhibitory-factor-related protein) from activated spleen cells: characterization of post-translational modifications and zinc binding.PMID:8645219mass spectrometric detection; chromatographic identification of PTC derivatives of 1'- and 3'-methylhistidine; the authors' source for the reference standard acknowledges that their name, 1'-methylhistidine, is a misnomer for the IUPAC standard name 3'-methylhistidineYao, X.Grade, S.Wriggers, W.Rubenstein, P.A.J. Biol. Chem. 274, 37443-37449, 1999His(73), often methylated, is an important structural determinant for actin. A mutagenic analysis of HIS(73) of yeast actin.DOI:10.1074/jbc.274.52.37443PMID:10601317Otterbein, L.R.Graceffa, P.Dominguez, R.Science 293, 708-711, 2001The crystal structure of uncomplexed actin in the ADP state.DOI:10.1126/science.1059700PMID:11474115Otterbein, L.R.Graceffa, P.Dominguez, R.submitted to the Protein Data Bank, May 2001Uncomplexed actin.PDB:1J6ZX-ray diffraction, 1.54 angstromsIn the older biochemical literature this is usually called 3-methylhistidine. See also RESID:AA0073.The crystallographic designation for the substituted nitrogen is epsilon-2, E2.S-adenosyl-L-methionine:protein-L-histidine N-tele-methyltransferase (EC 2.1.1.85)HGO:0018021GO:0042038PSI-MOD:00322methylated amino acidMOD_RES Tele-methylhistidineMOD_RES Methylhistidinethis UniProt feature is used when the isomeric structure has not been determinedAA031818-Jan-200218-Jan-200231-Dec-2011L-lysine methyl ester2,6-diaminohexanoic methyl esteralpha,epsilon-diaminocaproic methyl estermethyl L-lysinatemethyl (S)-2,6-diaminohexanoateCAS:687-64-9ChEBI:21354C 7 H 15 N 2 O 2159.21159.113353C 1 H 2 N 0 O 014.0314.015650Zobel-Thropp, P.Yang, M.C.Machado, L.Clarke, S.J. Biol. Chem. 275, 37150-37158, 2000A novel post-translational modification of yeast elongation factor 1A. Methylesterification at the C terminus.DOI:10.1074/jbc.M001005200PMID:10973948chemical characterizationprotein-lysine O-methyltransferase (EC 2.1.1.-)Kcarboxyl-terminalGO:0042034PSI-MOD:00323methylated carboxyl endMOD_RES Lysine methyl esterAA031931-Mar-200231-Mar-200231-Mar-2013L-serinyl molybdenum bis(molybdopterin guanine dinucleotide)2-amino-5,6-dimercapto-7-methyl-3,7,8a,9-tetrahydro-8-oxa-1,3,9,10-tetraazaanthracen-4-one guanosine dinucleotidebis[8-amino-1a,2,4a,5,6,7,10-heptahydro-2-(trihydrogen diphosphate 5'-ester with guanosine)methyl-6-oxo-3,4-disulfanyl-pteridino[6,7-5,6]pyranoato-S3,S4]-O3-serinyl-molybdenum oxideCAS:128007-95-4PDBHET:MGDPDBHET:MOC 43 H 52 Mo 1 N 21 O 29 P 4 S 41675.091676.012718C 40 H 47 Mo 1 N 20 O 27 P 4 S 41588.011588.980690Schindelin, H.Kisker, C.Hilton, J.Rajagopalan, K.V.Rees, D.C.Science 272, 1615-1621, 1996Crystal structure of DMSO reductase: redox-linked changes in molybdopterin coordination.DOI:10.1126/science.272.5268.1615PMID:8658134X-ray diffraction, 1.30 angstromsLi, H.-K.Temple, C.Rajagopalan, K.V.Schindelin, H.J. Am. Chem. Soc. 122, 7673-7680, 2000The 1.3 Å Crystal Structure of Rhodobacter sphaeroides Dimethyl Sulfoxide Reductase Reveals Two Distinct Molybdenum Coordination Environments.DOI:10.1021/ja000643eLi, H.K.Temple, K.Rajagopalan, K.V.Schindelin, H.submitted to the Protein Data Bank, April 2000The crystal structure of Rhodobacter sphaeroides dimethylsulfoxide reductase reveals two distinct molybdenum coordination environments.PDB:1EU1X-ray diffraction, 1.30 angstromsOne possible structure of a reduced form (+4H) is shown. The fully reduced form would be 1a,2,3,4,4a,5,6,7,10-nonahydro. The fully oxidized form would be 2,6,7-trihydro.There is a distantly bound oxygen, which could exist as an oxide, a hydroxide or as a coordinating water. It is shown as an oxide.SGO:0042258PSI-MOD:00324metalloproteinmolybdenummolybdopterinphosphoproteinACT_SITEthis UniProt feature lacks a descriptive representationAA032031-Mar-200231-Mar-200231-Mar-20123-(methylthio)-L-asparagine2,4-diamino-3-(methylsulfanyl)-4-oxobutanoic acid3-carboxamido-S-methyl-cysteinebeta-(methylthio)asparagine(2R,3Xi)-2-amino-3-(methylsulfanyl)-4-butanediamic acidC 5 H 8 N 2 O 2 S 1160.19160.030649C 1 H 2 N 0 O 0 S 146.0945.987721Carr, J.F.Hamburg, D.M.Gregory, S.T.Limbach, P.A.Dahlberg, A.E.J. Bacteriol. 188, 2020-2023, 2006Effects of streptomycin resistance mutations on posttranslational modification of ribosomal protein S12.DOI:10.1128/JB.188.5.2020-2023.2006PMID:16484214noting that mutations of the S12 methylthioaspartic acid were lethal in Thermus thermophilus, the Bacillus subtilis S12 gene was resequenced and found to differ from the reported genome sequenceLauber, M.A.Running, W.E.Reilly, J.P.J. Proteome Res. 8, 4193-4206, 2009B. subtilis Ribosomal Proteins: Structural Homology and Post-Translational Modifications.DOI:10.1021/pr801114kPMID:19653700numerous genome sequencing errors are noted, including the S12 methylthioaspartic acid site; B. subtilis lacks the RimO modifying enzyme, and the S12 invariant aspartic acid is not modifiedThere is a second chiral center. The (2R,3R) form is shown.This modification was predicted for ribosomal protein S12 in Bacillus subtilis when the sequence in the original version of the genome was reported to have asparagine rather than aspartic acid at the position of the methylthioaspartic acid modification (see RESID:AA0232). Two groups independently confirmed that the genome sequence was erroroneous. The sequence in the revised genome has aspartic acid at that position.NGO:0042259PSI-MOD:00325thioether bondNot availablethis modification is not annotated in UniProt featuresAA032124-May-200224-May-200231-May-2018L-pyrrolysine2-azanyl-6-[(2R,3R)-3-methyl-3,4-dihydro-2H-pyrrol-2-ylcarbonyl]azanylhexanoic acidmonomethylamine methyltransferase cofactor lysine adductN6-(4-methyl-1,2-didehydropyrrolidine-5-carboxyl)-L-lysineN6-(4-methyl-delta-1-pyrroline-5-carboxyl)-L-lysineN6-([(2R,3R)-3-methyl-3,4-dihydro-2H-pyrrol-2-yl]carbonyl)-L-lysine(2S)-2-amino-6-[(2R,3R)-3-methyl-3,4-dihydro-2H-pyrrol-2-ylcarbonyl]aminohexanoic acidCAS:448235-52-7ChEBI:21860PDBHET:BGXPDBHET:PYHPDBHET:X7OC 12 H 19 N 3 O 2237.30237.147727C 0 H 0 N 0 O 00.000.000000C 6 H 7 N 1 O 1109.13109.052764James, C.M.Ferguson, T.K.Leykam, J.F.Krzycki, J.A.J. Biol. Chem. 276, 34252-34258, 2001The amber codon in the gene encoding the monomethylamine methyltransferase isolated from Methanosarcina barkeri is translated as a sense codon.DOI:10.1074/jbc.M102929200PMID:11435424Hao, B.Gong, W.Ferguson, T.K.James, C.M.Krzycki, J.A.Chan, M.K.Science 296, 1462-1466, 2002A new UAG-encoded residue in the structure of a methanogen methyltransferase.DOI:10.1126/science.1069556PMID:12029132Srinivasan, G.James, C.M.Krzycki, J.A.Science 296, 1459-1462, 2002Pyrrolysine encoded by UAG in Archaea: charging of a UAG-decoding specialized tRNA.DOI:10.1126/science.1069588PMID:12029131Hao, B.Gong, W.Ferguson, T.K.James, C.M.Krzycki, J.A.Chan, M.K.submitted to the Protein Data Bank, February 2002Crystal Structure of the Methanosarcina barkeri Monomethylamine Methyltransferase (MtmB).PDB:1L2QX-ray diffraction, 1.55 angstromsHao, B.Gong, W.Ferguson, T.K.James, C.M.Krzycki, J.A.Chan, M.K.submitted to the Protein Data Bank, January 2003Crystal Structure of the Methanosarcina barkeri Monomethylamine Methyltransferase (MtmB).PDB:1NTHX-ray diffraction, 1.55 angstromsBlight, S.K.Larue, R.C.Mahapatra, A.Longstaff, D.G.Chang, E.Zhao, G.Kang, P.T.Green-Church, K.B.Chan, M.K.Krzycki, J.A.Nature 431, 333-335, 2004Direct charging of tRNA(CUA) with pyrrolysine in vitro and in vivo.DOI:10.1038/nature02895PMID:15329732Polycarpo, C.Ambrogelly, A.Berube, A.Winbush, S.M.McCloskey, J.A.Crain, P.F.Wood, J.L.Soell, D.Proc. Natl. Acad. Sci. U.S.A. 101, 12450-12454, 2004An aminoacyl-tRNA synthetase that specifically activates pyrrolysine.DOI:10.1073/pnas.0405362101PMID:15314242Krzycki, J.A.Curr. Opin. Chem. Biol. 8, 484-491, 2004Function of genetically encoded pyrrolysine in corrinoid-dependent methylamine methyltransferases.DOI:10.1016/j.cbpa.2004.08.012PMID:15450490proposed functional role of pyrrolysine in methylamine methyltransferasesSoares, J.A.Zhang, L.Pitsch, R.L.Kleinholz, N.M.Jones, R.B.Wolff, J.J.Amster, J.Green-Church, K.B.Krzycki, J.A.J. Biol. Chem. 280, 36962-36969, 2005The residue mass of L-pyrrolysine in three distinct methylamine methyltransferases.DOI:10.1074/jbc.M506402200PMID:16096277mass spectrometric characterization; the substituent at the 3 position on the pyrrol ring is established as a methyl groupHeinemann, I.U.O'Donoghue, P.Madinger, C.Benner, J.Randau, L.Noren, C.J.Söll, D.Proc. Natl. Acad. Sci. U.S.A. 106, 21103-21108, 2009The appearance of pyrrolysine in tRNAHis guanylyltransferase by neutral evolution.DOI:10.1073/pnas.0912072106PMID:19965368report of a pyrrolysine apparently incorporated for termination suppression and not catalytically activeGaston, M.A.Zhang, L.Green-Church, K.B.Krzycki, J.A.Nature 471, 647-650, 2011The complete biosynthesis of the genetically encoded amino acid pyrrolysine from lysine.DOI:10.1038/nature09918PMID:21455182mass spectrometric identification of intermediate using (13)C and (15)N labelsPyrrolysine is encoded by the UAG codon in some genetic systems.Although the single letter symbol O is recommended by IUBMB, most software applications fail to recognize it, and many sequence databases use the single letter symbol K.Proposed enzyme names are presented. There is evidence for the third reaction with an ornithine substrate, but not yet for the 3-methylornithine substrate, and the redox cofactor has not been identified.lysine--tRNA(Pyl) ligase (EC 6.1.1.25)pyrrolysine--tRNA(Pyl) ligase (EC 6.1.1.26)(3R)-3methyl-D-ornithine carboxy-aminomethylmutase, PylB (EC 5.4.99.-)(3R)-3-methyl-D-ornithine--L-lysine ligase, PylC (EC 6.3.2.-)N6-[(3R)-3-methyl-D-ornithinyl]-L-lysine N5-ornithine dehydrogenase, PylD (EC 1.4.1.-)OPylGO:0030631PSI-MOD:01187KPSI-MOD:00326pyrrolysineNON_STD PyrrolysineAA032231-May-200231-May-200231-Dec-20083-hydroxy-L-tryptophan3-hydroxytryptophanbeta-hydroxytryptophan(2S,3S)-2-amino-3-hydroxy-3-(1H-indol-3-yl)propanoic acidPDBHET:HTRPDBHET:HYDC 11 H 10 N 2 O 2202.21202.074228C 0 H 0 N 0 O 116.0015.994915Choinowski, T.Blodig, W.Winterhalter, K.H.Piontek, K.J. Mol. Biol. 286, 809-827, 1999The crystal structure of lignin peroxidase at 1.70 A resolution reveals a hydroxy group on the Cbeta of tryptophan 171: a novel radical site formed during the redox cycle.DOI:10.1006/jmbi.1998.2507PMID:10024453X-ray diffraction, 1.7 angstromsChoinowski, T.H.Piontek, K.Glumoff, T.submitted to the Protein Data Bank, November 1995Lignin peroxidase (isozyme H2) pI=4.15.PDB:1LLPX-ray diffraction, 1.7 angstroms; it is uncertain whether this modification is required for enzyme activity, or is the byproduct of a redox cycle involving formation of a tryptophyl radicalLiu, A.Ho, R.Y.Que Jr., L.Ryle, M.J.Phinney, B.S.Hausinger, R.P.J. Am. Chem. Soc. 123, 5126-5127, 2001Alternative reactivity of an alpha-ketoglutarate-dependent iron(II) oxygenase: enzyme self-hydroxylation.DOI:10.1021/ja005879xPMID:11457355resonance Raman spectroscopic detection; mass spectrometric identification; the modification is shown to be autocatalytic, requires ascorbate, and converts alpha-ketoglutarate to succinate and CO2WGO:0045325PSI-MOD:00327hydroxylationMOD_RES 3-hydroxytryptophanAA032330-Jun-200230-Jun-200230-Apr-2010O4'-(phospho-3'-DNA)-L-tyrosineO4'-L-tyrosine 3'-DNA phosphodiester(S)-2-amino-3-[4-(3'-deoxyribonucleic acid phosphonoxy)phenyl]propanoic acidC 9 H 10 N 1 O 5 P 1 +243.15 +243.029659 +C 0 H 1 N 0 O 3 P 1 +79.98 +79.966331 +Evans, B.R.Chen, J.W.Parsons, R.L.Bauer, T.K.Teplow, D.B.Jayaram, M.J. Biol. Chem. 265, 18504-18510, 1990Identification of the active site tyrosine of Flp recombinase. Possible relevance of its location to the mechanism of recombination.PMID:2211714The keyword "phosphoprotein" is not used with polynucleotide-linked intermediate modifications.YGO:0045326PSI-MOD:00328*phosphoproteingenome-linked proteinACT_SITE O-(3'-phospho-DNA)-tyrosine intermediateAA032430-Jun-200230-Jun-200231-Dec-2010hydroxyheme-L-glutamate ester5-hydroxymethyl protoporphyrin IX 5-glutamate estercytochrome P450 CYP4A family heme cofactor[3-[(S)-(4-amino-4-carboxy)butanoyloxymethyl]-7,12-diethenyl-8,13,17-trimethyl-21H,23H-porphine-2,18-bis(2-carboxyethyl)-N21,N22,N23,N24]-ferrateCOMe:BIM000314C 39 Fe 1 H 37 N 5 O 7743.60743.204236C 34 Fe 1 H 30 N 4 O 4614.48614.161643Hoch, U.Ortiz De Montellano, P.R.J. Biol. Chem. 276, 11339-11346, 2001Covalently linked heme in cytochrome P4504A fatty acid hydroxylases.DOI:10.1074/jbc.M009969200PMID:11139583LeBrun, L.A.Hoch, U.Ortiz de Montellano, P.R.J. Biol. Chem. 277, 12755-12761, 2002Autocatalytic mechanism and consequences of covalent heme attachment in the cytochrome P4504A family.DOI:10.1074/jbc.M112155200PMID:11821421LeBrun, L.A.Xu, F.Y.Kroetz, D.L.Ortiz de Montellano, P.R.Biochemistry 41, 5931-5937, 2002Covalent attachment of the heme prosthetic group in the CYP4F cytochrome P450 family.DOI:10.1021/bi025527yPMID:11980497autocatalyticEGO:0045328PSI-MOD:00329chromoproteinhemehydroxylationironmetalloproteinBINDING Heme (covalent; via 1 link)AA032512-Jul-200212-Jul-200231-Dec-20111'-(phospho-5'-guanosine)-L-histidineL-histidine 5'-guanosine phosphoramidesterL-histidine monoanhydride with 5'-guanylic acidN(tau)-5'-guanylic-L-histidineN1'-guanylylated histidinetele-5'-guanylic-L-histidine(2S)-2-amino-3-(1-(5'-adenosine phosphono)imidazol-4-yl)propanoic acidPDBHET:5GPC 16 H 19 N 8 O 8 P 1482.35482.106346C 10 H 12 N 5 O 7 P 1345.21345.047434O'Toole, G.A.Escalante-Semerena, J.C.J. Biol. Chem. 270, 23560-23569, 1995Purification and characterization of the bifunctional CobU enzyme of Salmonella typhimurium LT2. Evidence for a CobU-GMP intermediate.DOI:10.1074/jbc.270.40.23560PMID:7559521chemical evidence for guanylyl phosphoramide intermediateThompson, T.B.Thomas, M.G.Escalante-Semerena, J.C.Rayment, I.Biochemistry 38, 12995-13005, 1999Three-dimensional structure of adenosylcobinamide kinase/adenosylcobinamide phosphate guanylyltransferase (CobU) complexed with GMP: evidence for a substrate-induced transferase active site.DOI:10.1021/bi990910xPMID:10529169X-ray diffraction, 2.2 angstromsThompson, T.B.Thomas, M.G.Escalante-Semerena, J.C.Rayment, I.submitted to the Protein Data Bank, August 1999The three-dimensional structure of adenosylcobinamide kinase/adenosylcobinamide phosphate guanylyltransferase (CobU) complexed with GMP: evidence for a substrate-induced transferase active site.PDB:1C9KX-ray diffraction, 2.2 angstromsThomas, M.G.Thompson, T.B.Rayment, I.Escalante-Semerena, J.C.J. Biol. Chem. 275, 27576-27586, 2000Analysis of the adenosylcobinamide kinase/adenosylcobinamide-phosphate guanylyltransferase (CobU) enzyme of Salmonella typhimurium LT2. Identification of residue His-46 as the site of guanylylation.DOI:10.1074/jbc.M000977200PMID:10869342location of histidine modificationIt is not known whether the phosphoramide bond is formed with the tele- or pros-nitrogen of histidine. The tele-linked form is presented.HGO:0045427PSI-MOD:00330phosphoproteinACT_SITE GMP-histidine intermediateAA032602-Aug-200202-Aug-200231-Dec-2009tetrakis-L-cysteinyl triiron tetrasulfidebis[bis-L-cysteinyl iron disulfido]irontetra-mu-sulfido tetrakis-S-L-cysteinyl triirontetrakis-L-cysteinyl linear [3Fe-4S] clustertetrakis-L-cysteinyl triiron tetrasulfide D2 clusterdi-mu-1:2kappaS-sulfido di-mu-2:3kappaS-sulfido iron bis(bis-S-cysteinyliron)COMe:BIM000318PDBHET:F3SC 12 Fe 3 H 16 N 4 O 4 S 83-704.30703.700181C 0 Fe 3 H -4 N 0 O 0 S 43-291.74291.663442Kennedy, M.C.Kent, T.A.Emptage, M.Merkle, H.Beinert, H.Munck, E.J. Biol. Chem. 259, 14463-14471, 1984Evidence for the formation of a linear [3Fe-4S] cluster in partially unfolded aconitase.PMID:6094558Plank, D.W.Kennedy, M.C.Beinert, H.Howard, J.B.J. Biol. Chem. 264, 20385-20393, 1989Cysteine labeling studies of beef heart aconitase containing a 4Fe, a cubane 3Fe, or a linear 3Fe cluster.PMID:2511202Gailer, J.George, G.N.Pickering, I.J.Prince, R.C.Kohlhepp, P.Zhang, D.Walker, F.A.Winzerling, J.J.J. Am. Chem. Soc. 123, 10121-10122, 2001Human cytosolic iron regulatory protein 1 contains a linear iron-sulfur cluster.DOI:10.1021/ja0158915PMID:11592901X-ray absorption fine structure spectroscopyJones, K.Gomes, C.M.Huber, H.Teixeira, M.Wittung-Stafshede, P.J. Biol. Inorg. Chem. 7, 357-362, 2002Formation of a linear [3Fe-4S] cluster in a seven-iron ferredoxin triggered by polypeptide unfolding.DOI:10.1007/s00775-001-0304-4PMID:11941493The linear 3Fe-4S cluster may form from the reconfiguration of trigonal 3Fe-4S clusters. See RESID:AA0139.C, C, C, Ccross-link 4GO:0045459PSI-MOD:003313Fe-4Siron-sulfur proteinmetalloproteinNot availablethis modification is not annotated in UniProt featuresAA032706-Sep-200206-Sep-200231-May-2018omega-N-glucosyl-L-arginineNG-beta-D-glucosylarginineomega-N-(beta-D-glucosyl)-L-arginineomega-N-glycosyl-L-arginine(2S)-2-amino-5-(beta-D-glucopyranosyl[imino(methylamino)methyl]amino)pentanoic acidC 12 H 22 N 4 O 6318.33318.153934C 6 H 10 N 0 O 5162.14162.052823Singh, D.G.Lomako, J.Lomako, W.M.Whelan, W.J.Meyer, H.E.Serwe, M.Metzger, J.W.FEBS Lett. 376, 61-64, 1995beta-Glucosylarginine: a new glucose-protein bond in a self-glucosylating protein from sweet corn.DOI:10.1016/0014-5793(95)01247-6PMID:8521968sequence analysis; mass spectrometric and linkage analysisDelgado, I.J.Wang, Z.de Rocher, A.Keegstra, K.Raikhel, N.V.Plant Physiol. 116, 1339-1350, 1998Cloning and characterization of AtRGP1. A reversibly autoglycosylated arabidopsis protein implicated in cell wall biosynthesis.DOI:10.1104/pp.116.4.1339PMID:9536051Although proposed as the origin for plant starch, the anomeric isomer was beta, rather than alpha, and only a monosaccharide was observed.amylogenin glucosyltransferase (EC 2.4.1.-)RGO:0042543PSI-MOD:00332glycoproteinCARBOHYD N-linked (Glc...) arginineAA032811-Oct-200211-Oct-200225-Feb-2011(3-aminopropyl)(L-aspartyl-1-amino)phosphoryl-5'-adenosine9-(5'-O-[(3-aminopropoxy)(L-aspart-1-ylamino)phosphoryl]-beta-D-ribofuranosyl)adeninemicrocin C7 asparagine modificationN-(aspart-1-yl)-O-(3-aminopropyl)-O-(5'-adenosyl)phosphoramide5'-O-[(3-aminopropoxy)(L-aspart-1-ylamino)phosphoryl]adenosineChEBI:60869C 17 H 26 N 8 O 9 P 1517.42517.156036C 13 H 19 N 6 O 6 P 1386.30386.110369Gonzalez-Pastor, J.E.San Millan, J.L.Moreno, F.Nature 369, 281, 1994The smallest known gene.DOI:10.1038/369281a0PMID:8183363Metlitskaya, A.Z.Katrukha, G.S.Shashkov, A.S.Zaitsev, D.A.Egorov, Ts.A.Khmel, I.A.FEBS Lett. 357, 235-238, 1995Structure of microcin C51, a new antibiotic with a broad spectrum of activity.DOI:10.1016/0014-5793(94)01345-2PMID:7835418the proposed structure of the peptide has an N4-propylphosphoryl-5'-ribosylisopurine asparagine, and a highly unstable aminoxy-threonine; the initials of "T.A. Egorov" in the PubMed citation are correctedGuijarro, J.I.Gonzalez-Pastor, J.E.Baleux, F.San Millan, J.L.Castilla, M.A.Rico, M.Moreno, F.Delepierre, M.J. Biol. Chem. 270, 23520-23532, 1995Chemical structure and translation inhibition studies of the antibiotic microcin C7.DOI:10.1074/jbc.270.40.23520PMID:7559516the proposed structure of the peptide has a relatively unstable aspartyl-phosphoramidate diester with 3-aminopropanol and 5'-adenosineRoush, R.F.Nolan, E.M.Löhr, F.Walsh, C.T.J. Am. Chem. Soc. 130, 3603-3609, 2008Maturation of an Escherichia coli ribosomal peptide antibiotic by ATP-consuming N-P bond formation in microcin C7.DOI:10.1021/ja7101949PMID:18290647biosynthesisRegni, C.A.Roush, R.F.Miller, D.J.Nourse, A.Walsh, C.T.Schulman, B.A.EMBO J. 28, 1953-1964, 2009How the MccB bacterial ancestor of ubiquitin E1 initiates biosynthesis of the microcin C7 antibiotic.DOI:10.1038/emboj.2009.146PMID:19494832biosynthesisThe structure shown has been independently confirmed. Asparagine is converted to an aspartyl-1-amide by a process requiring two ATP molecules and the formation of a peptidyl-succinimide intermediate.The phosphorus atom is a chiral center that has not been resolved.Ncarboxyl-terminalGO:0046550PSI-MOD:00333blocked carboxyl endphosphoproteinMOD_RES Aspartic acid 1-[(3-aminopropyl)(5'-adenosyl)phosphono]amideAA032931-Dec-200231-Dec-200930-Apr-20101'-heme-L-histidine2-[1-(N1'-histidyl)ethyl]protoporphyrin IXN(epsilon)-histidyl hemeN(tau)-histidyl hemeN1'-histidyl hemetele-histidyl heme(S)-[7-ethenyl-12-[1-((2-amino-2-carboxyethyl)-1H-imidazol-1-yl)ethyl]-3,8,13,17-tetramethyl-21H,23H-porphine-2,18-bis(2-carboxyethyl)-N21,N22,N23,N24]-ferrateCOMe:BIM000351PDBHET:HEMC 40 Fe 1 H 39 N 7 O 5753.64753.236205C 34 Fe 1 H 32 N 4 O 4616.50616.177293Scott, N.L.Falzone, C.J.Vuletich, D.A.Zhao, J.Bryant, D.A.Lecomte, J.T.Biochemistry 41, 6902-6910, 2002Truncated hemoglobin from the cyanobacterium Synechococcus sp. PCC 7002: evidence for hexacoordination and covalent adduct formation in the ferric recombinant protein.DOI:10.1021/bi025609mPMID:12033922NOESY, 2QF-COSY, and TOCSY NMR detection; it is possible that the cross-link forms abnormally in the recombinant systemVu, B.C.Jones, A.D.Lecomte, J.T.J. Am. Chem. Soc. 124, 8544-8545, 2002Novel histidine-heme covalent linkage in a hemoglobin.DOI:10.1021/ja026569cPMID:12121092mass spectrometric characterization; (1)H-(15)N-HMQC NMR identificationFalzone, C.J.Vu, B.C.Scott, N.L.Lecomte, J.T.J. Mol. Biol. 324, 1015-1029, 2002The solution structure of the recombinant hemoglobin from the cyanobacterium Synechocystis sp. PCC 6803 in its hemichrome state.DOI:10.1016/S0022-2836(02)01093-8PMID:12470956(1)H-NMR and (15)N-NMR characterization; the initials of "C.B. Vu" in the PubMed citation are correctedFalzone, C.J.Vu, B.C.Scott, N.L.Lecomte, J.T.submitted to the Protein Data Bank, September 2002Solution structure of the recombinant hemoglobin from the cyanobacterium Synechocystis sp. PCC 6803 in its hemichrome state.PDB:1MWBconformation by (1)H-NMR and (15)N-NMRHoy, J.A.Kundu, S.Trent III, J.T.Ramaswamy, S.Hargrove, M.S.J. Biol. Chem. 279, 16535-16542, 2004The crystal structure of Synechocystis hemoglobin with a covalent heme linkage.DOI:10.1074/jbc.M313707200PMID:14736872X-ray diffraction, 1.8 angstroms; the spelling "Trent, J.T. 3rd", in the PubMed citation is correctedHoy, J.A.Kundu, S.Trent, J.T.Ramaswamy, S.Hargrove, M.S.submitted to the Protein Data Bank, December 2003Crystal structure of Synechocystis hemoglobin with a covalent heme linkage.PDB:1RTXX-ray diffraction, 1.8 angstromsHGO:0046805PSI-MOD:00334chromoproteinhemeironmetalloproteinBINDING Heme (covalent; via tele nitrogen)AA033031-Dec-200231-Dec-200231-Mar-20133-methyl-L-lanthionine sulfoxide(2S,3S,4Xi,6R)-2,6-diamino-3-methyl-4-oxo-4-thiaheptanedioic acid3-methyl-L-lanthionine S-oxideS-oxy-3-methyllanthionine(2S,3S,SXi)-2-amino-3-([(R)-2-amino-2-carboxyethyl]sulfinyl)butanoic acidC 7 H 10 N 2 O 3 S 1202.23202.041213C 0 H -2 N 0 O 0 S 0-2.02-2.015650Zimmermann, N.Metzger, J.W.Jung, G.Eur. J. Biochem. 228, 786-797, 1995The tetracyclic lantibiotic actagardine. 1H-NMR and 13C-NMR assignments and revised primary structure.DOI:10.1111/j.1432-1033.1995.tb20324.xPMID:7737178Zimmermann, N.Jung, G.Eur. J. Biochem. 246, 809-819, 1997The three-dimensional solution structure of the lantibiotic murein-biosynthesis-inhibitor actagardine determined by NMR.DOI:10.1111/j.1432-1033.1997.00809.xPMID:9219543Zimmermann, N.Jung, G.submitted to the Protein Data Bank, May 1997NMR structure of the lantibiotic actagardine, 15 structures.PDB:1AJ1conformation by (1)H-NMR; the sulfoxide is not modeled in the NMR-determined structureShi, Y.Bueno, A.van der Donk, W.A.Chem. Commun. (Camb.) 48, 10966-10968, 2012Heterologous production of the lantibiotic Ala(0)actagardine in Escherichia coli.DOI:10.1039/c2cc36336dPMID:23034674use of GarO, a luciferase-like monooxygenase, to produce the sulfoxideThe S-oxide of 3-methyl-L-lanthionine is a chiral center, and the stereoisomer has not been determined.C, Tcross-link 2GO:0046804PSI-MOD:00335lanthioninethioether bondCROSSLNK Beta-methyllanthionine sulfoxide (Thr-Cys)AA033121-Feb-200321-Feb-200331-Dec-2009tris-L-cysteinyl L-aspartato diiron disulfidedi-mu-sulfido(bis-S-cysteinyliron)(S-cysteinyl-O4-aspartatoiron)COMe:BIM000062PDBHET:FESC 13 Fe 2 H 16 N 4 O 6 S 52-596.28595.838311C 0 Fe 2 H -4 N 0 O 0 S 22-171.78171.783814Werth, M.T.Sices, H.Cecchini, G.Schroeder, I.Lasage, S.Gunsalus, R.P.Johnson, M.K.FEBS Lett. 299, 1-4, 1992Evidence for non-cysteinyl coordination of the [2Fe-2S] cluster in Escherichia coli succinate dehydrogenase.DOI:10.1016/0014-5793(92)80086-VPMID:1312028Meyer, J.Fujinaga, J.Gaillard, J.Lutz, M.Biochemistry 33, 13642-13650, 1994Mutated forms of the [2Fe-2S] ferredoxin from Clostridium pasteurianum with noncysteinyl ligands to the iron-sulfur cluster.DOI:10.1021/bi00250a014PMID:7947772an atypical 2Fe-2S cluster; three of four ligands are determinedHagen, W.R.Silva, P.J.Amorim, M.A.Hagedoorn, P.L.Wassink, H.Haaker, H.Robb, F.T.J. Biol. Inorg. Chem. 5, 527-534, 2000Novel structure and redox chemistry of the prosthetic groups of the iron-sulfur flavoprotein sulfide dehydrogenase from Pyrococcus furiosus; evidence for a [2Fe-2S] cluster with Asp(Cys)3 ligands.DOI:10.1007/s007750050013PMID:10968624The occurrence of aspartic acid rather than cysteine in an otherwise strongly conserved homology domain known to bind the 2Fe-2S cluster in other proteins suggests that aspartic acid may also bind iron-sulfur clusters.C, C, C, Dcross-link 4GO:0046869PSI-MOD:003362Fe-2Siron-sulfur proteinmetalloproteinMETAL Iron-sulfur (2Fe-2S)AA033214-Mar-200314-Mar-200320-Nov-2009S-carbamoyl-L-cysteine2-amino-3-(aminocarbonyl)sulfanylpropanoic acid2-amino-3-(aminocarbonyl)thiopropanoic acidalpha-amino-beta-carbamylthiopropionic acidbeta-carbamylthioalanineS-(aminocarbonyl)cysteineS-carbamoylcysteineS-carbamylcysteineS-cysteinyl carbamate ester(R)-2-amino-3-(carbamoylsulfanyl)propanoic acidCAS:2072-71-1C 4 H 6 N 2 O 2 S 1146.16146.014998C 1 H 1 N 1 O 1 S 043.0243.005814Anderson, P.M.Carlson, J.D.Biochemistry 14, 3688-3694, 1975Reversible reaction of cyanate with a reactive sulfhydryl group at the glutamine binding site of carbamyl phosphate synthetase.DOI:10.1021/bi00687a027PMID:240389Reissmann, S.Hochleitner, E.Wang, H.Paschos, A.Lottspeich, F.Glass, R.S.Bock, A.Science 299, 1067-1070, 2003Taming of a Poison: Biosynthesis of the NiFe-Hydrogenase Cyanide Ligands.DOI:10.1126/science.1080972PMID:12586941the modification is observed when dehydration, an auto-catalyzed process using ATP in the HypE protein, is blockedThis modification can undergo dehydration to produce S-cyanocysteine. See RESID:AA0333.Carbamoylation of the sulfhydryl group can be artifactual, in particular when urea buffers are used.CGO:0046891PSI-MOD:00337MOD_RES S-carbamoylcysteineAA033314-Mar-200314-Mar-200330-Sep-2011S-cyano-L-cysteinealpha-amino-beta-thiocyanatopropionic acidbeta-thiocyanatoalanineS-cyanocysteineserine thiocyanic acid ester(2R)-2-amino-3-thiocyanatopropanoic acidCAS:5652-31-3C 4 H 4 N 2 O 1 S 1128.15128.004434C 1 H -1 N 1 O 0 S 025.0124.995249Degani, Y.Patchornik, A.Biochemistry 13, 1-11, 1974Cyanylation of sulfhydryl groups by 2-nitro-5-thiocyanobenzoic acid. High-yield modification and cleavage of peptides at cysteine residues.DOI:10.1021/bi00698a001PMID:4808702modification by reagent of cysteine in the presence of cystineReissmann, S.Hochleitner, E.Wang, H.Paschos, A.Lottspeich, F.Glass, R.S.Bock, A.Science 299, 1067-1070, 2003Taming of a Poison: Biosynthesis of the NiFe-Hydrogenase Cyanide Ligands.DOI:10.1126/science.1080972PMID:12586941the modification is observed when cyanide transfer to iron is blockedThis modification is produced naturally when the HypE protein undergoes an auto-catalyzed dehydration, using ATP, of its carboxy-terminal S-carbamoyl cysteine. See RESID:AA0332.CGO:0046892PSI-MOD:00338MOD_RES S-cyanocysteineAA033414-Mar-200331-Dec-201331-Dec-2013L-cysteinyl hydrogenase diiron subcluster1,7-biscarbonyl-1-(cystein-S-yl)-8-oxo-4-aza-2lambda(3),6 lambda(3)-dithia-1,7-diferratricyclo[4.2.0.0(2,7)]octane-1,7-dicarbonitrilemu-carbonyl-dicarbonyl-1kappaC,2kappaC-dicyanido-1kappaC,2kappaC-cysteinato-1kS-1,2-azadimethanthiol-1kS,2kS'-diironPDBHET:HCNC 10 Fe 2 H 9 N 4 O 4 S 3457.08456.848468C 7 Fe 2 H 4 N 3 O 3 S 2353.94353.839283Peters, J.W.Lanzilotta, W.N.Lemon, B.J.Seefeldt, L.C.Science 282, 1853-1858, 1998X-ray crystal structure of the Fe-only hydrogenase (CpI) from Clostridium pasteurianum to 1.8 angstrom resolution.DOI:10.1126/science.282.5395.1853PMID:9836629X-ray diffraction, 1.80 angstroms; a heterologous ligand containing sulfur is modeledPeters, J.W.Lanzilotta, W.N.Lemon, B.J.Seefeldt, L.C.submitted to the Protein Data Bank, June 1993Fe-only hydrogenase from Clostridium pasteurianum.PDB:1FEHX-ray diffraction, 1.80 angstromsNicolet, Y.Piras, C.Legrand, P.Hatchikian, C.E.Fontecilla-Camps, J.C.Structure 7, 13-23, 1999Desulfovibrio desulfuricans iron hydrogenase: the structure shows unusual coordination to an active site Fe binuclear center.PMID:10368269X-ray diffraction, 1.60 angstroms; in the iron-only hydrogenase from a related species the heterologous group is modeled as propane-1,3-dithiolNicolet, Y.Piras, C.Legrand, P.Hatchikian, C.E.Fontecilla-Camps, J.C.submitted to the Protein Data Bank, November 19981.6 A resolution structure of the Fe-only hydrogenase from Desulfovibrio desulfuricans.PDB:1HFEX-ray diffraction, 1.60 angstromsPandey, A.S.Harris, T.V.Giles, L.J.Peters, J.W.Szilagyi, R.K.J. Am. Chem. Soc. 130, 4533-4540, 2008Dithiomethylether as a ligand in the hydrogenase h-cluster.DOI:10.1021/ja711187ePMID:18324814X-ray diffraction, 1.39 angstroms; the heterologous group is modeled using density functional theory as oxydimethanethiolPandey, A.S.Lemon, B.J.Peters, J.W.submitted to the Protein Data Bank, February 20081.39 Angstrom crystal structure of FE-only hydrogenase.PDB:3C8YX-ray diffraction, 1.39 angstromsBerggren, G.Adamska, A.Lambertz, C.Simmons, T.R.Esselborn, J.Atta, M.Gambarelli, S.Mouesca, J.M.Reijerse, E.Lubitz, W.Happe, T.Artero, V.Fontecave, M.Nature 499, 66-69, 2013Biomimetic assembly and activation of [FeFe]-hydrogenases.DOI:10.1038/nature12239PMID:23803769determination of molecular structure by partial chemical synthesis of intermediatesEsselborn, J.Lambertz, C.Adamska-Venkatesh, A.Simmons, T.Berggren, G.Noth, J.Siebel, J.Hemschemeier, A.Artero, V.Reijerse, E.Fontecave, M.Lubitz, W.Happe, T.Nature Chem. Biol. 9, 607-609, 2013Spontaneous activation of [FeFe]-hydrogenases by an inorganic [2Fe] active site mimic.DOI:10.1038/nchembio.1311PMID:23934246a synthetic iron subcluster is incorporated and supports full enzyme activityThe structure of the metal cluster in this enzyme may vary in related organisms. The structure of the small heterologous ligand has been determined by incorporation of synthetic intermediates.Because of possible variations in the structure, a formal charge cannot be calculated.The cysteine sulfur is a mu(3) ligand that also ligates a 4Fe-4S cluster. For the metabolic source of the carbon monoxide and cyanide components of the cluster, see RESID:AA0332 and RESID:AA0333.Cincidental to RESID:AA0140GO:0046893PSI-MOD:00339iron-sulfur proteinmetalloproteinMETAL Diiron subclusterAA033514-Mar-200314-Mar-200331-Mar-2012S-amidino-L-cysteine2-amino-3-amidinosulfanylpropanoic acid2-amino-3-amidinothiopropanoic acidalpha-amino-beta-amidinothiopropionic acidbeta-(S-isothiourea)alaninebeta-amidinothioalanineS-amidinocysteine(2R)-2-amino-3-(carbamimidoylsulfanyl)propanoic acidC 4 H 7 N 3 O 1 S 1145.18145.030983C 1 H 2 N 2 O 0 S 042.0442.021798Humm, A.Fritsche, E.Mann, K.Goehl, M.Huber, R.Biochem. J. 322, 771-776, 1997Recombinant expression and isolation of human L-arginine:glycine amidinotransferase and identification of its active-site cysteine residue.PMID:9148748glycine amidinotransferase (EC 2.1.4.1)CGO:0046894PSI-MOD:00340ACT_SITE Amidino-cysteine intermediateAA033614-Mar-200314-Mar-200330-Jun-2010N-methyl-L-isoleucineN-methylisoleucine(2S,3S)-2-methylamino-3-methylpentanoic acidCAS:4125-98-8PDBHET:IMLC 7 H 13 N 1 O 1127.19127.099714C 1 H 2 N 0 O 014.0314.015650Strom, M.S.Lory, S.J. Biol. Chem. 266, 1656-1664, 1991Amino acid substitutions in pilin of Pseudomonas aeruginosa. Effect on leader peptide cleavage, amino-terminal methylation, and pilus assembly.PMID:1671038the amino-terminal methyltransferase activity of prepilin peptidase is not specific for phenylalanineThis modification is predicted for proteins homologous to pilin in certain organisms where the position corresponding to N-methylphenylalanine instead encodes isoleucine.Polypeptides with monomethylated amino terminals can undergo premature cleavage during the coupling step of an Edman degradation. This can result in "preview" with both a residue and the following residue being seen from the first step on through a sequence.prepilin peptidase (EC 3.4.23.43)IGO:0046895PSI-MOD:00341methylated amino endMOD_RES N-methylisoleucineAA033714-Mar-200314-Mar-200331-May-2018N-methyl-L-leucine2-(methylamino)-4-methyl-valeric acidN-methylleucine(S)-2-methylamino-4-methylpentanoic acidCAS:3060-46-6PDBHET:MLEC 7 H 13 N 1 O 1127.19127.099714C 1 H 2 N 0 O 014.0314.015650Strom, M.S.Lory, S.J. Biol. Chem. 266, 1656-1664, 1991Amino acid substitutions in pilin of Pseudomonas aeruginosa. Effect on leader peptide cleavage, amino-terminal methylation, and pilus assembly.PMID:1671038the amino-terminal methyltransferase activity of prepilin peptidase is not specific for phenylalanineArmirotti, A.Damonte, G.Pozzolini, M.Mussino, F.Cerrano, C.Salis, A.Benatti, U.Giovine, M.J. Proteome Res. 8, 3995-4004, 2009Primary structure and post-translational modifications of silicatein beta from the marine sponge Petrosia ficiformis (Poiret, 1789).DOI:10.1021/pr900342yPMID:19522542mass spectrometric identification; the authors do not provide numeric data to support their mass-spectrometric interpretationsThis modification is predicted for proteins homologous to pilin in certain organisms where the position corresponding to N-methylphenylalanine instead encodes leucine.Polypeptides with monomethylated amino terminals can undergo premature cleavage during the coupling step of an Edman degradation. This can result in "preview" with both a residue and the following residue being seen from the first step on through a sequence.prepilin peptidase (EC 3.4.23.43)LGO:0046896PSI-MOD:00342methylated amino endMOD_RES N-methylleucineAA033814-Mar-200314-Mar-200329-Oct-2010N-methyl-L-tyrosineN-methyltyrosine(2S)-3-(4-hydroxyphenyl)-2-(methylamino)propanoic acidCAS:537-49-5C 10 H 11 N 1 O 2177.20177.078979C 1 H 2 N 0 O 014.0314.015650Strom, M.S.Lory, S.J. Biol. Chem. 266, 1656-1664, 1991Amino acid substitutions in pilin of Pseudomonas aeruginosa. Effect on leader peptide cleavage, amino-terminal methylation, and pilus assembly.PMID:1671038the amino-terminal methyltransferase activity of prepilin peptidase is not specific for phenylalanineThis modification is predicted for proteins homologous to pilin in certain organisms where the position corresponding to N-methylphenylalanine instead encodes tyrosine.Polypeptides with monomethylated amino terminals can undergo premature cleavage during the coupling step of an Edman degradation. This can result in "preview" with both a residue and the following residue being seen from the first step on through a sequence.prepilin peptidase (EC 3.4.23.43)YGO:0046897PSI-MOD:00343methylated amino endMOD_RES N-methyltyrosineAA033925-Apr-200325-Apr-200330-Sep-2011N-palmitoyl-glycine(hexadecanamido)acetic acid(hexadecanoylamino)acetic acidN-(1-oxohexadecyl)glycine(hexadecanoylamino)ethanoic acidCAS:2441-41-0PDBHET:140C 18 H 34 N 1 O 2296.47296.258954C 16 H 30 N 0 O 1 S 0238.41238.229666Kleuss, C.Krause, E.EMBO J. 22, 826-832, 2003Galpha(s) is palmitoylated at the N-terminal glycine.DOI:10.1093/emboj/cdg095PMID:12574119mass spectrometric characterizationThis modification should not be confused with N-myristoyl-glycine (see RESID:AA0059).glycylpeptide N-palmitoyltransferase (EC 2.3.1.-)Gamino-terminalincidental to RESID:AA0060GO:0046918PSI-MOD:00344blocked amino endlipoproteinpalmitoylationLIPID N-palmitoyl glycineAA034009-May-200309-May-200331-Mar-20112-(L-cystein-S-yl)-L-phenylalanine(2R,5R)-2,5-diamino-3-thia-2-phenylmethylhexanedioic acidalpha-(L-cystein-S-yl)-L-phenylalanine(2R)-2-amino-2-[(2R)-2-amino-2-carboxyethyl]sulfanyl-3-phenylpropanoic acidC 12 H 12 N 2 O 2 S 1248.30248.061949C 0 H -2 N 0 O 0 S 0-2.02-2.015650Babasaki, K.Takao, T.Shimonishi, Y.Kurahashi, K.J. Biochem. 98, 585-603, 1985Subtilosin A, a new antibiotic peptide produced by Bacillus subtilis 168: isolation, structural analysis, and biogenesis.PMID:3936839Kawulka, K.Sprules, T.McKay, R.T.Mercier, P.Diaper, C.M.Zuber, P.Vederas, J.C.J. Am. Chem. Soc. 125, 4726-4727, 2003Structure of subtilosin A, an antimicrobial peptide from Bacillus subtilis with unusual posttranslational modifications linking cysteine sulfurs to alpha-carbons of phenylalanine and threonine.DOI:10.1021/ja029654tPMID:12696888Kawulka, K.E.Sprules, T.Diaper, C.M.Whittal, R.M.McKay, R.T.Mercier, P.Zuber, P.Vederas, J.C.Biochemistry 43, 3385-3395, 2004Structure of subtilosin A, a cyclic antimicrobial peptide from Bacillus subtilis with unusual sulfur to alpha-carbon cross-links: formation and reduction of alpha-thio-alpha-amino acid derivatives.DOI:10.1021/bi0359527PMID:15035610mass spectrometric, (1)H-NMR, (13)C-NMR and (15)N-NMR identificationKawulka, K.E.Sprules, T.McKay, R.T.Mercier, P.Diaper, C.M.Zuber, P.Vederas, J.C.submitted to the Protein Data Bank, July 2003Structure of subtilosin A.PDB:1PXQconformation by (1)H-NMR, (13)C-NMR and (15)N-NMRThe L-stereoisomer of the 2-S-cysteinyl substituted phenylalanine has R configuration.C, Fcross-link 2GO:0046924PSI-MOD:00345thioether bondCROSSLNK 2-cysteinyl-L-phenylalanine (Cys-Phe)AA034109-May-200309-May-200320-May-20112-(L-cystein-S-yl)-D-phenylalanine(2S,5R)-2,5-diamino-3-thia-2-phenylmethylhexanedioic acidalpha-(L-cystein-S-yl)-D-phenylalanine(2S)-2-amino-2-[(2R)-2-amino-2-carboxyethyl]sulfanyl-3-phenylpropanoic acidC 12 H 12 N 2 O 2 S 1248.30248.061949C 0 H -2 N 0 O 0 S 0-2.02-2.015650Babasaki, K.Takao, T.Shimonishi, Y.Kurahashi, K.J. Biochem. 98, 585-603, 1985Subtilosin A, a new antibiotic peptide produced by Bacillus subtilis 168: isolation, structural analysis, and biogenesis.PMID:3936839Kawulka, K.Sprules, T.McKay, R.T.Mercier, P.Diaper, C.M.Zuber, P.Vederas, J.C.J. Am. Chem. Soc. 125, 4726-4727, 2003Structure of subtilosin A, an antimicrobial peptide from Bacillus subtilis with unusual posttranslational modifications linking cysteine sulfurs to alpha-carbons of phenylalanine and threonine.DOI:10.1021/ja029654tPMID:12696888Kawulka, K.E.Sprules, T.Diaper, C.M.Whittal, R.M.McKay, R.T.Mercier, P.Zuber, P.Vederas, J.C.Biochemistry 43, 3385-3395, 2004Structure of subtilosin A, a cyclic antimicrobial peptide from Bacillus subtilis with unusual sulfur to alpha-carbon cross-links: formation and reduction of alpha-thio-alpha-amino acid derivatives.DOI:10.1021/bi0359527PMID:15035610mass spectrometric, (1)H-NMR, (13)C-NMR and (15)N-NMR identificationKawulka, K.E.Sprules, T.McKay, R.T.Mercier, P.Diaper, C.M.Zuber, P.Vederas, J.C.submitted to the Protein Data Bank, July 2003Structure of subtilosin A.PDB:1PXQconformation by (1)H-NMR, (13)C-NMR and (15)N-NMRThe D-stereoisomer of the 2-S-cysteinyl substituted phenylalanine has S configuration.C, Fcross-link 2GO:0046925PSI-MOD:00346D-amino acidthioether bondCROSSLNK 2-cysteinyl-D-phenylalanine (Cys-Phe)AA034209-May-200309-May-200331-Dec-20132-(L-cystein-S-yl)-D-allo-threonine(2R,5S,6R)-2,5-diamino-5-carboxy-6-hydroxy-4-thiaheptanoic acidalpha-(L-cystein-S-yl)-D-allo-threonine(2S,3R)-2-amino-2-[(2R)-2-amino-2-carboxyethyl]sulfanyl-3-hydroxybutanoic acidC 7 H 10 N 2 O 3 S 1202.23202.041213C 0 H -2 N 0 O 0 S 0-2.02-2.015650Babasaki, K.Takao, T.Shimonishi, Y.Kurahashi, K.J. Biochem. 98, 585-603, 1985Subtilosin A, a new antibiotic peptide produced by Bacillus subtilis 168: isolation, structural analysis, and biogenesis.PMID:3936839Kawulka, K.Sprules, T.McKay, R.T.Mercier, P.Diaper, C.M.Zuber, P.Vederas, J.C.J. Am. Chem. Soc. 125, 4726-4727, 2003Structure of subtilosin A, an antimicrobial peptide from Bacillus subtilis with unusual posttranslational modifications linking cysteine sulfurs to alpha-carbons of phenylalanine and threonine.DOI:10.1021/ja029654tPMID:12696888Kawulka, K.E.Sprules, T.Diaper, C.M.Whittal, R.M.McKay, R.T.Mercier, P.Zuber, P.Vederas, J.C.Biochemistry 43, 3385-3395, 2004Structure of subtilosin A, a cyclic antimicrobial peptide from Bacillus subtilis with unusual sulfur to alpha-carbon cross-links: formation and reduction of alpha-thio-alpha-amino acid derivatives.DOI:10.1021/bi0359527PMID:15035610mass spectrometric, (1)H-NMR, (13)C-NMR and (15)N-NMR identificationKawulka, K.E.Sprules, T.McKay, R.T.Mercier, P.Diaper, C.M.Zuber, P.Vederas, J.C.submitted to the Protein Data Bank, July 2003Structure of subtilosin A.PDB:1PXQ(1)H-NMR, (13)C-NMR and (15)N-NMR geometry constraint modeling; stereochemical determinationSit, C.S.van Belkum, M.J.McKay, R.T.Worobo, R.W.Vederas, J.C.Angew. Chem. Int. Ed. Engl. 50, 8718-8721, 2011The 3D solution structure of thurincin H, a bacteriocin with four sulfur to α-carbon crosslinks.DOI:10.1002/anie.201102527PMID:21786372mass spectrometric, (1)H-NMR, (13)C-NMR and (15)N-NMR identificationSit, C.S.van Belkum, M.J.McKay, R.T.Worobo, R.W.Vederas, J.C.submitted to the Protein Data Bank, April 2011Thurincin H.PDB:2LBZ(1)H-NMR, (13)C-NMR and (15)N-NMR geometry constraint modeling; stereochemical determinationThe D-stereoisomer of the 2-S-cysteinyl substituted threonine has S configuration. The second chiral center of the threonine is not inverted from the L-threo diastereomer (J.C. Vederas, private communication, 2003), and is thus D-allo.C, Tcross-link 2GO:0046926PSI-MOD:00347D-amino acidthioether bondCROSSLNK 2-cysteinyl-D-allo-threonine (Cys-Thr)AA034330-May-200330-May-200331-Dec-2008N-carbamoyl-L-alanine2-ureidopropanoic acidN-carbamylalanine(S)-2-(carbamoylamino)propanoic acidC 4 H 7 N 2 O 2115.11115.050752C 1 H 1 N 1 O 143.0243.005814Van Driessche, G.Vandenberghe, I.Jacquemotte, F.Devreese, B.Van Beeumen, J.J.J. Mass Spectrom. 37, 858-866, 2002Mass spectrometric identification of in vivo carbamylation of the amino terminus of Ectothiorhodospira mobilis high-potential iron-sulfur protein, isozyme 1.DOI:10.1002/jms.348PMID:12203680an apparently natural alpha-amino carbamoylation; mass spectrometric detection and characterization by collision-induced dissociation (CID) MS/MS; identification by synthesisCarbamoylation of the alpha-amino group can be artifactual, especially when urea buffers are used.Aamino-terminalGO:0046945PSI-MOD:00348blocked amino endMOD_RES N-carbamoylalanineAA034430-Jun-200330-Jun-200330-Jun-2011N,N-(L-cysteine-1,S-diyl)-L-serine2-(4-amino-3-oxo-isothiazolidin-2-yl)-3-hydroxy-propanoic acid4-amino-3-isothiazolidinone-L-serineserine-cysteine sulfenyl amide cross-linkserine-cysteine sulphenyl amide cross-link(2S)-2-[(4R)-4-amino-3-oxo-1,2-thiazolidin-2-yl]-3-hydroxypropanoic acidC 6 H 8 N 2 O 3 S 1188.20188.025563C 0 H -2 N 0 O 0 S 0-2.02-2.015650Salmeen, A.Andersen, J.N.Myers, M.P.Meng, T.C.Hinks, J.A.Tonks, N.K.Barford, D.Nature 423, 769-773, 2003Redox regulation of protein tyrosine phosphatase 1B involves a sulphenyl-amide intermediate.DOI:10.1038/nature01680PMID:12802338X-ray diffraction, 1.8 angstroms; (18)O labeling; mass spectrometric identificationSalmeen, A.Andersen, J.N.Myers, M.P.Meng, T.C.Hinks, J.A.Tonks, N.K.Barford, D.submitted to the Protein Data Bank, March 2003PTP1B with the catalytic cysteine oxidized to a sulfenyl-amide bond.PDB:1OEMX-ray diffraction, 1.8 angstromsvan Montfort, R.L.M.Congreve, M.Tisi, D.Carr, R.Jhoti, H.Nature 423, 773-777, 2003Oxidation state of the active-site cysteine in protein tyrosine phosphatase 1B.DOI:10.1038/nature01681PMID:12802339van Montfort, R.L.M.Congreve, M.Tisi, D.Carr, R.Jhoti, H.submitted to the Protein Data Bank, March 2003Oxidation state of protein tyrosine phosphatase 1B.PDB:1OESX-ray diffraction, 2.2 angstromsThis cross-link is formed by the condensation of a cysteine sulfenic acid with the alpha-amido of the following residue. It can apparently be reversed by simple disulfhydryl reduction under physiological conditions.autocatalyticC, Scross-link 1GO:0048109PSI-MOD:00349isothiazole ringCROSSLNK N,N-(cysteine-1,S-diyl)serine (Cys-Ser)AA034505-Sep-200305-Sep-200330-Apr-2010L-threonyl-pentaglycyl-murein peptidoglycan(2R,6S)-2-(N-mureinyl-(R)-alanyl-(S)-isoglutamyl)amino-6-(threonyl-pentaglycyl)amino-pimeloyl-(S)-alanyl-(S)-alanineC 14 H 22 N 6 O 7 +386.37 +386.154997 +C 10 H 14 N 5 O 4 +268.25 +268.104579 +Schneewind, O.Model, P.Fischetti, V.A.Cell 70, 267-281, 1992Sorting of protein A to the staphylococcal cell wall.DOI:10.1016/0092-8674(92)90101-HPMID:1638631Novick, R.P.Trends Microbiol. 8, 148-151, 2000Sortase: the surface protein anchoring transpeptidase and the LPXTG motif.DOI:10.1016/S0966-842X(00)01741-8PMID:10754567reviewSome bacterial proteins containing the sequence motif LPXTG are covalently attached to the cell wall murein. These proteins are cleaved after the threonine and transacylated to a pentaglycyl "crossbridge" peptide attached to the 6(D)-amino of meso-2,6-diaminopimelic acid in the murein peptidoglycan. In some gram-positive bacteria the meso-2,6-diaminopimelic acid is replaced by L-lysine. The form with meso-2,6-diaminopimelic acid is shown.sortase aminoacyltransferase (EC 2.3.2.-)Tcarboxyl-terminalGO:0042902PSI-MOD:00350blocked carboxyl endglycoproteinpeptidoglycanMOD_RES Pentaglycyl murein peptidoglycan amidated threonineAA034630-Sep-200330-Sep-200331-Mar-2009N-glycyl-1-(phosphatidyl)ethanolamineN-glycyl-1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine(R)-1-hexadecanoyloxy-2-((Z)-9-octadecenoyloxy)-3-[2-(aminoacetylamino)ethyloxyphospho]propaneC 41 H 78 N 2 O 9 P 1 +774.05 +773.544494 +C 39 H 74 N 1 O 7 P 1 +699.99 +699.520290 +Ichimura, Y.Kirisako, T.Takao, T.Satomi, Y.Shimonishi, Y.Ishihara, N.Mizushima, N.Tanida, I.Kominami, E.Ohsumi, M.Noda, T.Ohsumi, Y.Nature 408, 488-492, 2000A ubiquitin-like system mediates protein lipidation.DOI:10.1038/35044114PMID:11100732A representative phospholipid structure is shown.Cleavage of a carboxyl terminal propeptide accompanies transamidation.Gcarboxyl-terminalGO:0050495PSI-MOD:00351blocked carboxyl endlipoproteinphosphoproteinLIPID Phosphatidylethanolamine amidated glycineAA034730-Sep-200330-Sep-200329-Jan-2010L-glutamyl 5-omega-hydroxyceramide ester2-[30-(isoglutamyloxy)triacontanoyl]icosasphingosine(S)-2-amino-5-[30-((2S,3R,4E)-1,3-dihydroxyicos-4-en-2-ylamino)-30-oxotriacontan-1-yloxy]-5-oxopentanoic acidC 55 H 104 N 2 O 6 +889.44 +888.789439 +C 50 H 96 N 0 O 4 +761.31 +760.730862 +Marekov, L.N.Steinert, P.M.J. Biol. Chem. 273, 17763-17770, 1998Ceramides are bound to structural proteins of the human foreskin epidermal cornified cell envelope.DOI:10.1074/jbc.273.28.17763PMID:9651377Nemes, Z.Marekov, L.N.Fesus, L.Steinert, P.M.Proc. Natl. Acad. Sci. U.S.A. 96, 8402-8407, 1999A novel function for transglutaminase 1: attachment of long-chain omega-hydroxyceramides to involucrin by ester bond formation.DOI:10.1073/pnas.96.15.8402PMID:10411887This lipid modification is thought to span the lipid bilayer.A representative structure is shown.QGO:0050496PSI-MOD:00352lipoproteinLIPID Omega-hydroxyceramide glutamate esterAA034831-Oct-200331-Oct-200331-Dec-2009S-[5'-(L-tryptoph-6'-yl)-L-tyrosin-3'-yl]-L-methionin-S-ium5'-(6'-tryptophyl)-tyrosin-3'-yl-methionin-S-iumC 25 H 25 N 4 O 4 S 11+477.56477.159103C 0 H -3 N 0 O 0 S 01+-3.02-3.024024Yamada, Y.Fujiwara, T.Sato, T.Igarashi, N.Tanaka, N.Nature Struct. Biol. 9, 691-695, 2002The 2.0 A crystal structure of catalase-peroxidase from Haloarcula marismortui.DOI:10.1038/nsb834PMID:12172540X-ray diffraction, 2.0 angstromsYamada, Y.Fujiwara, T.Sato, T.Igarashi, N.Tanaka, N.submitted to the Protein Data Bank, January 2002Crystal structure of catalase-peroxidase from Haloarcula marismortui.PDB:1ITKX-ray diffraction, 2.0 angstromsGhiladi, R.A.Medzihradszky, K.F.Ortiz de Montellano, P.R.Biochemistry 44, 15093-15105, 2005Role of the Met-Tyr-Trp cross-link in Mycobacterium tuberculosis catalase-peroxidase (KatG) as revealed by KatG(M255I).DOI:10.1021/bi051463qPMID:16285713chemical characterization; directed mutation analysisThis modification is produced auto-catalytically.M, W, Ycross-link 3GO:0050739PSI-MOD:00353CROSSLNK Tryptophyl-tyrosyl-methioninium (Trp-Tyr) (with M-...)CROSSLNK Tryptophyl-tyrosyl-methioninium (Tyr-Met) (with W-...)AA034931-Oct-200331-Oct-200331-May-2018O-(riboflavin phosphoryl)-L-threonineO3-threonyl flavin mononucleotideO3-threonyl FMN(2S,3R)-2-amino-3-(riboflavin 5'-hydrogen phosphonoxy)butanoic acidChEBI:74346C 21 H 26 N 5 O 10 P 1539.44539.141729C 17 H 19 N 4 O 8 P 1438.33438.094050Zhou, W.Bertsova, Y.V.Feng, B.Tsatsos, P.Verkhovskaya, M.L.Gennis, R.B.Bogachev, A.V.Barquera, B.Biochemistry 38, 16246-16252, 1999Sequencing and preliminary characterization of the Na+-translocating NADH:ubiquinone oxidoreductase from Vibrio harveyi.DOI:10.1021/bi991664sPMID:10587447original identification as 1'-(8alpha-FMN)-histidineHayashi, M.Nakayama, Y.Yasui, M.Maeda, M.Furuishi, K.Unemoto, T.FEBS Lett. 488, 5-8, 2001FMN is covalently attached to a threonine residue in the NqrB and NqrC subunits of Na(+)-translocating NADH-quinone reductase from Vibrio alginolyticus.DOI:10.1016/S0014-5793(00)02404-2PMID:11163785Barquera, B.Haese, C.C.Gennis, R.B.FEBS Lett. 492, 45-49, 2001Expression and mutagenesis of the NqrC subunit of the NQR respiratory Na(+) pump from Vibrio cholerae with covalently attached FMN.DOI:10.1016/S0014-5793(01)02224-4PMID:11248234cloning and expression of the gene in Escherichia coli results in the production of an unmodified protein, which may indicate that an enzyme required for this modification is not presentBackiel, J.Juárez, O.Zagorevski, D.V.Wang, Z.Nilges, M.J.Barquera, B.Biochemistry 47, 11273-11284, 2008Covalent binding of flavins to RnfG and RnfD in the Rnf complex from Vibrio cholerae.DOI:10.1021/bi800920jPMID:18831535mass spectrometric detection; EPR spectrographic analysis; mass spectrometric data presented in Figure 4 (but not discussed by the authors) of a phosphopeptide resulting from neutral loss of riboflavin provides proof of the phosphodiester linkageTGO:0050740PSI-MOD:00354flavoproteinFMNphosphoproteinMOD_RES FMN phosphoryl threonineAA035031-Oct-200331-Oct-200305-Dec-2008O-(riboflavin phosphoryl)-L-serineO3-seryl flavin mononucleotideO3-seryl FMN(R)-2-amino-3-(riboflavin 5'-hydrogen phosphonoxy)propanoic acidC 20 H 24 N 5 O 10 P 1525.41525.126079C 17 H 19 N 4 O 8 P 1438.33438.094050This modification is predicted for proteins homologous to Na(+)-translocating NADH:quinone oxidoreductase B and C chains in certain organisms where the position corresponding to O3-(ribofavin phosphoryl)-threonine instead encodes serine.SGO:0050741PSI-MOD:00355flavoproteinFMNphosphoproteinMOD_RES FMN phosphoryl serineAA035131-Oct-200331-Oct-200330-Apr-2010S-(4a-FMN)-L-cysteine4a-(S-cysteinyl)flavin mononucleotide4a-(S-cysteinyl)FMN(R)-2-amino-3-(4a-riboflavin 5'-dihydrogen phosphate)sulfanylpropanoic acidPDBHET:FMNC 20 H 26 N 5 O 10 P 1 S 1559.49559.113800C 17 H 21 N 4 O 9 P 1 S 0456.35456.104615Chlumsky, L.J.Zhang, L.Ramsey, A.J.Jorns, M.S.Biochemistry 32, 11132-11142, 1993Preparation and properties of recombinant corynebacterial sarcosine oxidase: evidence for posttranslational modification during turnover with sarcosine.DOI:10.1021/bi00092a024PMID:7692961detection of 4a-FMN cysteinyl adduct as an intermediateFedorov, R.Schlichting, I.Hartmann, E.Domratcheva, T.Fuhrmann, M.Hegemann, P.Biophys. J. 84, 2474-2482, 2003Crystal Structures and Molecular Mechanism of a Light-Induced Signaling Switch: The Phot-LOV1 Domain from Chlamydomonas reinhardtii.DOI:10.1021/bi0345135PMID:12668455Iwata, T.Nozaki, D.Tokutomi, S.Kagawa, T.Wada, M.Kandori, H.Biochemistry 42, 8183-8191, 2003Light-induced structural changes in the LOV2 domain of Adiantum phytochrome3 studied by low-temperature FTIR and UV-visible spectroscopy.DOI:10.1021/bi0345135PMID:12846567Nakasako, M.Zikihara, K.Matsuoka, D.Katsura, H.Tokutomi, S.J. Mol. Biol. 381, 718-733, 2008Structural basis of the LOV1 dimerization of Arabidopsis phototropins 1 and 2.DOI:10.1016/j.jmb.2008.06.033PMID:18585389X-ray diffraction, 2.00 angstromsNakasako, M.Matsuoka, D.Tokutomi, S.submitted to the Protein Data Bank, July 2007Crystal structure of LOV1 domain of phototropin2 from Arabidopsis thaliana.PDB:2Z6DX-ray diffraction, 2.00 angstroms; the covalent linkage is not annotated in the PDB entriesThis modification forms as an intermediate in light transduction and some redox reactions.The keyword "phosphoprotein" is not used with flavin modifications linked through the flavin.autocatalyticCGO:0050742PSI-MOD:00356*phosphoproteinflavoproteinFMNthioether bondMOD_RES S-4a-FMN cysteineAA035231-Oct-200331-Oct-200330-Apr-20101'-(8alpha-FMN)-L-histidine8alpha-(N(epsilon)-histidyl)FMN8alpha-(N1'-histidyl)FMNN(tau)-(8alpha-FMN)-histidinetele-(8alpha-FMN)-histidine(S)-2-amino-3-(1-[8alpha riboflavin 5'-dihydrogen phosphate]imidazol-4-yl)propanoic acidC 23 H 26 N 7 O 10 P 1591.47591.147877C 17 H 19 N 4 O 9 P 1454.33454.088965Willie, A.Edmondson, D.E.Jorns, M.S.Biochemistry 35, 5292-5299, 1996Sarcosine oxidase contains a novel covalently bound FMN.DOI:10.1021/bi952995hPMID:8611516(31)P-NMR, enzymatic and spectrographic characterizationMukouyama, E.B.Ohsawa, H.Suzuki, H.J. Protein Chem. 21, 59-64, 2002Cofactors in sarcosine oxidase from Corynebacterium sp. U-96.DOI:10.1023/A:1014135216860PMID:11902668mass spectrometric, enzymatic and spectrographic characterizationThe arrangement of the attachment has not been completely established in some cases.The keyword "phosphoprotein" is not used with flavin modifications linked through the flavin.autocatalyticHGO:0050743PSI-MOD:00357*phosphoproteinflavoproteinFMNMOD_RES Tele-8alpha-FMN histidineAA035331-Oct-200331-Oct-200330-Apr-20103'-(8alpha-FMN)-L-histidine8alpha-(N(delta)-histidyl)FMN8alpha-(N3'-histidyl)FMNN(pi)-(8alpha-FMN)-histidinepros-(8alpha-FMN)-histidine(S)-2-amino-3-(3-[8alpha riboflavin 5'-dihydrogen phosphate]imidazol-4-yl)propanoic acidC 23 H 26 N 7 O 10 P 1591.47591.147877C 17 H 19 N 4 O 9 P 1454.33454.088965Bandeiras, T.M.Salgueiro, C.Kletzin, A.Gomes, C.M.Teixeira, M.FEBS Lett. 531, 273-277, 2002Acidianus ambivalens type-II NADH dehydrogenase: genetic characterisation and identification of the flavin moiety as FMN.DOI:10.1016/S0014-5793(02)03514-7PMID:12417325(31)P-NMR, enzymatic and spectrographic characterizationBrito, J.A.Sousa, F.L.Stelter, M.Bandeiras, T.M.Vonrhein, C.Teixeira, M.Pereira, M.M.Archer, M.Biochemistry 48, 5613-5622, 2009Structural and functional insights into sulfide:quinone oxidoreductase.DOI:10.1021/bi9003827PMID:19438211X-ray diffraction, 2.57 angstroms; reassessment of original reportIn a later publication the authors changed the enzyme activity, the connection from a histidine nitrogen to a cysteine sulfur, and the identity of the flavin from FMN to FAD. They now believe the modification is S-(8alpha-FAD)-L-cysteine, see RESID:AA0143.The keyword "phosphoprotein" is not used with flavin modifications linked through the flavin.HGO:0050744PSI-MOD:00358*phosphoproteinflavoproteinFMNNot availablethis modification is not annotated in UniProt featuresAA035428-Nov-200328-Nov-200328-Aug-2009N2-acetyl-L-arginine2-acetamido-5-guanidinopentanoic acid2-acetylamino-5-guanidinopentanoic acidacetylargininealpha-acetylamino-delta-guanidinovaleric acidN(alpha)-acetylarginine(S)-2-acetamido-5-carbamimidamidopentanoic acidCAS:155-84-0PDBHET:ACEC 8 H 15 N 4 O 2199.23199.119501C 2 H 2 N 0 O 142.0442.010565Michel, H.Griffin, P.R.Shabanowitz, J.Hunt, D.F.Bennett, J.J. Biol. Chem. 266, 17584-17591, 1991Tandem mass spectrometry identifies sites of three post-translational modifications of spinach light-harvesting chlorophyll protein II. Proteolytic cleavage, acetylation, and phosphorylation.PMID:1894641mass spectrometric identification; chemical synthesisHansson, M.Vener, A.V.Mol. Cell. Proteomics 2, 550-559, 2003Identification of Three Previously Unknown in Vivo Protein Phosphorylation Sites in Thylakoid Membranes of Arabidopsis thaliana.DOI:10.1074/mcp.M300050-MCP200PMID:12883043mass spectrometric identificationThe common peptide alpha-N-acetyltransferase does not acetylate basic residues, so another alpha-acetyltransferase activity must be producing this modification in a thylakoid protein.arginylpeptide alpha-N-acetyltransferase (EC 2.3.1.-)Ramino-terminalGO:0048275PSI-MOD:00359acetylated amino endMOD_RES N2-acetylarginineAA035506-Feb-200406-Feb-200431-Dec-2008L-cysteinyl copper sulfido molybdopterin cytosine dinucleotidecysteinyl copper mu-sulfido Mo-pterin cytosine dinucleotide[8-amino-1a,2,4a,5,6,7,10-heptahydro-2-(trihydrogen diphosphate 5'-ester with cytosine)methyl-6-oxo-3,4-dimercapto-pteridino[6,7-5,6]pyranoato-S3,S4]-cysteinyl-S-copper-mu-sulfido-molybdenum hydroxide oxideCOMe:BIM000360PDBHET:CUNPDBHET:MCNC 22 Cu 1 H 29 Mo 1 N 9 O 16 P 2 S 41025.201025.844039C 19 Cu 1 H 24 Mo 1 N 8 O 15 P 2 S 3922.07922.834854Dobbek, H.Gremer, L.Kiefersauer, R.Huber, R.Meyer, O.Proc. Natl. Acad. Sci. U.S.A. 99, 15971-15976, 2002Catalysis at a dinuclear [CuSMo(==O)OH] cluster in a CO dehydrogenase resolved at 1.1-A resolution.DOI:10.1073/pnas.212640899PMID:12475995X-ray diffraction, 1.50 angstromsDobbek, H.Gremer, L.Kiefersauer, R.Huber, R.Meyer, O.submitted to the Protein Data Bank, November 2002Crystal structure of the Cu,Mo-CO dehydrogenase (CODH); oxidized form.PDB:1N5WX-ray diffraction, 1.50 angstromsDobbek, H.Gremer, L.Kiefersauer, R.Huber, R.Meyer, O.submitted to the Protein Data Bank, November 2002Crystal structure of the Cu,Mo-CO dehydrogenase (CODH); carbon monoxide reduced state.PDB:1N63X-ray diffraction, 1.21 angstromsA hydrogenated (+4H) structure is shown. The fully oxidized form would be the corresponding 4,9,10-trihydro form.CGO:0050834GO:0050842PSI-MOD:00360coppermetalloproteinmolybdenummolybdopterinphosphoproteinNot availablethis modification is not annotated in UniProt featuresAA035606-Feb-200406-Feb-200425-Feb-2011tris-L-cysteinyl S-adenosylmethion-N,O-diyl tetrairon tetrasulfidetetra-mu3-sulfido(S-adenosylmethion-N,O-diyliron)tris(S-cysteinyliron)COMe:BIM000462PDBHET:SAMPDBHET:SF4C 24 Fe 4 H 34 N 9 O 8 S 81-1056.451055.769901C 15 Fe 4 H 19 N 6 O 5 S 51-747.03746.742346Berkovitch, F.Nicolet, Y.Wan, J.T.Jarrett, J.T.Drennan, C.L.Science 303, 76-79, 2004Crystal structure of biotin synthase, an S-adenosylmethionine-dependent radical enzyme.DOI:10.1126/science.1088493PMID:14704425X-ray diffraction, 3.4 angstromsBerkovitch, F.Nicolet, Y.Wan, J.T.Jarrett, J.T.Drennan, C.L.submitted to the Protein Data Bank, September 2003The crystal structure of biotin synthase, an S-adenosylmethionine-dependent radical enzyme.PDB:1R30X-ray diffraction, 3.4 angstromsSofia, H.J.Chen, G.Hetzler, B.G.Reyes-Spindola, J.F.Miller, N.E.Nucleic Acids Res. 29, 1097-1106, 2001Radical SAM, a novel protein superfamily linking unresolved steps in familiar biosynthetic pathways with radical mechanisms: functional characterization using new analysis and information visualization methods.DOI:10.1093/nar/29.5.1097PMID:11222759review articleC, C, Ccross-link 3GO:0050835PSI-MOD:003614Fe-4Siron-sulfur proteinmetalloproteinS-adenosyl-L-methionineMETAL Iron-sulfur (4Fe-4S-S-AdoMet)AA035706-Feb-200406-Feb-200431-Dec-2009tris-L-cysteinyl L-arginyl diiron disulfidedi-mu-sulfido(N(eta1)-arginyl-S-cysteinyliron)(bis-S-cysteinyliron)COMe:BIM000469PDBHET:FESC 15 Fe 2 H 24 N 7 O 4 S 52-638.39637.920304C 0 Fe 2 H -3 N 0 O 0 S 22-172.79172.791639Berkovitch, F.Nicolet, Y.Wan, J.T.Jarrett, J.T.Drennan, C.L.Science 303, 76-79, 2004Crystal structure of biotin synthase, an S-adenosylmethionine-dependent radical enzyme.DOI:10.1126/science.1088493PMID:14704425X-ray diffraction, 3.4 angstromsBerkovitch, F.Nicolet, Y.Wan, J.T.Jarrett, J.T.Drennan, C.L.submitted to the Protein Data Bank, September 2003The crystal structure of biotin synthase, an S-adenosylmethionine-dependent radical enzyme.PDB:1R30X-ray diffraction, 3.4 angstromsC, C, C, Rcross-link 4GO:0050836PSI-MOD:003622Fe-2Siron-sulfur proteinmetalloproteinMETAL Iron-sulfur (2Fe-2S)AA035806-Feb-200406-Feb-200431-Mar-2010L-cysteinyl-L-selenocysteine(R,R)-2-amino-3-[3-(2-aminopropanoic acid)sulfanyl]selanylpropanoic acidC 6 H 8 N 2 O 2 S 1 Se 1251.17251.947170C 0 H -2 N 0 O 0 S -1 Se 144.9045.928800C 0 H -2 N 0 O 0 S 0 Se 0-2.02-2.015650Zhong, L.Arner, E.S.Holmgren, A.Proc. Natl. Acad. Sci. U.S.A. 97, 5854-5859, 2000Structure and mechanism of mammalian thioredoxin reductase: the active site is a redox-active selenolthiol/selenenylsulfide formed from the conserved cysteine-selenocysteine sequence.DOI:10.1073/pnas.100114897PMID:10801974mass spectrometric detection of selenide-sulfide bondMa, S.Hill, K.E.Burk, R.F.Caprioli, R.M.Biochemistry 42, 9703-9711, 2003Mass spectrometric identification of N- and O-glycosylation sites of full-length rat selenoprotein P and determination of selenide-sulfide and disulfide linkages in the shortest isoform.DOI:10.1021/bi0346300PMID:12911312mass spectrometric detection of selenide-sulfide bondMetanis, N.Keinan, E.Dawson, P.E.J. Am. Chem. Soc. 128, 16684-16691, 2006Synthetic seleno-glutaredoxin 3 analogues are highly reducing oxidoreductases with enhanced catalytic efficiency.DOI:10.1021/ja0661414PMID:17177418comparative redox potentials of cystine, cysteinylselenocysteine and selenocystine in synthetic glutaredoxins with a [C/U]XX[C/U] motifThe experimental redox potential of cysteinylselenocysteine in synthetic glutaredoxin 3 is -260 to -275 mV. See RESID:AA0025 and RESID:AA0437.C, Ccross-link 2secondary to RESID:AA0022GO:0050837PSI-MOD:00867C, Ucross-link 2PSI-MOD:00363redox-active centerseleniumselenocysteineCROSSLNK Cysteinyl-selenocysteine (Cys-Sec)CROSSLNK Cysteinyl-selenocysteine (Sec-Cys)AA035906-Feb-200406-Feb-200431-May-20135-hydroxy-N6,N6,N6-trimethyl-L-lysine(2Xi,5S)-5-amino-5-carboxy-2-hydroxy-N,N,N-trimethylpentanaminium(2Xi,5S)-5-azanyl-5-carboxy-2-hydroxy-N,N,N-trimethylpentanazanium5-hydroxy-N(zeta)-trimethyllysine5-hydroxy-N6,N6,N6-trimethyllysin-N6-ium5-hydroxy-N6,N6,N6-trimethyllysine cationalpha-amino-epsilon-dimethylamino-delta-hydroxycaproic aciddelta-hydroxy-epsilon-N,N,N-trimethyllysinelysine derivative Lys(z)(2R,5Xi)-5-amino-5-carboxy-2-hydroxy-N,N,N-trimethylpentan-1-aminiumC 9 H 19 N 2 O 21+187.26187.144104C 3 H 7 N 0 O 11+59.0959.049141Kroeger, N.Deutzmann, R.Sumper, M.J. Biol. Chem. 276, 26066-26070, 2001Silica-precipitating peptides from diatoms. The chemical structure of silaffin-A from Cylindrotheca fusiformis.DOI:10.1074/jbc.M102093200PMID:11349130chromatographic and mass spectrometric identificationHydroxylation at C-5 is assumed. Neither the position of the hydroxylation nor the stereochemistry for the second chiral center it produces have been determined. The (2S,5R) diastereomer is shown.Consult FAQ at http://pir.georgetown.edu/resid/faq.shtml#q12 concerning calculation of the difference formula.Kincidental to RESID:AA0278secondary to RESID:AA0028secondary to RESID:AA0074GO:0050838GO:0050841PSI-MOD:00364hydroxylationmethylated amino acidMOD_RES N6,N6,N6-trimethyl-5-hydroxylysineAA036027-Feb-200427-Feb-200429-Oct-2010N-(L-isoglutamyl)-glycine2-amino-N5-(carboxymethyl)-pentanediamic acidisoglutamyl glycineN-gamma-glutamylglycine(S)-2-amino-5-(carboxymethyl)amino-5-oxopentanoic acidCAS:1948-29-4C 7 H 9 N 2 O 3169.16169.061317C 0 H -2 N 0 O -1-18.02-18.010565Bayro, M.J.Mukhopadhyay, J.Swapna, G.V.T.Huang, J.Y.Ma, L.-C.Sineva, E.Dawson, P.E.Montelione, G.T.Ebright, R.H.J. Am. Chem. Soc. 125, 12382-12383, 2003Structure of antibacterial peptide microcin J25: a 21-residue lariat protoknot.DOI:10.1021/ja036677ePMID:14531661the initials of G.V.T. Swapna in the PubMed citation are correctedBayro, M.J.Swapna, G.V.T.Huang, J.Y.Ma, L.-C.Mukhopadhyay, J.Ebright, R.H.Montelione, G.T.submitted to the Protein Data Bank, June 2003Structure of antibacterial peptide microcin J25: a 21-residue lariat protoknot.PDB:1PP5solution structure by (1)H-, (13)C- and (15)N-NMRWilson, K.A.Kalkum, M.Ottesen, J.Yuzenkova, J.Chait, B.T.Landick, R.Muir, T.Severinov, K.Darst, S.A.J. Am. Chem. Soc. 125, 12475-12483, 2003Structure of microcin J25, a peptide inhibitor of bacterial RNA polymerase, is a lassoed tail.DOI:10.1021/ja036756qPMID:14531691mass spectrometric and (1)H-NMR identification; chemical synthesisFor the "lariat" or "lasso" cross-link between glycine and aspartic acid, see RESID:AA0126.E, Gamino-terminalcross-link 2GO:0050986PSI-MOD:00365blocked amino endisopeptide bondCROSSLNK Isoglutamyl glycine isopeptide (Gly-Glu)AA036127-Feb-200427-Feb-200431-Dec-2008O-sulfo-L-serine2-amino-3-hydroxypropanoic acid 3-sulfateO3-sulfonoserineO3-sulfoserineserine sulfate ester(2S)-2-amino-3-(sulfooxy)propanoic acidCAS:626-69-7PDBHET:OSEC 3 H 5 N 1 O 5 S 1167.13166.988843C 0 H 0 N 0 O 3 S 180.0679.956815Medzihradszky, K.F.Darula, Z.Perlson, E.Fainzilber, M.Chalkley, R.J.Ball, H.Greenbaum, D.Bogyo, M.Tyson, D.R.Bradshaw, R.A.Burlingame, A.L.Mol. Cell. Proteomics 3, 429-440, 2004O-Sulfonation of serine and threonine - mass spectrometric detection and characterization of a new posttranslational modification in diverse proteins throughout the eukaryotes.DOI:10.1074/mcp.M300140-MCP200PMID:14752058chromatographic detection; mass spectrometric identificationSGO:0050984GO:0050987PSI-MOD:00366sulfoproteinMOD_RES SulfoserineAA036227-Feb-200427-Feb-200431-Dec-2008O-sulfo-L-threonine2-amino-3-hydroxybutanoic acid 3-sulfateO3-sulfonothreonineO3-sulfothreoninethreonine sulfate ester(2S,3R)-2-amino-3-(sulfooxy)butanoic acidC 4 H 7 N 1 O 5 S 1181.16181.004493C 0 H 0 N 0 O 3 S 180.0679.956815Medzihradszky, K.F.Darula, Z.Perlson, E.Fainzilber, M.Chalkley, R.J.Ball, H.Greenbaum, D.Bogyo, M.Tyson, D.R.Bradshaw, R.A.Burlingame, A.L.Mol. Cell. Proteomics 3, 429-440, 2004O-Sulfonation of serine and threonine - mass spectrometric detection and characterization of a new posttranslational modification in diverse proteins throughout the eukaryotes.DOI:10.1074/mcp.M300140-MCP200PMID:14752058chromatographic detection; mass spectrometric identificationTGO:0050985GO:0050991PSI-MOD:00367sulfoproteinMOD_RES SulfothreonineAA036327-Feb-200427-Feb-200431-Dec-2011N-carboxy-L-methionine2-carbamic-4-(methylsulfanyl)butanoic acid2-carbamic-4-(methylthio)butanoic acidN-carboxymethionine(S)-2-carboxyamino-4-(methylsulfanyl)butanoic acidChEBI:61924PDBHET:CXMPDBHET:FMTC 6 H 10 N 1 O 3 S 1176.21176.038139C 1 H 0 N 0 O 2 S 044.0143.989829Fauman, E.B.Rutenber, E.E.Maley, G.F.Maley, F.Stroud, R.M.Biochemistry 33, 1502-1511, 1994Water-mediated substrate/product discrimination: the product complex of thymidylate synthase at 1.83 A.DOI:10.1021/bi00172a029PMID:8312270X-ray diffraction, 1.83 angstroms; the modification is described as "a carbamate involving the N-terminal nitrogen"Fauman, E.Rutenber, E.Stroud, R.submitted to the Protein Data Bank, May 1993Thymidylate synthase (E.C.2.1.1.45) mutant with Cys 146 replaced by Ser (C146S).PDB:1TYSX-ray diffraction, 1.83 angstroms; the modification is described as "a formate group bound to N of Met 1 forming a carbamate group"Benini, S.Rypniewski, W.R.Wilson, K.S.Miletti, S.Ciurli, S.Mangani, S.Structure 7, 205-216, 1999A new proposal for urease mechanism based on the crystal structures of the native and inhibited enzyme from Bacillus pasteurii: why urea hydrolysis costs two nickels.DOI:10.1016/S0969-2126(99)80026-4PMID:10368287X-ray diffraction, 2.0 angstroms; the modification is described as "a formate group bound to N of Met 1 forming a carbamate group"Benini, S.Rypniewski, W.R.Wilson, K.S.Ciurli, S.Mangani, S.submitted to the Protein Data Bank, April 2001Phosphate inhibited Bacillus pasteurii urease crystal structure.PDB:1IE7X-ray diffraction, 1.85 angstroms; modeled earlier as an acetyl group in PDB:2UBPPapiz, M.Z.Prince, S.M.Howard, T.Cogdell, R.J.Isaacs, N.W.J. Mol. Biol. 326, 1523-1538, 2003The structure and thermal motion of the B800-850 LH2 complex from Rps. acidophila at 2.0 angstroms resolution and 100 K: new structural features and functionally relevant motions.DOI:10.1016/S0022-2836(03)00024-XPMID:12595263X-ray diffraction, 2.0 angstroms; the formyl group ligand is remodeled with two oxygens as a carboxyl group, but appears to be tetrahedral rather than trigonal planarPapiz, M.Z.Prince, S.M.Howard, T.Cogdell, R.J.Isaacs, N.W.submitted to the Protein Data Bank, September 1994Crystal structure LH2 B800-850 from Rps. acidophila at 2.0 angstrom resolution.PDB:1NKZX-ray diffraction, 2.0 angstroms; the formyl group ligand is remodeled with two oxygens as a carboxyl group, but appears to be tetrahedral rather than trigonal planarAt least three protein crystallographic structures have been reported with this modification. However, no chemical evidence for this modification is provided, there were no reports of this modification before these crystallographic reports, and there is no metabolic explanation for the conversion of a formyl group to a carboxy group. There is confusion in its description, and misnaming is common.This modification is probably a misidentification of N-(dihydroxymethyl)methionine, the hydrated form of N-formylmethionine. See RESID:AA0493.Mamino-terminalGO:0050988PSI-MOD:00368blocked amino endNot availablethis dubious modification is not currently annotated in UniProt featuresAA036431-Mar-200431-Mar-200431-Mar-2010O-acetyl-L-serineO-acetylserineserine acetate ester(2S)-3-(acetyloxy)-2-aminopropanoic acidCAS:4985-36-8ChEBI:17981PDBHET:OASC 5 H 7 N 1 O 3129.12129.042593C 2 H 2 N 0 O 142.0442.010565Rudman, D.Chawla, R.K.Hollins, B.M.J. Biol. Chem. 254, 10102-10108, 1979N,O-Diacetylserine-1 alpha-melanocyte-stimulating hormone, a naturally occurring melanotropic peptide.PMID:489587Buckley, D.I.Houghten, R.A.Ramachandran, J.Int. J. Pept. Protein Res. 17, 508-513, 1981Isolation of alpha-melanotropin and N, O-diacetylserine1-alpha-melanotropin from porcine pituitary extracts.PMID:7309355in this report it is not clear whether O-acetylation is separately catalyzed from N-acetylation, or follows from it by internal transacetylationMukherjee, S.Keitany, G.Li, Y.Wang, Y.Ball, H.L.Goldsmith, E.J.Orth, K.Science 312, 1211-1214, 2006Yersinia YopJ acetylates and inhibits kinase activation by blocking phosphorylation.DOI:10.1126/science.1126867PMID:16728640O-acetylation of serine in host kinases is catalyzed by yersinia toxin blocking the normal phosphorylationSincidental to RESID:AA0051GO:0030919PSI-MOD:00369PSI-MOD:00648MOD_RES O-acetylserineAA036531-Mar-200431-Mar-200431-Dec-2011(E)-2,3-didehydrotyrosineamino-(para-hydroxybenzylidenyl)acetic acidblue non-fluorescent pocilloporin chromophorepara-hydroxybenzylidene-imidazolidinone chromophoretrans-dehydrotyrosine(2E)-2-amino-3-(4-hydroxyphenyl)prop-2-enoic acidPDBHET:CRKPDBHET:CRQPDBHET:NRQC 9 H 7 N 1 O 2161.16161.047678C 0 H -2 N 0 O 0-2.02-2.015650Prescott, M.Ling, M.Beddoe, T.Oakley, A.J.Dove, S.Hoegh-Guldberg, O.Devenish, R.J.Rossjohn, J.Structure 11, 275-284, 2003The 2.2 A crystal structure of a pocilloporin pigment reveals a nonplanar chromophore conformation.DOI:10.1016/S0969-2126(03)00028-5PMID:12623015X-ray diffraction, 2.2 angstromsPrescott, M.Ling, M.Beddoe, T.Oakley, A.J.Dove, S.Hoegh-Guldberg, O.Devenish, R.J.Rossjohn, J.submitted to the Protein Data Bank, September 2002Crystal structure of coral pigment.PDB:1MOUX-ray diffraction, 2.2 angstromsYincidental to RESID:AA0184incidental to RESID:AA0187incidental to RESID:AA0188incidental to RESID:AA0189incidental to RESID:AA0378incidental to RESID:AA0379incidental to RESID:AA0380incidental to RESID:AA0381GO:0018251GO:0030922PSI-MOD:00370MOD_RES (E)-2,3-didehydrotyrosineMOD_RES 2,3-didehydrotyrosinethis UniProt feature is used when the isomeric structure has not been determinedAA036631-Mar-200431-Mar-200401-Mar-2013bis-L-aspartato tris-L-glutamato L-histidino calcium tetramanganese tetroxide4Mn-Ca-4O clusterphotosystem II catalytic clustermu3-1:2:3kappaO-oxido-mu3-1:3:4kappaO-oxido-mu3-2:3:4kappaO-oxido-mu4-1:2:4:5kappaO-oxido-N1'-histidino-O5-glutamato 2-manganese-O5,O5-glutamato 3-manganese-O4-aspartato 4-manganese-O4-aspartato-O5-glutamato 5-manganesePDBHET:OECC 29 Ca 1 H 32 Mn 4 N 8 O 201072.441071.888057C 0 Ca 1 H -6 Mn 4 N 0 O 4317.78317.647480Ferreira, K.N.Iverson, T.M.Maghlaoui, K.Barber, J.Iwata, S.Science 303, 1831-1838, 2004Architecture of the photosynthetic oxygen-evolving center.DOI:10.1126/science.1093087PMID:14764885X-ray diffraction, 3.5 angstromsFerreira, K.N.Iverson, T.M.Maghlaoui, K.Barber, J.Iwata, S.submitted to the Protein Data Bank, January 2004Architecture of the photosynthetic oxygen evolving center.PDB:1S5LX-ray diffraction, 3.5 angstromsThe metal cluster was modeled as a three manganese, calcium, four oxygen cubane with one oxygen ligating the calcium also ligating a fourth manganese. The reactive center for converting several water molecules to dioxygen may be between the calcium and the fourth manganese where electron density was modeled as bicarbonate and chloride ions.Because of the uncertainty in the structure, a formal charge cannot be calculated.This model for the photosystem II catalytic cluster has been superseded by RESID:AA0600.D, D, E, E, E, Hcross-link 6GO:0030926GO:0030927PSI-MOD:00371calciummanganesemetalloproteinNot availablethis modification is not annotated in UniProt featuresAA036730-Jun-200430-Jun-200430-Jun-20123'-(L-tyros-3'-yl)-L-tyrosine6,6'-dihydroxy-(1,1'-biphenyl)-3,3'-bis(2-aminopropanoic acid)alpha,alpha'-diamino-6,6'-dihydroxy-(1,1'-biphenyl)-3,3'-dipropanoic acidbityrosineo,o-dityrosine(2S,2'S)-3,3'-(6,6'-dihydroxybiphenyl-3,3'-diyl)bis(2-aminopropanoic acid)CAS:980-21-2C 18 H 16 N 2 O 4324.34324.111007C 0 H -2 N 0 O 0-2.02-2.015650Andersen, S.O.Biochim. Biophys. Acta 93, 213-215, 1964The cross-links in resilin identified as dityrosine and trityrosine.DOI:10.1016/0304-4165(64)90289-2PMID:14249161DeVore, D.P.Gruebel, R.J.Biochem. Biophys. Res. Commun. 80, 993-999, 1978Dityrosine in adhesive formed by the sea mussel, Mytilus edulis.DOI:10.1016/0006-291X(78)91343-8PMID:637884Malencik, D.A.Sprouse, J.F.Swanson, C.A.Anderson, S.R.Anal. Biochem. 242, 202-213, 1996Dityrosine: preparation, isolation, and analysis.DOI:10.1006/abio.1996.0454PMID:8937563Jacob, J.S.Cistola, D.P.Hsu, F.F.Muzaffar, S.Mueller, D.M.Hazen, S.L.Heinecke, J.W.J. Biol. Chem. 271, 19950-19956, 1996Human phagocytes employ the myeloperoxidase-hydrogen peroxide system to synthesize dityrosine, trityrosine, pulcherosine, and isodityrosine by a tyrosyl radical-dependent pathway.DOI:10.1074/jbc.271.33.19950PMID:8702710biosynthesisThis cross-link can be produced as an oxidation artifact, or enzymatically by enzymes like myeloperoxidase. Since the enzymatic reaction proceeds by a free-radical mechanism, the cross-link can be aleatoric with 2, 3 or 4 tyrosines rings becoming linked in several possible ways. See also RESID:AA0368.myeloperoxidase (EC 1.11.1.7)Y, Ycross-link 2GO:0030959PSI-MOD:00372aleatoric crosslinkNot availablethis modification is not annotated in UniProt featuresAA036830-Jun-200430-Jun-200430-Jun-20123'-(L-tyros-O4'-yl)-L-tyrosine2-amino-3-[4-(5-[(2S)-2-amino-2-carboxyethyl]-2-hydroxyphenoxy)phenyl]propanoic acidisodityrosineO-(5-(2-amino-2-carboxyethyl)-2-hydroxyphenyl)-L-tyrosine(2S)-2-amino-3-[3-(4-[(2S)-2-amino-2-carboxyethyl]phenoxy)-4-hydroxyphenyl]propanoic acidCAS:83118-65-4C 18 H 16 N 2 O 4324.34324.111007C 0 H -2 N 0 O 0-2.02-2.015650Fry, S.C.Biochem. J. 204, 449-455, 1982Isodityrosine, a new cross-linking amino acid from plant cell-wall glycoprotein.PMID:7115340Jacob, J.S.Cistola, D.P.Hsu, F.F.Muzaffar, S.Mueller, D.M.Hazen, S.L.Heinecke, J.W.J. Biol. Chem. 271, 19950-19956, 1996Human phagocytes employ the myeloperoxidase-hydrogen peroxide system to synthesize dityrosine, trityrosine, pulcherosine, and isodityrosine by a tyrosyl radical-dependent pathway.DOI:10.1074/jbc.271.33.19950PMID:8702710biosynthesisMilani, M.Savard, P.Y.Ouellet, H.Ascenzi, P.Guertin, M.Bolognesi, M.Proc. Natl. Acad. Sci. U.S.A. 100, 5766-5771, 2003A TyrCD1/TrpG8 hydrogen bond network and a TyrB10--TyrCD1 covalent link shape the heme distal site of Mycobacterium tuberculosis hemoglobin O.DOI:10.1073/pnas.1037676100PMID:12719529X-ray diffraction, 2.1 angstroms; mass spectrometric detection; this is an apparently specific formation of the isodityrosine cross-linkMilani, M.Savard, P.-Y.Ouellet, H.Ascenzi, P.Guertin, M.Bolognesi, M.submitted to the Protein Data Bank, May 2003Crystallographic structure of Mycobacterium tuberculosis hemoglobin O.PDB:1NGKX-ray diffraction, 2.11 angstromsThis cross-link can be produced as an oxidation artifact, or enzymatically by enzymes like myeloperoxidase. Since the enzymatic reaction proceeds by a free-radical mechanism, the cross-link can be aleatoric with 2, 3 or 4 tyrosines rings becoming linked in several possible ways. See also RESID:AA0367.myeloperoxidase (EC 1.11.1.7)Y, Ycross-link 2secondary to RESID:AA0146GO:0030960PSI-MOD:00373aleatoric crosslinkCROSSLNK Isodityrosine (Tyr-Tyr)AA036930-Jun-200430-Jun-200424-Oct-20083,4-dihydroxy-L-arginine2-amino-5-guanidino-3,4-dihydroxypentanoic acidbeta,gamma-dihydroxyarginine(2S,3Xi,4Xi)-2-amino-5-carbamimidamido-3,4-dihydroxypentanoic acidC 6 H 12 N 4 O 3188.19188.090940C 0 H 0 N 0 O 232.0031.989829Taylor, S.W.Craig, A.G.Fischer, W.H.Park, M.Lehrer, R.I.J. Biol. Chem. 275, 38417-38426, 2000Styelin D, an extensively modified antimicrobial peptide from ascidian hemocytes.DOI:10.1074/jbc.M006762200PMID:10978343Hydroxylations at C-3 and C-4 are assumed. Neither the positions of the hydroxylations nor the stereochemistry for the chiral centers they produce have been determined. The (2S,3R,4R) stereoisomer is shown.RGO:0030961PSI-MOD:00374hydroxylationMOD_RES 3,4-dihydroxyarginineAA037030-Jun-200430-Jun-200430-Sep-20084,5-dihydroxy-L-lysinealpha,epsilon-diamino-delta,gamma-dihydroxycaproic aciddelta,gamma-dihydroxylysine(2S,4Xi,5Xi)-2,6-diamino-4,5-dihydroxyhexanoic acidC 6 H 12 N 2 O 3160.17160.084792C 0 H 0 N 0 O 232.0031.989829Taylor, S.W.Craig, A.G.Fischer, W.H.Park, M.Lehrer, R.I.J. Biol. Chem. 275, 38417-38426, 2000Styelin D, an extensively modified antimicrobial peptide from ascidian hemocytes.DOI:10.1074/jbc.M006762200PMID:10978343Hydroxylations at C-4 and C-5 are assumed. Neither the positions of the hydroxylations nor the stereochemistry for the chiral centers they produce have been determined. The (2S,4R,5R) stereoisomer is shown.KGO:0030963PSI-MOD:00375hydroxylationMOD_RES 4,5-dihydroxylysineAA037130-Jul-200430-Jul-200431-Dec-20111'-(phospho-5'-adenosine)-L-histidineL-histidine 5'-adenosine phosphoramidesterL-histidine monoanhydride with 5'-adenylic acidN(tau)-5'-adenylic-L-histidineN1'-adenylylated histidinetele-5'-adenylic-L-histidine(2S)-2-amino-3-[1-(5'-adenosine phosphono)imidazol-4-yl]propanoic acidPDBHET:AMPC 16 H 19 N 8 O 7 P 1466.35466.111432C 10 H 12 N 5 O 6 P 1329.21329.052520Lima, C.D.Klein, M.G.Hendrickson, W.A.Science 278, 286-290, 1997Structure-based analysis of catalysis and substrate definition in the HIT protein family.DOI:10.1126/science.278.5336.286PMID:9323207X-ray diffraction, 1.8 angstroms; chemical evidence for adenylyl phosphoramide intermediateHuang, K.Arabshahi, A.Wei, Y.Frey, P.A.Biochemistry 43, 7637-7642, 2004The mechanism of action of the fragile histidine triad, Fhit: isolation of a covalent adenylyl enzyme and chemical rescue of H96G-Fhit.DOI:10.1021/bi049762nPMID:15182206chemical evidence for adenylyl phosphoramide intermediateMcCoy, J.G.Arabshahi, A.Bitto, E.Bingman, C.A.Ruzicka, F.J.Frey, P.A.Phillips Jr., G.N.Biochemistry 45, 3154-3162, 2006Structure and mechanism of an ADP-glucose phosphorylase from Arabidopsis thaliana.DOI:10.1021/bi052232mPMID:16519510X-ray diffraction, 1.83 angstromsMcCoy, J.G.Bitto, E.Phillips Jr., G.N.Bingman, C.A.Bingman, C.A.Center for Eukaryotic Structural Genomics (CESG)submitted to the Protein Data Bank, March 2005X-ray structure of GalTt-like protein from Arabidopsis thaliana At5g18200.PDB:1Z84X-ray diffraction, 1.83 angstroms, of the the trapped covalent intermediateThe phosphoramide bond is probably formed with the tele-nitrogen of histidine in most cases.HGO:0051111GO:0051112GO:0051113PSI-MOD:00376phosphoproteinACT_SITE Tele-AMP-histidine intermediateACT_SITE AMP-histidine intermediatethis UniProt feature is used when the isomeric structure has not been determinedAA037230-Jul-200430-Jul-200431-Jul-20091'-(phospho-5'-uridine)-L-histidineL-histidine 5'-uridine phosphoramidesterL-histidine monoanhydride with 5'-uridylic acidN(tau)-5'-uridylic-L-histidineN1'-uridylylated histidinetele-5'-uridylic-L-histidine(S)-2-amino-3-[1-(5'-uridine phosphono)imidazol-4-yl]propanoic acidPDBHET:U5PC 15 H 18 N 5 O 9 P 1443.31443.084214C 9 H 11 N 2 O 8 P 1306.17306.025302Wong, L.J.Sheu, K.F.Lee, S.L.Frey, P.A.Biochemistry 16, 1010-1016, 1977Galactose-1-phosphate uridylyltransferase: isolation and properties of a uridylyl-enzyme intermediate.DOI:10.1021/bi00624a032PMID:321007chemical evidence for uridylyl phosphoramide intermediateYang, S.L.Frey, P.A.Biochemistry 18, 2980-2984, 1979Nucleophile in the active site of Escherichia coli galactose-1-phosphate uridylyltransferase: degradation of the uridylyl-enzyme intermediate to N3-phosphohistidine.DOI:10.1021/bi00581a011PMID:380639chemical evidence for tele-nitrogen uridylyl phosphoramide intermediate; the 1'-nitrogen is called N(3)Wedekind, J.E.Frey, P.A.Rayment, I.Biochemistry 35, 11560-11569, 1996The structure of nucleotidylated histidine-166 of galactose-1-phosphate uridylyltransferase provides insight into phosphoryl group transfer.DOI:10.1021/bi9612677PMID:8794735X-ray diffraction, 1.86 angstromsWedekind, J.E.Frey, P.A.Rayment, I.submitted to the Protein Data Bank, June 1996The structure of nucleotidylated galactose-1-phosphate uridylyltransferase from Escherichia coli at 1.86 Angstroms resolution.PDB:1HXQX-ray diffraction, 1.86 angstromsHGO:0051110GO:0051114GO:0051115PSI-MOD:00377phosphoproteinACT_SITE Tele-UMP-histidine intermediateAA037330-Sep-200430-Sep-200430-Sep-2008L-aspartyl aldehydeL-aminosuccinaldehydic acidL-aminosuccinic acid semialdehydeL-aspartate-beta-semialdehydeL-aspartic beta-semialdehydeL-beta-formylalanine(S)-2-amino-4-oxobutanoic acidCAS:498-20-4C 4 H 5 N 1 O 299.0999.032028C 0 H 0 N 0 O -1-16.00-15.994915Anderson, L.B.Ouellette, A.J.Eaton-Rye, J.Maderia, M.MacCoss, M.J.Yates 3rd, J.R.Barry, B.A.J. Am. Chem. Soc. 126, 8399-8405, 2004Evidence for a post-translational modification, aspartyl aldehyde, in a photosynthetic membrane protein.DOI:10.1021/ja0478781PMID:15237995amine and hydrazine derivatization; chemical characterization and mass spectrometric identificationDGO:0051203PSI-MOD:00378MOD_RES Aspartyl aldehydeAA037422-Oct-200422-Oct-200405-Dec-2008L-serine microcin E492 siderophore esterN-[5-(6-O-seryl-beta-glucosyl)-2,3-dihydroxybenzoyl]-O-[N-(2,3-dihydroxybenzoyl)-O-[N-(2,3-dihydroxybenzoyl)seryl]seryl]serineC 39 H 43 N 4 O 23935.78935.231809C 36 H 37 N 3 O 20831.69831.197041Thomas, X.Destoumieux-Garzón, D.Peduzzi, J.Afonso, C.Blond, A.Birlirakis, N.Goulard, C.Dubost, L.Thai, R.Tabet, J.C.Rebuffat, S.J. Biol. Chem. 279, 28233-28242, 2004Siderophore peptide, a new type of post-translationally modified antibacterial peptide with potent activity.DOI:10.1074/jbc.M400228200PMID:15102848mass spectrometric, (1)H-NMR, and (13)C-NMR identification; the encoding of an author's name in the PubMed citation is corrected to UTF8Nolan, E.M.Walsh, C.T.Biochemistry 47, 9289-9299, 2008Investigations of the MceIJ-catalyzed posttranslational modification of the microcin E492 C-terminus: linkage of ribosomal and nonribosomal peptides to form “trojan horse” antibiotics.DOI:10.1021/bi800826jPMID:18690711biosynthesisScarboxyl-terminalGO:0051263PSI-MOD:00379blocked carboxyl endMOD_RES Serine microcin E492 siderophore esterAA037512-Nov-200412-Nov-200431-Mar-2013L-aspartyl molybdenum bis(molybdopterin guanine dinucleotide)2-amino-5,6-dimercapto-7-methyl-3,7,8a,9-tetrahydro-8-oxa-1,3,9,10-tetraazaanthracen-4-one guanosine dinucleotidenitrate reductase A aspartyl Mo-bisMGD cofactorphosphoric acid 4-(2-amino-4-oxo-3,4,5,6,-tetrahydro-pteridin-6-yl)-2-hydroxy-3,4-dimercapto-but-3-en-yl ester guanylate esterbis[8-amino-1a,2,4a,5,6,7,10-heptahydro-2-(trihydrogen diphosphate 5'-ester with guanosine)methyl-6-oxo-3,4-disulfanyl-pteridino[6,7-5,6]pyranoato-S3,S4]-aspartyl-molybdenumPDBHET:MGDPDBHET:MOC 44 H 52 Mo 1 N 21 O 29 P 4 S 41687.101688.012718C 40 H 47 Mo 1 N 20 O 26 P 4 S 41572.021572.985775Bertero, M.G.Rothery, R.A.Palak, M.Hou, C.Lim, D.Blasco, F.Weiner, J.H.Strynadka, N.C.J.Nature Struct. Biol. 10, 681-687, 2003Insights into the respiratory electron transfer pathway from the structure of nitrate reductase A.DOI:10.1038/nsb969PMID:12910261X-ray diffraction, 1.90 angstromsBertero, M.G.Strynadka, N.C.J.submitted to the Protein Data Bank, July 2003Crystal structure of nitrate reductase A, NarGHI, from Escherichia coli.PDB:1Q16X-ray diffraction, 1.90 angstromsJormakka, M.Richardson, D.Byrne, B.Iwata, S.Structure 12, 95-104, 2004Architecture of NarGH reveals a structural classification of Mo-bisMGD enzymes.DOI:10.1016/j.str.2003.11.020PMID:14725769X-ray diffraction, 2.00 angstromsJormakka, M.Richardson, D.Byrne, B.Iwata, S.submitted to the Protein Data Bank, September 2003Crystal structure of NarGH complex.PDB:1R27X-ray diffraction, 2.00 angstromsOne possible structure of a reduced form (+4H) is shown. The fully reduced form would be 1a,2,3,4,4a,5,6,7,10-nonahydro. The fully oxidized form would be 2,6,7-trihydro.The model is based on the structure of 1Q16 in which one of the molybdopterin ring systems is in the tricyclic form, and the other is in a bicyclic form with an opened pyran ring.DGO:0051217PSI-MOD:00380metalloproteinmolybdenummolybdopterinphosphoproteinMETAL Molybdenumthis UniProt feature has a structural misrepresentationAA037612-Nov-200412-Nov-200431-Mar-2013L-selenocysteinyl tungsten bis(molybdopterin guanine dinucleotide)2-amino-5,6-dimercapto-7-methyl-3,7,8a,9-tetrahydro-8-oxa-1,3,9,10-tetraazaanthracen-4-one guanosine dinucleotideformate dehydrogenase selenocysteine W-bisMGD cofactorguanylate-O'-phosphoric acid mono-(2-amino-5,6-dimercapto-4-oxo-3,5,6,7,8a,9,10,10a-octahydro-4h-8-oxa-1,3,9,10-tetraaza-anthracen-7-ylmethyl) esterbis[8-amino-1a,2,4a,5,6,7,10-heptahydro-2-(trihydrogen diphosphate 5'-ester with guanosine)methyl-6-oxo-3,4-disulfanyl-pteridino[6,7-5,6]pyranoato-S3,S4]-selenocysteinyl-Se-tungsten sulfidePDBHET:2MDPDBHET:MGDPDBHET:WC 43 H 52 N 21 O 27 P 4 S 5 Se 1 W 11842.021841.957004C 40 H 47 N 20 O 26 P 4 S 4 Se 1 W 11738.881738.947820C 40 H 47 N 20 O 26 P 4 S 5 Se 0 W 11691.971691.003369Raaijmakers, H.Teixeira, S.Dias, J.M.Almendra, M.J.Brondino, C.D.Moura, I.Moura, J.J.G.Romao, M.J.J. Biol. Inorg. Chem. 6, 398-404, 2001Tungsten-containing formate dehydrogenase from Desulfovibrio gigas: metal identification and preliminary structural data by multi-wavelength crystallography.DOI:10.1007/s007750100215PMID:11372198Raaijmakers, H.Macieira, S.Dias, J.M.Teixeira, S.Bursakov, S.Huber, R.Moura, J.J.G.Moura, I.Romao, M.J.Structure 10, 1261-1272, 2002Gene sequence and the 1.8 A crystal structure of the tungsten-containing formate dehydrogenase from Desulfovibrio gigas.DOI:10.1016/S0969-2126(02)00826-2PMID:12220497Raaijmakers, H.C.A.submitted to the Protein Data Bank, June 2002Tungsten containing formate dehydrogenase from Desulfovibrio gigas.PDB:1H0HX-ray diffraction, 1.8 angstromsOne possible structure of a reduced form (+4H) is shown. The fully reduced form would be 1a,2,3,4,4a,5,6,7,10-nonahydro. The fully oxidized form would be 2,6,7-trihydro.Csecondary to RESID:AA0022GO:0051218PSI-MOD:01469UPSI-MOD:00381metalloproteinmolybdopterinphosphoproteinseleniumselenocysteinetungstenMETAL Tungstenthis UniProt feature has a structural misrepresentationAA037731-Dec-200431-Dec-200424-Oct-20083-(2-methylthio)ethyl-6-(4-hydroxybenzylidene)-5-iminopiperazin-2-one3-(2-methylthio)ethyl-6-(4-hydroxybenzylidene)-5-amino-3,6-didehydropyrazin-2-olGFP-like chromoprotein asFP595 chromophoreL-methionyl-L-tyrosyl-2-keto-5-iminopiperazine3-(2-methylsulfanyl)ethyl-6-(4-hydroxybenzylidene)-5-iminopiperazin-2-oneC 14 H 15 N 2 O 2 S 1275.35275.085424C 0 H -4 N 0 O -1 S 0-20.03-20.026215Lukyanov, K.A.Fradkov, A.F.Gurskaya, N.G.Matz, M.V.Labas, Y.A.Savitsky, A.P.Markelov, M.L.Zaraisky, A.G.Zhao, X.Fang, Y.Tan, W.Lukyanov, S.A.J. Biol. Chem. 275, 25879-25882, 2000Natural animal coloration can be determined by a nonfluorescent green fluorescent protein homolog.DOI:10.1074/jbc.C000338200PMID:10852900Martynov, V.I.Savitsky, A.P.Martynova, N.Y.Savitsky, P.A.Lukyanov, K.A.Lukyanov, S.A.J. Biol. Chem. 276, 21012-21016, 2001Alternative cyclization in GFP-like proteins family. The formation and structure of the chromophore of a purple chromoprotein from Anemonia sulcata.DOI:10.1074/jbc.M100500200PMID:11259412Zagranichny, V.E.Rudenko, N.V.Gorokhovatsky, A.Y.Zakharov, M.V.Balashova, T.A.Arseniev, A.S.Biochemistry 43, 13598-13603, 2004Traditional GFP-type cyclization and unexpected fragmentation site in a purple chromoprotein from Anemonia sulcata, asFP595.DOI:10.1021/bi0488247PMID:15491166The correct structure for the asFP595 chromophore is now thought to be a para-hydroxybenzylidene-5-imidazolidinone. See RESID:AA0379.The diagram presents structures for two tautomeric forms with the glycine, which is linked by either an imino or amino group, shown in gray. In the correct structure, the glycine amino group forms part of a 5-member ring.M, Yamino-terminalcarboxamidinecross-link 1GO:0051357PSI-MOD:00382blocked amino endhydroxylationNot availablethis dubious modification is not currently annotated in UniProt featuresAA037831-Dec-200431-Dec-200420-May-20112-imino-glutamic acid 5-imidazolinone glycine2,N-didehydroglutamyl-5-imidazolinone glycine2-(3-carboxy-1-iminopropyl)-1-carboxymethyl-1-imidazolin-5-one2-imino-glutamyl-5-imidazolinone glycinepara-hydroxybenzylidene-imidazolidinone chromophore[2-(3-carboxy-1-iminopropyl)-5-oxo-4,5-dihydro-imidazol-1-yl]-acetic acid4-[1-(carboxymethyl)-5-oxo-4,5-dihydro-1H-imidazol-2-yl]-4-iminobutanoic acidPDBHET:CRUC 7 H 6 N 2 O 3166.14166.037842C 0 H -4 N 0 O -1-20.03-20.026215Gurskaya, N.G.Fradkov, A.F.Terskikh, A.Matz, M.V.Labas, Y.A.Martynov, V.I.Yanushevich, Y.G.Lukyanov, K.A.Lukyanov, S.A.FEBS Lett. 507, 16-20, 2001GFP-like chromoproteins as a source of far-red fluorescent proteins.DOI:10.1016/S0014-5793(01)02930-1PMID:11682051Wilmann, P.G.Petersen, J.Pettikiriarachchi, A.Buckle, A.M.Smith, S.C.Olsen, S.Perugini, M.A.Devenish, R.J.Prescott, M.Rossjohn, J.J. Mol. Biol. 349, 223-237, 2005The 2.1A crystal structure of the far-red fluorescent protein HcRed: inherent conformational flexibility of the chromophore.DOI:10.1016/j.jmb.2005.03.020PMID:15876379spectrofluorimetric analysis; X-ray diffraction, 2.10 angstromsWilmann, P.G.Petersen, J.Pettikiriarachchi, A.Buckle, A.M.Devenish, R.J.Prescott, M.Rossjohn, J.submitted to the Protein Data Bank, February 2005The 2.1A crystal structure of the far-red fluorescent protein HcRed: inherent conformational flexibility of the chromophore.PDB:1YZWX-ray diffraction, 2.10 angstromsThis entry represents the cross-link of the peptide backbone from the alpha-carboxyl carbon of residue N, a glutamic acid, to the alpha-amino nitrogen of residue N+2, a glycine, coupled with the formation of a double bond to the alpha-amino nitrogen of residue N, and the loss of a molecule of water.This cross-link is accompanied by modification of residue N+1. The modified residue N+1 is presented in a separate entry and is not included in the mass accounting of this entry. The backbone atoms of residue N+1 are shown in gray in the diagram.autocatalyticE, Gcarboxamidinecross-link 1incidental to RESID:AA0183incidental to RESID:AA0365GO:0051358PSI-MOD:00383chromoproteinimidazolinone/oxazolinone ringCROSSLNK 2-iminomethyl-5-imidazolinone (Glu-Gly)AA037931-Dec-200431-Dec-200420-May-20112-imino-methionine 5-imidazolinone glycine(2-[1-imino-3-(methylsulfanyl)propyl]-5-oxo-4,5-dihydro-imidazol-1-yl)acetic acid2,N-didehydromethionyl-5-imidazolinone glycine2-imino-methionyl-5-imidazolinone glycine2-[1-imino-3-(methylsulfanyl)propyl]-1-carboxymethyl-1-imidazolin-5-oneGFP-like chromoprotein asFP595 chromophorepara-hydroxybenzylidene-imidazolidinone chromophorered fluorescent protein eqFP611 chromophore(2-[3-(methylsulfanyl)propanimidoyl]-5-oxo-4,5-dihydro-1H-imidazol-1-yl)acetic acidPDBHET:NRQC 7 H 8 N 2 O 1 S 1168.21168.035734C 0 H -4 N 0 O -1 S 0-20.03-20.026215Lukyanov, K.A.Fradkov, A.F.Gurskaya, N.G.Matz, M.V.Labas, Y.A.Savitsky, A.P.Markelov, M.L.Zaraisky, A.G.Zhao, X.Fang, Y.Tan, W.Lukyanov, S.A.J. Biol. Chem. 275, 25879-25882, 2000Natural animal coloration can be determined by a nonfluorescent green fluorescent protein homolog.DOI:10.1074/jbc.C000338200PMID:10852900Wiedenmann, J.Schenk, A.Roecker, C.Girod, A.Spindler, K.-D.Nienhaus, G.U.Proc. Natl. Acad. Sci. U.S.A. 99, 11646-11651, 2002A far-red fluorescent protein with fast maturation and reduced oligomerization tendency from Entacmaea quadricolor (Anthozoa, Actinaria).DOI:10.1073/pnas.182157199PMID:12185250the punctuation of "Spindler, K.D." in the PubMed citation is correctedPetersen, J.Wilmann, P.G.Beddoe, T.Oakley, A.J.Devenish, R.J.Prescott, M.Rossjohn, J.J. Biol. Chem. 278, 44626-44631, 2003The 2.0-A crystal structure of eqFP611, a far red fluorescent protein from the sea anemone Entacmaea quadricolor.DOI:10.1074/jbc.M307896200PMID:12909624X-ray diffraction, 2.00 angstromsPetersen, J.Wilmann, P.G.Beddoe, T.Oakley, A.J.Devenish, R.J.Prescott, M.Rossjohn, J.submitted to the Protein Data Bank, July 2003The 2.0 crystal structure of eqFP611, a far-red fluorescent protein from the sea anemone Entacmaea quadricolor.PDB:1UISX-ray diffraction, 2.00 angstromsWilmann, P.G.Petersen, J.Devenish, R.J.Prescott, M.Rossjohn, J.J. Biol. Chem. 280, 2401-2404, 2005Variations on the GFP chromophore: A polypeptide fragmentation within the chromophore revealed in the 2.1-A crystal structure of a nonfluorescent chromoprotein from Anemonia sulcata.DOI:10.1074/jbc.C400484200PMID:15542608X-ray diffraction, 2.10 angstromsPetersen, J.Wilmann, P.G.Beddoe, T.Oakley, A.J.Devenish, R.J.Prescott, M.Rossjohn, J.submitted to the Protein Data Bank, October 2004Variations on the GFP chromophore: A fragmented 5-membered heterocycle revealed in the 2.1A crystal structure of a non-fluorescent chromoprotein.PDB:1XQMX-ray diffraction, 2.10 angstromsThis entry represents the cross-link of the peptide backbone from the alpha-carboxyl carbon of residue N, a methionine, to the alpha-amino nitrogen of residue N+2, a glycine, coupled with the formation of a double bond to the alpha-amino nitrogen of residue N, and the loss of a molecule of water.This cross-link is accompanied by modification of residue N+1. The modified residue N+1 is presented in a separate entry and is not included in the mass accounting of this entry. The backbone atoms of residue N+1 are shown in gray in the diagram.In the asFP595 chromoprotein, the peptide chain is cleaved at the methionine alpha-amino. For a previously proposed structure of the asFP595 chromoprotein, see RESID:AA0377.autocatalyticG, Mcarboxamidinecross-link 1incidental to RESID:AA0183incidental to RESID:AA0365GO:0051359PSI-MOD:00384chromoproteinimidazolinone/oxazolinone ringCROSSLNK 2-iminomethyl-5-imidazolinone (Met-Gly)AA038031-Dec-200431-Dec-200420-May-2011L-asparagine 5-imidazolinone glycine2-[(S)-1,3-diamino-3-oxopropyl]-1-carboxymethyl-1-imidazolin-5-oneasparaginyl-5-imidazolinone glycinepara-hydroxybenzylidene-imidazolidinone chromophoreZoanthus sp. fluorescent protein FP506 chromophore[2-(1,3-diamino-3-oxopropyl)-5-oxo-4,5-dihydro-imidazol-1-yl]-acetic acid(2-[(1S)-1,3-diamino-3-oxopropyl]-5-oxo-4,5-dihydro-1H-imidazol-1-yl)acetic acidPDBHET:NYGC 6 H 7 N 3 O 2153.14153.053826C 0 H -2 N 0 O -1-18.02-18.010565Matz, M.V.Fradkov, A.F.Labas, Y.A.Savitsky, A.P.Zaraisky, A.G.Markelov, M.L.Lukyanov, S.A.Nature Biotechnol. 17, 969-973, 1999Fluorescent proteins from nonbioluminescent Anthozoa species.DOI:10.1038/13657PMID:10504696Pletneva, N.Pletnev, V.Tikhonova, T.Pakhomov, A.A.Popov, V.Martynov, V.I.Wlodawer, A.Dauter, Z.Pletnev, S.Acta Crystallogr. D Biol. Crystallogr. 63, 1082-1093, 2007Refined crystal structures of red and green fluorescent proteins from the button polyp Zoanthus.DOI:10.1107/S0907444907042461PMID:17881826X-ray diffraction, 2.20 angstromsPletneva, N.Pletnev, V.Tikhonova, T.Pletnev, S.submitted to the Protein Data Bank, January 2007Crystal structures of green fluorescent proteins from Zoanthus sp. at 2.2 A resolution.PDB:2OJKX-ray diffraction, 2.20 angstromsThis entry represents the cross-link of the peptide backbone from the alpha-carboxyl carbon of residue N, an asparagine, to the alpha-amino nitrogen of residue N+2, a glycine, coupled with the formation of a double bond to the alpha-amino nitrogen of residue N+1 which loses one hydrogen, and the loss of a molecule of water.This cross-link is accompanied by modification of residue N+1. The modified residue N+1 is presented in a separate entry and is not included in the mass accounting of this entry. The backbone atoms of residue N+1 are shown in gray in the diagram.autocatalyticG, Ncarboxamidinecross-link 1incidental to RESID:AA0183incidental to RESID:AA0365GO:0051360PSI-MOD:00385chromoproteinimidazolinone/oxazolinone ringCROSSLNK 5-imidazolinone (Asn-Gly)AA038131-Dec-200431-Dec-200420-May-2011L-lysine 5-imidazolinone glycine2-[(S)-1,5-diaminopentanyl]-1-carboxymethyl-1-imidazolin-5-oneAnemonia majano fluorescent protein FP486 chromophorelysyl-5-imidazolinone glycinepara-hydroxybenzylidene-imidazolidinone chromophore[2-(1,5-diaminopentanyl)-5-oxo-4,5-dihydro-imidazol-1-yl]-acetic acid(2-[(1S)-1,5-diaminopentyl]-5-oxo-4,5-dihydro-1H-imidazol-1-yl)acetic acidPDBHET:CR7C 8 H 13 N 3 O 1167.21167.105862C 0 H -2 N 0 O -1-18.02-18.010565Matz, M.V.Fradkov, A.F.Labas, Y.A.Savitsky, A.P.Zaraisky, A.G.Markelov, M.L.Lukyanov, S.A.Nature Biotechnol. 17, 969-973, 1999Fluorescent proteins from nonbioluminescent Anthozoa species.DOI:10.1038/13657PMID:10504696Henderson, J.N.Remington, S.J.Proc. Natl. Acad. Sci. U.S.A. 102, 12712-12717, 2005Crystal structures and mutational analysis of amFP486, a cyan fluorescent protein from Anemonia majano.DOI:10.1073/pnas.0502250102PMID:16120682spectrofluorimetric analysis; X-ray diffraction, 1.65 angstromsHenderson, J.N.Remington, S.J.submitted to the Protein Data Bank, June 2005Crystal structures of amFP486, a cyan fluorescent protein from Anemonia majano, and variants.PDB:2A46X-ray diffraction, 1.65 angstromsThis entry represents the cross-link of the peptide backbone from the alpha-carboxyl carbon of residue N, a lysine, to the alpha-amino nitrogen of residue N+2, a glycine, coupled with the formation of a double bond to the alpha-amino nitrogen of residue N+1 which loses one hydrogen, and the loss of a molecule of water.This cross-link is accompanied by modification of residue N+1. The modified residue N+1 is presented in a separate entry and is not included in the mass accounting of this entry. The backbone atoms of residue N+1 are shown in gray in the diagram.autocatalyticG, Kcarboxamidinecross-link 1incidental to RESID:AA0183incidental to RESID:AA0365GO:0051361PSI-MOD:00386chromoproteinimidazolinone/oxazolinone ringCROSSLNK 5-imidazolinone (Lys-Gly)AA038225-Feb-200525-Feb-200530-Jun-20122-tetrahydropyridinyl-5-imidazolinone glycine2-(3,4,5,6-tetrahydropyridin-2-yl)-1-carboxymethyl-1-imidazolin-5-one2-(tetrahydropyrid-2-yl)-5-imidazolinone glycinepara-hydroxybenzylidene-imidazolidinone chromophoreZoanthus sp. fluorescent protein zFP538 chromophore[5-oxo-2-(3,4,5,6-tetrahydropyridin-2-yl)-4,5-dihydro-1H-imidazol-1-yl]acetic acid[5-oxo-2-(3,4,5,6-tetrahydropyridin-2-yl)-4,5-dihydro-1H-imidazol-1-yl]acetic acidPDBHET:CH7C 8 H 9 N 2 O 1149.17149.071488C 0 H -7 N -1 O -1-37.06-37.052764Matz, M.V.Fradkov, A.F.Labas, Y.A.Savitsky, A.P.Zaraisky, A.G.Markelov, M.L.Lukyanov, S.A.Nature Biotechnol. 17, 969-973, 1999Fluorescent proteins from nonbioluminescent Anthozoa species.DOI:10.1038/13657PMID:10504696Remington, S.J.Wachter, R.M.Yarbrough, D.K.Branchaud, B.Anderson, D.C.Kallio, K.Lukyanov, K.A.Biochemistry 44, 202-212, 2005zFP538, a yellow-fluorescent protein from Zoanthus, contains a novel three-ring chromophore.DOI:10.1021/bi048383rPMID:15628861X-ray diffraction, 2.70 angstromsRemington, S.J.Wachter, R.M.Yarbrough, D.K.Branchaud, B.Anderson, D.C.Kallio, K.Lukyanov, K.A.submitted to the Protein Data Bank, August 2004Crystal Structure of Wild Type Yellow Fluorescent Protein zFP538 from Zoanthus.PDB:1XAEX-ray diffraction, 2.70 angstromsThis entry represents the cross-link of the peptide backbone from the alpha-carboxyl carbon of residue N, a lysine, to the alpha-amino nitrogen of residue N+2, a glycine, coupled with the formation of a double bond to the alpha-amino nitrogen of residue N+1 which loses one hydrogen, and the loss of a molecule of water. In addition, the residue N lysine undergoes cyclization. The alpha-amino nitrogen is replaced by the epsilon-amino nitrogen, the peptide chain is broken, residue N-1 is released as an amide, and a double bond is formed between the alpha-carbon and the nitrogen so that a tetrahydropyridine ring results.This cross-link is accompanied by modification of residue N+1. The modified residue N+1 is presented in a separate entry and is not included in the mass accounting of this entry. The backbone atoms of residue N+1 are shown in gray in the diagram.autocatalyticG, Kamino-terminalcarboxamidinecross-link 1incidental to RESID:AA0183incidental to RESID:AA0365GO:0051362PSI-MOD:00387chromoproteinimidazolinone/oxazolinone ringpyridine ringCROSSLNK 2-tetrahydro-2-pyridyl-5-imidazolinone (Lys-Gly)AA038325-Feb-200525-Feb-200530-Apr-2010L-alanyl-pentaglycyl-murein peptidoglycan(2R,6S)-2-(N-mureinyl-(R)-alanyl-(S)-isoglutamyl)amino-6-(alanyl-pentaglycyl)amino-pimeloyl-(S)-alanyl-(S)-alanineC 13 H 20 N 6 O 6 +356.34 +356.144432 +C 10 H 14 N 5 O 4 +268.25 +268.104579 +de Chateau, M.Bjoerck, L.J. Biol. Chem. 269, 12147-12151, 1994Protein PAB, a mosaic albumin-binding bacterial protein representing the first contemporary example of module shuffling.PMID:8163519This modification may be unique to the species Finegoldia magna (Peptostreptococcus magnus).sortase aminoacyltransferase (EC 2.3.2.-)Acarboxyl-terminalGO:0051363PSI-MOD:00388blocked carboxyl endglycoproteinpeptidoglycanMOD_RES Pentaglycyl murein peptidoglycan amidated alanineAA038425-Feb-200525-Feb-200531-Dec-2011N-formyl-L-proline1-formyl-2-pyrrolidinecarboxylic acid1-formylproline(2S)-1-formylpyrrolidine-2-carboxylic acidCAS:13200-83-4C 6 H 8 N 1 O 2126.14126.055504C 1 H 0 N 0 O 128.0127.994915Fujiki, H.Braunitzer, G.Rudloff, V.Hoppe-Seyler's Z. Physiol. Chem. 351, 901-902, 1970N-Formylproline as N-terminal amino acid of lamprey haemoglobin.DOI:10.1515/bchm2.1970.351.2.893PMID:5464655this reported modification is probably artifactual; the publisher's DOI is incorrectly processed, the article can be accessed with the preceeding article beginning at page 893Fuchigami, T.Misumi, S.Takamune, N.Takahashi, I.Takama, M.Shoji, S.Biochem. Biophys. Res. Commun. 293, 1107-1113, 2002Acid-labile formylation of amino terminal proline of human immunodeficiency virus type 1 p24(gag) was found by proteomics using two-dimensional gel electrophoresis and matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry.DOI:10.1016/S0006-291X(02)00329-7PMID:12051774it is not demonstrated that this modification is enzymatically producedGevaert, K.Goethals, M.Martens, L.Van Damme, J.Staes, A.Thomas, G.R.Vandekerckhove, J.Nature Biotechnol. 21, 566-569, 2003Exploring proteomes and analyzing protein processing by mass spectrometric identification of sorted N-terminal peptides.DOI:10.1038/nbt810PMID:12665801the peptide proposed to have an N-formylproline was supposedly isolated from human tissue, but the sequence identified by mass analysis was the product of an engineered, artificial gene sequence; the identification has been acknowledged to be spurious (by private communication) and no alternative interpretation has been offeredPamino-terminalGO:0051364PSI-MOD:00389blocked amino endformylationNot availablethis modification is not annotated in UniProt featuresAA038527-May-200527-May-200525-Feb-2011O-decanoyl-L-serineL-serine decanoate esterO3-decanoyl-L-serine(2S)-2-amino-3-(decanoyloxy)propanoic acidC 13 H 23 N 1 O 3241.33241.167794C 10 H 18 N 0 O 1154.25154.135765Kaiya, H.Kojima, M.Hosoda, H.Riley, L.G.Hirano, T.Grau, E.G.Kangawa, K.J. Endocrinol. 176, 415-423, 2003Amidated fish ghrelin: purification, cDNA cloning in the Japanese eel and its biological activity.DOI:10.1677/joe.0.1760415PMID:12630926mass spectrometric identificationghrelin O-acyltransferase, GOAT (EC 2.3.1.-)SGO:0042050GO:0051367PSI-MOD:00390lipoproteinLIPID O-decanoyl serineAA038627-May-200527-May-200530-Sep-2011O-octanoyl-L-threonineL-threonine octanoate esterO3-octanoyl-L-threonine(2S)-2-amino-3-(octanoyloxy)butanoic acidC 12 H 21 N 1 O 3227.30227.152144C 8 H 14 N 0 O 1126.20126.104465Kaiya, H.Kojima, M.Hosoda, H.Koda, A.Yamamoto, K.Kitajima, Y.Matsumoto, M.Minamitake, Y.Kikuyama, S.Kangawa, K.J. Biol. Chem. 276, 40441-40448, 2001Bullfrog ghrelin is modified by n-octanoic acid at its third threonine residue.DOI:10.1074/jbc.M105212200PMID:11546772mass spectrometric identificationghrelin O-acyltransferase, GOAT (EC 2.3.1.-)TGO:0042050GO:0051368PSI-MOD:00391lipoproteinLIPID O-octanoyl threonineAA038727-May-200527-May-200525-Feb-2011O-decanoyl-L-threonineL-threonine decanoate esterO3-decanoyl-L-threonine(2S)-2-amino-3-(decanoyloxy)propanoic acidC 14 H 25 N 1 O 3255.36255.183444C 10 H 18 N 0 O 1154.25154.135765Kaiya, H.Kojima, M.Hosoda, H.Koda, A.Yamamoto, K.Kitajima, Y.Matsumoto, M.Minamitake, Y.Kikuyama, S.Kangawa, K.J. Biol. Chem. 276, 40441-40448, 2001Bullfrog ghrelin is modified by n-octanoic acid at its third threonine residue.DOI:10.1074/jbc.M105212200PMID:11546772mass spectrometric identificationghrelin O-acyltransferase, GOAT (EC 2.3.1.-)TGO:0042050GO:0051369PSI-MOD:00392lipoproteinLIPID O-decanoyl threonineAA038828-Oct-200528-Oct-200530-Sep-20084-hydroxy-D-valineD-gamma-hydroxyvaline(2R,3Xi)-2-amino-4-hydroxy-3-methylbutanoic acidC 5 H 9 N 1 O 2115.13115.063329C 0 H 0 N 0 O 116.0015.994915Pisarewicz, K.Mora, D.Pflueger, F.C.Fields, G.B.Mari, F.J. Am. Chem. Soc. 127, 6207-6215, 2005Polypeptide chains containing D-gamma-hydroxyvaline.DOI:10.1021/ja050088mPMID:15853325mass spectrographic, and 1D- and 2D-TOCSY NMR analysis; both the (2R,3R) and the (2R,3S) diastereomeric forms are apparently producedVsecondary to RESID:AA0200PSI-MOD:00756D-amino acidhydroxylationMOD_RES D-4-hydroxyvalineAA038928-Oct-200528-Oct-200531-May-2018O4-galactosyl-L-hydroxyproline4-(beta-D-galactopyranosyloxy)proline4-(galactosyloxy)prolinebeta-galactopyranosyl-4-hydroxyprolineO4-glycosyl-hydroxyproline(2S,4R)-4-(beta-D-galactopyranosyloxy)pyrrolidine-2-carboxylic acidC 11 H 17 N 1 O 7 +275.26 +275.100502 +C 6 H 10 N 0 O 6 +178.14 +178.047738 +Fincher, G.B.Stone, B.A.Annu. Rev. Plant Physiol. 34, 47-70, 1983Arabinogalactan-proteins: structure, biosynthesis, and function.DOI:10.1146/annurev.pp.34.060183.000403reviewVan den Bulck, K.Loosveld, A.M.A.Courtin, C.M.Proost, P.Van Damme, J.Robben, J.Mort, A.Delcour, J.A.Cereal Chem. 79, 329-331, 2002Amino acid sequence of wheat flour arabinogalactan-peptide is identical to part of grain softness protein GSP-1, leads to an improved structural model.DOI:10.1094/CCHEM.2002.79.3.329See also RESID:AA0212 and RESID:AA0390 for other O4-glycosylated 4-hydroxyprolines.Psecondary to RESID:AA0030PSI-MOD:00757glycoproteinhydroxylationCARBOHYD O-linked (Gal...) hydroxyprolineAA039028-Oct-200528-Oct-200531-May-2018O4-(N-acetylamino)glucosyl-L-hydroxyproline4-(N-acetylglucosaminyloxy)proline4-[(2-N-acetylamino)-alpha-D-glucopyranosyl]oxyprolinealpha-2-(N-acetylamino)glucopyranosyl-4-hydroxyprolineO4-glycosyl-hydroxyproline(2S,4R)-4-[2-acetamido-2-deoxy-alpha-D-glucopyranosyloxy]pyrrolidine-2-carboxylic acidCAS:10036-64-3C 13 H 20 N 2 O 7 +316.31 +316.127051 +C 8 H 13 N 1 O 6 +219.19 +219.074287 +Teng-umnuay, P.Morris, H.R.Dell, A.Panico, M.Paxton, T.West, C.M.J. Biol. Chem. 273, 18242-18249, 1998The cytoplasmic F-box binding protein SKP1 contains a novel pentasaccharide linked to hydroxyproline in Dictyostelium.DOI:10.1074/jbc.273.29.18242PMID:9660787the polysaccharide structure is described with N-acetylglucosamine glycosylating hydroxyprolineWest, C.M.Van Der Wel, H.Sassi, S.Gaucher, E.A.Biochim. Biophys. Acta 1673, 29-44, 2004Cytoplasmic glycosylation of protein-hydroxyproline and its relationship to other glycosylation pathways.DOI:10.1016/j.bbagen.2004.04.007PMID:15238247the initial enzymatic reactions are described and the modification is identified as O4-alpha-(N-acetylamino)glucosyl-hydroxyprolineSee also RESID:AA0212 and RESID:AA0389 for other O4-glycosylated 4-hydroxyprolines.Psecondary to RESID:AA0030PSI-MOD:00758glycoproteinhydroxylationCARBOHYD O-linked (GlcNAc...) hydroxyprolineCARBOHYD O-linked (HexNAc...) hydroxyprolinethis UniProt feature is used when the identity of the sugar has not been determinedAA039102-Dec-200502-Dec-200531-Dec-20132-(S-L-cysteinyl)pyruvic acid O-phosphothioketal2-([(2R)-2-amino-2-carboxyethyl]sulfanyl)-2-(phosphonooxy)propanoic acid2-([(2R)-2-azanyl-2-carboxyethyl]sulfanyl)-2-(phosphonooxy)propanoic acidcysteinyl pyruvate O-phosphothioketalphosphoenolpyruvate cysteine adductphospholactoyl cysteine adductS-[1-carboxy-1-(phosphonooxy)ethyl]cysteine(2R)-2-amino-3-[1-carboxy-1-(phosphonooxy)ethyl]sulfanylpropanoic acidPDBHET:QPAC 6 H 10 N 1 O 7 P 1 S 1271.18270.991559C 3 H 5 N 0 O 6 P 1 S 0168.04167.982375Cassidy, P.J.Kahan, F.M.Biochemistry 12, 1364-1374, 1973A stable enzyme-phosphoenolpyruvate intermediate in the synthesis of uridine-5'-diphospho-N-acetyl-2-amino-2-deoxyglucose 3-O-enolpyruvyl ether.DOI:10.1021/bi00731a017PMID:4696757Ramilo, C.Appleyard, R.J.Wanke, C.Krekel, F.Amrhein, N.Evans, J.N.Biochemistry 33, 15071-15079, 1994Detection of the covalent intermediate of UDP-N-acetylglucosamine enolpyruvyl transferase by solution-state and time-resolved solid-state NMR spectroscopy.DOI:10.1021/bi00254a016PMID:7999765Kim, D.H.Lees, W.J.Kempsell, K.E.Lane, W.S.Duncan, K.Walsh, C.T.Biochemistry 35, 4923-4928, 1996Characterization of a Cys115 to Asp substitution in the Escherichia coli cell wall biosynthetic enzyme UDP-GlcNAc enolpyruvyl transferase (MurA) that confers resistance to inactivation by the antibiotic fosfomycin.DOI:10.1021/bi952937wPMID:8664284it is demonstrated that Cys-115 acts catalytically as a proton donor, but that formation of the covalent adduct with phosphoenolpyruvate is not required for catalysisZhu, J.Y.Yang, Y.Han, H.Betzi, S.Olesen, S.H.Marsilio, F.Schönbrunn, E.J. Biol. Chem. 287, 12657-12667, 2012Functional consequence of covalent reaction of phosphoenolpyruvate with UDP-N-acetylglucosamine 1-carboxyvinyltransferase (MurA).DOI:10.1074/jbc.M112.342725PMID:22378791X-ray diffraction, 1.81 angstromsZhu, J.Y.Schonbrunn, E.submitted to the Protein Data Bank, August 1996Aquifex aeolicus MurA in complex with UDP-N-acetylmuramic acid and covalent adduct of PEP with Cys124.PDB:3SWGX-ray diffraction, 1.81 angstroms; an alternative model to PDB:2YVW3-phosphoshikimate 1-carboxyvinyltransferase (EC 2.5.1.19)UDP-N-acetylglucosamine 1-carboxyvinyltransferase (EC 2.5.1.7)CPSI-MOD:00797phosphoproteinthioether bondMOD_RES 2-(S-cysteinyl)pyruvic acid O-phosphothioketalAA039202-Dec-200502-Dec-200531-May-2018S-galactosyl-L-cysteineS-(beta-D-galactopyranosyl)cysteineS-glycosyl-cysteine(2R)-2-amino-3-(D-galactopyranosylsulfanyl)propanoic acidC 9 H 15 N 1 O 6 S 1 +265.28 +265.062008 +C 6 H 10 N 0 O 5 S 0 +162.14 +162.052823 +Lote, C.J.Weiss, J.B.FEBS Lett. 16, 81-85, 1971Identification of digalactosylcysteine in a glycopeptide isolated from urine by a new preparative technique.DOI:10.1016/0014-5793(71)80337-XPMID:11945907chromatographic detection and chemical characterization; S-galactosylcysteine peptide; the peptide was not isolated or characterized in subsequent work, and the reported peptide sequence has not been found in the human proteomeThe beta form is shown.See also RESID:AA0152 and RESID:AA0560 for other S-glycosylated cysteines.CPSI-MOD:00799glycoproteinthioether bondCARBOHYD S-linked (Gal...) cysteineCARBOHYD S-linked (Hex...) cysteinethis UniProt feature is used when the identity of the sugar has not been determinedAA039331-Dec-200531-Dec-201131-Dec-2011L-cysteinyl-L-histidino-homocitryl vanadium heptairon nonasulfide carbidenitrogenase iron-vanadium cofactorC 17 Fe 7 H 18 N 4 O 9 S 10 V 11184.811184.316610C 8 Fe 7 H 6 N 0 O 7 S 9 V 1944.53944.248513Joerger, R.D.Loveless, T.M.Pau, R.N.Mitchenall, L.A.Simon, B.H.Bishop, P.E.J. Bacteriol. 172, 3400-3408, 1990Nucleotide sequences and mutational analysis of the structural genes for nitrogenase 2 of Azotobacter vinelandii.PMID:2345152The structure is presumed to be analagous to the molybendum-iron-sulfur cluster (see RESID:AA0141). Cysteine binds one iron of a 4Fe-3S cluster; the other three irons are connected by three mu(2)-sulfides and one mu(6)-carbon to three irons of a V-3Fe-3S cluster; the vanadium is further bound by the 2-oxide and 2-carboxylate of homocitrate (2-hydroxy-1,2,4-butanetricarboxylic acid) and the pros-N of histidine.C, Hcross-link 2incidental to RESID:AA0300PSI-MOD:00800iron-sulfur proteinmetalloproteinvanadiumMETAL Vanadium-iron-sulfur (7Fe-V-9S-X-homocitryl)these UniProt features have not been revisedMETAL Vanadium-iron-sulfur (7Fe-V-9S-X-homocitryl); via pros nitrogenthese UniProt features have not been revisedAA039431-Dec-200531-Dec-201131-Dec-2011L-cysteinyl-L-histidino-homocitryl octairon nonasulfide carbidenitrogenase iron-iron cofactorC 17 Fe 8 H 18 N 4 O 9 S 102-1189.711189.308685C 8 Fe 8 H 6 N 0 O 7 S 92-949.43949.240588Pau, R.N.Eldridge, M.E.Lowe, D.J.Mitchenall, L.A.Eady, R.R.Biochem. J. 293, 101-107, 1993Molybdenum-independent nitrogenases of Azotobacter vinelandii: a functional species of alternative nitrogenase-3 isolated from a molybdenum-tolerant strain contains an iron-molybdenum cofactor.PMID:8392330The structure is presumed to be analagous to the molybendum-iron-sulfur cluster (see RESID:AA0141). Cysteine binds one iron of a 4Fe-3S cluster; the other three irons are connected by three mu-sulfides and one mu(6)-carbon to three irons of a Mo-3Fe-3S cluster; the molybdenum is further bound by the 2-oxide and 2-carboxylate of homocitrate (2-hydroxy-1,2,4-butanetricarboxylic acid) and the pros-N of histidine.C, Hcross-link 2incidental to RESID:AA0300PSI-MOD:00801iron-sulfur proteinmetalloproteinMETAL Iron-sulfur (8Fe-9S-X-homocitryl)these UniProt features have not been revisedMETAL Iron-sulfur (8Fe-9S-X-homocitryl); via pros nitrogenthese UniProt features have not been revisedAA039531-Mar-200631-Mar-200631-Jul-2009L-histidino vanadium tetraoxide(4-[(2S)-2-amino-2-carboxyethyl]-1H-imidazol-1-yl) (dihydroxy)dioxovanadium1'-vanadato-L-histidinebromoperoxidase vanadium cofactorchloroperoxidase vanadium cofactorhaloperoxidase vanadium cofactorhistidine-1-vanadatehistidine-N(epsilon)-vanadatehistidine-N1'-vanadateN(tau)-vanadatohistidinetele-vanadatohistidinedihydrogen (4-[(2S)-2-amino-2-carboxyethyl]-1H-imidazol-1-yl) (tetraoxido)vanadateCAS:14333-18-7COMe:BIM000195PDBHET:VO4C 6 H 9 N 3 O 5 V 1254.10253.998180C 0 H 2 N 0 O 4 V 1116.95116.939268Messerschmidt, A.Wever, R.Proc. Natl. Acad. Sci. U.S.A. 93, 392-396, 1996X-ray structure of a vanadium-containing enzyme: chloroperoxidase from the fungus Curvularia inaequalis.DOI:10.1073/pnas.93.1.392PMID:8552646X-ray diffraction, 2.1 angstromsMesserschmidt, A.Prade, L.Wever, R.submitted to the Protein Data Bank, April 2001Crystal structure of native vanadium-containing chloroperoxidase from Curvularia inaequalis.PDB:1IDQX-ray diffraction, 2.03 angstromsWeyand, M.Hecht, H.Kiess, M.Liaud, M.Vilter, H.Schomburg, D.J. Mol. Biol. 293, 595-611, 1999X-ray structure determination of a vanadium-dependent haloperoxidase from Ascophyllum nodosum at 2.0 A resolution.DOI:10.1006/jmbi.1999.3179PMID:10543953X-ray diffraction, 2.0 angstromsWeyand, M.Hecht, H.J.Kiess, M.Liaud, M.F.Vilter, H.Schomburg, D.submitted to the Protein Data Bank, June 1999X-ray SIRAS structure determination of a vanadium-dependent haloperoxidase from Ascophyllum nodosum at 2.0 A resolution.PDB:1QI9X-ray diffraction, 2.05 angstromsRaugei, S.Carloni, P.J. Phys. Chem. B 110, 3747-3758, 2006Structure and function of vanadium haloperoxidase.DOI:10.1021/jp054901bPMID:16494433quantum and molecular mechanics model study of electon configuartion, protonation and enzyme mechanismThe resting state electron configuration and protonation probably corresponds to dihydrogen (tetraoxido)vanadate(6+).HPSI-MOD:00802metalloproteinvanadiumMETAL Vanadiumthis UniProt feature has a structural misrepresentationAA039631-Mar-200631-Mar-200631-Mar-20123-(L-cystein-S-yl)-L-tyrosine2-amino-3-(2-amino-2-carboxyethylthio)-3-(4-hydroxyphenyl)propanoic acidS-(tyros-3'-yl)cysteine(2S,3R)-2-amino-3-([(2R)-2-amino-2-carboxyethyl]sulfanyl)-3-(4-hydroxyphenyl)propanoic acidC 12 H 12 N 2 O 3 S 1264.30264.056863C 0 H -2 N 0 O 0 S 0-2.02-2.015650Diaz, A.Horjales, E.Rudino-Pinera, E.Arreola, R.Hansberg, W.J. Mol. Biol. 342, 971-985, 2004Unusual Cys-Tyr covalent bond in a large catalase.DOI:10.1016/j.jmb.2004.07.027PMID:15342250X-ray diffraction, 1.75 angstromsDiaz, A.Horjales, E.Rudio-Piera, E.Arreola, R.Hansberg, W.submitted to the Protein Data Bank, April 2004Crystal structure of the catalase-1 from Neurospora crassa, native structure at 1.75A resolution.PDB:1SY7X-ray diffraction, 1.75 angstromsThis modification should not be confused with 3'-(S-L-cysteinyl)-L-tyrosine (see RESID:AA0113).C, Ycross-link 2PSI-MOD:00803thioether bondCROSSLNK 3-(S-cysteinyl)-tyrosine (Cys-Tyr)AA039731-Mar-200631-Mar-200631-May-2018O-glucosyl-L-serineO-glycosylserineO3-glucosylserine(2S)-2-amino-3-(beta-D-glucopyranosyloxy)propanoic acidC 9 H 15 N 1 O 7 +249.22 +249.084852 +C 6 H 10 N 0 O 5 +162.14 +162.052823 +Nishimura, H.Kawabata, S.Kisiel, W.Hase, S.Ikenaka, T.Takao, T.Shimonishi, Y.Iwanaga, S.J. Biol. Chem. 264, 20320-20325, 1989Identification of a disaccharide (Xyl-Glc) and a trisaccharide (Xyl2-Glc) O-glycosidically linked to a serine residue in the first epidermal growth factor-like domain of human factors VII and IX and protein Z and bovine protein Z.PMID:2511201Hase, S.Nishimura, H.Kawabata, S.Iwanaga, S.Ikenaka, T.J. Biol. Chem. 265, 1858-1861, 1990The structure of (xylose)2glucose-O-serine 53 found in the first epidermal growth factor-like domain of bovine blood clotting factor IX.PMID:2105311structural analysis; this modification has a beta-glycosidic linkageMoloney, D.J.Shair, L.H.Lu, F.M.Xia, J.Locke, R.Matta, K.L.Haltiwanger, R.S.J. Biol. Chem. 275, 9604-9611, 2000Mammalian Notch1 is modified with two unusual forms of O-linked glycosylation found on epidermal growth factor-like modules.DOI:10.1074/jbc.275.13.9604PMID:10734111See also RESID:AA0154, RESID:AA0208, RESID:AA0209, RESID:AA0210, RESID:AA0291, RESID:AA0296, RESID:AA0297, RESID:AA0397, RESID:AA0398, RESID:AA0400, RESID:AA0402, RESID:AA0404, RESID:AA0406, and RESID:AA0422 for other O-glycosylated serines.SPSI-MOD:00804glycoproteinCARBOHYD O-linked (Glc) serineCARBOHYD O-linked (Glc...) serineCARBOHYD O-linked (Hex) serinethis UniProt feature is used when the identity of the sugar has not been determinedCARBOHYD O-linked (Hex...) serinethis UniProt feature is used when the identity of the sugar has not been determinedAA039831-Mar-200631-Mar-200631-May-2018O-(N-acetylamino)glucosyl-L-serineO-(2-acetylamino-2-deoxy-beta-D-glucopyranosyl)-L-serineO-(N-acetylglucosaminyl)serineO-glycosylserineO-seryl-beta-N-acetylglucosaminideO3-(2-acetamido-2-deoxy-beta-D-glucopyranosyl)-L-serineO3-(N-acetylglucosaminyl)serine(2S)-2-amino-3-(2-acetamido-2-deoxy-beta-D-glucopyranosyloxy)propanoic acidCAS:17041-36-0ChEBI:90838PDBHET:NAGC 11 H 18 N 2 O 7 +290.27 +290.111401 +C 8 H 13 N 1 O 5 +203.19 +203.079373 +Torres, C.R.Hart, G.W.J. Biol. Chem. 259, 3308-3317, 1984Topography and polypeptide distribution of terminal N-acetylglucosamine residues on the surfaces of intact lymphocytes. Evidence for O-linked GlcNAc.PMID:6421821D'Onofrio, M.Starr, C.M.Park, M.K.Holt, G.D.Haltiwanger, R.S.Hart, G.W.Hanover, J.A.Proc. Natl. Acad. Sci. U.S.A. 85, 9595-9599, 1988Partial cDNA sequence encoding a nuclear pore protein modified by O-linked N-acetylglucosamine.DOI:10.1073/pnas.85.24.9595PMID:3200844enzymatic radiolabeling and sequencing evidence for intracellular O-GlcNAc glycosylation of serineHaynes, P.A.Gooley, A.A.Ferguson, M.A.Redmond, J.W.Williams, K.L.Eur. J. Biochem. 216, 729-737, 1993Post-translational modifications of the Dictyostelium discoideum glycoprotein PsA. Glycosylphosphatidylinositol membrane anchor and composition of O-linked oligosaccharides.DOI:10.1111/j.1432-1033.1993.tb18192.xPMID:8404891Butkinaree, C.Park, K.Hart, G.W.Biochim. Biophys. Acta 1800, 96-106, 2010O-linked beta-N-acetylglucosamine (O-GlcNAc): Extensive crosstalk with phosphorylation to regulate signaling and transcription in response to nutrients and stress.DOI:10.1016/j.bbagen.2009.07.018PMID:19647786review of regulatory GlcNAc O-glycosylationLazarus, M.B.Nam, Y.Jiang, J.Sliz, P.Walker, S.Nature 469, 564-567, 2011Structure of human O-GlcNAc transferase and its complex with a peptide substrate.DOI:10.1038/nature09638PMID:21240259X-ray diffraction of generating enzyme with substrate, at 1.95 and 2.78 angstromsSee also RESID:AA0154, RESID:AA0208, RESID:AA0209, RESID:AA0210, RESID:AA0291, RESID:AA0296, RESID:AA0297, RESID:AA0397, RESID:AA0400, RESID:AA0402, RESID:AA0404, RESID:AA0406, and RESID:AA0422 for other O-glycosylated serines.protein O-GlcNAc transferase (EC 2.4.1.255)SPSI-MOD:00805glycoproteinCARBOHYD O-linked (GlcNAc) serineCARBOHYD O-linked (GlcNAc...) serineCARBOHYD O-linked (HexNAc) serinethis UniProt feature is used when the identity of the sugar has not been determinedCARBOHYD O-linked (HexNAc...) serinethis UniProt feature is used when the identity of the sugar has not been determinedAA039931-Mar-200631-Mar-200631-May-2018O-(N-acetylamino)glucosyl-L-threonineO-(2-acetylamino-2-deoxy-beta-D-glucopyranosyl)-L-threonineO-(N-acetylglucosaminyl)-L-threonineO-glycosylthreonineO-threonyl-beta-N-acetylglucosaminideO3-(2-acetamido-2-deoxy-beta-D-glucopyranosyl)-L-threonineO3-(N-acetylglucosaminyl)threonine(2S,3R)-2-amino-3-(2-acetamido-2-deoxy-beta-D-glucopyranosyloxy)butanoic acidChEBI:90840PDBHET:NDGC 12 H 20 N 2 O 7 +304.30 +304.127051 +C 8 H 13 N 1 O 5 +203.19 +203.079373 +Torres, C.R.Hart, G.W.J. Biol. Chem. 259, 3308-3317, 1984Topography and polypeptide distribution of terminal N-acetylglucosamine residues on the surfaces of intact lymphocytes. Evidence for O-linked GlcNAc.PMID:6421821Haynes, P.A.Gooley, A.A.Ferguson, M.A.Redmond, J.W.Williams, K.L.Eur. J. Biochem. 216, 729-737, 1993Post-translational modifications of the Dictyostelium discoideum glycoprotein PsA. Glycosylphosphatidylinositol membrane anchor and composition of O-linked oligosaccharides.DOI:10.1111/j.1432-1033.1993.tb18192.xPMID:8404891Butkinaree, C.Park, K.Hart, G.W.Biochim. Biophys. Acta 1800, 96-106, 2010O-linked beta-N-acetylglucosamine (O-GlcNAc): Extensive crosstalk with phosphorylation to regulate signaling and transcription in response to nutrients and stress.DOI:10.1016/j.bbagen.2009.07.018PMID:19647786review of regulatory GlcNAc O-glycosylationLazarus, M.B.Nam, Y.Jiang, J.Sliz, P.Walker, S.Nature 469, 564-567, 2011Structure of human O-GlcNAc transferase and its complex with a peptide substrate.DOI:10.1038/nature09638PMID:21240259X-ray diffraction of generating enzyme with substrate, at 1.95 and 2.78 angstromsSee also RESID:AA0155, RESID:AA0247, RESID:AA0401, RESID:AA0403, RESID:AA0405, and RESID:AA0515 for other O-glycosylated threonines.The PDB has some entries with threonine apparently alpha-glycosylated with N-acetylglucosamine. These are low resolution structures and appear to be erroneous.protein O-GlcNAc transferase (EC 2.4.1.255)TPSI-MOD:00806glycoproteinCARBOHYD O-linked (GlcNAc) threonineCARBOHYD O-linked (GlcNAc...) threonineCARBOHYD O-linked (HexNAc) threoninethis UniProt feature is used when the identity of the sugar has not been determinedCARBOHYD O-linked (HexNAc...) threoninethis UniProt feature is used when the identity of the sugar has not been determinedAA040031-Mar-200631-Mar-200631-May-2018O-galactosyl-L-serineO-glycosylserineO3-galactosylserine(2S)-2-amino-3-(alpha-D-galactopyranosyloxy)propanoic acidC 9 H 15 N 1 O 7249.22249.084852C 6 H 10 N 0 O 5162.14162.052823Allen, A.K.Desai, N.N.Neuberger, A.Creeth, J.M.Biochem. J. 171, 665-674, 1978Properties of potato lectin and the nature of its glycoprotein linkages.PMID:666730the modification is identified as O3-(alpha-galactosyl)-serineSee also RESID:AA0154, RESID:AA0208, RESID:AA0209, RESID:AA0210, RESID:AA0291, RESID:AA0296, RESID:AA0297, RESID:AA0397, RESID:AA0398, RESID:AA0402, RESID:AA0404, RESID:AA0406, and RESID:AA0422 for other O-glycosylated serines.galactosyltransferase (EC 2.4.1.-)SPSI-MOD:00808glycoproteinCARBOHYD O-linked (Gal) serineCARBOHYD O-linked (Gal...) serineCARBOHYD O-linked (Hex) serinethis UniProt feature is used when the identity of the sugar has not been determinedCARBOHYD O-linked (Hex...) serinethis UniProt feature is used when the identity of the sugar has not been determinedAA040131-Mar-200631-Mar-200631-May-2018O-galactosyl-L-threonineO-glycosylthreonineO3-galactosylthreonine(2S,3R)-2-amino-3-(alpha-D-galactopyranosyloxy)butanoic acidC 10 H 17 N 1 O 7 +263.25 +263.100502 +C 6 H 10 N 0 O 5 +162.14 +162.052823 +Lechner, J.Wieland, F.Annu. Rev. Biochem. 58, 173-194, 1989Structure and biosynthesis of prokaryotic glycoproteins.DOI:10.1146/annurev.bi.58.070189.001133PMID:2673008See also RESID:AA0155, RESID:AA0247, RESID:AA0399, RESID:AA0403, RESID:AA0405, and RESID:AA0515 for other O-glycosylated threonines.galactosyltransferase (EC 2.4.1.-)TPSI-MOD:00809glycoproteinCARBOHYD O-linked (Gal) threonineCARBOHYD O-linked (Gal...) threonineCARBOHYD O-linked (Hex) threoninethis UniProt feature is used when the identity of the sugar has not been determinedCARBOHYD O-linked (Hex...) threoninethis UniProt feature is used when the identity of the sugar has not been determinedAA040231-Mar-200631-Mar-200631-May-2018O-mannosyl-L-serineO-glycosylserineO-mannopyranosylserineO3-mannosylserine(2S)-2-amino-3-(alpha-D-mannopyranosyloxy)propanoic acidCAS:78609-14-0ChEBI:137321C 9 H 15 N 1 O 7 +249.22 +249.084852 +C 6 H 10 N 0 O 5 +162.14 +162.052823 +Bause, E.Lehle, L.Eur. J. Biochem. 101, 531-540, 1979Enzymatic N-glycosylation and O-glycosylation of synthetic peptide acceptors by dolichol-linked sugar derivatives in yeast.DOI:10.1111/j.1432-1033.1979.00531.pp.xPMID:391559the enzyme was shown to produce alpha anomeric glycosidesSee also RESID:AA0154, RESID:AA0208, RESID:AA0209, RESID:AA0210, RESID:AA0291, RESID:AA0296, RESID:AA0297, RESID:AA0397, RESID:AA0398, RESID:AA0400, RESID:AA0404, RESID:AA0406, and RESID:AA0422 for other O-glycosylated serines.dolichyl-phosphate-mannose-protein mannosyltransferase (EC 2.4.1.109)SPSI-MOD:00810glycoproteinCARBOHYD O-linked (Man) serineCARBOHYD O-linked (Man...) serineCARBOHYD O-linked (Hex) serinethis UniProt feature is used when the identity of the sugar has not been determinedCARBOHYD O-linked (Hex...) serinethis UniProt feature is used when the identity of the sugar has not been determinedAA040331-Mar-200631-Mar-200631-May-2018O-mannosyl-L-threonineO-glycosylthreonineO3-mannosylthreonine(2S,3R)-2-amino-3-(alpha-D-mannopyranosyloxy)butanoic acidChEBI:137323C 10 H 17 N 1 O 7 +263.25 +263.100502 +C 6 H 10 N 0 O 5 +162.14 +162.052823 +Bause, E.Lehle, L.Eur. J. Biochem. 101, 531-540, 1979Enzymatic N-glycosylation and O-glycosylation of synthetic peptide acceptors by dolichol-linked sugar derivatives in yeast.DOI:10.1111/j.1432-1033.1979.00531.pp.xPMID:391559the enzyme was shown to produce alpha anomeric glycosidesSee also RESID:AA0155, RESID:AA0247, RESID:AA0399, RESID:AA0401, RESID:AA0405, and RESID:AA0515 for other O-glycosylated threonines.dolichyl-phosphate-mannose-protein mannosyltransferase (EC 2.4.1.109)TPSI-MOD:00811glycoproteinCARBOHYD O-linked (Man) threonineCARBOHYD O-linked (Man...) threonineCARBOHYD O-linked (Hex) threoninethis UniProt feature is used when the identity of the sugar has not been determinedCARBOHYD O-linked (Hex...) threoninethis UniProt feature is used when the identity of the sugar has not been determinedAA040431-Mar-200631-Mar-200631-May-2018O-fucosyl-L-serineO-glycosylserineO3-fucosylserine(2S)-2-amino-3-(6-deoxy-alpha-D-galactopyranosyloxy)propanoic acidC 9 H 15 N 1 O 6 +233.22 +233.089937 +C 6 H 10 N 0 O 4 +146.14 +146.057909 +Bjoern, S.Foster, D.C.Thim, L.Wiberg, F.C.Christensen, M.Komiyama, Y.Pedersen, A.H.Kisiel, W.J. Biol. Chem. 266, 11051-11057, 1991Human plasma and recombinant factor VII. Characterization of O-glycosylations at serine residues 52 and 60 and effects of site-directed mutagenesis of serine 52 to alanine.PMID:1904059detection by carbohydrate analysis; location by radioisotope labeling; characterized as a single fucose glycosylationNishimura, H.Takao, T.Hase, S.Shimonishi, Y.Iwanaga, S.J. Biol. Chem. 267, 17520-17525, 1992Human factor IX has a tetrasaccharide O-glycosidically linked to serine 61 through the fucose residue.PMID:1517205detection by carbohydrate analysis; characterized as a tetrasaccharide glycosylationMoloney, D.J.Shair, L.H.Lu, F.M.Xia, J.Locke, R.Matta, K.L.Haltiwanger, R.S.J. Biol. Chem. 275, 9604-9611, 2000Mammalian Notch1 is modified with two unusual forms of O-linked glycosylation found on epidermal growth factor-like modules.DOI:10.1074/jbc.275.13.9604PMID:10734111Hofsteenge, J.Huwiler, K.G.Macek, B.Hess, D.Lawler, J.Mosher, D.F.Peter-Katalinic, J.J. Biol. Chem. 276, 6485-6498, 2001C-mannosylation and O-fucosylation of the thrombospondin type 1 module.DOI:10.1074/jbc.M008073200PMID:11067851mass spectrographic and linkage analysis; characterized as a tetrasaccharide glycosylationGonzalez de Peredo, A.Klein, D.Macek, B.Hess, D.Peter-Katalinic, J.Hofsteenge, J.Mol. Cell. Proteomics 1, 11-18, 2002C-mannosylation and o-fucosylation of thrombospondin type 1 repeats.DOI:10.1074/mcp.M100011-MCP200PMID:12096136See also RESID:AA0154, RESID:AA0208, RESID:AA0209, RESID:AA0210, RESID:AA0291, RESID:AA0296, RESID:AA0297, RESID:AA0397, RESID:AA0398, RESID:AA0400, RESID:AA0402, RESID:AA0406, and RESID:AA0422 for other O-glycosylated serines.peptide-O-fucosyltransferase (EC 2.4.1.221)SPSI-MOD:00812glycoproteinCARBOHYD O-linked (Fuc) serineCARBOHYD O-linked (Fuc...) serineCARBOHYD O-linked (dHex) serinethis UniProt feature is used when the identity of the sugar has not been determinedCARBOHYD O-linked (dHex...) serinethis UniProt feature is used when the identity of the sugar has not been determinedAA040531-Mar-200631-Mar-200631-May-2018O-fucosyl-L-threonineO-glycosylthreonineO3-fucosylthreonine(2S,3R)-2-amino-3-(6-deoxy-alpha-D-galactopyranosyloxy)butanoic acidC 10 H 17 N 1 O 6 +247.25 +247.105587 +C 6 H 10 N 0 O 4 +146.14 +146.057909 +Harris, R.J.Leonard, C.K.Guzzetta, A.W.Spellman, M.W.Biochemistry 30, 2311-2314, 1991Tissue plasminogen activator has an O-linked fucose attached to threonine-61 in the epidermal growth factor domain.DOI:10.1021/bi00223a004PMID:1900431this modification has an alpha-glycosidic linkageNakakura, N.Hietter, H.Van Dorsselaer, A.Luu, B.Eur. J. Biochem. 204, 147-153, 1992Isolation and structural determination of three peptides from the insect Locusta migratoria. Identification of a deoxyhexose-linked peptide.DOI:10.1111/j.1432-1033.1992.tb16617.xPMID:1740125chromatographic and mass spectrometric identification of fucosyl threonineSee also RESID:AA0155, RESID:AA0247, RESID:AA0399, RESID:AA0401, RESID:AA0403, and RESID:AA0515 for other O-glycosylated threonines.peptide-O-fucosyltransferase (EC 2.4.1.221)TPSI-MOD:00813glycoproteinCARBOHYD O-linked (Fuc) threonineCARBOHYD O-linked (Fuc...) threonineCARBOHYD O-linked (dHex) threoninethis UniProt feature is used when the identity of the sugar has not been determinedCARBOHYD O-linked (dHex...) threoninethis UniProt feature is used when the identity of the sugar has not been determinedAA040631-Mar-200631-Mar-200620-Apr-2012O-xylosyl-L-serineO-(beta-D-xylopyranosyl)-L-serineO-glycosylserineO3-xylosylserine(2S)-2-amino-3-(alpha-D-xylopyranosyloxy)propanoic acidCAS:6050-71-1PDBHET:XYSC 8 H 13 N 1 O 6219.19219.074287C 5 H 8 N 0 O 4132.12132.042259Sundaramoorthy, M.Terner, J.Poulos, T.L.Structure 3, 1367-1377, 1995The crystal structure of chloroperoxidase: a heme peroxidase--cytochrome P450 functional hybrid.DOI:10.1016/S0969-2126(01)00274-XPMID:8747463Sundaramoorthy, M.Poulos, T.L.submitted to the Protein Data Bank, February 1996Chloroperoxidase.PDB:1CPOX-ray diffraction, 1.9 angstromsSundaramoorthy, M.Poulos, T.L.submitted to the Protein Data Bank, February 1996Chloroperoxidase.PDB:2CPOX-ray diffraction, 2.16 angstromsOne glycosylated serine with weak electron density was modeled as O3-alpha-xylosylserine, while O3-alpha-mannosyl serine and threonine were modeled at ten other positions. The authors do not discuss this exception or provide chemical evidence for it. Since an O3-xylosyl serine modification has not been reported in any other fungal proteins, the modification is probably also an O3-alpha-mannosyl serine (see RESID:AA0402).See also RESID:AA0154, RESID:AA0208, RESID:AA0209, RESID:AA0210, RESID:AA0291, RESID:AA0296, RESID:AA0297, RESID:AA0397, RESID:AA0398, RESID:AA0400, RESID:AA0402, RESID:AA0404, and RESID:AA0422 for other O-glycosylated serines.SPSI-MOD:00814glycoproteinNot availablethis dubious modification is not currently annotated in UniProt featuresAA040731-Mar-200631-Mar-200630-Sep-2008S-stearoyl-L-cysteine2-amino-3-(octadecanoylthio)propanoic acidcysteine octadecanoate thioestercysteine stearate thioester(R)-2-amino-3-(octadecanoylsulfanyl)propanoic acidC 21 H 39 N 1 O 2 S 1369.61369.270150C 18 H 34 N 0 O 1 S 0266.47266.260966Schmidt, M.Schmidt, M.F.Rott, R.J. Biol. Chem. 263, 18635-18639, 1988Chemical identification of cysteine as palmitoylation site in a transmembrane protein (Semliki Forest virus E1).PMID:3143715misidentification of modification as S-palmitoyl cysteine after use of radiolabeled palmitate without accounting for metabolic conversionBach, R.Konigsberg, W.H.Nemerson, Y.Biochemistry 27, 4227-4231, 1988Human tissue factor contains thioester-linked palmitate and stearate on the cytoplasmic half-cystine.DOI:10.1021/bi00412a004PMID:3166978identification of modification produced by an enzyme with relaxed specificityVeit, M.Herrler, G.Schmidt, M.F.Rott, R.Klenk, H.D.Virology 177, 807-811, 1990The hemagglutinating glycoproteins of influenza B and C viruses are acylated with different fatty acids.DOI:10.1016/0042-6822(90)90554-5PMID:2371783recognition of preferential modification formation of S-stearoyl cysteineVeit, M.Reverey, H.Schmidt, M.F.Biochem. J. 318, 163-172, 1996Cytoplasmic tail length influences fatty acid selection for acylation of viral glycoproteins.PMID:8761467chemical characterization; examines conditions for selection of stearate in preference to palmitateAlthough the predominant palmitoyl transferase in mammalian systems appears to utilize a mixture of saturated and unsaturated fatty acids, some systems may be more specific in their incorporation of other fatty acids. See RESID:AA0307 and RESID:AA0308.This modification may be misidentified as S-palmitoyl-cysteine (see RESID:AA0106) when labeled palmitate is used without determining whether metabolic conversion has occurred.protein-cysteine S-stearoyltransferase (EC 2.3.1.-)CPSI-MOD:00816lipoproteinstearatethioester bondLIPID S-stearoyl cysteineAA040831-Mar-200631-Mar-200631-Dec-20123'-geranyl-2',3'-dihydro-2',N2-cyclo-L-tryptophan(2S,3R)-3-geranyl-2,3-dihydro-2,N(alpha)-cyclo-L-tryptophan(2S,3aR,8aS)-3a-[(2E)-3,7-dimethylocta-2,6-dien-1-yl]-1,2,3,3a,8,8a-hexahydropyrrolo[2,3-b]indole-2-carboxylic acidChEBI:35304C 21 H 26 N 2 O 1322.45322.204513C 10 H 16 N 0 O 0136.24136.125201Magnuson, R.Solomon, J.Grossman, A.D.Cell 77, 207-216, 1994Biochemical and genetic characterization of a competence pheromone from B. subtilis.DOI:10.1016/0092-8674(94)90313-1PMID:8168130peptide structure and identification as a tryptophan modificationOkada, M.Sato, I.Cho, S.J.Iwata, H.Nishio, T.Dubnau, D.Sakagami, Y.Nature Chem. Biol. 1, 23-24, 2005Structure of the Bacillus subtilis quorum-sensing peptide pheromone ComX.DOI:10.1038/nchembio709PMID:16407988mass spectrographic, (1)H-NMR, DQF-COSY, and ROESY identification; chemical synthesisOkada, M.Biosci. Biotechnol. Biochem. 75, 1413-1417, 2011Post-translational isoprenylation of tryptophan.PMID:21821957review articleWPSI-MOD:00817lipoproteinprenylationLIPID 3'-geranyl-2',N2-cyclotryptophanAA040926-May-200626-May-200625-Feb-2011L-2-aminobutanoic acidL-2-amino-n-butyric acidL-2-aminobutyric acidL-alpha-amino-n-butyric acidL-alpha-aminobutyric acidL-butyrine(S)-2-aminobutanoic acidCAS:1492-24-6ChEBI:35619PDBHET:ABAC 4 H 7 N 1 O 185.1185.052764C -1 H 0 N 0 O -2-44.01-43.989829van Thor, J.J.Gensch, T.Hellingwerf, K.J.Johnson, L.N.Nature Struct. Biol. 9, 37-41, 2002Phototransformation of green fluorescent protein with UV and visible light leads to decarboxylation of glutamate 222.DOI:10.1038/nsb739PMID:11740505X-ray diffraction, 1.80 angstromsvan Thor, J.J.Gensch, T.Hellingwerf, K.J.Johnson, L.submitted to the Protein Data Bank, May 2001Photoproduct of the wild-type Aequorea victoria green fluorescent protein.PDB:1HCJX-ray diffraction, 1.80 angstroms; the modification is mentioned in the PDB entry but is presented as glutamic acidExposure of green fluorescent protein to 254 nm UV light or to 390 nm visible light causes gamma decarboxylation of glutamic acid 222.Unlike the threonine in 3-methylanthionine, the L configuration (S chirality) of the 2-aminobutanoate skeleton is maintained.autocatalyticEincidental to RESID:AA0183incidental to RESID:AA0184PSI-MOD:00819Not availablethis modification is not annotated in UniProt featuresAA041026-May-200626-May-200620-May-20112-imino-alanine 5-imidazolinone glycine2,N-didehydroalanyl-5-imidazolinone glycine2-(1-iminoethyl)-1-carboxymethyl-1-imidazolin-5-one2-imino-alanyl-5-imidazolinone glycinealanyl-5-imidazolinone glycinepara-hydroxybenzylidene-imidazolidinone chromophorered fluorescent protein zRFP574 chromophore[2-(1-iminoethyl)-5-oxo-4,5-dihydro-imidazol-1-yl]-acetic acid(2-ethanimidoyl-5-oxo-4,5-dihydro-1H-imidazol-1-yl)acetic acidPDBHET:XYGC 5 H 4 N 2 O 1108.10108.032363C -1 H -4 N 0 O -3-64.04-64.016044Pletneva, N.Pletnev, S.Tikhonova, T.Popov, V.Martynov, V.Pletnev, V.Acta Crystallogr. D Biol. Crystallogr. 62, 527-532, 2006Structure of a red fluorescent protein from Zoanthus, zRFP574, reveals a novel chromophore.DOI:10.1107/S0907444906007852PMID:16627946the authors have not published the sequencePletneva, N.Pletnev, S.Tikhonova, T.Popov, V.Martynov, V.Pletnev, V.submitted to the Protein Data Bank, January 2006Crystal structure of red fluorescent protein from Zoanthus, zRFP574, at 2.4 A resolution.PDB:2FL1X-ray diffraction, 2.40 angstromsThis entry represents the cross-link of the peptide backbone from the alpha-carboxyl carbon of residue N, an aspartic acid, to the alpha-amino nitrogen of residue N+2, a glycine, coupled with the formation of a double bond to the alpha-amino nitrogen of residue N, the loss of a molecule of water, and the beta-decarboxylation of the aspartic acid.This cross-link is accompanied by modification of residue N+1. The modified residue N+1 is presented in a separate entry and is not included in the mass accounting of this entry. The backbone atoms of residue N+1 are shown in gray in the diagram.autocatalyticD, Gcarboxamidinecross-link 1incidental to RESID:AA0183incidental to RESID:AA0365PSI-MOD:00820chromoproteinimidazolinone/oxazolinone ringNot availablethis modification is not annotated in UniProt featuresAA041126-May-200626-May-200631-Dec-2011S-(L-alanyl)-L-cysteinealanine cysteine thioesterS-(2-aminopropanoyl)cysteine(2R)-2-amino-3-([(2S)-2-aminopropanoyl]sulfanyl)propanoic acidC 6 H 9 N 2 O 2 S 1173.21173.038474C 0 H -2 N 0 O -1 S 0-18.02-18.010565Dufour, P.Jarraud, S.Vandenesch, F.Greenland, T.Novick, R.P.Bes, M.Etienne, J.Lina, G.J. Bacteriol. 184, 1180-1186, 2002High genetic variability of the agr locus in Staphylococcus species.DOI:10.1128/jb.184.4.1180-1186.2002PMID:11807079These are thioester cross-links formed between cysteine residues and the alanine carboxyl end of a peptide.This modification is predicted for proteins homologous to autoinducing peptides in certain organisms where the position corresponding to the carboxyl end encodes alanine.A, Ccarboxyl-terminalcross-link 2PSI-MOD:00821blocked carboxyl endthioester bondCROSSLNK Alanyl cysteine thioester (Cys-Ala)AA041226-May-200626-May-200631-Dec-2011S-(L-leucyl)-L-cysteineleucine cysteine thioesterS-(2-amino-4-methylpentanoyl)cysteine(2R)-2-amino-3-([(2S)-2-amino-4-methylpentanoyl]sulfanyl)propanoic acidC 9 H 15 N 2 O 2 S 1215.29215.085424C 0 H -2 N 0 O -1 S 0-18.02-18.010565Kalkum, M.Lyon, G.J.Chait, B.T.Proc. Natl. Acad. Sci. U.S.A. 100, 2795-2800, 2003Detection of secreted peptides by using hypothesis-driven multistage mass spectrometry.DOI:10.1073/pnas.0436605100PMID:12591958These are thioester cross-links formed between cysteine residues and the leucine carboxyl end of a peptide.C, Lcarboxyl-terminalcross-link 2PSI-MOD:00822blocked carboxyl endthioester bondCROSSLNK Leucyl cysteine thioester (Cys-Leu)AA041326-May-200626-May-200631-Dec-2011S-(L-methionyl)-L-cysteinemethionine cysteine thioesterS-(2-amino-4-methylthiobutanoyl)cysteine(2R)-2-amino-3-([(2S)-2-amino-4-(methylsulfanyl)butanoyl]sulfanyl)propanoic acidC 8 H 13 N 2 O 2 S 2233.32233.041845C 0 H -2 N 0 O -1 S 0-18.02-18.010565Lyon, G.J.Wright, J.S.Muir, T.W.Novick, R.P.Biochemistry 41, 10095-10104, 2002Key determinants of receptor activation in the agr autoinducing peptides of Staphylococcus aureus.DOI:10.1021/bi026049uPMID:12146974These are thioester cross-links formed between cysteine residues and the methionine carboxyl end of a peptide.C, Mcarboxyl-terminalcross-link 2PSI-MOD:00823blocked carboxyl endthioester bondCROSSLNK Methionyl cysteine thioester (Cys-Met)AA041426-May-200626-May-200631-Dec-2011S-(L-phenylalanyl)-L-cysteinephenylalanine cysteine thioesterS-(2-amino-3-phenylpropanoyl)cysteine(2R)-2-amino-3-([(2S)-2-amino-3-phenylpropanoyl]sulfanyl)propanoic acidC 12 H 13 N 2 O 2 S 1249.31249.069774C 0 H -2 N 0 O -1 S 0-18.02-18.010565Kalkum, M.Lyon, G.J.Chait, B.T.Proc. Natl. Acad. Sci. U.S.A. 100, 2795-2800, 2003Detection of secreted peptides by using hypothesis-driven multistage mass spectrometry.DOI:10.1073/pnas.0436605100PMID:12591958These are thioester cross-links formed between cysteine residues and the phenylalanine carboxyl end of a peptide.C, Fcarboxyl-terminalcross-link 2PSI-MOD:00825blocked carboxyl endthioester bondCROSSLNK Phenylalanyl cysteine thioester (Cys-Phe)AA041526-May-200626-May-200631-Dec-2011S-(L-threonyl)-L-cysteineS-(2-amino-3-hydroxybutanoyl)cysteinethreonine cysteine thioester(2R)-2-amino-3-([(2S,3R)-2-amino-3-hydroxybutanoyl]sulfanyl)propanoic acidC 7 H 11 N 2 O 3 S 1203.24203.049038C 0 H -2 N 0 O -1 S 0-18.02-18.010565Sakinc, T.Kulczak, P.Henne, K.Gatermann, S.G.FEMS Microbiol. Lett. 237, 157-161, 2004Cloning of an agr homologue of Staphylococcus saprophyticus.DOI:10.1016/j.femsle.2004.06.030PMID:15268951These are thioester cross-links formed between cysteine residues and the threonine carboxyl end of a peptide.This modification is predicted for proteins homologous to autoinducing peptides in certain organisms where the position corresponding to the carboxyl end encodes threonine.C, Tcarboxyl-terminalcross-link 2PSI-MOD:00826blocked carboxyl endthioester bondCROSSLNK Threonyl cysteine thioester (Cys-Thr)AA041626-May-200626-May-200631-Dec-2011S-(L-tyrosyl)-L-cysteineS-[2-amino-3-(4-hydoxyphenyl)propanoyl]cysteinetyrosine cysteine thioester(2R)-2-amino-3-([(2S)-2-amino-3-(4-hydroxyphenyl)propanoyl]sulfanyl)propanoic acidC 12 H 13 N 2 O 3 S 1265.31265.064688C 0 H -2 N 0 O -1 S 0-18.02-18.010565Dufour, P.Jarraud, S.Vandenesch, F.Greenland, T.Novick, R.P.Bes, M.Etienne, J.Lina, G.J. Bacteriol. 184, 1180-1186, 2002High genetic variability of the agr locus in Staphylococcus species.DOI:10.1128/jb.184.4.1180-1186.2002PMID:11807079These are thioester cross-links formed between cysteine residues and the tyrosine carboxyl end of a peptide.This modification is predicted for proteins homologous to autoinducing peptides in certain organisms where the position corresponding to the carboxyl end encodes tyrosine.C, Ycarboxyl-terminalcross-link 2PSI-MOD:00827blocked carboxyl endthioester bondCROSSLNK Tyrosyl cysteine thioester (Cys-Tyr)AA041726-May-200626-May-200631-Dec-2011S-(L-tryptophanyl)-L-cysteineS-[2-amino-3-(1H-indol-3-yl)propanoyl]cysteinetryptophan cysteine thioester(2R)-2-amino-3-([(2S)-2-amino-3-(1H-indol-3-yl)propanoyl]sulfanyl)propanoic acidC 14 H 14 N 3 O 2 S 1288.35288.080673C 0 H -2 N 0 O -1 S 0-18.02-18.010565Sturme, M.H.Nakayama, J.Molenaar, D.Murakami, Y.Kunugi, R.Fujii, T.Vaughan, E.E.Kleerebezem, M.de Vos, W.M.J. Bacteriol. 187, 5224-5235, 2005An agr-like two-component regulatory system in Lactobacillus plantarum is involved in production of a novel cyclic peptide and regulation of adherence.DOI:10.1128/JB.187.15.5224-5235.2005PMID:16030216These are thioester cross-links formed between cysteine residues and the tryptophan carboxyl end of a peptide.C, Wcarboxyl-terminalcross-link 2PSI-MOD:00828blocked carboxyl endthioester bondCROSSLNK Tryptophanyl cysteine thioester (Cys-Trp)AA041826-May-200626-May-200631-Dec-2011O-(L-phenylalanyl)-L-serineO-(2-amino-3-phenylpropanoyl)serinephenylalanine serine ester(2S)-2-amino-3-([(2S)-2-amino-3-phenylpropanoyl]oxy)propanoic acidC 12 H 13 N 2 O 3233.25233.092617C 0 H -2 N 0 O -1-18.02-18.010565Kalkum, M.Lyon, G.J.Chait, B.T.Proc. Natl. Acad. Sci. U.S.A. 100, 2795-2800, 2003Detection of secreted peptides by using hypothesis-driven multistage mass spectrometry.DOI:10.1073/pnas.0436605100PMID:12591958These are ester cross-links formed between serine residues and the phenylalanine carboxyl end of a peptide.F, Scarboxyl-terminalcross-link 2PSI-MOD:00829blocked carboxyl endCROSSLNK Phenylalanyl serine ester (Ser-Phe)AA041926-May-200626-May-200631-May-2018N-methyl-L-proline1-methylpyrrolidine-2-carboxylic acidhygric acid(S)-1-methylpyrrolidine-2-carboxylic acidCAS:475-11-6C 6 H 10 N 1 O 1112.15112.076239C 1 H 2 N 0 O 014.0314.015650Desrosiers, R.Tanguay, R.M.J. Biol. Chem. 263, 4686-4692, 1988Methylation of Drosophila histones at proline, lysine, and arginine residues during heat shock.PMID:3127388N-terminal RCC1 methyltransferaseprotein N-terminal methyltransferaseS-adenosyl-L-methionine:N-terminal-(A,P,S)PK-[protein] methyltransferase (EC 2.1.1.244)protein N-terminal monomethyltransferaseS-adenosyl-L-methionine:N-terminal-(A,P,S)PK-[protein] monomethyltransferase (EC 2.1.1.299)Pamino-terminalGO:0035568PSI-MOD:00830blocked amino endmethylated amino endMOD_RES N-methylprolineAA042026-May-200626-May-200631-May-2018N4-(N-acetylamino)galactosyl-L-asparagineN4-(2-acetamido-2-deoxy-beta-D-galactopyranosyl)-L-asparagineN4-(2-acetylamino-2-deoxy-beta-D-galactopyranosyl)-L-asparagineN4-(N-acetylgalactosaminyl)asparagineN4-asparagine-beta-N-acetylgalactosaminideN4-glycosyl-L-asparagineN4-glycosylasparagine(2S)-2-amino-4-(2-acetamido-2-deoxy-beta-D-galactopyranosyl)amino-4-oxobutanoic acidCAS:100991-94-4C 12 H 19 N 3 O 7 +317.30 +317.122300 +C 8 H 13 N 1 O 5 +203.19 +203.079373 +Kaercher, U.Schroeder, H.Haslinger, E.Allmaier, G.Schreiner, R.Wieland, F.Haselbeck, A.Koenig, H.J. Biol. Chem. 268, 26821-26826, 1993Primary structure of the heterosaccharide of the surface glycoprotein of Methanothermus fervidus.PMID:8262914probably an alpha-N-glycosidic linkageThis modification occurs in archaebacterial cell surface proteins with an NX[ST] motif.See also RESID:AA0151 and RESID:AA0421 for other N4-glycosylated asparagines.NPSI-MOD:00832glycoproteinCARBOHYD N-linked (GalNAc...) asparagineCARBOHYD N-linked (GalNAc...) (glycosaminoglycan) asparagineAA042126-May-200626-May-200631-May-2018N4-glucosyl-L-asparagineN4-(D-glucopyranosyl)-L-asparagineN4-(D-glucopyranosyl)-L-asparagineN4-asparagine-glucosideN4-glucosylasparagineN4-glycosyl-L-asparagineN4-glycosylasparagine(2S)-2-amino-4-(D-glucopyranosyl)amino-4-oxobutanoic acidC 10 H 16 N 2 O 7 +276.25 +276.095751 +C 6 H 10 N 0 O 5 +162.14 +162.052823 +Shibata, S.Takeda, T.Natori, Y.J. Biol. Chem. 263, 12483-12485, 1988The structure of nephritogenoside. A nephritogenic glycopeptide with alpha-N-glycosidic linkage.PMID:3410849glycopeptide with trisaccharide glucose attached by an alpha-N-glycosidic linkage, and the NX[ST] motif is not presentMengele, R.Sumper, M.J. Biol. Chem. 267, 8182-8185, 1992Drastic differences in glycosylation of related S-layer glycoproteins from moderate and extreme halophiles.PMID:1569073the anomeric form was not determinedThe alpha anomeric form is shown.See also RESID:AA0151 and RESID:AA0420 for other N4-glycosylated asparagines.NPSI-MOD:00833glycoproteinCARBOHYD N-linked (Glc) asparagineCARBOHYD N-linked (Glc...) asparagineAA042226-May-200626-May-200631-May-2018O-(N-acetylamino)fucosyl-L-serineO-(2-acetylamino-2-deoxy-beta-D-fucopyranosyl)-L-serineO-(N-acetylfucosaminyl)serineO-seryl-beta-N-acetylfucosaminideO3-(2-acetamido-2-deoxy-beta-D-fucopyranosyl)-L-serineO3-(N-acetylfucosaminyl)serine(2S)-2-amino-3-(2-acetamido-2-deoxy-beta-D-fucopyranosyloxy)propanoic acidC 11 H 18 N 2 O 6274.27274.116486C 8 H 13 N 1 O 4187.19187.084458Castric, P.Cassels, F.J.Carlson, R.W.J. Biol. Chem. 276, 26479-26485, 2001Structural characterization of the Pseudomonas aeruginosa 1244 pilin glycan.DOI:10.1074/jbc.M102685200PMID:11342554Comer, J.E.Marshall, M.A.Blanch, V.J.Deal, C.D.Castric, P.Infect. Immun. 70, 2837-2845, 2002Identification of the Pseudomonas aeruginosa 1244 pilin glycosylation site.DOI:10.1128/IAI.70.6.2837-2845.2002PMID:12010970beta-N-glycosidic linkageSee also RESID:AA0154, RESID:AA0208, RESID:AA0209, RESID:AA0210, RESID:AA0291, RESID:AA0296, RESID:AA0297, RESID:AA0397, RESID:AA0398, RESID:AA0400, RESID:AA0402, RESID:AA0404, and RESID:AA0406 for other O-glycosylated serines.SPSI-MOD:00834glycoproteinCARBOHYD O-linked (FucNAc...) serineCARBOHYD O-linked (dHexNAc...) serinethis UniProt feature is used when the identity of the sugar has not been determinedAA042330-Jun-200630-Jun-200630-Jun-2010O-acetyl-L-threonineO-acetylthreoninethreonine acetate ester(2S,3R)-3-(acetyloxy)-2-aminobutanoic acidCAS:17012-42-9PDBHET:TH5C 6 H 9 N 1 O 3143.14143.058243C 2 H 2 N 0 O 142.0442.010565Mukherjee, S.Keitany, G.Li, Y.Wang, Y.Ball, H.L.Goldsmith, E.J.Orth, K.Science 312, 1211-1214, 2006Yersinia YopJ acetylates and inhibits kinase activation by blocking phosphorylation.DOI:10.1126/science.1126867PMID:16728640Iqbal, A.Clifton, I.J.Bagonis, M.Kershaw, N.J.Domene, C.Claridge, T.D.Wharton, C.W.Schofield, C.J.J. Am. Chem. Soc. 131, 749-757, 2009Anatomy of a simple acyl intermediate in enzyme catalysis: combined biophysical and modeling studies on ornithine acetyl transferase.DOI:10.1021/ja807215uPMID:19105697O-acetylation of threonine in host kinases is catalyzed by yersinia toxin blocking the normal phosphorylation.TPSI-MOD:01171MOD_RES O-acetylthreonineACT_SITE O-acetylthreonine intermediateAA042430-Jun-200630-Jun-200630-Apr-2010N-alanyl-glycosylsphingolipidinositolethanolamineC 5 H 12 N 2 O 5 P 1 +211.13 +211.048383 +C 2 H 6 N 1 O 3 P 1 +123.05 +123.008530 +Fontaine, T.Magnin, T.Melhert, A.Lamont, D.Latge, J.P.Ferguson, M.A.Glycobiology 13, 169-177, 2003Structures of the glycosylphosphatidylinositol membrane anchors from Aspergillus fumigatus membrane proteins.DOI:10.1093/glycob/cwg004PMID:12626404This modification is predicted for proteins with sequence characteristics for the GPI-like-anchor modification with sphingolipid, and with alanine at the cleavage and anchor attachment site.A representative glycan core structure is shown.Cleavage of a carboxyl terminal propeptide accompanies transamidation.Acarboxyl-terminalPSI-MOD:01172blocked carboxyl endglycoproteinlipoproteinphosphoproteinsphingolipidinositol linkageLIPID GPI-like-anchor amidated alanineAA042530-Jun-200630-Jun-200630-Apr-2010N-asparaginyl-glycosylsphingolipidinositolethanolamineC 6 H 13 N 3 O 6 P 1 +254.16 +254.054197 +C 2 H 6 N 1 O 3 P 1 +123.05 +123.008530 +Stevens, B.A.White, I.J.Hames, B.D.Hooper, N.M.Biochim. Biophys. Acta 1511, 317-329, 2001The carboxyl terminus of Dictyostelium discoideum protein 1I encodes a functional glycosyl-phosphatidylinositol signal sequence.DOI:10.1016/S0005-2736(01)00289-9PMID:11286975evidence for asparagine at the cleavage and anchor attachment site; lipid resistance to phospholipase C indicates it does not contain phosphatidylinositolFontaine, T.Magnin, T.Melhert, A.Lamont, D.Latge, J.P.Ferguson, M.A.Glycobiology 13, 169-177, 2003Structures of the glycosylphosphatidylinositol membrane anchors from Aspergillus fumigatus membrane proteins.DOI:10.1093/glycob/cwg004PMID:12626404This modification is predicted for proteins with sequence characteristics for the GPI-like anchor modification with sphingolipid, and with asparagine at the cleavage and anchor attachment site.A representative glycan core structure is shown.Cleavage of a carboxyl terminal propeptide accompanies transamidation.Ncarboxyl-terminalPSI-MOD:01173blocked carboxyl endglycoproteinlipoproteinphosphoproteinsphingolipidinositol linkageLIPID GPI-like-anchor amidated asparagineAA042630-Jun-200630-Jun-200620-May-2011S-(15-deoxy-Delta12,14-prostaglandin J2-9-yl)-L-cysteine(2R)-2-amino-3-([(5Z,9Xi,12E,14Z)-1-hydroxy-1,11-oxoprosta-5,12,14-trien-9-yl]sulfanyl)propanoic acid(5Z,9Xi,12E,14Z)-9-([(2R)-2-amino-3-carboxyethyl]sulfanyl)-11-oxoprosta-5,12,14-trien-1-oic acidCAS:60203-57-8ChEBI:27485C 23 H 33 N 1 O 4 S 1419.58419.213030C 20 H 28 N 0 O 3 S 0316.44316.203845Cernuda-Morollon, E.Pineda-Molina, E.Canada, F.J.Perez-Sala, D.J. Biol. Chem. 276, 35530-35536, 200115-Deoxy-(Delta)12,14-prostaglandin J2 inhibition of NF-(kappa)B-DNA binding through covalent modification of the p50 subunit.DOI:10.1074/jbc.M104518200PMID:11466314mass spectrometric detection; directed mutation analysisOliva, J.L.Perez-Sala, D.Castrillo, A.Martinez, N.Canada, F.J.Bosca, L.Rojas, J.M.Proc. Natl. Acad. Sci. U.S.A. 100, 4772-4777, 2003The cyclopentenone 15-deoxy-(delta)12,14-prostaglandin J2 binds to and activates H-Ras.DOI:10.1073/pnas.0735842100PMID:12684535mass spectrometric detection; directed mutation analysisautocatalyticCPSI-MOD:01174lipoproteinprostaglandinthioether bondLIPID S-(15-deoxy-Delta12,14-prostaglandin J2-9-yl)cysteineAA042730-Sep-200630-Sep-200630-Sep-2008S-phycourobilin-L-cysteine18-ethenyl-3-[1-(2-amino-2-carboxyethylsulfanyl)ethyl]-2,3,15,16-dihydro-2,7,13,17-tetramethyl-1,19-dioxo-(21H,22H,24H)-bilin-8,12-dipropanoic acidphycourobilin cysteine adductPUB(2S,3R,16R)-18-ethenyl-3-[(1R)-1-([(R)-2-amino-2-carboxyethyl]sulfanyl)ethyl]-8,12-bis(2-carboxyethyl)-2,7,13,17-tetramethyl-4,5,15,16-tetrahydrobiline-1,19(21H,22H,24H)-dioneCAS:61932-71-6C 36 H 43 N 5 O 7 S 1689.83689.288320C 33 H 38 N 4 O 6 S 0586.69586.279135Nagy, J.O.Bishop, J.E.Klotz, A.V.Glazer, A.N.Rapoport, H.J. Biol. Chem. 260, 4864-4868, 1985Bilin attachment sites in the alpha, beta, and gamma subunits of R-phycoerythrin. Structural studies on singly and doubly linked phycourobilins.PMID:3838747Moss, G.P.Eur. J. Biochem. 178, 277-328, 1988IUPAC-IUB Joint Commission on Biochemical Nomenclature (JCBN). Nomenclature of tetrapyrroles. Recommendations 1986.DOI:10.1111/j.1432-1033.1988.tb14453.xPMID:3208761Ong, L.J.Glazer, A.N.J. Biol. Chem. 266, 9515-9527, 1991Phycoerythrins of marine unicellular cyanobacteria. I. Bilin types and locations and energy transfer pathways in Synechococcus spp. phycoerythrins.PMID:1903388There are additional chiral centers at C-3alpha, C-4, and C-16.CPSI-MOD:01175chromoproteinphycourobilinthioether bondBINDING Phycourobilin chromophore (covalent; via 1 link)AA042830-Jun-200830-Jun-200831-Mar-2009S-15,16-dihydrobiliverdin-L-cysteine15,16-Dhbv15,16-dihydrobiliverdin cysteine adduct15,16-dihydrobiliverdin IXalpha18-ethenyl-8,12-bis(2-carboxyethyl)-3-(2-(cysteinyl-S)-ethyl)-2,7,13,17-tetramethylbiladiene-ab-1,19(16H,21H)-dione3'-cysteinyl-15,16-dihydrobiliverdin3alpha-cysteinyl-15,16-dihydrobiliverdinDBV(16R)-18-ethenyl-8,12-bis(2-carboxyethyl)-3-[(1R)-1-(((2R)-2-amino-2-carboxy)ethylsulfanyl)ethyl]-2,7,13,17-tetramethyl-15,16-dihydrobilin-1,19(21H,24H)-dioneCAS:137429-14-2PDBHET:DBVC 36 H 41 N 5 O 7 S 1687.81687.272670C 33 H 36 N 4 O 6 S 0584.67584.263485Moss, G.P.Eur. J. Biochem. 178, 277-328, 1988IUPAC-IUB Joint Commission on Biochemical Nomenclature (JCBN). Nomenclature of tetrapyrroles. Recommendations 1986.DOI:10.1111/j.1432-1033.1988.tb14453.xPMID:3208761Wedemayer, G.J.Kidd, D.G.Wemmer, D.E.Glazer, A.N.J. Biol. Chem. 267, 7315-7331, 1992Phycobilins of cryptophycean algae. Occurrence of dihydrobiliverdin and mesobiliverdin in cryptomonad biliproteins.PMID:1559975a "cryptoviolin-like" chromophore is identified as 15,16-dihydrobiliverdinWilk, K.E.Harrop, S.J.Jankova, L.Edler, D.Keenan, G.Sharples, F.Hiller, R.G.Curmi, P.M.G.Proc. Natl. Acad. Sci. U.S.A. 96, 8901-8906, 1999Evolution of a light-harvesting protein by addition of new subunits and rearrangement of conserved elements: crystal structure of a cryptophyte phycoerythrin at 1.63-A resolution.DOI:10.1073/pnas.96.16.8901PMID:10430868X-ray diffraction, 1.63 angstroms; the initials of "P.M. Curmi" in the PubMed citation are correctedHarrop, S.J.Wilk, K.E.Hiller, R.G.Curmi, P.M.G.submitted to the Protein Data Bank, May 1999Crystal structure of phycoerythrin 545 from the marine cryptophyte Rhodomonas CS24.PDB:1QGWX-ray diffraction, 1.63 angstromsDoust, A.B.Marai, C.N.J.Harrop, S.J.Wilk, K.E.Curmi, P.M.G.Scholes, G.D.J. Mol. Biol. 344, 135-153, 2004Developing a structure-function model for the cryptophyte phycoerythrin 545 using ultrahigh resolution crystallography and ultrafast laser spectroscopy.DOI:10.1016/j.jmb.2004.09.044PMID:15504407X-ray diffraction, 1.63 angstroms; the initials of "C.N. Marai" and "P.M. Curmi" in the PubMed citation are correctedDoust, A.B.Marai, C.N.J.Harrop, S.J.Wilk, K.E.Curmi, P.M.G.Scholes, G.D.submitted to the Protein Data Bank, September 2004High resolution crystal structure of phycoerythrin 545 from the marine cryptophyte Rhodomonas CS24.PDB:1XF6X-ray diffraction, 1.10 angstromsDoust, A.B.Marai, C.N.J.Harrop, S.J.Wilk, K.E.Curmi, P.M.G.Scholes, G.D.submitted to the Protein Data Bank, September 2004High resolution crystal structure of phycoerythrin 545 from the marine cryptophyte Rhodomonas CS24.PDB:1XG0X-ray diffraction, 0.97 angstroms15,16-dihydrobiliverdin transmits violet.CPSI-MOD:01142chromoproteindihydrobiliverdinthioether bondBINDING 15,16-dihydrobiliverdin (covalent; via 1 link)AA042930-Jun-200830-Jun-200830-Jan-200915,16-dihydrobiliverdin-bis-L-cysteine15,16-Dhbv15,16-dihydrobiliverdin cysteine adduct15,16-dihydrobiliverdin IXalpha3'',18'-biscysteinyl-15,16-dihydrobiliverdin3beta,18alpha-biscysteinyl-15,16-dihydrobiliverdin8,12-bis(2-carboxyethyl)-3-(2-(cysteinyl-S)-ethyl)-18-(1-(cysteinyl-S)-ethyl)-2,7,13,17-tetramethylbiladiene-ab-1,19(16H,21H)-dioneDBV(16R)-8,12-bis(2-carboxyethyl)-3-[2-(((2R)-2-amino-2-carboxy)ethylsulfanyl)ethyl]-18-[(1Xi)-1-(((2R)-2-amino-2-carboxy)ethylsulfanyl)ethyl]-2,7,13,17-tetramethyl-15,16-dihydrobilin-1,19(21H,24H)-dioneCAS:137429-14-2PDBHET:DBVC 39 H 46 N 6 O 8 S 2790.95790.281854C 33 H 36 N 4 O 6 S 0584.67584.263485Moss, G.P.Eur. J. Biochem. 178, 277-328, 1988IUPAC-IUB Joint Commission on Biochemical Nomenclature (JCBN). Nomenclature of tetrapyrroles. Recommendations 1986.DOI:10.1111/j.1432-1033.1988.tb14453.xPMID:3208761Sidler, W.Nutt, H.Kumpf, B.Frank, G.Suter, F.Brenzel, A.Wehrmeyer, W.Zuber, H.Biol. Chem. Hoppe-Seyler 371, 537-547, 1990The complete amino-acid sequence and the phylogenetic origin of phycocyanin-645 from the cryptophytan alga Chroomonas sp.PMID:2222853a double-linked, "cryptoviolin-like" chromophore is detectedWedemayer, G.J.Kidd, D.G.Wemmer, D.E.Glazer, A.N.J. Biol. Chem. 267, 7315-7331, 1992Phycobilins of cryptophycean algae. Occurrence of dihydrobiliverdin and mesobiliverdin in cryptomonad biliproteins.PMID:1559975the "cryptoviolin-like" chromophore is identified as 15,16-dihydrobiliverdinWemmer, D.E.Wedemayer, G.J.Glazer, A.N.J. Biol. Chem. 268, 1658-1669, 1993Phycobilins of cryptophycean algae. Novel linkage of dihydrobiliverdin in a phycoerythrin 555 and a phycocyanin 645.PMID:8420941by mass spectrometric, (1)H-NMR, and (13)C-NMR analysis, the 15,16-dihydrobiliverdin is determined to be attached to Cys-50 by C18', and to Cys-61 by C33''This bilin transmits violet.The stereochemistry for the 18' chiral center has not been resolved.C, Ccross-link 2PSI-MOD:01143chromoproteindihydrobiliverdinthioether bondBINDING 15,16-dihydrobiliverdin (covalent; via 2 links)AA043030-Sep-200630-Sep-200630-Jun-2012L-dehydrolysinonorleucine6-(N6-L-didehydrolysino)-L-norleucinedehydrolysinorleucine [misspelling]dehydrolysylnorleucinedidehydrolysinonorleucineN6-[(5S)-5-amino-5-carboxypentylidene]-L-lysine(2S)-2-amino-6-([(5S)-5-amino-5-carboxypentylidene]amino)hexanoic acidCAS:31504-14-0ChEBI:64748C 12 H 19 N 3 O 2237.30237.147727C 0 H -5 N -1 O 0-19.05-19.042199Franzblau, C.Sinex, F.M.Faris, B.Lampidis, R.Biochem. Biophys. Res. Commun. 21, 575-581, 1965Identification of a new crosslinking amino acid in elastin.PMID:5879466isolation of reduced form; chemical characterization and naming of lysinonorleucineFranzblau, C.Faris, B.Papaioannou, R.Biochemistry 8, 2833-2837, 1969Lysinonorleucine. A new amino acid from hydrolysates of elastin.PMID:5817620mass spectrometric and chemical characterization of the reduced form; stereochemical determinationLent, R.Franzblau, C.Biochem. Biophys. Res. Commun. 26, 43-50, 1967Studies on the reduction of bovine elastin: evidence for the presence of Delta-6,7-dehydrolysinonorleucine.PMID:6030254observation of the aldimine formBailey, A.J.Peach, C.M.Biochem. J. 121, 257-259, 1971The chemistry of the collagen cross-links. The absence of reduction of dehydrolysinonorleucine and dehydrohydroxylysinonorleucine in vivo.PMID:5117030the non-reduced aldimine form is the predominant form in collagen, and in insoluble collagens there is less hydroxylation; the predominant form in elastin is the reduced lysinonorleucineDuff, A.P.Cohen, A.E.Ellis, P.J.Hilmer, K.Langley, D.B.Dooley, D.M.Freeman, H.C.Guss, J.M.Acta Crystallogr. D Biol. Crystallogr. 62, 1073-1084, 2006The 1.23 A structure of Pichia pastoris lysyl oxidase reveals a lysine-lysine cross-link.DOI:10.1107/S0907444906026333PMID:16929109X-ray diffraction, 1.23 angstroms; the authors estimate that 35% of the protein molecules in the crystal contain this cross-linkDuff, A.P.Cohen, A.E.Ellis, P.J.Guss, J.M.submitted to the Protein Data Bank, September 2004PPLO at 1.23 angstroms.PDB:1W7CX-ray diffraction, 1.23 angstromsAlthough it should not be possible to distinguish dehydrolysinonorleucine from lysinonorleucine in the X-ray structure, the cross-link was probably not reduced.After the oxidation of a lysine to allysine (see RESID:AA0121), this cross-link forms spontaneously with a Schiff-base reaction. In this aleatoric modification two peptide chains may be crosslinked with the peptides contributing a lysine in either biosynthetic position.The lysines forming the cross-link may also be hydroxylated and glycosylated (see RESID:AA0028 and RESID:AA0153).lysyl oxidase (EC 1.4.3.13)K, Kcross-link 2incidental to RESID:AA0028incidental to RESID:AA0147secondary to RESID:AA0121PSI-MOD:01176aleatoric crosslinkCROSSLNK Dehydrolysinonorleucine (Lys-Lys)AA043131-Dec-200631-Dec-200629-Jan-20101'-(1,2,3-trihydroxyprop-2-yl)-L-histidine1-[1,2-dihydroxy-1-(hydroxymethyl)ethyl]-L-histidineN(epsilon)-histidine dihydroxyacetone adductN(tau)-(1,2,3-trihydroxypropan-2-yl)histidinetele-(1,2,3-trihydroxypropan-2-yl)histidine(S)-2-amino-3-[1-(1,2,3-trihydroxypropan-2-yl)-1H-imidazol-4-yl]propanoic acidPDBHET:HIQC 9 H 13 N 3 O 4227.22227.090606C 3 H 6 N 0 O 390.0890.031694Christen, S.Srinivas, A.Baehler, P.Zeller, A.Pridmore, D.Bieniossek, C.Baumann, U.Erni, B.J. Biol. Chem. 281, 23129-23137, 2006Regulation of the Dha operon of Lactococcus lactis: a deviation from the rule followed by the Tetr family of transcription regulators.DOI:10.1074/jbc.M603486200PMID:16760471X-ray diffraction, 1.96 angstromsSrinivas, A.Christen, S.Baumann, U.Erni, B.submitted to the Protein Data Bank, May 2006Dihydroxyacetone kinase operon co-activator Dha-dhaQ.PDB:2IU4X-ray diffraction, 1.96 angstromsHPSI-MOD:01177MOD_RES Tele-(1,2,3-trihydroxypropan-2-yl)histidineAA043230-Sep-200730-Sep-200730-Jun-2009S-(aspart-4-yloxy) thiocarbonate4-aspartyloxysulfanylcarbonateO-carboxysulfanyl-4-oxo-L-homoserine(2S)-2-amino-4-(carboxysulfanyl)oxy-4-oxobutanoic acidPDBHET:OHSC 5 H 5 N 1 O 5 S 1191.16190.988843C 1 H 0 N 0 O 2 S 176.0775.961900Shimon, L.J.Goihberg, E.Peretz, M.Burstein, Y.Frolow, F.Acta Crystallogr. D Biol. Crystallogr. 62, 541-547, 2006Structure of alcohol dehydrogenase from Entamoeba histolytica.DOI:10.1107/S0907444906009292PMID:16627948X-ray diffraction, 1.8 angstromsShimon, L.J.Peretz, M.Goihberg, E.Burstein, Y.Frolow, F.submitted to the Protein Data Bank, December 2004Alcohol dehydrogenase from Entamoeba histolotica in complex with cacodylate.PDB:1Y9AX-ray diffraction, 1.81 angstromsGoihberg, E.Dym, O.Tel-Or, S.Shimon, L.Frolow, F.Peretz, M.Burstein, Y.Proteins 72, 711-719, 2008Thermal stabilization of the protozoan Entamoeba histolytica alcohol dehydrogenase by a single proline substitution.DOI:10.1002/prot.21946PMID:18260103X-ray diffraction, 1.77 angstroms; the modification is not mentionedFrolow, F.Shimon, L.Burstein, Y.Goihberg, E.Peretz, M.Dym, O.submitted to the Protein Data Bank, February 2007D275P mutant of alcohol dehydrogenase from protozoa Entamoeba histolytica.PDB:2OUIX-ray diffraction, 1.77 angstroms; the modification is not presented in the modelThis modification was originally observed in the enzyme expressed in Escherichia coli. It was not chemically confirmed or characterized. It did not appear in a later model at higher resolution by the same group.DPSI-MOD:01178Not availablethis dubious modification is not currently annotated in UniProt featuresAA043330-Sep-200730-Sep-200731-May-2018N,N-dimethyl-L-alanine(S)-1-carboxy-N,N-dimethylaminoethaneN,N-dimethylalanine(S)-2-(dimethylamino)propanoic acidCAS:2812-31-9C 5 H 10 N 1 O 1100.14100.076239C 2 H 4 N 0 O 028.0528.031300Alix, J.H.Hayes, D.Lontie, J.F.Colson, C.Glatigny, A.Lederer, F.Biochimie 61, 671-679, 1979Methylated amino acids in ribosomal proteins from Escherichia coli treated with ethionine and from a mutant lacking methylation of protein L11.DOI:10.1016/S0300-9084(79)80165-0PMID:387091N,N-dimethylalanine identified in ribosomal protein L11 after ethionine treatmentMinami, Y.Yoshida, K.Azuma, R.Urakawa, A.Kawauchi, T.Otani, T.Komiyama, K.Omura, S.Tetrahedron Lett. 35, 8001-8004, 1994Structure of cypemycin, a new peptide antibiotic.DOI:10.1016/0040-4039(94)80033-2mass spectrometric, (1)H-NMR, and (13)C-NMR identificationBergmüller, E.Gehrig, P.M.Gruissem, W.J. Proteome Res. 6, 3655-3668, 2007Characterization of Post-Translational Modifications of Histone H2B-Variants Isolated from Arabidopsis thaliana.DOI:10.1021/pr0702159PMID:17691833Claesen, J.Bibb, M.Proc. Natl. Acad. Sci. U.S.A. 107, 16297-16302, 2010Genome mining and genetic analysis of cypemycin biosynthesis reveal an unusual class of posttranslationally modified peptides.DOI:10.1073/pnas.1008608107PMID:20805503gene sequence for the encoded peptideribosomal protein L11 methyltransferase prmA (EC 2.1.1.-)N-terminal RCC1 methyltransferaseprotein N-terminal methyltransferaseS-adenosyl-L-methionine:N-terminal-(A,P,S)PK-[protein] methyltransferase (EC 2.1.1.244)Aamino-terminalGO:0018011PSI-MOD:01179blocked amino endmethylated amino endMOD_RES N,N-dimethylalanineAA043430-Sep-200730-Sep-200731-May-20182-hydroxyglycinealpha-hydroxyglycineaminohydroxyacetic acidamino(hydroxy)acetic acidCAS:4746-62-7ChEBI:38048C 2 H 3 N 1 O 273.0573.016378C 0 H 0 N 0 O 116.0015.994915Young, S.D.Tamburini, P.P.J. Am. Chem. Soc. 111, 1933-1934, 1989Enzymatic peptidyl alpha-amidation proceeds through formation of an alpha-hydroxyglycine intermediate.DOI:10.1021/ja00187a088demonstration that the first step of peptide amide formation is the monooxidation of peptidylglycine to 2-hydroxyglycineHoefnagel, A.J.van Bekkum, H.Peters, J.A.J. Org. Chem. 57, 3916-3921, 1992The reaction of glyoxylic acid with ammonia revisited.DOI:10.1021/jo00040a035synthesis of hydoxyglycine peptides and observation of their decompositionHagelin, G.J. Mass Spectrom. 40, 1287-1299, 2005Structure investigation of Maltacine D1a, D1b and D1c-cyclic peptide lactones of the Maltacine complex from Bacillus subtilis.DOI:10.1002/jms.897PMID:16178056reported mass spectrometric detection of hydroxyglycine in an antibiotic peptideAsara, J.M.Schweitzer, M.H.Freimark, L.M.Phillips, M.Cantley, L.C.Science 316, 280-285, 2007Protein sequences from mastodon and Tyrannosaurus rex revealed by mass spectrometry.DOI:10.1126/science.1137614PMID:17431180reported mass spectrometric detection of hydroxyglycine in archaeological samples of collagen peptidesAsara, J.M.Garavelli, J.S.Slatter, D.A.Schweitzer, M.H.Freimark, L.M.Phillips, M.Cantley, L.C.Science 317, 1324-1325, 2007Interpreting Sequences from Mastodon and T. rex.DOI:10.1126/science.317.5843.1324PMID:17823333reinterpretation of mass spectrograms of collagen peptidesThe S form, produced by peptidylglycine alpha-hydroxylating monooxygenase, is shown.peptidylglycine monooxygenase (EC 1.14.17.3)GPSI-MOD:01180hydroxylationNot availablethis dubious modification is not currently annotated in UniProt featuresAA043530-Sep-200730-Sep-200730-Sep-2008L-aspartic acid 4-methyl ester2-aminobutanedioic acid 4-methyl ester4-methyl L-2-aminosuccinic acid4-methyl L-aspartate4-methyl L-hydrogen aspartateaspartic acid 4-methyl esteraspartic acid beta-methyl ester(2S)-2-amino-4-methoxy-4-oxobutanoic acidCAS:16856-13-6C 5 H 7 N 1 O 3129.12129.042593C 1 H 2 N 0 O 014.0314.015650Lowenson, J.D.Clarke, S.J. Biol. Chem. 267, 5985-5995, 1992Recognition of D-aspartyl residues in polypeptides by the erythrocyte L-isoaspartyl/D-aspartyl protein methyltransferase. Implications for the repair hypothesis.PMID:1556110repair enzyme acts on L-isoaspartyl and D-aspartyl peptidesHaebel, S.Albrecht, T.Sparbier, K.Walden, P.Körner, R.Steup, M.Electrophoresis 19, 679-686, 1998Electrophoresis-related protein modification: alkylation of carboxy residues revealed by mass spectrometry.DOI:10.1002/elps.1150190513PMID:9629898artifactual production of aspartyl and glutamyl methyl estersHoelz, D.J.Arnold, R.J.Dobrolecki, L.E.Abdel-Aziz, W.Loehrer, A.P.Novotny, M.V.Schnaper, L.Hickey, R.J.Malkas, L.H.Proteomics 6, 4808-4816, 2006The discovery of labile methyl esters on proliferating cell nuclear antigen by MS/MS.DOI:10.1002/pmic.200600142PMID:16888766aspartate methyl ester is reported, but not located, resolved as either D- or L-aspartate, or otherwise chemically characterizedAn enzyme acting to form the methyl ester of L-aspartyl peptides might interfere with the D-aspartyl peptide repair mechanism.DPSI-MOD:01181Not availablethis dubious modification is not currently annotated in UniProt featuresAA043609-Nov-200709-Nov-200730-Apr-20106-(S-L-cysteinyl)-8alpha-(N3'-L-histidino)-FAD6-(S-cysteinyl)-8alpha-(N(delta1)-histidyl)-FAD6-(S-cysteinyl)-8alpha-(N(pi)-histidyl)-FAD6-(S-cysteinyl)-8alpha-(N3'-histidyl)-FAD6-(S-cysteinyl)-8alpha-(pros-histidyl)-FAD6-((R)-2-amino-2-carboxyethyl)sulfanyl-8alpha-[4-((S)-2-amino-2-carboxyethyl)imidazol-3-yl]-riboflavin 5'-(trihydrogen diphosphate) 5'->5'-ester with adenosinePDBHET:FADC 36 H 41 N 13 O 17 P 2 S 11021.811021.193931C 27 H 29 N 9 O 15 P 2 S 0781.52781.125835Huang, C.H.Lai, W.L.Lee, M.H.Chen, C.J.Vasella, A.Tsai, Y.C.Liaw, S.H.J. Biol. Chem. 280, 38831-38838, 2005Crystal structure of glucooligosaccharide oxidase from Acremonium strictum: a novel flavinylation of 6-S-cysteinyl, 8alpha-N1-histidyl FAD.DOI:10.1074/jbc.M506078200PMID:16154992Huang, C.-H.Lai, W.-L.Vasella, A.Tsai, Y.-C.Liaw, S.-H.submitted to the Protein Data Bank, September 2005Crystal structure of glucooligosaccharide oxidase from Acremonium strictum: a novel flavinylation of 6-S-cysteinyl, 8alpha-N1-histidyl FAD.PDB:2AXRX-ray diffraction, 1.98 angstromsAlexeev, I.Sultana, A.Mäntsälä, P.Niemi, J.Schneider, G.Proc. Natl. Acad. Sci. U.S.A. 104, 6170-6175, 2007Aclacinomycin oxidoreductase (AknOx) from the biosynthetic pathway of the antibiotic aclacinomycin is an unusual flavoenzyme with a dual active site.DOI:10.1073/pnas.0700579104PMID:17395717X-ray diffraction, 1.65 angstromsThe keyword "phosphoprotein" is not used with flavin modifications linked through the flavin.autocatalyticC, Hcross-link 2PSI-MOD:01182*phosphoproteinFADflavoproteinthioether bondBINDING FAD (covalent; via 2 links, pros nitrogen)BINDING FAD (covalent; via 2 links)AA043709-Nov-200709-Nov-200730-Jun-2013L-selenocystine3,3'-diselenobis(2-aminopropanoic acid)3,3'-diselenobisalanine3,3'-diselenodialaninebeta,beta'-diamino-beta,beta'-dicarboxydiethyldiselenidebeta,beta'-diselenodialaninebis(alpha-aminopropionic acid)-beta-diselenidebis(beta-amino-beta-carboxyethyl)diselenidediselenocysteineselenium cystine(R,R)-3,3'-diselane-1,2-diylbis(2-aminopropanoic acid)CAS:1464-43-3ChEBI:28553C 6 H 8 N 2 O 2 Se 2298.08299.891620C 0 H -2 N 0 O 0 Se 0-2.02-2.015650C 0 H -2 N 0 O 0 S -2 Se 291.8193.873250Huber, R.E.Criddle, R.S.Arch. Biochem. Biophys. 122, 164-173, 1967Comparison of the chemical properties of selenocysteine and selenocystine with their sulfur analogs.DOI:10.1016/0003-9861(67)90136-1PMID:6076213Shchedrina, V.A.Novoselov, S.V.Malinouski, M.Y.Gladyshev, V.N.Proc. Natl. Acad. Sci. U.S.A. 104, 13919-13924, 2007Identification and characterization of a selenoprotein family containing a diselenide bond in a redox motif.DOI:10.1073/pnas.0703448104PMID:17715293Metanis, N.Keinan, E.Dawson, P.E.J. Am. Chem. Soc. 128, 16684-16691, 2006Synthetic seleno-glutaredoxin 3 analogues are highly reducing oxidoreductases with enhanced catalytic efficiency.DOI:10.1021/ja0661414PMID:17177418comparative redox potentials of cystine, cysteinylselenocysteine and selenocystine in synthetic glutaredoxins with a [C/U]XX[C/U] motifThe experimental redox potential of selenocystine in synthetic glutaredoxin 3 is -309 mV. See RESID:AA0025 and RESID:AA0358.U, Ucross-link 2PSI-MOD:01183C, Ccross-link 2secondary to RESID:AA0022PSI-MOD:01184redox-active centerseleniumCROSSLNK Selenocystine (Sec-Sec)AA043831-Dec-200731-Dec-200720-Apr-2012tris-L-cysteinyl L-histidino diiron disulfideCDGSH domain iron-sulfur clusterdi-mu-sulfido(bis-S-cysteinyliron)(S-cysteinyl-N3'-histidinoiron)PDBHET:FESC 15 Fe 2 H 18 N 6 O 4 S 52-618.34617.870280C 0 Fe 2 H -4 N 0 O 0 S 22-171.78171.783814Paddock, M.L.Wiley, S.E.Axelrod, H.L.Cohen, A.E.Roy, M.Abresch, E.C.Capraro, D.Murphy, A.N.Nechushtai, R.Dixon, J.E.Jennings, P.A.Proc. Natl. Acad. Sci. U.S.A. 104, 14342-14347, 2007MitoNEET is a uniquely folded 2Fe 2S outer mitochondrial membrane protein stabilized by pioglitazone.DOI:10.1073/pnas.0707189104PMID:17766440X-ray diffraction, 1.50 angstromsPaddock, M.L.Wiley, S.E.Axelrod, H.L.Cohen, A.E.Roy, M.Abresch, E.C.Capraro, D.Murphy, A.N.Nechushtai, R.Dixon, J.E.Jennings, P.A.submitted to the Protein Data Bank, June 2007MitoNEET is a uniquely folded 2Fe 2S outer mitochondrial membrane protein stabilized by pioglitazone.PDB:2QH7X-ray diffraction, 1.50 angstromsLin, J.Zhou, T.Ye, K.Wang, J.Proc. Natl. Acad. Sci. U.S.A. 104, 14640-14645, 2007Crystal structure of human mitoNEET reveals distinct groups of iron sulfur proteins.DOI:10.1073/pnas.0702426104PMID:17766439X-ray diffraction, 1.81 angstromsThe CDGSH homology domain containing this iron-sulfur cluster had been predicted to be a "zinc finger".C, C, C, Hcross-link 4PSI-MOD:008642Fe-2Siron-sulfur proteinmetalloproteinMETAL Iron-sulfur (2Fe-2S)METAL Iron-sulfur (2Fe-2S); via pros nitrogenAA043931-Dec-200731-Dec-200730-Apr-2010N-aspartyl-glycosylsphingolipidinositolethanolamineC 6 H 12 N 2 O 7 P 1 +255.14 +255.038212 +C 2 H 6 N 1 O 3 P 1 +123.05 +123.008530 +This modification is predicted for proteins with sequence characteristics for the GPI-like anchor modification with sphingolipid, and with asparatic acid at the cleavage and anchor attachment site.A representative glycan core structure is shown.Cleavage of a carboxyl terminal propeptide accompanies transamidation.Dcarboxyl-terminalPSI-MOD:00865blocked carboxyl endglycoproteinlipoproteinphosphoproteinsphingolipidinositol linkageLIPID GPI-like-anchor amidated aspartateAA044031-Mar-200831-Mar-200826-Feb-2010N6-(L-threonyl)-L-lysineN6-threonyl-lysine(2S)-2-amino-6-([(2S,3R)-2-amino-3-hydroxybutanoyl]amino)hexanoic acidC 10 H 18 N 3 O 3228.27228.134816C 0 H -2 N 0 O -1-18.02-18.010565Kang, H.J.Coulibaly, F.Clow, F.Proft, T.Baker, E.N.Science 318, 1625-1628, 2007Stabilizing isopeptide bonds revealed in gram-positive bacterial pilus structure.DOI:10.1126/science.1145806PMID:18063798X-ray diffraction, 2.2 angstroms; evidence for multiple intrachain isoaspartyl lysine isopeptide cross-linksKang, H.J.Coulibaly, F.Proft, T.Baker, E.N.submitted to the Protein Data Bank, October 2007Crystal structure of the major pilin from Streptococcus pyogenes.PDB:3B2MX-ray diffraction, 2.22 angstromsThis interchain cross-link is formed between a lysine residue and a threonine residue in polymerized streptococcal pilin.K, Tcarboxyl-terminalcross-link 2incidental to RESID:AA0345PSI-MOD:00924blocked carboxyl endisopeptide bondCROSSLNK Threonyl lysine isopeptide (Lys-Thr) (interchain with T-...)CROSSLNK Threonyl lysine isopeptide (Thr-Lys) (interchain with K-...)AA044131-Mar-200831-Mar-200830-Jun-2012(2-aminosuccinimidyl)acetic acid(3-amino-2,5-dioxo-1-pyrrolidinyl)acetic acidanhydroaspartyl glycineaspartimide glycineN-(2-aminosuccinyl)glycine[(3S)-3-amino-2,5-dioxopyrrolidin-1-yl]acetic acidChEBI:45890PDBHET:ACYPDBHET:SNNPDBHET:SUIC 6 H 6 N 2 O 3154.13154.037842C 0 H -3 N -1 O 0-17.03-17.026549C 0 H -2 N 0 O -1-18.02-18.010565IUPAC-IUB Joint Commission on Biochemical Nomenclature (JCBN)Eur. J. Biochem. 183, 1-4, 1989Nomenclature Committee of IUB (NC-IUB) and IUPAC-IUB Joint Commission on Biochemical Nomenclature (JCBN), newsletter 1989.DOI:10.1111/j.1432-1033.1989.tb14887.xHøjrup, P.Gerola, P.Hansen, H.F.Mikkelsen, J.M.Shahed, A.E.Knudsen, J.Roepstorff, P.Olson, J.M.Biochim. Biophys. Acta 1077, 220-224, 1991The amino acid sequence of a major protein component in the light harvesting complex of the green photosynthetic bacterium Chlorobium limicola f. thiosulfatophilum.DOI:10.1016/0167-4838(91)90061-4PMID:2015294detection of a blocked N-terminal Asn-Gly sequence with a mass loss of "approx. 18 Da"; the formation of (2-aminosuccinimidyl)acetic acid, with a mass loss of 17 Da, would probably block imidazolinone cyclizationHernandez, J.F.Gagnon, J.Chiche, L.Nguyen, T.M.Andrieu, J.P.Heitz, A.Trinh Hong, T.Pham, T.T.Le Nguyen, D.Biochemistry 39, 5722-5730, 2000Squash trypsin inhibitors from Momordica cochinchinensis exhibit an atypical macrocyclic structure.DOI:10.1021/bi9929756 S0006-2960(99)02975-XPMID:10801322probable mass spectrometric detection of cyclic anhydride formed from aspartic acidFitzgerald, P.M.D.Sharma, N.submitted to the Protein Data Bank, July 2001IMP-1 metallo beta-lactamase from Pseudomonas aeruginosa in complex with a biaryl succinic acid inhibitor (1).PDB:1JJTX-ray diffraction, 1.80 angstroms; the cross-link is mentioned in the PDB entry and not in the publicationErskine, P.T.Coates, L.Mall, S.Gill, R.S.Wood, S.P.Myles, D.A.A.Cooper, J.B.Protein Sci. 12, 1741-1749, 2003Atomic resolution analysis of the catalytic site of an aspartic proteinase and an unexpected mode of binding by short peptides.DOI:10.1110/ps.0305203PMID:12876323X-ray diffraction, 0.9 angstromsCoates, L.Erskine, P.T.Mall, S.Gill, R.S.Wood, S.P.Myles, D.A.A.Cooper, J.B.submitted to the Protein Data Bank, March 2003Atomic resolution structure of native endothiapepsin.PDB:1OEWX-ray diffraction, 0.9 angstromsThis cross-link is formed by the condensation of an aspartic acid or asparagine residue with the alpha-amido of the following residue.autocatalyticG, Ncross-link 1PSI-MOD:01624D, Gcross-link 1PSI-MOD:00952succinimide ringCROSSLNK (2-aminosuccinimidyl)acetic acid (Asn-Gly)CROSSLNK (2-aminosuccinimidyl)acetic acid (Asp-Gly)AA044208-Aug-200808-Aug-200830-Jan-2009(2S)-4-hydroxyleucinegamma-hydroxyleucine(2S)-2-amino-4-hydroxy-4-methylpentanoic acidC 6 H 11 N 1 O 2129.16129.078979C 0 H 0 N 0 O 116.0015.994915Wieland, T.Faulstich, H.C.R.C. Crit. Rev. Biochem. 5, 185-260, 1978Amatoxins, phallotoxins, phallolysin, and antamanide: the biologically active components of poisonous Amanita mushrooms.PMID:363352described as a constituent of the phallotoxin phalloinFu, S.L.Dean, R.T.Biochem. J. 324, 41-48, 1997Structural characterization of the products of hydroxyl-radical damage to leucine and their detection on proteins.PMID:9164839LPSI-MOD:01372hydroxylationNot availablethis modification is not annotated in UniProt featuresAA044308-Aug-200808-Aug-200830-Sep-2010(2S,4R)-5-hydroxyleucine(4R)-5-hydroxyleucinedelta-hydroxyleucine(2S,4R)-2-amino-5-hydroxy-4-methylpentanoic acidC 6 H 11 N 1 O 2129.16129.078979C 0 H 0 N 0 O 116.0015.994915Wilson, J.B.Brennan, S.O.Allen, J.Shaw, J.G.Gu, L.H.Huisman, T.H.J. Chromatogr. 617, 37-42, 1993The M gamma chain of human fetal hemoglobin is an A gamma chain with an in vitro modification of gamma 141 leucine to hydroxyleucine.DOI:10.1016/0378-4347(93)80418-4PMID:7690768Fu, S.L.Dean, R.T.Biochem. J. 324, 41-48, 1997Structural characterization of the products of hydroxyl-radical damage to leucine and their detection on proteins.PMID:9164839Sundheim, O.Vågbø, C.B.Bjørås, M.Sousa, M.M.L.Talstad, V.Aas, P.A.Drabløs, F.Krokan, H.E.Tainer, J.A.Slupphaug, G.EMBO J. 25, 3389-3397, 2006Human ABH3 structure and key residues for oxidative demethylation to reverse DNA/RNA damage.DOI:10.1038/sj.emboj.7601219PMID:16858410X-ray diffraction, 1.50 angstromsSundheim, O.Vagbo, C.B.Bjoras, M.DeSousa, M.M.L.Talstad, V.Aas, P.A.Drablos, F.Krokan, H.E.Tainer, J.A.Slupphaug, G.submitted to the Protein Data Bank, June 2006Human ABH3 structure and key residues for oxidative demethylation to reverse DNA/RNA damage.PDB:2IUWX-ray diffraction, 1.50 angstromsThe oxidation artifacts 5-hydroxyleucine and 5-oxoleucine can form autocatalytically and stereospecifically, but not selectively. It is not clear whether the modified residue subsequently takes part in catalytic reactions at the active site of alpha-ketoglutarate-dependent dioxygenase alkB homolog 3 (ABH3).LPSI-MOD:01373hydroxylationNot availablethis modification is not annotated in UniProt featuresAA044408-Aug-200808-Aug-200831-May-2018(2S,4R)-5-oxoleucine(4R)-5-oxo-L-leucine(2S,4R)-2-amino-4-methyl-5-oxopentanoic acidChEBI:43739PDBHET:LEDC 6 H 9 N 1 O 2127.14127.063329C 0 H -2 N 0 O 113.9813.979265Sundheim, O.Vågbø, C.B.Bjørås, M.Sousa, M.M.L.Talstad, V.Aas, P.A.Drabløs, F.Krokan, H.E.Tainer, J.A.Slupphaug, G.EMBO J. 25, 3389-3397, 2006Human ABH3 structure and key residues for oxidative demethylation to reverse DNA/RNA damage.DOI:10.1038/sj.emboj.7601219PMID:16858410X-ray diffraction, 1.50 angstromsSundheim, O.Vagbo, C.B.Bjoras, M.DeSousa, M.M.L.Talstad, V.Aas, P.A.Drablos, F.Krokan, H.E.Tainer, J.A.Slupphaug, G.submitted to the Protein Data Bank, June 2006Human ABH3 structure and key residues for oxidative demethylation to reverse DNA/RNA damage.PDB:2IUWX-ray diffraction, 1.50 angstromsThe oxidation artifacts 5-hydroxyleucine and 5-oxoleucine can form autocatalytically and stereospecifically, but not selectively. It is not clear whether the modified residue subsequently takes part in catalytic reactions at the active site of alpha-ketoglutarate-dependent dioxygenase alkB homolog 3 (ABH3).LPSI-MOD:01374MOD_RES (4R)-5-oxoleucineAA044508-Aug-200808-Aug-200830-Jan-2009(2S,4R)-4,5-dihydroxyleucine(4R)-4,5-dihydroxyleucinegamma,delta-dihydroxyleucine(2S,4R)-2-amino-4,5-dihydroxy-4-methylpentanoic acidC 6 H 11 N 1 O 3145.16145.073893C 0 H 0 N 0 O 232.0031.989829Georgi, V.Wieland, T.Justus Liebigs Ann. Chem. 700, 149-156, 1966Über die Inhaltsstoffe des grünen Knollenblätterpilzes. XXIX. Synthese von gamma-delta-Dihydroxy-isoleucin, der lactonisierenden Aminosäure von alpha- und beta-Amanitin. [On the ingredients of the green amanita. XXIX. Synthesis of gamma-delta-dihydroxyleucine, the lactonizing amino acid of alpha- and beta-amanitin].DOI:10.1002/jlac.19667000118PMID:6010785article in GermanFaulstich, H.Buku, A.Bodenmüller, H.Wieland, T.Biochemistry 19, 3334-3343, 1980Virotoxins: actin-binding cyclic peptides of Amanita virosa mushrooms.DOI:10.1021/bi00555a036PMID:6893271LPSI-MOD:01375hydroxylationMOD_RES (4R)-4,5-dihydroxyleucineAA044631-Mar-200931-Mar-200930-Jun-2009(2S,4S)-4,5-dihydroxyleucine(4S)-4,5-dihydroxyleucinegamma,delta-dihydroxyleucine(2S,4S)-2-amino-4,5-dihydroxy-4-methylpentanoic acidC 6 H 11 N 1 O 3145.16145.073893C 0 H 0 N 0 O 232.0031.989829Little, M.C.Preston III, J.F.Jackson, C.Bonetti, S.King, R.W.Taylor, L.C.Biochemistry 25, 2867-2872, 1986Alloviroidin, the naturally occurring toxic isomer of the cyclopeptide viroidin.DOI:10.1021/bi00358a019PMID:3718926the name of J.F. Preston III in the PubMed citation is correctedLPSI-MOD:01432hydroxylationNot availablethis modification is not annotated in UniProt featuresAA044724-Oct-200824-Oct-200830-Apr-2010(2S,3S,4R)-3,4-dihydroxyisoleucine(3S,4R)-3,4-dihydroxyisoleucinebeta,gamma-dihydroxyisoleucine(2S,3S,4R)-2-amino-3,4-dihydroxy-3-methylpentanoic acidPDBHET:TSIC 6 H 11 N 1 O 3145.16145.073893C 0 H 0 N 0 O 232.0031.989829Bond, C.S.Shaw, M.P.Alphey, M.S.Hunter, W.N.Acta Crystallogr. D Biol. Crystallogr. 57, 755-758, 2001Structure of the macrocycle thiostrepton solved using the anomalous dispersion contribution of sulfur.DOI:10.1107/S0907444901003134PMID:11320328Bond, C.S.Shaw, M.P.Alphey, M.S.Hunter, W.N.submitted to the Protein Data Bank, October 2000Structure of the macrocycle thiostrepton solved using the anomalous dispersion contribution of sulfur.PDB:1E9WX-ray diffraction, 1.02 angstromsMukai, A.Fukai, T.Hoshino, Y.Yazawa, K.Harada, K.-I.Mikami, Y.J. Antibiot. 62, 613-619, 2009Nocardithiocin, a novel thiopeptide antibiotic, produced by pathogenic Nocardia pseudobrasiliensis IFM 0757.DOI:10.1038/ja.2009.90PMID:19745839the initials of K.-I. Harada in the PubMed citation are correctedIn some cases the stereochemistry for the second and third chiral centers have not been resolved.Iincidental to RESID:AA0466PSI-MOD:01376hydroxylationMOD_RES (3S,4R)-3,4-dihydroxyisoleucineMOD_RES 3,4-dihydroxyisoleucinethis UniProt feature is used when the stereochemistry has not been determinedAA044808-Aug-200808-Aug-200830-Sep-2010(2S,3R,4S)-4-hydroxyisoleucine(2S,3R,4S)-2-amino-3-methyl-4-hydroxyvaleric acid(3R,4S)-4-hydroxyisoleucinegamma-hydroxyisoleucine(2S,3R,4S)-2-amino-4-hydroxy-3-methylpentanoic acidC 6 H 11 N 1 O 2129.16129.078979C 0 H 0 N 0 O 116.0015.994915Gieren, A.Narayana, P.Hoppe, W.Hasan, M.Michl, K.Wieland, T.Smith, H.O.Jung, G.Breitmai, E.Justus Liebigs Ann. Chem. 1974, 1561-1569, 1974Über die Inhaltsstoffe des grünen Knollenblätterpilzes. XLIV. Die Konfiguration der hydroxylierten Isoleucine der Amatoxine. [Components of Green Deathcap Toadstool, Amanita Phalloides. XLIV. Configuration of hydroxylated isoleucines from Amatoxins].DOI:10.1002/jlac.197419741004article in GermanWieland, T.Faulstich, H.C.R.C. Crit. Rev. Biochem. 5, 185-260, 1978Amatoxins, phallotoxins, phallolysin, and antamanide: the biologically active components of poisonous Amanita mushrooms.PMID:363352described as a constituent of the amatoxin gamma-amanitinIn peptide sequencing work prior to 1968, this modification was reported as a beta-methylleucine derivative that could arise by either beta-methylation of leucine or gamma-methylation of isoleucine. The correct structure has been determined to be derived from isoleucine without methylation.IPSI-MOD:01377hydroxylationMOD_RES (3R,4S)-4-hydroxyisoleucineAA044908-Aug-200808-Aug-200830-Sep-2010(2S,3R,4R)-4,5-dihydroxyisoleucine(3R,4R)-4,5-dihydroxyisoleucinegamma,delta-dihydroxyisoleucine(2S,3R,4R)-2-amino-4,5-dihydroxy-3-methylpentanoic acidPDBHET:ILXC 6 H 11 N 1 O 3145.16145.073893C 0 H 0 N 0 O 232.0031.989829Gieren, A.Narayana, P.Hoppe, W.Hasan, M.Michl, K.Wieland, T.Smith, H.O.Jung, G.Breitmai, E.Justus Liebigs Ann. Chem. 1974, 1561-1569, 1974Über die Inhaltsstoffe des grünen Knollenblätterpilzes, XLIV. Die Konfiguration der hydroxylierten Isoleucine der Amatoxine. [Components of Green Deathcap Toadstool, Amanita Phalloides. XLIV. Configuration of hydroxylated isoleucines from Amatoxins].DOI:10.1002/jlac.197419741004article in GermanWieland, T.Faulstich, H.C.R.C. Crit. Rev. Biochem. 5, 185-260, 1978Amatoxins, phallotoxins, phallolysin, and antamanide: the biologically active components of poisonous Amanita mushrooms.PMID:363352described as a constituent of the amatoxin alpha-amanitinBushnell, D.A.Cramer, P.Kornberg, R.D.Proc. Natl. Acad. Sci. U.S.A. 99, 1218-1222, 2002Structural basis of transcription: alpha-amanitin-RNA polymerase II cocrystal at 2.8 A resolution.DOI:10.1073/pnas.251664698PMID:11805306X-ray diffraction with modeled peptide, 2.80 angstromsBushnell, D.A.Cramer, P.Kornberg, R.D.submitted to the Protein Data Bank, October 2001Crystal structure of yeast RNA polymerase II complexed with the inhibitor alpha amanitin.PDB:1K83X-ray diffraction with modeled peptide, 2.80 angstromsBrueckner, F.Cramer, P.Nature Struct. Mol. Biol. 15, 811-818, 2008Structural basis of transcription inhibition by alpha-amanitin and implications for RNA polymerase II translocation.DOI:10.1038/nsmb.1458PMID:18552824X-ray diffraction, 3.40 angstromsBrueckner, F.Cramer, P.submitted to the Protein Data Bank, May 2008Alpha-amanitin inhibited complete RNA polymerase II elongation complex.PDB:2VUMX-ray diffraction, 3.40 angstromsIn peptide sequencing work prior to 1968, this modification was reported as a beta-methylleucine derivative that could arise by either beta-methylation of leucine or gamma-methylation of isoleucine. The correct structure has been determined to be derived from isoleucine without methylation.IPSI-MOD:01378hydroxylationMOD_RES (3R,4R)-4,5-dihydroxyisoleucineAA045008-Aug-200808-Aug-200830-Jan-20092'-methylsulfonyl-L-tryptophan2-methylsulfonyl-3-((2S)-2-amino-2-carboxyethyl)-1H-indoleC 12 H 12 N 2 O 3 S 1264.30264.056863C 1 H 2 N 0 O 2 S 178.0977.977550Faulstich, H.Buku, A.Bodenmüller, H.Wieland, T.Biochemistry 19, 3334-3343, 1980Virotoxins: actin-binding cyclic peptides of Amanita virosa mushrooms.DOI:10.1021/bi00555a036PMID:6893271In virotoxin this modified tryptophan is formed after a 2'-(S-cysteinyl)tryptophan crosslink is broken.WPSI-MOD:01379MOD_RES 2'-methylsulfonyltryptophanAA045108-Aug-200808-Aug-200831-May-20182'-(S-L-cysteinyl)-6'-hydroxy-L-tryptophan sulfoxide6'-hydroxy-S-oxo-tryptathionine2-{(R)-[(2R)-2-amino-2-carboxyethyl]sulfinyl}-3-[(2S)-2-amino-2-carboxyethyl]-6-hydroxy-1H-indolePDBHET:CSXPDBHET:TRXC 14 H 13 N 3 O 4 S 1319.33319.062677C 0 H -2 N 0 O 2 S 029.9829.974179Wieland, T.Science 159, 946-952, 1968Poisonous principles of mushrooms of the genus Amanita. Four-carbon amines acting on the central nervous system and cell-destroying cyclic peptides are produced.DOI:10.1126/science.159.3818.946PMID:4865716Wieland, T.Faulstich, H.C.R.C. Crit. Rev. Biochem. 5, 185-260, 1978Amatoxins, phallotoxins, phallolysin, and antamanide: the biologically active components of poisonous Amanita mushrooms.PMID:363352described as a constituent of the amatoxins alpha- and gamma-amanitinBushnell, D.A.Cramer, P.Kornberg, R.D.Proc. Natl. Acad. Sci. U.S.A. 99, 1218-1222, 2002Structural basis of transcription: alpha-amanitin-RNA polymerase II cocrystal at 2.8 A resolution.DOI:10.1073/pnas.251664698PMID:11805306X-ray diffraction with modeled peptide, 2.80 angstromsBushnell, D.A.Cramer, P.Kornberg, R.D.submitted to the Protein Data Bank, October 2001Crystal structure of yeast RNA polymerase II complexed with the inhibitor alpha amanitin.PDB:1K83X-ray diffraction with modeled peptide, 2.80 angstromsBrueckner, F.Cramer, P.Nature Struct. Mol. Biol. 15, 811-818, 2008Structural basis of transcription inhibition by alpha-amanitin and implications for RNA polymerase II translocation.DOI:10.1038/nsmb.1458PMID:18552824X-ray diffraction, 3.40 angstromsBrueckner, F.Cramer, P.submitted to the Protein Data Bank, May 2008Alpha-amanitin inhibited complete RNA polymerase II elongation complex.PDB:2VUMX-ray diffraction, 3.40 angstromsC, Wcross-link 2PSI-MOD:01380hydroxylationCROSSLNK 2'-cysteinyl-6'-hydroxytryptophan sulfoxide (Trp-Cys)AA045508-Aug-200808-Aug-200831-May-2018O-palmitoleoyl-L-serineL-serine cis-9-hexadecenoate esterO3-palmitoleoyl-serine(2S)-2-amino-3-((9Z)-9-hexadecenoyloxy)propanoic acidChEBI:85189PDBHET:PAMC 19 H 33 N 1 O 3323.48323.246044C 16 H 28 N 0 O 1236.40236.214016Takada, R.Satomi, Y.Kurata, T.Ueno, N.Norioka, S.Kondoh, H.Takao, T.Takada, S.Dev. Cell 11, 791-801, 2006Monounsaturated fatty acid modification of Wnt protein: its role in Wnt secretion.DOI:10.1016/j.devcel.2006.10.003PMID:17141155Janda, C.Y.Waghray, D.Levin, A.M.Thomas, C.Garcia, K.C.Science 337, 59-64, 2012Structural Basis of Wnt Recognition by Frizzled.DOI:10.1126/science.1222879PMID:22653731X-ray diffraction, 3.25 angstroms; the modification was produced with Xenopus laevis Wnt8 expressed in Drosophila melanogasterJanda, C.Y.Waghray, D.Levin, A.M.Thomas, C.Garcia, K.C.submitted to the Protein Data Bank, May 2012Crystal structure of XWnt8 in complex with the cysteine-rich domain of Frizzled 8.PDB:4F0AX-ray diffraction, 3.25 angstroms; electron density of the lipid is incomplete and the model does not have the expected geometryO-palmitoleoyl transferase(9Z)-hexadec-9-enoyl-CoA:[Wnt]-L-serine O-hexadecenoyltransferase (EC 2.3.1.250)SPSI-MOD:01381lipoproteinLIPID O-palmitoleyl serineAA045629-Aug-200829-Aug-200831-May-2013N,N,N-trimethyl-L-methionine(1S)-1-carboxy-N,N,N-trimethyl-3-(methylsulfanyl)propanazanium2-trimethylammonio-4-(methylthio)butanoic acidN,N,N-trimethylmethionine cationN,N,N-trimethylmethioninium(1S)-1-carboxy-N,N,N-trimethyl-3-(methylsulfanyl)propanaminiumPDBHET:4MMC 8 H 17 N 1 O 1 S 11+175.29175.102537C 3 H 7 N 0 O 0 S 01+43.0943.054227Demirci, H.Gregory, S.T.Dahlberg, A.E.Jogl, G.Structure 16, 1059-1066, 2008Multiple-site trimethylation of ribosomal protein L11 by the PrmA methyltransferase.DOI:10.1016/j.str.2008.03.016PMID:18611379X-ray diffraction, 1.75 angstroms; the model submitted as PDB 3CJU was corrected and replaced by 3EGVDemirci, H.Gregory, S.T.Dahlberg, A.E.Jogl, G.submitted to the Protein Data Bank, September 2008Ribosomal protein L11 methyltransferase (PrmA) in complex with trimethylated ribosomal protein L11.PDB:3EGVX-ray diffraction, 1.75 angstromsAlthough appropriate, the keyword "thioether bond" normally does not appear for this amino acid.Consult FAQ at http://pir.georgetown.edu/resid/faq.shtml#q12 concerning calculation of the difference formula.ribosomal protein L11 methyltransferase (EC 2.1.1.-)Mamino-terminalGO:0018014PSI-MOD:01382*thioether bondblocked amino endmethylated amino endMOD_RES N,N,N-trimethylmethionineAA045729-Aug-200829-Aug-200826-Feb-2010L-cystine S-oxidecystine sulfoxideS-cysteinyl 3-(oxidosulfanyl)alanineS-[(2R)-2-amino-3-oxopropyl] (2R)-2-amino-3-oxopropane-1-sulfinothioate(2R)-2-amino-3-[([(2R)-2-amino-2-carboxyethyl]sulfanyl)sulfinyl]propanoic acidC 6 H 8 N 2 O 3 S 2220.26219.997634C 0 H -2 N 0 O 1 S 013.9813.979265Oke, M.Ching, R.T.Y.Carter, L.G.Johnson, K.A.Liu, H.McMahon, S.A.White, M.F.Bloch Jr., C.Botting, C.H.Walsh, M.A.Latiff, A.A.Kennedy, M.W.Cooper, A.Naismith, J.H.Angew. Chem. Int. Ed. Engl. 47, 7853-7856, 2008Unusual chromophore and cross-links in ranasmurfin: a blue protein from the foam nests of a tropical frog.DOI:10.1002/anie.200802901PMID:18781570X-ray diffraction, 1.16 angstroms; the authors' names in the PubMed citation are correctedOke, M.Ching, R.Y.Carter, L.G.Johnson, K.A.Liu, H.McMahon, S.A.Bloch Jr., C.Botting, C.H.Walsh, M.A.Latiff, A.A.Kennedy, M.W.Cooper, A.Naismith, J.H.submitted to the Protein Data Bank, November 2007Ranasmurfin.PDB:2VH3X-ray diffraction, 1.16 angstromsThis modification in the modeled protein has not been chemically confirmed.C, Ccross-link 2PSI-MOD:01383disulfide bondCROSSLNK S-cysteinyl 3-(oxidosulfanyl)alanine (Cys-Cys)AA045829-Aug-200829-Aug-200826-Feb-2010aminomalonic acid2-carboxyglycineAmaaminopropanedioic acidCAS:1068-84-4PDBHET:FGLC 3 H 3 N 1 O 3101.06101.011293C 0 H -2 N 0 O 1 S 013.9813.979265Thanassi, J.W.Biochemistry 9, 525-532, 1970Aminomalonic acid. Spontaneous decarboxylation and reaction with 5-deoxypyridoxal.DOI:10.1021/bi00805a011PMID:5415959Hauschka, P.V.Henson, E.B.Gallop, P.M.Anal. Biochem. 108, 57-63, 1980Quantitative analysis and comparative decarboxylation of aminomalonic acid, beta-carboxyaspartic acid, and gamma-carboxyglutamic acid.DOI:10.1016/0003-2697(80)90691-0PMID:7457858Van Buskirk, J.J.Kirsch, W.M.Kleyer, D.L.Barkley, R.M.Koch, T.H.Proc. Natl. Acad. Sci. U.S.A. 81, 722-725, 1984Aminomalonic acid: identification in Escherichia coli and atherosclerotic plaque.DOI:10.1073/pnas.81.3.722PMID:6366787Copley, S.D.Frank, E.Kirsch, W.M.Koch, T.H.Anal. Biochem. 201, 152-157, 1992Detection and possible origins of aminomalonic acid in protein hydrolysates.DOI:10.1016/0003-2697(92)90188-DPMID:1621954Oke, M.Ching, R.T.Y.Carter, L.G.Johnson, K.A.Liu, H.McMahon, S.A.White, M.F.Bloch Jr., C.Botting, C.H.Walsh, M.A.Latiff, A.A.Kennedy, M.W.Cooper, A.Naismith, J.H.Angew. Chem. Int. Ed. Engl. 47, 7853-7856, 2008Unusual chromophore and cross-links in ranasmurfin: a blue protein from the foam nests of a tropical frog.DOI:10.1002/anie.200802901PMID:18781570X-ray diffraction, 1.16 angstroms; the authors' names in the PubMed citation are correctedOke, M.Ching, R.Y.Carter, L.G.Johnson, K.A.Liu, H.McMahon, S.A.Bloch Jr., C.Botting, C.H.Walsh, M.A.Latiff, A.A.Kennedy, M.W.Cooper, A.Naismith, J.H.submitted to the Protein Data Bank, November 2007Ranasmurfin.PDB:2VH3X-ray diffraction, 1.16 angstromsThis modification in the modeled protein has not been chemically confirmed.As a free amino acid, aminomalonic acid is achiral. However, originating from (2S)-serine in a protein, the residue would be named as a (2R)-2,3-diamino-3-oxopropanoic acid, with the serine carbon-3 carboxyl taking precedence, becoming carbon-1, and changing the stereochemical designation.The PDB Hetgroup FGL was originally designated as the "C(alpha)-formyl glycine" active site residue L-3-oxoalanine (see RESID:AA0185) observed in its hydrated form. That structure, a gem-diol with an sp(3) carbon, was misinterpreted as a carboxyl with an sp(2) carbon and assigned to aminomalonic acid instead.SPSI-MOD:01384MOD_RES Aminomalonic acid (Ser)AA045926-Feb-201026-Feb-201029-Oct-20105'-(L-tyros-5'-yl)amino-L-tyrosine5'-tyrosyl-5'-aminotyrosine5'-[(tyros-5'-yl)amino]tyrosinebis(LTQ) linkage(2S,2'S)-3,3'-[iminobis(4-hydroxybenzene-3,1-diyl)]bis(2-aminopropanoic acid)PDBHET:TY2C 18 H 17 N 3 O 4339.35339.121906C 0 H -1 N 1 O 013.0012.995249Oke, M.Ching, R.T.Y.Carter, L.G.Johnson, K.A.Liu, H.McMahon, S.A.White, M.F.Bloch Jr., C.Botting, C.H.Walsh, M.A.Latiff, A.A.Kennedy, M.W.Cooper, A.Naismith, J.H.Angew. Chem. Int. Ed. Engl. 47, 7853-7856, 2008Unusual chromophore and cross-links in ranasmurfin: a blue protein from the foam nests of a tropical frog.DOI:10.1002/anie.200802901PMID:18781570X-ray diffraction, 1.16 angstroms; the authors' names in the PubMed citation are correctedOke, M.Ching, R.Y.Carter, L.G.Johnson, K.A.Liu, H.McMahon, S.A.Bloch Jr., C.Botting, C.H.Walsh, M.A.Latiff, A.A.Kennedy, M.W.Cooper, A.Naismith, J.H.submitted to the Protein Data Bank, November 2007Ranasmurfin.PDB:2VH3X-ray diffraction, 1.16 angstromsThis structure represents the cross-linked tyrosine portion of a four residue bis(lysine tyrosylquinone) structure which is itself part of a zinc binding complex with two histidine residues.This modification in the modeled protein has not been chemically confirmed.Y, Ycross-link 2secondary to RESID:AA0233PSI-MOD:01787CROSSLNK 5'-tyrosyl-5'-aminotyrosine (Tyr-Tyr) (interchain)AA046224-Oct-200824-Oct-200826-Feb-20103-hydroxy-L-phenylalanine3-hydoxyphenylalanine3-phenyl-L-serinebeta-hydroxyphenylalaninebeta-phenylserineL-threo-3-phenylserine(2S,3S)-2-amino-3-hydroxy-3-phenylpropanoic acidCAS:1078-17-7CAS:587-33-7CAS:6254-48-4ChEBI:16795C 9 H 9 N 1 O 2163.18163.063329C 0 H 0 N 0 O 116.0015.994915Lin, T.S.Kolattukudy, P.E.Eur. J. Biochem. 106, 341-351, 1980Structural studies on cutinase, a glycoprotein containing novel amino acids and glucuronic acid amide at the N terminus.DOI:10.1111/j.1432-1033.1980.tb04580.xPMID:7398618the location of the modification in the sequence was not determined; all crystallographic determinations have used proteins not expressed in the original species, and thus lacking the modificationKettenring, J.Colombo, L.Ferrari, P.Tavecchia, P.Nebuloni, M.Vekey, K.Gallo, G.G.Selva, E.J. Antibiot. 44, 702-715, 1991Antibiotic GE2270 A: a novel inhibitor of bacterial protein synthesis. II. Structure elucidation.PMID:1880060mass spectrometric, (1)H-NMR, (13)C-NMR, and IR identificationTavecchia, P.Gentili, P.Kurz, M.Sottani, C.Bonfichi, R.Lociuro, S.Selva, E.J. Antibiot. 47, 1564-1567, 1994Revised structure of the antibiotic GE 2270A.PMID:7844053Heffron, S.E.Jurnak, F.Biochemistry 39, 37-45, 2000Structure of an EF-Tu complex with a thiazolyl peptide antibiotic determined at 2.35 A resolution: atomic basis for GE2270A inhibition of EF-Tu.DOI:10.1021/bi9913597PMID:10625477Heffron, S.E.Jurnak, F.submitted to the Protein Data Bank, October 1999Crystal structure of elongation factor, Tu (EF-Tu-MGGDP) complexed with GE2270A, a thiazolyl peptide antibiotic.PDB:1D8TX-ray diffraction, 2.35 angstroms; in this low resolution, dimeric structure the modification was modeled as the (2S,3R) diastereomer in one molecule and (2S,3S) in the otherHeckmann, G.Bach, T.Angew. Chem. Int. Ed. Engl. 44, 1199-1201, 2005Synthesis of the heterocyclic core of the GE 2270 antibiotics and structure elucidation of a major degradation product.DOI:10.1002/anie.200461715PMID:15651011(1)H-NMR, specific rotation analysis, and chemical synthesis; establishes that the modification is the (2S,3S) diastereomerParmeggiani, A.Krab, I.M.Okamura, S.Nielsen, R.C.Nyborg, J.Nissen, P.Biochemistry 45, 6846-6857, 2006Structural basis of the action of pulvomycin and GE2270 A on elongation factor Tu.DOI:10.1021/bi0525122PMID:16734421X-ray diffraction, 1.60 angstromsParmeggiani, A.Krab, I.M.Okamura, S.Nielsen, R.C.Nyborg, J.Nissen, P.submitted to the Protein Data Bank, November 2005EF-Tu complexed with a GTP analog and the antibiotic GE2270 A.PDB:2C77X-ray diffraction, 1.60 angstromsFPSI-MOD:01385hydroxylationMOD_RES 3-hydroxyphenylalanineAA046324-Oct-200824-Oct-200830-Jan-20093-hydroxy-L-valine3-hydroxyvaline(2S)-2-amino-3-hydroxy-3-methylbutanoic acidC 5 H 9 N 1 O 2115.13115.063329C 0 H 0 N 0 O 116.0015.994915Shoji, J.Kato, T.Yoshimura, Y.Tori, K.J. Antibiot. 34, 1126-1136, 1981Structural studies on thiocillins I, II and III (studies on antibiotics from the genus Bacillus XXIX).PMID:7328054VPSI-MOD:01386hydroxylationMOD_RES 3-hydroxyvalineAA046424-Oct-200824-Oct-200831-Dec-2009O-methyl-L-threonineO-methyl threoninethreonine methyl ether(2S,3R)-2-amino-3-methoxybutanoic acidCAS:4385-90-4PDBHET:OLTC 5 H 9 N 1 O 2115.13115.063329C 1 H 2 N 0 O 014.0314.015650Shoji, J.Kato, T.Yoshimura, Y.Tori, K.J. Antibiot. 34, 1126-1136, 1981Structural studies on thiocillins I, II and III (studies on antibiotics from the genus Bacillus XXIX).PMID:7328054Tincidental to RESID:AA0483PSI-MOD:01387methylated amino acidMOD_RES O-methylthreonineAA046524-Oct-200824-Oct-200830-Jan-20091-amino-2-propanol1-amino-2-hydroxypropane1-methyl-2-aminoethanol2-amino-1-methylethanol2-hydroxy-1-propylamine2-hydroxypropanamine2-hydroxypropylaminealpha-aminoisopropyl alcoholdecarboxylated threonineisopropanolaminethreamine(2R)-1-aminopropan-2-olCAS:35320-23-1ChEBI:15675C 3 H 8 N 1 O 174.1074.060589C -1 H 0 N 0 O -2-44.01-43.989829Shoji, J.Kato, T.Yoshimura, Y.Tori, K.J. Antibiot. 34, 1126-1136, 1981Structural studies on thiocillins I, II and III (studies on antibiotics from the genus Bacillus XXIX).PMID:7328054Tcarboxyl-terminalPSI-MOD:01388blocked carboxyl endMOD_RES Decarboxylated threonineAA046624-Oct-200824-Oct-200830-Sep-2011L-isoleucine thiazole-4-carboxylic acid2-[1-zanyl-2-methylbutyl]-1,3-thiazole-4-carboxylic acid2-[(1S,2S)-1-amino-2-methylbutyl]-1,3-thiazole-4-carboxylic acidPDBHET:BB9C 9 H 12 N 2 O 1 S 1196.27196.067034C 0 H -4 N 0 O -1 S 0-20.03-20.026215Bond, C.S.Shaw, M.P.Alphey, M.S.Hunter, W.N.Acta Crystallogr. D Biol. Crystallogr. 57, 755-758, 2001Structure of the macrocycle thiostrepton solved using the anomalous dispersion contribution of sulfur.DOI:10.1107/S0907444901003134PMID:11320328Bond, C.S.Shaw, M.P.Alphey, M.S.Hunter, W.N.submitted to the Protein Data Bank, October 2000Structure of the macrocycle thiostrepton solved using the anomalous dispersion contribution of sulfur.PDB:1E9WX-ray diffraction, 1.02 angstromsFormed by the condensation of a cysteine thiol with the carbonyl of the preceding residue and alpha-beta dehydrogenation.peptidyl-cysteine cyclase (EC 4.2.1.-)peptidyl-thiazoline dehydrogenase (EC 1.3.-.-)C, Icross-link 1PSI-MOD:01389oxazole/thiazole ringthioether bondCROSSLNK Thiazole-4-carboxylic acid (Ile-Cys)AA046724-Oct-200824-Oct-200830-Sep-2011L-valine thiazole-4-carboxylic acid2-[1-azanyl-2-methylpropyl]-1,3-thiazole-4-carboxylic acid2-[(1S)-1-amino-2-methylpropyl]-1,3-thiazole-4-carboxylic acidPDBHET:BB9C 8 H 10 N 2 O 1 S 1182.24182.051384C 0 H -4 N 0 O -1 S 0-20.03-20.026215Shoji, J.Kato, T.Yoshimura, Y.Tori, K.J. Antibiot. 34, 1126-1136, 1981Structural studies on thiocillins I, II and III (studies on antibiotics from the genus Bacillus XXIX).PMID:7328054Formed by the condensation of a cysteine thiol with the carbonyl of the preceding residue and alpha-beta dehydrogenation.peptidyl-cysteine cyclase (EC 4.2.1.-)peptidyl-thiazoline dehydrogenase (EC 1.3.-.-)C, Vcross-link 1PSI-MOD:01390oxazole/thiazole ringthioether bondCROSSLNK Thiazole-4-carboxylic acid (Val-Cys)AA046824-Oct-200830-Jan-200925-Feb-2011L-valine 5-(methoxymethyl)thiazole-4-carboxylic acid2-[1-azanyl-2-methylpropyl]-5-(methoxymethyl)-1,3-thiazole-4-carboxylic acid2-[(1S)-1-amino-2-methylpropyl]-5-(methoxymethyl)-1,3-thiazole-4-carboxylic acidC 10 H 14 N 2 O 2 S 1226.29226.077599C 2 H 0 N 0 O 0 S 024.0224.000000Kettenring, J.Colombo, L.Ferrari, P.Tavecchia, P.Nebuloni, M.Vekey, K.Gallo, G.G.Selva, E.J. Antibiot. 44, 702-715, 1991Antibiotic GE2270 A: a novel inhibitor of bacterial protein synthesis. II. Structure elucidation.PMID:1880060mass spectrometric, (1)H-NMR, (13)C-NMR, and IR identificationTavecchia, P.Gentili, P.Kurz, M.Sottani, C.Bonfichi, R.Lociuro, S.Selva, E.J. Antibiot. 47, 1564-1567, 1994Revised structure of the antibiotic GE 2270A.PMID:7844053Heffron, S.E.Jurnak, F.Biochemistry 39, 37-45, 2000Structure of an EF-Tu complex with a thiazolyl peptide antibiotic determined at 2.35 A resolution: atomic basis for GE2270A inhibition of EF-Tu.DOI:10.1021/bi9913597PMID:10625477Heffron, S.E.Jurnak, F.submitted to the Protein Data Bank, October 1999Crystal structure of elongation factor, Tu (EF-Tu-MGGDP) complexed with GE2270A, a thiazolyl peptide antibiotic.PDB:1D8TX-ray diffraction, 2.35 angstromsFormed by the condensation of a cysteine thiol with the carbonyl of the preceding residue and alpha-beta dehydrogenation.peptidyl-cysteine cyclase (EC 4.2.1.-)peptidyl-thiazoline dehydrogenase (EC 1.3.-.-)C, Vcross-link 1PSI-MOD:01391methylated amino acidoxazole/thiazole ringthioether bondCROSSLNK 5-(methoxymethyl)thiazole-4-carboxylic acid (Val-Cys)AA046924-Oct-200824-Oct-200825-Feb-2011L-asparagine 5-methylthiazole-4-carboxylic acid2-[(1S)-1,3-bisazanyl-3-oxopropyl]-5-methyl-1,3-thiazole-4-carboxylic acid2-[(1S)-1,3-diamino-3-oxopropyl]-5-methyl-1,3-thiazole-4-carboxylic acidC 8 H 9 N 3 O 2 S 1211.24211.041548C 1 H -2 N 0 O -1 S 0-6.00-6.010565Kettenring, J.Colombo, L.Ferrari, P.Tavecchia, P.Nebuloni, M.Vekey, K.Gallo, G.G.Selva, E.J. Antibiot. 44, 702-715, 1991Antibiotic GE2270 A: a novel inhibitor of bacterial protein synthesis. II. Structure elucidation.PMID:1880060mass spectrometric, (1)H-NMR, (13)C-NMR, and IR identificationTavecchia, P.Gentili, P.Kurz, M.Sottani, C.Bonfichi, R.Lociuro, S.Selva, E.J. Antibiot. 47, 1564-1567, 1994Revised structure of the antibiotic GE 2270A.PMID:7844053Heffron, S.E.Jurnak, F.Biochemistry 39, 37-45, 2000Structure of an EF-Tu complex with a thiazolyl peptide antibiotic determined at 2.35 A resolution: atomic basis for GE2270A inhibition of EF-Tu.DOI:10.1021/bi9913597PMID:10625477Heffron, S.E.Jurnak, F.submitted to the Protein Data Bank, October 1999Crystal structure of elongation factor, Tu (EF-Tu-MGGDP) complexed with GE2270A, a thiazolyl peptide antibiotic.PDB:1D8TX-ray diffraction, 2.35 angstromsFormed by the condensation of a cysteine thiol with the carbonyl of the preceding residue and alpha-beta dehydrogenation.peptidyl-cysteine cyclase (EC 4.2.1.-)peptidyl-thiazoline dehydrogenase (EC 1.3.-.-)C, Ncross-link 1PSI-MOD:01392methylated amino acidoxazole/thiazole ringthioether bondCROSSLNK 5-methylthiazole-4-carboxylic acid (Asn-Cys)AA047024-Oct-200824-Oct-200829-Nov-2010L-cysteine pyridine-2,5-dicarboxylic acid6-[(1R)-1-amino-2-sulfanylethyl]pyridine-2,5-dicarboxylic acidPDBHET:GEAC 9 H 7 N 2 O 2 S 1207.23207.022823C 0 H -8 N -1 O -3 S 0-70.07-70.050418Kettenring, J.Colombo, L.Ferrari, P.Tavecchia, P.Nebuloni, M.Vekey, K.Gallo, G.G.Selva, E.J. Antibiot. 44, 702-715, 1991Antibiotic GE2270 A: a novel inhibitor of bacterial protein synthesis. II. Structure elucidation.PMID:1880060mass spectrometric, (1)H-NMR, (13)C-NMR, and IR identificationTavecchia, P.Gentili, P.Kurz, M.Sottani, C.Bonfichi, R.Lociuro, S.Selva, E.J. Antibiot. 47, 1564-1567, 1994Revised structure of the antibiotic GE 2270A.PMID:7844053Heffron, S.E.Jurnak, F.Biochemistry 39, 37-45, 2000Structure of an EF-Tu complex with a thiazolyl peptide antibiotic determined at 2.35 A resolution: atomic basis for GE2270A inhibition of EF-Tu.DOI:10.1021/bi9913597PMID:10625477Heffron, S.E.Jurnak, F.submitted to the Protein Data Bank, October 1999Crystal structure of elongation factor, Tu (EF-Tu-MGGDP) complexed with GE2270A, a thiazolyl peptide antibiotic.PDB:1D8TX-ray diffraction, 2.35 angstromsFormed by the metathesis of two didehydroalanines made from serines, condensation with a cysteine carbonyl and dehydrogenation.This modification is currently represented in the PDB as part of the HET group for the entire molecule of antibiotic GE2270 A.C, S, Scross-link 3incidental to RESID:AA0244PSI-MOD:01393pyridine ringCROSSLNK Pyridine-2,5-dicarboxylic acid (Ser-Ser) (with C-...)CROSSLNK Pyridine-2,5-dicarboxylic acid (Ser-Cys) (with S-...)AA047124-Oct-200824-Oct-200830-Jun-2009L-cysteine 5-amino-3,4,5,6-tetrahydropyridine-2,5-dicarboxylic acidL-cysteine 5-aminopiperideine-2,5-dicarboxylic acid(5R,6R)-5-amino-6-[(1R)-1-amino-2-sulfanylethyl]-3,4,5,6-tetrahydropyridine-2,5-dicarboxylic acidPDBHET:XBBC 9 H 11 N 3 O 2 S 1225.27225.057198C 0 H -5 N 0 O -3 S 0-53.04-53.023869Bond, C.S.Shaw, M.P.Alphey, M.S.Hunter, W.N.Acta Crystallogr. D Biol. Crystallogr. 57, 755-758, 2001Structure of the macrocycle thiostrepton solved using the anomalous dispersion contribution of sulfur.DOI:10.1107/S0907444901003134PMID:11320328Bond, C.S.Shaw, M.P.Alphey, M.S.Hunter, W.N.submitted to the Protein Data Bank, October 2000Structure of the macrocycle thiostrepton solved using the anomalous dispersion contribution of sulfur.PDB:1E9WX-ray diffraction, 1.02 angstromsFormed by the metathesis of two didehydroalanines made from serines, condensation with a cysteine carbonyl and dehydrogenation.C, S, Scross-link 3amino-terminalincidental to RESID:AA0244PSI-MOD:01394blocked amino endpyridine ringCROSSLNK 5-amino-piperideine-2,5-dicarboxylic acid (Ser-Cys) (with S-...)CROSSLNK 5-amino-piperideine-2,5-dicarboxylic acid (Ser-Ser) (with C-...)AA047224-Oct-200824-Oct-200828-Oct-20114-(1-hydroxyethyl)-7-isoleucino-2-(threonin-O3-ylcarbonyl)-7,8-dihydroquinolin-8-ol(7R,8S)-7-[(1S,2S)-1-carboxy-2-methylbutyl]amino-2-([(1S,2R)-1-amino-1-carboxypropan-2-yl]oxy)carbonyl-8-hydroxy-4-[(1S)-1-hydroxyethyl]-7,8-dihydroquinolinePDBHET:QUAC 22 H 28 N 3 O 6430.48430.197811C 12 H 9 N 1 O 3215.21215.058243Bond, C.S.Shaw, M.P.Alphey, M.S.Hunter, W.N.Acta Crystallogr. D Biol. Crystallogr. 57, 755-758, 2001Structure of the macrocycle thiostrepton solved using the anomalous dispersion contribution of sulfur.DOI:10.1107/S0907444901003134PMID:11320328Bond, C.S.Shaw, M.P.Alphey, M.S.Hunter, W.N.submitted to the Protein Data Bank, October 2000Structure of the macrocycle thiostrepton solved using the anomalous dispersion contribution of sulfur.PDB:1E9WX-ray diffraction, 1.02 angstromsI, Tamino-terminalcross-link 2PSI-MOD:01395blocked amino endBINDING 4-(1-hydroxyethyl)-7,8-dihydroquinolin-8-ol (covalent; via 2 links)AA047305-Dec-200805-Dec-200828-Oct-20115-hydroxy-3-methyl-L-proline5-hydroxy-3-methylprolinebeta-methyl-delta-hydroxyproline(2S,3S,5Xi)-5-hydroxy-3-methylpyrrolidine-2-carboxylic acidC 6 H 9 N 1 O 2127.14127.063329C 0 H -2 N 0 O 113.9813.979265Stella, S.Montanini, N.Le Monnier, F.Ferrari, P.Colombo, L.Marinelli, F.Landini, P.Ciciliato, I.Goldstein, B.P.Selva, E.J. Antibiot. 48, 780-786, 1995Antibiotic GE37468 A: a new inhibitor of bacterial protein synthesis. I. Isolation and characterization.PMID:7592021Ferrari, P.Colombo, L.Stella, S.Selva, E.Zerilli, L.F.J. Antibiot. 48, 1304-1311, 1995Antibiotic GE37468 A: a novel inhibitor of bacterial protein synthesis. II. Structure elucidation.PMID:8557573mass spectrometric, (1)H-NMR and (13)C-NMR analysis; chemical characterizationYoung, T.S.Walsh, C.T.Proc. Natl. Acad. Sci. U.S.A. 108, 13053-13058, 2011Identification of the thiazolyl peptide GE37468 gene cluster from Streptomyces ATCC 55365 and heterologous expression in Streptomyces lividans.DOI:10.1073/pnas.1110435108PMID:21788474gene sequence for the encoded peptide; mass spectrometric identification, isotope labeling and (1)H-NMR identification; biosynthesisThe stereochemistry at C3 and C5 has not been resolved, but (3S) can be assumed by derivation from L-isoleucine. The (3S,5S) form is shown.LPSI-MOD:01897hydroxylationMOD_RES 5-hydroxy-3-methylproline (Ile)AA047405-Dec-200805-Dec-200825-Feb-2011L-serine 5-methyloxazole-4-carboxylic acid2-[1-azanyl-2-hydroxyethyl]-5-methyl-1,3-oxazole-4-carboxylic acid2-[(1S)-1-amino-2-hydroxyethyl]-5-methyl-1,3-oxazole-4-carboxylic acidC 7 H 8 N 2 O 3168.15168.053492C 0 H -4 N 0 O -1-20.03-20.026215Stella, S.Montanini, N.Le Monnier, F.Ferrari, P.Colombo, L.Marinelli, F.Landini, P.Ciciliato, I.Goldstein, B.P.Selva, E.J. Antibiot. 48, 780-786, 1995Antibiotic GE37468 A: a new inhibitor of bacterial protein synthesis. I. Isolation and characterization.PMID:7592021Ferrari, P.Colombo, L.Stella, S.Selva, E.Zerilli, L.F.J. Antibiot. 48, 1304-1311, 1995Antibiotic GE37468 A: a novel inhibitor of bacterial protein synthesis. II. Structure elucidation.PMID:8557573mass spectrometric, (1)H-NMR and (13)C-NMR analysis; chemical characterizationFormed by the condensation of a threonine hydroxyl with the carbonyl of the preceding residue and alpha-beta dehydrogenation.peptidyl-threonine cyclase (EC 4.2.1.-)peptidyl-oxazoline dehydrogenase (EC 1.3.-.-)S, Tcross-link 1PSI-MOD:01397oxazole/thiazole ringCROSSLNK 5-methyloxazole-4-carboxylic acid (Ser-Thr)AA047505-Dec-200805-Dec-200831-Dec-2011N6-propanoyl-L-lysine2-amino-6-propionylaminocaproic acidepsilon-propanoyl-L-lysineepsilon-propionyl-L-lysineN(zeta)-propanoyllysineN6-(1-oxopropyl)-L-lysineN6-propionyllysine(2S)-2-amino-6-(propanoylamino)hexanoic acidCAS:1974-17-0PDBHET:PRKC 9 H 16 N 2 O 2184.24184.121178C 3 H 4 N 0 O 156.0656.026215Kawai, Y.Fujii, H.Okada, M.Tsuchie, Y.Uchida, K.Osawa, T.J. Lipid Res. 47, 1386-1398, 2006Formation of Nepsilon-(succinyl)lysine in vivo: a novel marker for docosahexaenoic acid-derived protein modification.DOI:10.1194/jlr.M600091-JLR200PMID:16582421chromatographic detection; mass spectrometric identification; a major product after radical-catalyzed peroxidation of docosahexaenoic acidChen, Y.Sprung, R.Tang, Y.Ball, H.Sangras, B.Kim, S.C.Falck, J.R.Peng, J.Gu, W.Zhao, Y.Mol. Cell. Proteomics 6, 812-819, 2007Lysine propionylation and butyrylation are novel post-translational modifications in histones.DOI:10.1074/mcp.M700021-MCP200PMID:17267393the modification is not chemically characterized and isobaric alternatives are not eliminatedGarrity, J.Gardner, J.G.Hawse, W.Wolberger, C.Escalante-Semerena, J.C.J. Biol. Chem. 282, 30239-30245, 2007N-lysine propionylation controls the activity of propionyl-CoA synthetase.DOI:10.1074/jbc.M704409200PMID:17684016Vollmuth, F.Geyer, M.Angew. Chem. Int. Ed. Engl. 49, 6768-6772, 2010Interaction of propionylated and butyrylated histone H3 lysine marks with Brd4 bromodomains.DOI:10.1002/anie.201002724PMID:20715035X-ray diffraction, 1.75 angstroms; iosthermal titration calorimetry; binding of propanoylated lysine histone peptide is found to be unspecific and weaker than for the corresponding acetylated peptideVollmuth, V.Geyer, M.submitted to the Protein Data Bank, May 2010Crystal structure of Brd4 bromodomain 1 with propionylated histone H3-K(buty)14.PDB:3MUKX-ray diffraction, 1.75 angstromsBheda, P.Wang, J.T.Escalante-Semerena, J.C.Wolberger, C.Protein Sci. 20, 131-139, 2011Structure of Sir2Tm bound to a propionylated peptide.DOI:10.1002/pro.544PMID:21080423X-ray diffraction, 1.8 angstroms; artificial peptide complexed with protein that naturally binds N6-acetyllysineWolberger, C.Bheda, P.submitted to the Protein Data Bank, October 2010Structure of Sir2Tm bound to a propionylated peptide.PDB:3PDHX-ray diffraction, 1.80 angstromsA metabolic source for propanoic acid in the nucleus is not evident; the modification would be isobaric with lactaldehyde adduct, an advanced glycation end product of artifactual nucleic acid degradationThis modification has been shown to be produced by Gcn-5-related N-acetyltransferases in some bacterial systems.In eukaryotes, a metabolic source for propanoic acid in the nucleus is not evident, and a responsible generating enzyme activity is not identified.lysine N6-acyltransferase, acetoin utilization protein AcuA (EC 2.3.1.-)KPSI-MOD:01398lipoproteinNot availablethis modification is not annotated in UniProt featuresAA047605-Dec-200805-Dec-200830-Jun-2009N6-(ADP-ribosyl)-L-lysine2-amino-6-(ADP-ribosyl)amino-hexanoic acidepsilon-ADP-ribosyllysineN(zeta)-ADP-ribosyllysineN6-alpha-D-ribofuranosyl-L-lysine 5'->5'-ester with adenosine 5'-(trihydrogen diphosphate)N6-[alpha-D-ribofuranoside 5'->5'-ester with adenosine 5'-(trihydrogen diphosphate)]-L-lysine(S)-2-amino-6-([adenosine 5'-(trihydrogen diphosphate) 5'->5'-ester with alpha-D-ribofuranosyl]amino)hexanoic acidC 21 H 33 N 7 O 14 P 2669.48669.156072C 15 H 21 N 5 O 13 P 2541.30541.061109Haenni, S.S.Hassa, P.O.Altmeyer, M.Fey, M.Imhof, R.Hottiger, M.O.Int. J. Biochem. Cell Biol. 40, 2274-2283, 2008Identification of lysines 36 and 37 of PARP-2 as targets for acetylation and auto-ADP-ribosylation.DOI:10.1016/j.biocel.2008.03.008PMID:18436469The alpha form is presented.The keyword "phosphoprotein" is not used with ADP-ribosylation.NAD(P)+--lysine ADP-ribosyltransferase (EC 2.4.2.-)KPSI-MOD:01399*phosphoproteinMOD_RES N6-(ADP-ribosyl)lysineAA047705-Dec-200805-Dec-200830-Jan-2009L-lysyl-poly(ADP-ribose)poly[2'-adenosine 5'-(trihydrogen diphosphate) 5'->5'-ester with 1alpha-D-ribofuranosyl] (2S)-2,6-diaminohexanoateCAS:26656-46-2C 21 H 34 N 7 O 15 P 2 +686.48 +686.158812 +C 15 H 21 N 5 O 13 P 2 +541.30 +541.061109 +Ogata, N.Ueda, K.Kagamiyama, H.Hayaishi, O.J. Biol. Chem. 255, 7616-7620, 1980ADP-ribosylation of histone H1. Identification of glutamic acid residues 2, 14, and the COOH-terminal lysine residue as modification sites.PMID:6772638The alpha form is presented.The keyword "phosphoprotein" is not used with ADP-ribosylation.NAD+ ADP-ribosyltransferase (EC 2.4.2.30)Kcarboxyl-terminalPSI-MOD:01400*phosphoproteinblocked carboxyl endpoly adenosine diphosphate riboseMOD_RES Lysyl poly(ADP-ribose)AA047831-Dec-200831-Dec-200831-May-2018(2S,3S)-3-hydroxyasparagine(2S,3S)-2,4-diamino-3-hydroxy-4-oxobutanoic acid(3S)-3-hydroxy-L-asparagineL-threo-beta-hydroxyasparagine(2S,3S)-2-amino-3-hydroxy-4-butanediamic acidChEBI:138107PDBHET:AHBC 4 H 6 N 2 O 3130.10130.037842C 0 H 0 N 0 O 116.0015.994915Lando, D.Peet, D.J.Whelan, D.A.Gorman, J.J.Whitelaw, M.L.Science 295, 858-861, 2002Asparagine hydroxylation of the HIF transactivation domain a hypoxic switch.DOI:10.1126/science.1068592PMID:11823643mass spectrometric detection; located in the C-terminal transactivation domain; the stereochemistry was not determinedHewitson, K.S.McNeill, L.A.Riordan, M.V.Tian, Y.M.Bullock, A.N.Welford, R.W.Elkins, J.M.Oldham, N.J.Bhattacharya, S.Gleadle, J.M.Ratcliffe, P.J.Pugh, C.W.Schofield, C.J.J. Biol. Chem. 277, 26351-26355, 2002Hypoxia-inducible factor (HIF) asparagine hydroxylase is identical to factor inhibiting HIF (FIH) and is related to the cupin structural family.DOI:10.1074/jbc.C200273200PMID:12042299characterization of the enzyme producing the modificationMcNeill, L.A.Hewitson, K.S.Claridge, T.D.Seibel, J.F.Horsfall, L.E.Schofield, C.J.Biochem. J. 367, 571-575, 2002Hypoxia-inducible factor asparaginyl hydroxylase (FIH-1) catalyses hydroxylation at the beta-carbon of asparagine-803.DOI:10.1042/BJ20021162PMID:12215170the modification is identified as the (2S,3S), threo, diastereomer Coleman, M.L.McDonough, M.A.Hewitson, K.S.Coles, C.Mecinovic, J.Edelmann, M.Cook, K.M.Cockman, M.E.Lancaster, D.E.Kessler, B.M.Oldham, N.J.Ratcliffe, P.J.Schofield, C.J.J. Biol. Chem. 282, 24027-24038, 2007Asparaginyl hydroxylation of the Notch ankyrin repeat domain by factor inhibiting hypoxia-inducible factor.DOI:10.1074/jbc.M704102200PMID:17573339mass spectrometric detection; X-ray diffraction, 2.35 angstroms; located in the ankyrin repeat domains of notch 1McDonough, M.A.Schofield, C.J.submitted to the Protein Data Bank, June 2007Mouse notch 1 ankyrin repeat intracellular domain.PDB:2QC9X-ray diffraction, 2.35 angstromsThis diastereomeric form has been found in the C-terminal transactivation domain (CAD) of hypoxia-inducible factor (HIF), and in the ankyrin repeat domains of notch 1, which probably also contains the other diastereomeric form of the modification in its EGF domains.The PDB group code includes models with both the (2S,3R) and the (2S,3S) stereoconfiguration.hypoxia-inducible factor-asparagine dioxygenase (EC 1.14.11.30)NPSI-MOD:01401hydroxylationMOD_RES (3S)-3-hydroxyasparagineAA047931-Dec-200831-Dec-200831-Mar-2009(2S,3R,4R)-3,4-dihydroxyproline2,3-trans-3,4-trans-3,4-dihydroxy-L-proline2-alpha-3-beta-4-alpha-3,4-dihydroxyproline(2S,3R,4R)-3,4-dihydroxypyrrolidine-2-carboxylic acidCAS:74644-88-5C 5 H 7 N 1 O 3129.12129.042593C 0 H 0 N 0 O 232.0031.989829Faulstich, H.Buku, A.Bodenmüller, H.Wieland, T.Biochemistry 19, 3334-3343, 1980Virotoxins: actin-binding cyclic peptides of Amanita virosa mushrooms.DOI:10.1021/bi00555a036PMID:6893271Buku, A.Faulstich, H.Wieland, T.Dabrowski, J.Proc. Natl. Acad. Sci. U.S.A. 77, 2370-2371, 19802,3-trans-3,4-trans-3,4-Dihydroxy-L-proline: An amino acid in toxic peptides of Amanita virosa mushrooms.DOI:10.1073/pnas.77.5.2370PMID:16592813chemical characteriztion, stereochemistry, (1)H-NMR identificationPPSI-MOD:01402hydroxylationMOD_RES (3R,4R)-3,4-dihydroxyprolineAA048031-Dec-200831-Dec-200830-Jan-2009(2S)-4,5,5'-trihydroxyleucine4,5,5'-trihydroxyleucinegamma,delta,delta'-trihydroxyleucine(2S)-2-amino-4,5-dihydroxy-4-(hydroxymethyl)pentanoic acidC 6 H 11 N 1 O 4161.16161.068808C 0 H 0 N 0 O 348.0047.984744Faulstich, H.Buku, A.Bodenmüller, H.Wieland, T.Biochemistry 19, 3334-3343, 1980Virotoxins: actin-binding cyclic peptides of Amanita virosa mushrooms.DOI:10.1021/bi00555a036PMID:6893271LPSI-MOD:01403hydroxylationMOD_RES 4,5,4'-trihydroxyleucineAA048130-Jan-200930-Jan-200925-Feb-2011L-asparagine thiazole-4-carboxylic acid2-[1,3-bisazanyl-3-oxopropyl]-1,3-thiazole-4-carboxylic acid2-[(1S)-1,3-diamino-3-oxopropyl]-1,3-thiazole-4-carboxylic acidC 7 H 7 N 3 O 2 S 1197.21197.025897C 0 H -4 N 0 O -1 S 0-20.03-20.026215Stella, S.Montanini, N.Le Monnier, F.Ferrari, P.Colombo, L.Marinelli, F.Landini, P.Ciciliato, I.Goldstein, B.P.Selva, E.J. Antibiot. 48, 780-786, 1995Antibiotic GE37468 A: a new inhibitor of bacterial protein synthesis. I. Isolation and characterization.PMID:7592021Ferrari, P.Colombo, L.Stella, S.Selva, E.Zerilli, L.F.J. Antibiot. 48, 1304-1311, 1995Antibiotic GE37468 A: a novel inhibitor of bacterial protein synthesis. II. Structure elucidation.PMID:8557573mass spectrometric, (1)H-NMR and (13)C-NMR analysis; chemical characterizationFormed by the condensation of a cysteine thiol with the carbonyl of the preceding residue and alpha-beta dehydrogenation.peptidyl-cysteine cyclase (EC 4.2.1.-)peptidyl-thiazoline dehydrogenase (EC 1.3.-.-)C, Ncross-link 1PSI-MOD:01404oxazole/thiazole ringthioether bondCROSSLNK Thiazole-4-carboxylic acid (Asn-Cys)AA048230-Jan-200930-Jan-200929-Nov-2010L-proline thiazole-4-carboxylic acid2-[(2S)-pyrrolidin-2-yl]-1,3-thiazole-4-carboxylic acidC 8 H 8 N 2 O 1 S 1180.22180.035734C 0 H -4 N 0 O -1 S 0-20.03-20.026215Stella, S.Montanini, N.Le Monnier, F.Ferrari, P.Colombo, L.Marinelli, F.Landini, P.Ciciliato, I.Goldstein, B.P.Selva, E.J. Antibiot. 48, 780-786, 1995Antibiotic GE37468 A: a new inhibitor of bacterial protein synthesis. I. Isolation and characterization.PMID:7592021Ferrari, P.Colombo, L.Stella, S.Selva, E.Zerilli, L.F.J. Antibiot. 48, 1304-1311, 1995Antibiotic GE37468 A: a novel inhibitor of bacterial protein synthesis. II. Structure elucidation.PMID:8557573mass spectrometric, (1)H-NMR and (13)C-NMR analysis; chemical characterizationFormed by the condensation of a cysteine thiol with the carbonyl of the preceding residue and alpha-beta dehydrogenation.peptidyl-cysteine cyclase (EC 4.2.1.-)peptidyl-thiazoline dehydrogenase (EC 1.3.-.-)C, Pcross-link 1PSI-MOD:01405oxazole/thiazole ringthioether bondCROSSLNK Thiazole-4-carboxylic acid (Pro-Cys)AA048330-Jan-200930-Jan-200931-Dec-2011L-threonine thiazole-4-carboxylic acid2-[1-azanyl-2-hydroxypropyl]-1,3-thiazole-4-carboxylic acid2-[(1S,2R)-1-amino-2-hydroxypropyl]-1,3-thiazole-4-carboxylic acidPDBHET:XAAC 7 H 8 N 2 O 2 S 1184.21184.030649C 0 H -4 N 0 O -1 S 0-20.03-20.026215Bond, C.S.Shaw, M.P.Alphey, M.S.Hunter, W.N.Acta Crystallogr. D Biol. Crystallogr. 57, 755-758, 2001Structure of the macrocycle thiostrepton solved using the anomalous dispersion contribution of sulfur.DOI:10.1107/S0907444901003134PMID:11320328Bond, C.S.Shaw, M.P.Alphey, M.S.Hunter, W.N.submitted to the Protein Data Bank, October 2000Structure of the macrocycle thiostrepton solved using the anomalous dispersion contribution of sulfur.PDB:1E9WX-ray diffraction, 1.02 angstromsKalyon, B.Helaly, S.E.Scholz, R.Nachtigall, J.Vater, J.Borriss, R.Süssmuth, R.D.Org. Lett. 13, 2996-2999, 2011Plantazolicin A and B: Structure Elucidation of Ribosomally Synthesized Thiazole/Oxazole Peptides from Bacillus amyloliquefaciens FZB42.DOI:10.1021/ol200809mPMID:21568297mass spectrometric, (1)H-NMR, (13)C-NMR and (15)N-NMR identificationMolohon, K.J.Melby, J.O.Lee, J.Evans, B.S.Dunbar, K.L.Bumpus, S.B.Kelleher, N.L.Mitchell, D.A.ACS Chem. Biol. 6, 1307-1313, 2011Structure determination and interception of biosynthetic intermediates for the plantazolicin class of highly discriminating antibiotics.DOI:10.1021/cb200339dPMID:21950656mass spectrometric, (1)H-NMR and (13)C-NMR identificationFormed by the condensation of a cysteine thiol with the carbonyl of the preceding residue and alpha-beta dehydrogenation.peptidyl-cysteine cyclase (EC 4.2.1.-)peptidyl-thiazoline dehydrogenase (EC 1.3.-.-)C, Tcross-link 1PSI-MOD:01406oxazole/thiazole ringthioether bondCROSSLNK Thiazole-4-carboxylic acid (Thr-Cys)AA048430-Jan-200930-Jan-200925-Feb-2011L-phenylalanine thiazoline-4-carboxylic acid2-[1-azanyl-2-phenylethyl]-4,5-dihydro-1,3-thiazole-4-carboxylic acid(4R)-2-[(1S)-1-amino-2-phenylethyl]-4,5-dihydro-1,3-thiazole-4-carboxylic acidC 12 H 12 N 2 O 1 S 1232.30232.067034C 0 H -2 N 0 O -1 S 0-18.02-18.010565Stella, S.Montanini, N.Le Monnier, F.Ferrari, P.Colombo, L.Marinelli, F.Landini, P.Ciciliato, I.Goldstein, B.P.Selva, E.J. Antibiot. 48, 780-786, 1995Antibiotic GE37468 A: a new inhibitor of bacterial protein synthesis. I. Isolation and characterization.PMID:7592021Ferrari, P.Colombo, L.Stella, S.Selva, E.Zerilli, L.F.J. Antibiot. 48, 1304-1311, 1995Antibiotic GE37468 A: a novel inhibitor of bacterial protein synthesis. II. Structure elucidation.PMID:8557573mass spectrometric, (1)H-NMR and (13)C-NMR analysis; chemical characterizationFormed by the condensation of a cysteine thiol with the carbonyl of the preceding residue.peptidyl-cysteine cyclase (EC 4.2.1.-)C, Fcross-link 1PSI-MOD:01407oxazole/thiazole ringthioether bondCROSSLNK Thiazoline-4-carboxylic acid (Phe-Cys)AA048530-Jan-200912-Jun-200931-Dec-2013L-threonine (4S)-thiazoline-4-carboxylic acid2-[1-azanyl-2-hydroxypropyl]-4,5-dihydro-1,3-thiazole-4-carboxylic acid(4S)-2-[(1S,2R)-1-amino-2-hydroxypropyl]-4,5-dihydro-1,3-thiazole-4-carboxylic acidPDBHET:BB9C 7 H 10 N 2 O 2 S 1186.23186.046299C 0 H -2 N 0 O -1 S 0-18.02-18.010565Bond, C.S.Shaw, M.P.Alphey, M.S.Hunter, W.N.Acta Crystallogr. D Biol. Crystallogr. 57, 755-758, 2001Structure of the macrocycle thiostrepton solved using the anomalous dispersion contribution of sulfur.DOI:10.1107/S0907444901003134PMID:11320328Bond, C.S.Shaw, M.P.Alphey, M.S.Hunter, W.N.submitted to the Protein Data Bank, October 2000Structure of the macrocycle thiostrepton solved using the anomalous dispersion contribution of sulfur.PDB:1E9WX-ray diffraction, 1.02 angstromsFormed by the condensation of a cysteine thiol with the carbonyl of the preceding residue. The ring may be oxidized to thiazole and then reduced from the opposite side effectively inverting the cysteine alpha-carbon chirality.peptidyl-cysteine cyclase (EC 4.2.1.-)C, Tcross-link 1PSI-MOD:01408oxazole/thiazole ringthioether bondCROSSLNK (4S)-thiazoline-4-carboxylic acid (Thr-Cys)AA048631-Mar-200931-Mar-200931-Mar-20091-amino-2-propanone1-aminopropan-2-oneaminoacetone1-aminopropanoneCAS:298-08-8ChEBI:17906C 3 H 6 N 1 O 172.0972.044939C -1 H -2 N 0 O -2-46.03-46.005479Suzumura, K.Yokoi, T.Funatsu, M.Nagai, K.Tanaka, K.Zhang, H.Suzuki, K.J. Antibiot. 56, 129-134, 2003YM-266183 and YM-266184, novel thiopeptide antibiotics produced by Bacillus cereus isolated from a marine sponge II. Structure elucidation.PMID:12715872mass spectrometric, (1)H-NMR, and (13)C-NMR identificationWieland Brown, L.C.Acker, M.G.Clardy, J.Walsh, C.T.Fischbach, M.A.Proc. Natl. Acad. Sci. U.S.A. 106, 2549-2553, 2009Thirteen posttranslational modifications convert a 14-residue peptide into the antibiotic thiocillin.DOI:10.1073/pnas.0900008106PMID:19196969Tcarboxyl-terminalPSI-MOD:01433blocked carboxyl endMOD_RES 1-amino-2-propanoneAA048731-Mar-200931-Mar-200930-Sep-20114-hydroxy-L-glutamic acidgamma-hydroxy glutaminic acidthreo-4-hydroxy-L-glutamic acid(2S,4Xi)-2-amino-4-hydroxypentanedioic acidCAS:3913-68-6PDBHET:3GLC 5 H 7 N 1 O 4145.11145.037508C 0 H 0 N 0 O 116.0015.994915Pascard, C.Ducruix, A.Lunel, J.Prangé, T.J. Am. Chem. Soc. 99, 6418-6423, 1977Highly modified cysteine-containing antibiotics. Chemical structure and configuration of nosiheptide.DOI:10.1021/ja00461a039PMID:893891X-ray diffraction; the resolution is not specified; the structure deposited in the Cambridge Structural Database (NOSHEP10) is presented as (2S,4R)Harms, J.M.Wilson, D.N.Schluenzen, F.Connell, S.R.Stachelhaus, T.Zaborowska, Z.Spahn, C.M.Fucini, P.Mol. Cell 30, 26-38, 2008Translational regulation via L11: molecular switches on the ribosome turned on and off by thiostrepton and micrococcin.DOI:10.1016/j.molcel.2008.01.009PMID:18406324X-ray diffraction, 2.50 angstromsHarms, J.M.Wilson, D.N.Schluenzen, F.Connell, S.R.Stachelhaus, T.Zaborowska, Z.Spahn, C.M.Fucini, P.submitted to the Protein Data Bank, March 2008Thiopeptide antibiotic nosiheptide bound to the large ribosomal subunit of Deinococcus radiodurans.PDB:2ZJPX-ray diffraction, 3.70 angstroms; the structure is presented as (2S,4S)This modification is currently represented in the PDB as part of the HET group for the entire molecule of nosiheptide.The chirality of C-4 is not settled. The (2S,4S) diastereomer is shown.Eincidental to RESID:AA0488incidental to RESID:AA0541PSI-MOD:01434MOD_RES 4-hydroxyglutamateAA048831-Mar-200931-Mar-200930-Sep-20112-(cystein-S-ylcarbonyl)-3-methyl-4-(glutam-5-yloxy)methylindole2-(cystein-S-ylcarbonyl)-4-[(glutam-5-yloxy)methyl]-3-methyl-1H-indole2-([(1R)-1-amino-1-carboxyeth-2-yl]sulfanyl)carbonyl-3-methyl-4-([(1S)-1-amino-1-carboxy-4-oxobutan-4-yl]oxy)methyl-1H-indolePDBHET:NO1C 19 H 19 N 3 O 5 S 1401.44401.104542C 11 H 7 N 1 O 1 S 0169.18169.052764Pascard, C.Ducruix, A.Lunel, J.Prangé, T.J. Am. Chem. Soc. 99, 6418-6423, 1977Highly modified cysteine-containing antibiotics. Chemical structure and configuration of nosiheptide.DOI:10.1021/ja00461a039PMID:893891X-ray diffraction; the resolution is not specified; the structure is deposited in the Cambridge Structural Database entry NOSHEP10Harms, J.M.Wilson, D.N.Schluenzen, F.Connell, S.R.Stachelhaus, T.Zaborowska, Z.Spahn, C.M.Fucini, P.Mol. Cell 30, 26-38, 2008Translational regulation via L11: molecular switches on the ribosome turned on and off by thiostrepton and micrococcin.DOI:10.1016/j.molcel.2008.01.009PMID:18406324X-ray diffraction, 2.50 angstromsHarms, J.M.Wilson, D.N.Schluenzen, F.Connell, S.R.Stachelhaus, T.Zaborowska, Z.Spahn, C.M.Fucini, P.submitted to the Protein Data Bank, March 2008Thiopeptide antibiotic nosiheptide bound to the large ribosomal subunit of Deinococcus radiodurans.PDB:2ZJPX-ray diffraction, 3.70 angstromsYu, Y.Duan, L.Zhang, Q.Liao, R.Ding, Y.Pan, H.Wendt-Pienkowski, E.Tang, G.Shen, B.Liu, W.ACS Chem. Biol. 4, 855-864, 2009Nosiheptide biosynthesis featuring a unique indole side ring formation on the characteristic thiopeptide framework.DOI:10.1021/cb900133xPMID:19678698This modification is currently represented in the PDB as part of the HET group for the entire molecule of nosiheptide.C, Ecross-link 2incidental to RESID:AA0487incidental to RESID:AA0541PSI-MOD:01435BINDING 3-methyl-4-hydroxymethylindole-2-carboxylic acid (covalent; via 2 links)AA048931-Mar-200931-Mar-200924-Aug-2012cyclo[(prolylserin)-O-yl] cysteinate(3,6-dioxopyrrolo[4,5-a]piperazin-2-yl)methyl cysteinate[(3S,8aS)-1,4-dioxooctahydropyrrolo[1,2-a]pyrazin-3-yl]methyl (2R)-2-amino-3-sulfanylpropanoateC 11 H 16 N 3 O 4 S 1286.33286.086152C 8 H 10 N 2 O 2 S 0166.18166.074228C 0 H -2 N 0 O -1 S 0-18.02-18.010565Shimanaka, K.Takahashi, Y.Iinuma, H.Naganawa, H.Takeuchi, T.J. Antibiot. 47, 1153-1159, 1994Novel antibiotics, amythiamicins. III. Structure elucidations of amythiamicins A, B and C.PMID:7961166This diketopiperazine ester is formed by cyclization of the C-terminal seryl-proline dipeptide and transesterification to cysteine.Although it is constructed from three C-terminal amino acids, for simplicity it is represented in the UniProt feature as a modification of cysteine and not as a crosslink.Ccarboxyl-terminalPSI-MOD:01436C, P, Scarboxyl-terminalcross-link 3PSI-MOD:01437blocked carboxyl enddiketopiperazine ringMOD_RES Cyclo[(prolylserin)-O-yl] cysteinateAA049012-Jun-200912-Jun-200912-Jun-20093-(O4'-L-tyrosyl)-L-valine(2S)-2-amino-3-(4-[(2S)-2-amino-2-carboxyethyl]phenoxy)-3-methylbutanoic acidC 14 H 16 N 2 O 3260.29260.116092C 0 H -2 N 0 O 0-2.02-2.015650Andersson, C.S.Högbom, M.Proc. Natl. Acad. Sci. U.S.A. 106, 5633-5638, 2009A Mycobacterium tuberculosis ligand-binding Mn/Fe protein reveals a new cofactor in a remodeled R2-protein scaffold.DOI:10.1073/pnas.0812971106PMID:19321420X-ray diffraction, 1.90 angstromsAndersson, C.S.Jones, T.A.Hogbom, M.submitted to the Protein Data Bank, September 2008R2-like ligand binding Mn/Fe oxidase from M. tuberculosis.PDB:3EE4X-ray diffraction, 1.90 angstromsThis cross-link may be formed by a free-radical process during maturation of a metal cluster.V, Ycross-link 2incidental to RESID:AA0491PSI-MOD:01442CROSSLNK 3-(O4'-tyrosyl)-valine (Val-Tyr)AA049112-Jun-200912-Jun-200931-Dec-2009tetrakis-L-glutamato bis-L-N1'-histidino lipid carboxylato manganese iron oxideC 46 Fe 1 H 65 Mn 1 N 10 O 171-1140.861140.326447C 14 Fe 1 H 23 Mn 1 N 0 O 31-350.12350.038251Andersson, C.S.Högbom, M.Proc. Natl. Acad. Sci. U.S.A. 106, 5633-5638, 2009A Mycobacterium tuberculosis ligand-binding Mn/Fe protein reveals a new cofactor in a remodeled R2-protein scaffold.DOI:10.1073/pnas.0812971106PMID:19321420X-ray diffraction, 1.90 angstromsAndersson, C.S.Jones, T.A.Hogbom, M.submitted to the Protein Data Bank, September 2008R2-like ligand binding Mn/Fe oxidase from M. tuberculosis.PDB:3EE4X-ray diffraction, 1.90 angstromsIt is not clear whether the lipid carboxylate is a cofactor or a substrate, and its identity is not certain. It was modeled as myristic acid.E, E, E, E, H, Hcross-link 6incidental to RESID:AA0490PSI-MOD:01443ironlipoproteinmanganesemetalloproteinMETAL IronMETAL Iron; via pros nitrogenMETAL ManganeseMETAL Manganese; via pros nitrogenAA049212-Jun-200912-Jun-200930-Sep-20113,3-dihydroxy-L-alanine2-(dihydroxymethyl)glycine3,3-dihydroxyalanine3-hydroxy-L-serine3-oxoalanine hydrateC(alpha)-formylglycine hydrate [misnomer](S)-2-amino-3,3-dihydroxypropanoic acidPDBHET:DDZPDBHET:FGLC 3 H 5 N 1 O 3103.08103.026943C 0 H 0 N 0 O 2 S -1-0.060.017758C 0 H 0 N 0 O 116.0015.994915Jackson, W.G.McLaughlin, G.M.Sargeson, A.M.Watson, A.D.J. Am. Chem. Soc. 105, 2426-2430, 1983Synthesis, molecular structure and chemistry of p-[CoIII(tren)(2-(dihydroxymethyl)glycinato)]ZnCl4.2H2O.DOI:10.1021/ja00346a052chemical synthesisWaldow, A.Schmidt, B.Dierks, T.von Bülow, R.von Figura, K.J. Biol. Chem. 274, 12284-12288, 1999Amino acid residues forming the active site of arylsulfatase A. Role in catalytic activity and substrate binding.DOI:10.1074/jbc.274.18.12284PMID:10212197Boltes, I.Czapinska, H.Kahnert, A.von Bülow, R.Dierks, T.Schmidt, B.von Figura, K.Kertesz, M.A.Usón, I.Structure 9, 483-491, 20011.3 A structure of arylsulfatase from Pseudomonas aeruginosa establishes the catalytic mechanism of sulfate ester cleavage in the sulfatase family.DOI:10.1016/S0969-2126(01)00609-8PMID:11435113X-ray diffraction, 1.3 angstroms; the active site residue is shown as a gem-diol and referred to as a "formylglycine hydrate"Boltes, I.Czapinska, H.Kahnert, A.von Buelow, R.Dierks, T.Schmidt, B.von Figura, K.Kertesz, M.A.Uson, I.submitted to the Protein Data Bank, November 2000Arylsulfatase from Pseudomonas aeruginosa.PDB:1HDHX-ray diffraction, 1.3 angstroms; the depositors refer to the modified residue as "formylglycine hydrate", but it is incorrectly annotated as FGL, 2-aminopropanedioic acidGhosh, D.Cell. Mol. Life Sci. 64, 2013-2022, 2007Human sulfatases: a structural perspective to catalysis.DOI:10.1007/s00018-007-7175-yPMID:17558559review article discussing the functioning of the dihydroxymethyl group in the active siteThis active site residue is formed by the spontaneous hydration of the aldehyde, 2-amino-3oxopropanoic acid. See RESID:AA0185.The PDB hetgroup FGL was originally designated as the "C(alpha)-formyl glycine" active site residue L-3-oxoalanine observed in its hydrated form. That structure, a gem-diol with an sp(3) carbon, was misinterpreted as a carboxyl with an sp(2) carbon, and assigned to aminomalonic acid (see RESID:AA0458) instead. The hetgroup DDZ is being introduced for 3,3-dihydroxyalanine.sulfatase maturing enzyme (sulfatase modifying factor, C-alpha-formylglycine-generating enzyme) (EC 1.1.99.-)sulfatase maturing enzyme (sulfatase modifying factor, C-alpha-formylglycine-generating enzyme) (EC 1.8.99.-)CPSI-MOD:01444PSI-MOD:01448SPSI-MOD:01445PSI-MOD:01448Not availablethis modification is not currently annotated in UniProt featuresAA049312-Jun-200912-Jun-200930-Sep-2011N-(dihydroxymethyl)-L-methionineN-formyl-L-methionine hydrateN-orthoformylmethionine(2S)-2-[(dihydroxymethyl)amino]-4-(methylsulfanyl)butanoic acidPDBHET:CXMC 6 H 12 N 1 O 3 S 1178.23178.053789C 0 H 2 N 0 O 1 S 018.0218.010565C 1 H 2 N 0 O 2 S 046.0346.005479Prince, S.M.Papiz, M.Z.Freer, A.A.McDermott, G.Hawthornthwaite-Lawless, A.M.Cogdell, R.J.Isaacs, N.W.J. Mol. Biol. 268, 412-423, 1997Apoprotein structure in the LH2 complex from Rhodopseudomonas acidophila strain 10050: modular assembly and protein pigment interactions.DOI:10.1006/jmbi.1997.0966PMID:9159480X-ray diffraction, 2.50 angstroms; an N-formyl carbonyl group axially ligates the magnesium ion of bacteriochlorophyll a in light-harvesting protein B-800/850 alpha chainCogdell, R.J.Freer, A.A.Isaacs, N.W.Hawthornthwaite-Lawless, A.M.McDermott, G.Papiz, M.Z.Prince, S.M.submitted to the Protein Data Bank, August 1996Integral membrane peripheral light harvesting complex from Rhodopseudomonas acidophila strain 10050.PDB:1KZUX-ray diffraction, 2.50 angstromsPapiz, M.Z.Prince, S.M.Howard, T.Cogdell, R.J.Isaacs, N.W.J. Mol. Biol. 326, 1523-1538, 2003The structure and thermal motion of the B800-850 LH2 complex from Rps. acidophila at 2.0 angstroms resolution and 100 K: new structural features and functionally relevant motions.DOI:10.1016/S0022-2836(03)00024-XPMID:12595263X-ray diffraction, 2.0 angstroms; the formyl group ligand is remodeled with two oxygens as a carboxyl group, but appears to be tetrahedral rather than trigonal planarPapiz, M.Z.Prince, S.M.Howard, T.Cogdell, R.J.Isaacs, N.W.submitted to the Protein Data Bank, January 2003Crystal structure of LH2 B800-850 from Rps. acidophila at 2.0 Angstrom resolution.PDB:1NKZX-ray diffraction, 2.00 angstromsDemirci, H.Larsen, L.H.Hansen, T.Rasmussen, A.Cadambi, A.Gregory, S.T.Kirpekar, F.Jogl, G.RNA 16, 1584-1596, 2010Multi-site-specific 16S rRNA methyltransferase RsmF from Thermus thermophilus.DOI:10.1261/rna.2088310PMID:20558545X-ray diffraction, 1.68 angstroms; the N-formylmethionine group observed with extra density is interpreted as N-(dihydroxymethyl)-L-methionineDemirci, H.Larsen, L.H.Hansen, T.Rasmussen, A.Cadambi, A.Gregory, S.T.Kirpekar, F.Jogl, G.submitted to the Protein Data Bank, March 2010Multi-site-specific 16S rRNA methyltransferase RsmF from Thermus thermophilus in space group P21212.PDB:3M6XX-ray diffraction, 1.68 angstromsThe formyl group of N-formylmethionine, as an aldehyde, may undergo spontaneous addition of water to form a dihydoxymethyl group. It is detectable by mass spectrometry and other methods.Although appropriate, the keyword "thioether bond" normally does not appear for this amino acid.methionine--tRNA ligase (EC 6.1.1.10)methionyl-tRNA formyltransferase (EC 2.1.2.9)Mamino-terminalPSI-MOD:01446Mamino-terminalPSI-MOD:01447*thioether bondblocked amino endformylationpretranslational modificationNot availablethis modification is not currently annotated in UniProt featuresAA049430-Jun-200930-Jun-200931-Mar-2010N-(DNA-1',2'-dideoxyribos-1'-ylidene)-L-proliniumDNA glycosylase proline Schiff base intermediate [misnomer](1Z,2S)-2-carboxy-1-[(3R,4R)-3,4-dihydroxy-5-(phosphonooxy)pentylidene]pyrrolidiniumPDBHET:PEDC 10 H 16 N 1 O 6 P 1 +1+277.21 +277.070975 +C 5 H 8 N 0 O 5 P 1 +1+179.09 +179.010386 +Zharkov, D.O.Rieger, R.A.Iden, C.R.Grollman, A.P.J. Biol. Chem. 272, 5335-5341, 1997NH2-terminal proline acts as a nucleophile in the glycosylase/AP-lyase reaction catalyzed by Escherichia coli formamidopyrimidine-DNA glycosylase (Fpg) protein.DOI:10.1074/jbc.272.8.5335PMID:9030608chemical identification and characterizationRieger, R.A.McTigue, M.M.Kycia, J.H.Gerchman, S.E.Grollman, A.P.Iden, C.R.J. Am. Soc. Mass Spectrom. 11, 505-515, 2000Characterization of a cross-linked DNA-endonuclease VIII repair complex by electrospray ionization mass spectrometry.DOI:10.1016/S1044-0305(00)00117-3PMID:10833024mass spectrometric detection and linkage analysisZharkov, D.O.Golan, G.Gilboa, R.Fernandes, A.S.Gerchman, S.E.Kycia, J.H.Rieger, R.A.Grollman, A.P.Shoham, G.EMBO J. 21, 789-800, 2002Structural analysis of an Escherichia coli endonuclease VIII covalent reaction intermediate.DOI:10.1093/emboj/21.4.789PMID:11847126X-ray diffraction, 1.25 angstromsGolan, G.Zharkov, D.O.Gilboa, R.Fernandes, A.S.Kycia, J.H.Gerchman, S.E.Rieger, R.A.Grollman, A.P.Shoham, G.submitted to the Protein Data Bank, October 2001Crystal structure of a trapped reaction intermediate of the DNA repair enzyme endonuclease VIII with DNA.PDB:1KZUX-ray diffraction, 1.42 angstromsThe modification is frequently referred to as a "Schiff base". As an iminium bonded to three carbons, this is not a Schiff base, defined in the IUPAC Compendium of Chemical Terminology, 2nd ed. ("the Gold Book", http://goldbook.iupac.org/index.html) as an imine (uncharged, double bonded nitrogen) bonded to two carbons. Chemically it is not a "base" because it cannot act as either a proton acceptor (a "Brønsted-Lowry base") or as an electron pair donor (a "Lewis base").The model has three open valences, one on the proline carboxyl group and two in the DNA nucleotide segment on the 5'-phosphate and the 3'-hydroxyl.The keyword "phosphoprotein" is not used with polynucleotide-linked intermediate modifications.formamidopyrimidine-DNA glycosylase (EC 3.2.2.23)Pamino-terminalPSI-MOD:01454*phosphoproteinblocked amino endACT_SITE Schiff-base intermediate with DNAthis UniProt feature has a structural misrepresentationAA049528-Aug-200928-Aug-200930-Sep-2010O-(glycyl)-L-serineO3-(aminoacetyl)serineserine glycinate ester(2S)-2-amino-3-[(aminoacetyl)oxy]propanoic acidC 5 H 7 N 2 O 3143.12143.045667C 0 H -2 N 0 O -1-18.02-18.010565Wang, X.Herr, R.A.Chua, W.J.Lybarger, L.Wiertz, E.J.Hansen, T.H.J. Cell Biol. 177, 613-624, 2007Ubiquitination of serine, threonine, or lysine residues on the cytoplasmic tail can induce ERAD of MHC-I by viral E3 ligase mK3.DOI:10.1083/jcb.200611063PMID:17502423chemical and directed mutation analysisThese are ester cross-links formed between internal serine residues and the carboxyl end of ubiquitin and other proteins.G, Scarboxyl-terminalcross-link 2PSI-MOD:01585blocked carboxyl endCROSSLNK Glycyl serine ester (Ser-Gly) (interchain with G-Cter ...)AA049628-Aug-200928-Aug-200930-Sep-2010O-(glycyl)-L-threonineO3-(2-aminoacetyl)threoninethreonine glycinate ester(2S,3R)-2-amino-3-[(aminoacetyl)oxy]butanoic acidC 6 H 9 N 2 O 3157.15157.061317C 0 H -2 N 0 O -1 S 0-18.02-18.010565Wang, X.Herr, R.A.Chua, W.J.Lybarger, L.Wiertz, E.J.Hansen, T.H.J. Cell Biol. 177, 613-624, 2007Ubiquitination of serine, threonine, or lysine residues on the cytoplasmic tail can induce ERAD of MHC-I by viral E3 ligase mK3.DOI:10.1083/jcb.200611063PMID:17502423chemical and directed mutation analysisThese are ester cross-links formed between internal threonine residues and the carboxyl end of ubiquitin and other proteins.G, Tcarboxyl-terminalcross-link 2PSI-MOD:01586blocked carboxyl endCROSSLNK Glycyl threonine ester (Thr-Gly) (interchain with G-Cter ...)AA049728-Aug-200928-Aug-200928-Aug-2009O-(2-aminoethylphosphoryl)-L-serineO3-(2-aminoethylphosphoryl)-L-serineO3-(phosphoethanolamine)-L-serineserine ethanolamine phosphateserine ethanolamine phosphodiester(2S)-2-amino-3-([(2-aminoethoxy)(hydroxy)phosphoryl]oxy)propanoic acidCAS:1186-34-1PDBHET:OPEC 5 H 11 N 2 O 5 P 1210.13210.040558C 2 H 6 N 1 O 3 P 1123.05123.008530Hegge, F.T.Hitchen, P.G.Aas, F.E.Kristiansen, H.Løvold, C.Egge-Jacobsen, W.Panico, M.Leong, W.Y.Bull, V.Virji, M.Morris, H.R.Dell, A.Koomey, M.Proc. Natl. Acad. Sci. U.S.A. 101, 10798-10803, 2004Unique modifications with phosphocholine and phosphoethanolamine define alternate antigenic forms of Neisseria gonorrhoeae type IV pili.DOI:10.1073/pnas.0402397101PMID:15249686mass spectrometric detectionAas, F.E.Egge-Jacobsen, W.Winther-Larsen, H.C.Løvold, C.Hitchen, P.G.Dell, A.Koomey, M.J. Biol. Chem. 281, 27712-27723, 2006Neisseria gonorrhoeae type IV pili undergo multisite, hierarchical modifications with phosphoethanolamine and phosphocholine requiring an enzyme structurally related to lipopolysaccharide phosphoethanolamine transferases.DOI:10.1074/jbc.M604324200PMID:16825186mass spectrometric identification, directed mutation analysisCraig, L.Volkmann, N.Arvai, A.S.Pique, M.E.Yeager, M.Egelman, E.H.Tainer, J.A.Mol. Cell 23, 651-662, 2006Type IV pilus structure by cryo-electron microscopy and crystallography: implications for pilus assembly and functions.DOI:10.1016/j.molcel.2006.07.004PMID:16949362X-ray diffraction, 2.30 angstromsCraig, L.Volkmann, N.Arvai, A.S.Pique, M.E.Yeager, M.Egelman, E.H.Tainer, J.A.submitted to the Protein Data Bank, June 2006Crystal structure of native Neisseria gonorrhoeae type IV pilin at 2.3 Angstroms resolution.PDB:2HI2X-ray diffraction, 2.30 angstromsSPSI-MOD:01587phosphoproteinMOD_RES O-(2-aminoethylphosphoryl)serineAA049828-Aug-200928-Aug-200931-May-2018O-cholinephosphoryl-L-serine2-[([(2S)-2-azanyl-2-carboxyethoxy][hydroxy]phosphoryl)oxy]-N,N,N-trimethylethanazaniumO3-phosphocholine-L-serineO3-[(2-[trimethylammonio]ethyl)phosphoryl]-L-serineserine choline phosphateserine choline phosphodiester2-[([(2S)-2-amino-2-carboxyethoxy][hydroxy]phosphoryl)oxy]-N,N,N-trimethylethanaminiumC 8 H 18 N 2 O 5 P 11+253.21253.094785C 5 H 13 N 1 O 3 P 11+166.14166.062756Hegge, F.T.Hitchen, P.G.Aas, F.E.Kristiansen, H.Løvold, C.Egge-Jacobsen, W.Panico, M.Leong, W.Y.Bull, V.Virji, M.Morris, H.R.Dell, A.Koomey, M.Proc. Natl. Acad. Sci. U.S.A. 101, 10798-10803, 2004Unique modifications with phosphocholine and phosphoethanolamine define alternate antigenic forms of Neisseria gonorrhoeae type IV pili.DOI:10.1073/pnas.0402397101PMID:15249686mass spectrometric detectionAas, F.E.Egge-Jacobsen, W.Winther-Larsen, H.C.Løvold, C.Hitchen, P.G.Dell, A.Koomey, M.J. Biol. Chem. 281, 27712-27723, 2006Neisseria gonorrhoeae type IV pili undergo multisite, hierarchical modifications with phosphoethanolamine and phosphocholine requiring an enzyme structurally related to lipopolysaccharide phosphoethanolamine transferases.DOI:10.1074/jbc.M604324200PMID:16825186mass spectrometric identification, directed mutation analysisCraig, L.Volkmann, N.Arvai, A.S.Pique, M.E.Yeager, M.Egelman, E.H.Tainer, J.A.Mol. Cell 23, 651-662, 2006Type IV pilus structure by cryo-electron microscopy and crystallography: implications for pilus assembly and functions.DOI:10.1016/j.molcel.2006.07.004PMID:16949362X-ray diffraction, 2.3 angstroms; this modification is discussed but not modeledIn Neisseria this is produced as a secondary modification by methylation of O-(2-aminoethylphosphoryl)-L-serine. See RESID:AA0497.phosphocholine transferase AnkX (EC 2.7.1.-)Ssecondary to RESID:AA0497PSI-MOD:01588phosphoproteinMOD_RES O-(2-cholinephosphoryl)serineAA049928-Aug-200928-Aug-200931-May-2018O-(2,4-diacetamido-2,4-dideoxy-D-glucosyl)-L-serineDADDGlcO-(2,4-diacetamido-2,4-dideoxy-beta-D-glucopyranosyl)-L-serineO-seryl-beta-2,4-bis(acetylamino)glucosideO-[2,4-bis(acetylamino)]glucosyl-L-serineO3-(2,4-diacetamido-2,4-dideoxy-beta-D-glucopyranosyl)-L-serine(2S)-2-amino-3-[(2,4-diacetamido-2,4-dideoxy-beta-D-glucopyranosyl)oxy]propanoic acidPDBHET:DT6C 13 H 21 N 3 O 7331.33331.137950C 10 H 16 N 2 O 5244.25244.105922Hegge, F.T.Hitchen, P.G.Aas, F.E.Kristiansen, H.Løvold, C.Egge-Jacobsen, W.Panico, M.Leong, W.Y.Bull, V.Virji, M.Morris, H.R.Dell, A.Koomey, M.Proc. Natl. Acad. Sci. U.S.A. 101, 10798-10803, 2004Unique modifications with phosphocholine and phosphoethanolamine define alternate antigenic forms of Neisseria gonorrhoeae type IV pili.DOI:10.1073/pnas.0402397101PMID:15249686mass spectrometric detection; reported as 2,4-diacetamido-2,4,6-trideoxyhexoside in Nesseria gonorrhoeae strain MS11Craig, L.Volkmann, N.Arvai, A.S.Pique, M.E.Yeager, M.Egelman, E.H.Tainer, J.A.Mol. Cell 23, 651-662, 2006Type IV pilus structure by cryo-electron microscopy and crystallography: implications for pilus assembly and functions.DOI:10.1016/j.molcel.2006.07.004PMID:16949362X-ray diffraction, 2.30 angstroms, cryoelectron microscopy, 12.5 angstroms; the modification is not chemically characterizedCraig, L.Volkmann, N.Arvai, A.S.Pique, M.E.Yeager, M.Egelman, E.H.Tainer, J.A.submitted to the Protein Data Bank, June 2006Crystal structure of native Neisseria gonorrhoeae type IV pilin at 2.3 Angstroms resolution.PDB:2HI2X-ray diffraction, 2.30 angstromsIt is not clear whether or not there is a chemical difference in the glycosylation of the two varieties of strain MS11 used in these experiments.For O-(2,4-diacetamido-2,4,6-trideoxy-D-glucosyl)-L-serine, see RESID:AA0607.SPSI-MOD:01589glycoproteinCARBOHYD O-linked (DADDGlc...) serineAA050028-Aug-200928-Aug-200901-Mar-20133'-farnesyl-2',3'-dihydro-2',N2-cyclo-L-tryptophan(2S,3aR,8aS)-3a-[(2E,6E)-3,7,11-trimethyldodeca-2,6,10-trien-1-yl]-1,2,3,3a,8,8a-hexahydropyrrolo[2,3-b]indole-2-carboxylic acidChEBI:52950C 26 H 34 N 2 O 1390.57390.267114C 15 H 24 N 0 O 0204.36204.187801Okada, M.Yamaguchi, H.Sato, I.Tsuji, F.Dubnau, D.Sakagami, Y.Biosci. Biotechnol. Biochem. 72, 914-918, 2008Chemical structure of posttranslational modification with a farnesyl group on tryptophan.DOI:10.1271/bbb.80006PMID:18323630Okada, M.Biosci. Biotechnol. Biochem. 75, 1413-1417, 2011Post-translational isoprenylation of tryptophan.DOI:10.1271/bbb.110087PMID:21821957review articleWPSI-MOD:01590lipoproteinprenylationLIPID 3'-farnesyl-2',N2-cyclotryptophanAA050130-Sep-200930-Sep-200931-May-2018S-(L-lysyl)-L-methionine sulfilimine(E)-N6-([(3S)-3-amino-3-carboxypropyl](methyl)-lambda(4)-sulfanylidene)-L-lysineS-lysyl-methionine(2S)-2-amino-6-([(E)-[(3S)-3-amino-3-carboxypropyl](methyl)-lambda(4)-sulfanylidene]amino)hexanoic acidC 11 H 19 N 3 O 2 S 1257.35257.119798C 0 H -2 N 0 O 0 S 0-2.02-2.015650Than, M.E.Henrich, S.Huber, R.Ries, A.Mann, K.Kühn, K.Timpl, R.Bourenkov, G.P.Bartunik, H.D.Bode, W.Proc. Natl. Acad. Sci. U.S.A. 99, 6607-6612, 2002The 1.9-A crystal structure of the noncollagenous (NC1) domain of human placenta collagen IV shows stabilization via a novel type of covalent Met-Lys cross-link.DOI:10.1073/pnas.062183499PMID:12011424X-ray diffraction, 1.9 angstroms; the cross-link is detected and postulated to be a thioetherThan, M.E.Henrich, S.Huber, R.Ries, A.Mann, K.Kuhn, K.Timpl, R.Bourenkov, G.P.Bartunik, H.D.Bode, W.submitted to the Protein Data Bank, April 2002The 1.9-a crystal structure of the noncollagenous (NC1) domain of human placenta collagen IV shows stabilization via a novel type of covalent Met-Lys cross-link.PDB:1LI1X-ray diffraction, 1.9 angstroms; although the cross-link is discussed as a thioether in the paper, it is not modeled in the PDB entryVanacore, R.M.Friedman, D.B.Ham, A.J.Sundaramoorthy, M.Hudson, B.G.J. Biol. Chem. 280, 29300-29310, 2005Identification of S-hydroxylysyl-methionine as the covalent cross-link of the noncollagenous (NC1) hexamer of the alpha1alpha1alpha2 collagen IV network: a role for the post-translational modification of lysine 211 to hydroxylysine 211 in hexamer assembly.DOI:10.1074/jbc.M502752200PMID:15951440mass spectrometric detection and linkage analysis; the linkage is reduced by dithiothreitol, but the proposed link is a thioetherVanacore, R.Ham, A.J.Voehler, M.Sanders, C.R.Conrads, T.P.Veenstra, T.D.Sharpless, K.B.Dawson, P.E.Hudson, B.G.Science 325, 1230-1234, 2009A sulfilimine bond identified in collagen IV.DOI:10.1126/science.1176811PMID:19729652mass spectrometric, (1)H-NMR, and (13)C-NMR identification; the proposed link is a sulfanylidene amine (-S=N-), referred to by the authors and Chemical Abstracts as a sulfilimine, and by IUPAC as a sulfimideOnčák, M.Berka, K.Slavíček, P.Chemphyschem 12, 3449-3457, 2011Novel covalent bond in proteins: calculations on model systems question the bond stability.DOI:10.1002/cphc.201100664PMID:22144375quantum mechanical molecular modelingBhave, G.Cummings, C.F.Vanacore, R.M.Kumagai-Cresse, C.Ero-Tolliver, I.A.Rafi, M.Kang, J.S.Pedchenko, V.Fessler, L.I.Fessler, J.H.Hudson, B.G.Nat. Chem. Biol. 8, 784-790, 2012Peroxidasin forms sulfilimine chemical bonds using hypohalous acids in tissue genesis.DOI:10.1038/nchembio.1038PMID:22842973bromine oxidized to hypobromous acid by peroxidasin in basement membranes generates methionine bromosulfoniun that spontaneously reacts with lysine to form sulfilimine cross-linkThe process for formation of the sulfanylimine bond has not been determined. It might involve the initial formation of methionine sulfoxide.The lysine involved in this cross-link in collagen IV is usually hydroxylated, but it is not subsequently glycosylated.K, Mcross-link 2incidental to RESID:AA0028PSI-MOD:01602CROSSLNK S-Lysyl-methionine sulfilimine (Lys-Met) (interchain with M-...)CROSSLNK S-Lysyl-methionine sulfilimine (Met-Lys) (interchain with K-...)AA050220-Nov-200920-Nov-200913-Sep-20135-glutamyl 2-aminoadipic acidN2-(gamma-glutamyl)-2-aminoadipic acidN2-(isoglutamyl)-2-aminoadipic acid(2S)-2-([(4S)-4-amino-4-carboxybutanoyl]amino)hexanedioic acidC 11 H 16 N 2 O 6272.26272.100836C 6 H 9 N 1 O 3143.14143.058243Horie, A.Tomita, T.Saiki, A.Kono, H.Taka, H.Mineki, R.Fujimura, T.Nishiyama, C.Kuzuyama, T.Nishiyama, M.Nature Chem. Biol. 5, 673-679, 2009Discovery of proteinaceous N-modification in lysine biosynthesis of Thermus thermophilus.DOI:10.1038/nchembio.198PMID:19620981mass spectrometric detection and linkage analysisOuchi, T.Tomita, T.Horie, A.Yoshida, A.Takahashi, K.Nishida, H.Lassak, K.Taka, H.Mineki, R.Fujimura, T.Kosono, S.Nishiyama, C.Masui, R.Kuramitsu, S.Albers, S.V.Kuzuyama, T.Nishiyama, M.Nature Chem. Biol. 9, 277-283, 2013Lysine and arginine biosyntheses mediated by a common carrier protein in Sulfolobus.DOI:10.1038/nchembio.1200PMID:23434852biosynthesis; mass spectrometric detectionalpha-aminoadipate--LysW ligase, LysX (EC 6.3.2.-)EPSI-MOD:01605MOD_RES 5-glutamyl 2-aminoadipic acidAA050320-Nov-200920-Nov-200913-Sep-20135-glutamyl 2-aminoadipic 6-phosphoric anhydride(2S)-2-([(4S)-4-amino-4-carboxybutanoyl]amino)-6-oxo-6-(phosphonooxy)hexanoic acidC 11 H 17 N 2 O 9 P 1352.24352.067167C 6 H 10 N 1 O 6 P 1223.12223.024574Horie, A.Tomita, T.Saiki, A.Kono, H.Taka, H.Mineki, R.Fujimura, T.Nishiyama, C.Kuzuyama, T.Nishiyama, M.Nature Chem. Biol. 5, 673-679, 2009Discovery of proteinaceous N-modification in lysine biosynthesis of Thermus thermophilus.DOI:10.1038/nchembio.198PMID:19620981Ouchi, T.Tomita, T.Horie, A.Yoshida, A.Takahashi, K.Nishida, H.Lassak, K.Taka, H.Mineki, R.Fujimura, T.Kosono, S.Nishiyama, C.Masui, R.Kuramitsu, S.Albers, S.V.Kuzuyama, T.Nishiyama, M.Nature Chem. Biol. 9, 277-283, 2013Lysine and arginine biosyntheses mediated by a common carrier protein in Sulfolobus.DOI:10.1038/nchembio.1200PMID:23434852biosynthesis; chemical detection using hydroxyl amine; mass spectrometric detectionLysW-L-glutamate/LysW-L-2-aminoadipate kinase, LysZ (EC 2.7.2.-)EPSI-MOD:01606phosphoproteinNot availablethis modification is not annotated in UniProt featuresAA050420-Nov-200920-Nov-200920-Nov-20095-glutamyl allysine2-(5-glutamyl)amino-6-oxohexanoic acidalpha-(gamma-glutamyl)allysineN2-(gamma-glutamyl)allysineN2-(isoglutamyl)allysine(2S)-2-([(4S)-4-amino-4-carboxybutanoyl]amino)-6-oxohexanoic acidC 11 H 16 N 2 O 5256.26256.105922C 6 H 9 N 1 O 2127.14127.063329Horie, A.Tomita, T.Saiki, A.Kono, H.Taka, H.Mineki, R.Fujimura, T.Nishiyama, C.Kuzuyama, T.Nishiyama, M.Nature Chem. Biol. 5, 673-679, 2009Discovery of proteinaceous N-modification in lysine biosynthesis of Thermus thermophilus.DOI:10.1038/nchembio.198PMID:19620981EPSI-MOD:01607Not availablethis modification is not annotated in UniProt featuresAA050520-Nov-200920-Nov-200920-Nov-2009N2-(L-isoglutamyl)-L-lysine5-glutamyl N2-lysinealpha-(gamma-glutamyl)lysinegamma-glutamyl N2-lysineN2-(gamma-glutamyl)lysine(2S)-6-amino-2-([(4S)-4-amino-4-carboxybutanoyl]amino)hexanoic acidCAS:5978-23-4C 11 H 19 N 3 O 4257.29257.137556C 6 H 12 N 2 O 1128.18128.094963Horie, A.Tomita, T.Saiki, A.Kono, H.Taka, H.Mineki, R.Fujimura, T.Nishiyama, C.Kuzuyama, T.Nishiyama, M.Nature Chem. Biol. 5, 673-679, 2009Discovery of proteinaceous N-modification in lysine biosynthesis of Thermus thermophilus.DOI:10.1038/nchembio.198PMID:19620981mass spectrometric detection and linkage analysisFor the cross-linking of a peptidyl glutamine or glutamic acid by isopeptide bond through the gamma-carboxyl group to the N6-amino of a peptidyl lysine, see RESID:AA0124.EPSI-MOD:01608isopeptide bondMOD_RES 5-glutamyl N2-lysineAA050620-Nov-200920-Nov-200931-May-20187'-hydroxy-2'-alpha-mannosyl-L-tryptophan(2S)-2-amino-3-[7-hydroxy-2-(alpha-D-mannopyranosyl)-1H-indol-3-yl]propanoic acidC 17 H 20 N 2 O 7364.35364.127051C 6 H 10 N 0 O 6178.14178.047738Zhao, H.Sagert, J.Hwang, D.S.Waite, J.H.J. Biol. Chem. 284, 23344-23352, 2009Glycosylated hydroxytryptophan in a mussel adhesive protein from Perna viridis.DOI:10.1074/jbc.M109.022517PMID:19584055mass spectrometric detection, spectrographic and chemical characterizationThe 7'-hydroxylation of tryptophan apparently makes it susceptible to oxidation and cross-linking, however these secondary products have not been characterized.Wsecondary to RESID:AA0217secondary to RESID:AA0521PSI-MOD:01609glycoproteinhydroxylationCARBOHYD C-linked (Man) hydroxytryptophanAA050731-Dec-200931-Dec-200930-Jun-2012L-threonine methyl estermethyl L-threoninatemethyl (2S,3R)-2-amino-3-hydroxybutanoateCAS:3373-59-9C 5 H 10 N 1 O 3132.14132.066068C 1 H 2 N 0 O 014.0314.015650Mukai, A.Fukai, T.Hoshino, Y.Yazawa, K.Harada, K.-I.Mikami, Y.J. Antibiot. 62, 613-619, 2009Nocardithiocin, a novel thiopeptide antibiotic, produced by pathogenic Nocardia pseudobrasiliensis IFM 0757.DOI:10.1038/ja.2009.90PMID:19745839the initials of K.-I. Harada in the PubMed citation are correctedTcarboxyl-terminalincidental to RESID:AA0182GO:0044608PSI-MOD:01610methylated carboxyl endNot availablethis modification is not annotated in UniProt featuresAA050831-Dec-200931-Dec-200930-Apr-20106-(S-L-cysteinyl)-8alpha-(N3'-L-histidino)-FMN6-(S-cysteinyl)-8alpha-(N(delta)-histidyl)-FMN6-(S-cysteinyl)-8alpha-(N(pi)-histidyl)-FMN6-(S-cysteinyl)-8alpha-(N3'-histidyl)-FMN6-(S-cysteinyl)-8alpha-(pros-histidyl)-FMN6-((R)-2-amino-2-carboxyethyl)sulfanyl-8alpha-[4-((S)-2-amino-2-carboxyethyl)imidazol-3-yl]-riboflavin 5'-trihydrogen phosphateC 26 H 29 N 8 O 11 P 1 S 1692.60692.141411C 17 H 17 N 4 O 9 P 1 S 0452.32452.073315Li, Y.S.Ho, J.Y.Huang, C.C.Lyu, S.Y.Lee, C.Y.Huang, Y.T.Wu, C.J.Chan, H.C.Huang, C.J.Hsu, N.S.Tsai, M.D.Li, T.L.J. Am. Chem. Soc. 129, 13384-13385, 2007A unique flavin mononucleotide-linked primary alcohol oxidase for glycopeptide A40926 maturation.DOI:10.1021/ja075748xPMID:17935335mass spectrometric identification, directed mutation analysisThe keyword "phosphoprotein" is not used with flavin modifications linked through the flavin.autocatalyticC, Hcross-link 2PSI-MOD:01611*phosphoproteinflavoproteinFMNthioether bondBINDING FMN (covalent; via 2 links, pros nitrogen)BINDING FMN (covalent; via 2 links)AA050931-Dec-200931-Dec-200931-May-20183'-iodo-L-tyrosine3-iodo-L-tyrosine3-iodotyrosine4-hydroxy-3-iodo-phenylalanineMIT(2S)-2-amino-3-(4-hydroxy-3-iodophenyl)propanoic acidCAS:70-78-0ChEBI:90870PDBHET:IYRC 9 H 8 I 1 N 1 O 2289.07288.959976C 0 H -1 I 1 N 0 O 0125.90125.896648Gentile, F.Ferranti, P.Mamone, G.Malorni, A.Salvatore, G.J. Biol. Chem. 272, 639-646, 1997Identification of hormonogenic tyrosines in fragment 1218-1591 of bovine thyroglobulin by mass spectrometry. Hormonogenic acceptor TYR-12donor TYR-1375.DOI:10.1074/jbc.272.1.639PMID:8995307mass spectrometric detectionYPSI-MOD:01612iodineMOD_RES IodotyrosineAA051031-Dec-200931-Dec-200931-May-20183',5'-diiodo-L-tyrosine3,5-diiodo-L-tyrosine3,5-diiodotyrosineDITiodogorgoic acid(2S)-2-amino-3-(4-hydroxy-3,5-diiodophenyl)propanoic acidCAS:300-39-0ChEBI:90871PDBHET:TYIC 9 H 7 I 2 N 1 O 2414.97414.856624C 0 H -2 I 2 N 0 O 0251.79251.793295Gentile, F.Ferranti, P.Mamone, G.Malorni, A.Salvatore, G.J. Biol. Chem. 272, 639-646, 1997Identification of hormonogenic tyrosines in fragment 1218-1591 of bovine thyroglobulin by mass spectrometry. Hormonogenic acceptor TYR-12donor TYR-1375.DOI:10.1074/jbc.272.1.639PMID:8995307mass spectrometric detectionYPSI-MOD:01613iodineMOD_RES DiiodotyrosineAA051131-Dec-200931-Dec-200920-May-2011glycyl phospho-5'-adenosine(2-aminoacetyl)oxy-([(2R,3R,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy)phosphinic acid([(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl)-2-aminoethanoate5'-adenylic-glyinateglycine monoanhydride with 5'-adenylic acidglycyl 5'-adenylateglycyl adenosine-5'-phosphateglycyladenylateaminoacetyl [5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl hydrogen phosphateCAS:35985-26-3PDBHET:AMPC 12 H 16 N 6 O 8 P 1403.27403.076723C 10 H 12 N 5 O 6 P 1329.21329.052520Taylor, S.V.Kelleher, N.L.Kinsland, C.Chiu, H.J.Costello, C.A.Backstrom, A.D.McLafferty, F.W.Begley, T.P.J. Biol. Chem. 273, 16555-16560, 1998Thiamin biosynthesis in Escherichia coli. Identification of ThiS thiocarboxylate as the immediate sulfur donor in the thiazole formation.DOI:10.1074/jbc.273.26.16555PMID:9632726mass spectrometric identification; the capitalization of ThiS in the PubMed citation is correctedLake, M.W.Wuebbens, M.M.Rajagopalan, K.V.Schindelin, H.Nature 414, 325-329, 2001Mechanism of ubiquitin activation revealed by the structure of a bacterial MoeB-MoaD complex.DOI:10.1038/35104586PMID:11713534X-ray diffraction, 2.10 angstromsLake, M.W.Wuebbens, M.M.Rajagopalan, K.V.Schindelin, H.submitted to the Protein Data Bank, September 2001Structure of the covalent acyl-adenylate form of the MoeB-MoaD protein complex.PDB:1JWBX-ray diffraction, 2.50 angstromsLehmann, C.Begley, T.P.Ealick, S.E.Biochemistry 45, 11-19, 2006Structure of the Escherichia coli ThiS-ThiF complex, a key component of the sulfur transfer system in thiamin biosynthesis.DOI:10.1021/bi051502yPMID:16388576X-ray diffraction, 1.98 angstroms, of the ThiS-ThiF complex with discussion of models of the proposed intermediatesGcarboxyl-terminalPSI-MOD:01614blocked carboxyl endphosphoproteinMOD_RES Glycyl adenylateAA051231-Dec-200931-Dec-200925-Feb-2011glycyl cysteine dithioester2-(glycyldithio)alanineS-glycyl cysteine persulfideS-glycyl thiocysteinethioglycine cysteine disulfide(2R)-2-amino-3-[(aminoacetyl)disulfanyl]propanoic acidC 5 H 7 N 2 O 2 S 2191.24190.994894C 0 H -2 N 0 O -1 S 114.0513.961506Xi, J.Ge, Y.Kinsland, C.McLafferty, F.W.Begley, T.P.Proc. Natl. Acad. Sci. U.S.A. 98, 8513-8518, 2001Biosynthesis of the thiazole moiety of thiamin in Escherichia coli: identification of an acyldisulfide-linked protein--protein conjugate that is functionally analogous to the ubiquitin/E1 complex.DOI:10.1073/pnas.141226698PMID:11438688mass spectrometric evidenceLehmann, C.Begley, T.P.Ealick, S.E.Biochemistry 45, 11-19, 2006Structure of the Escherichia coli ThiS-ThiF complex, a key component of the sulfur transfer system in thiamin biosynthesis.DOI:10.1021/bi051502yPMID:16388576X-ray diffraction, 1.98 angstroms, of the ThiS-ThiF complex with discussion of models of the proposed intermediatesThese are highly reactive dithioester cross-links formed between internal cysteine residues of ThiF and the carboxyl end of ThiS and other similar proteins.C, Gcarboxyl-terminalcross-link 2PSI-MOD:01615blocked carboxyl endthioester bondCROSSLNK Glycyl cysteine dithioester (Gly-Cys) (interchain with C-...)CROSSLNK Glycyl cysteine dithioester (Cys-Gly) (interchain with G-Cter ...)AA051329-Jan-201029-Jan-201029-Jan-2010trithiocystine3,3'-pentathiobisalaninebis(2-amino-2-carboxyethyl)pentasulfide(2R,2'R)-3,3'-pentasulfane-1,5-diylbis(2-aminopropanoic acid)PDBHET:S3HC 6 H 8 N 2 O 2 S 5300.44299.918933C 0 H -2 N 0 O 0 S 394.1693.900563Brito, J.A.Sousa, F.L.Stelter, M.Bandeiras, T.M.Vonrhein, C.Teixeira, M.Pereira, M.M.Archer, M.Biochemistry 48, 5613-5622, 2009Structural and functional insights into sulfide:quinone oxidoreductase.DOI:10.1021/bi9003827PMID:19438211X-ray diffraction, 2.57 angstromsBrito, J.A.Sousa, F.L.Stelter, M.Bandeiras, T.M.Vonrhein, C.Teixeira, M.Pereira, M.M.Archer, M.submitted to the Protein Data Bank, April 2009The first X-ray structure of a sulfide:quinone oxidoreductase: insights into sulfide oxidation mechanism.PDB:3H8LX-ray diffraction, 2.57 angstromsC, Ccross-link 2PSI-MOD:01616Not availablethis modification is not annotated in UniProt featuresAA051429-Jan-201029-Jan-201031-May-2018O-(6-phosphomannosyl)-L-threonineO3-(6-phosphomannosyl)threonine(2S,3R)-2-amino-3-[6-phosphonooxy-alpha-D-mannopyranosyloxy]butanoic acidC 10 H 18 N 1 O 10 P 1 +343.22 +343.066832 +C 6 H 11 N 0 O 8 P 1 +242.12 +242.019154 +Yoshida-Moriguchi, T.Yu, L.Stalnaker, S.H.Davis, S.Kunz, S.Madson, M.Oldstone, M.B.Schachter, H.Wells, L.Campbell, K.P.Science 327, 88-92, 2010O-mannosyl phosphorylation of alpha-dystroglycan is required for laminin binding.DOI:10.1126/science.1180512PMID:20044576mass spectrometric, (1)H-NMR, and (13)C-NMR identification; the structure was determined to be O3-[N-acetylgalactosaminyl-beta-1,3-N-acetylglucosaminyl-beta-1,4-(6-phospho-)mannosyl]threonineThe alpha anomeric form is shown.See also RESID:AA0155, RESID:AA0247, RESID:AA0399, RESID:AA0401, RESID:AA0403, and RESID:AA0405 for other O-glycosylated threonines.protein O-mannosyl transferase (EC 2.4.1.109)protein O-mannose beta-1,4-N-acetylglucosaminyltransferase (EC 2.4.1.-)protein O-(N-acetylglucosaminyl-beta-1,4)-mannose beta-1,4-N-acetylgalactosaminyltransferase (EC 2.4.1.-)protein O-mannose 6-phosphotransferase (EC 2.7.1.-)TPSI-MOD:01617glycoproteinphosphoproteinCARBOHYD O-linked (Man6P...) threonineAA051529-Jan-201029-Jan-201030-Jun-2011L-alanyl-L-isoaspartyl cyclopeptide1,4.2-anhydro(L-alanyl-L-aspartic acid)(2S,5S)-2-methyl-3,7-dioxo-1,4-diazepane-5-carboxylic acidC 7 H 9 N 2 O 3169.16169.061317C 0 H -3 N -1 O 0-17.03-17.026549Lura, R.Schirch, V.Biochemistry 27, 7671-7677, 1988Role of peptide conformation in the rate and mechanism of deamidation of asparaginyl residues.DOI:10.1021/bi00420a015PMID:3207697chemical and (1)H-NMR evidence for formation of a valyl-isoaspartyl cyclopeptide from a synthetic tetrapeptide valyl-asparaginyl-glycyl-alanineKita, M.Black, D.S.Ohno, O.Yamada, K.Kigoshi, H.Uemura, D.J. Am. Chem. Soc. 131, 18038-18039, 2009Duck-billed platypus venom peptides induce Ca2+ influx in neuroblastoma cells.DOI:10.1021/ja908148zPMID:19928958mass spectrometric detection of cyclic deamidation; an alternate cyclization is not ruled outThis is a proposed cyclization between asparagine and the free amino group of the preceding amino acid in a peptide. It is more probable that asparagine cyclizes with the amino group of the following glycine, see RESID:AA0441.A, Namino-terminalcross-link 1PSI-MOD:01618CROSSLNK Alanine isoaspartyl cyclopeptide (Ala-Asn)AA051626-Feb-201026-Feb-201029-May-2010N-[(12R)-12-hydroxymyristoyl]-L-cysteineN-[(12R)-12-hydroxytetradecanoyl]cysteine2-[(12R)-12-hydroxytetradecanoyl]amino-3-sulfanylpropanoic acidC 17 H 32 N 1 O 3 S 1330.51330.210290C 14 H 26 N 0 O 2 S 0226.36226.193280Whitson, E.L.Ratnayake, A.S.Bugni, T.S.Harper, M.K.Ireland, C.M.J. Org. Chem. 74, 1156-1162, 2009Isolation, structure elucidation, and synthesis of eudistomides A and B, lipopeptides from a Fijian ascidian Eudistoma sp.DOI:10.1021/jo8022582PMID:19053188mass spectrometric, (1)H-NMR, and (13)C-NMR identification; chemical synthesisCamino-terminalPSI-MOD:01690lipoproteinLIPID N-[(12R)-12-hydroxymyristoyl]cysteineAA051726-Feb-201026-Feb-201029-May-2010N-(12-ketomyristoyl)-L-cysteineN-(12-oxotetradecanoyl)cysteine2-(12-oxotetradecanoyl)amino-3-sulfanylpropanoic acidC 17 H 30 N 1 O 3 S 1328.49328.194640C 14 H 24 N 0 O 2 S 0224.34224.177630Whitson, E.L.Ratnayake, A.S.Bugni, T.S.Harper, M.K.Ireland, C.M.J. Org. Chem. 74, 1156-1162, 2009Isolation, structure elucidation, and synthesis of eudistomides A and B, lipopeptides from a Fijian ascidian Eudistoma sp.DOI:10.1021/jo8022582PMID:19053188mass spectrometric, (1)H-NMR, and (13)C-NMR identification; chemical synthesisCamino-terminalPSI-MOD:01691lipoproteinLIPID N-(12-oxomyristoyl)cysteineAA051831-Mar-201031-Mar-201029-Oct-2010N5-(ADP-ribosyl)-L-glutamineN5-alpha-D-ribofuranosyl-L-glutamine 5'->5'-ester with adenosine 5'-(trihydrogen diphosphate)N5-[alpha-D-ribofuranoside 5'->5'-ester with adenosine 5'-(trihydrogen diphosphate)]-L-glutamine(S)-2-amino-4-([adenosine 5'-(trihydrogen diphosphate) 5'->5'-ester with alpha-D-ribofuranosyl]amino)-5-oxopentanoic acidC 20 H 29 N 7 O 15 P 2669.43669.119687C 15 H 21 N 5 O 13 P 2541.30541.061109Lang, A.E.Schmidt, G.Schlosser, A.Hey, T.D.Larrinua, I.M.Sheets, J.J.Mannherz, H.G.Aktories, K.Science 327, 1139-1142, 2010Photorhabdus luminescens toxins ADP-ribosylate actin and RhoA to force actin clustering.DOI:10.1126/science.1184557PMID:20185726It is not known whether Photorhabdus luminescens toxin catalyzes formation of the alpha or beta isomer. The alpha form is presented.The keyword "phosphoprotein" is not used with toxin modification.NAD(P)+--glutamine ADP-ribosyltransferase TccC5 (EC 2.4.2.-)QPSI-MOD:01662*phosphoproteinNot availablethis modification is not annotated in UniProt featuresAA051931-Mar-201031-Mar-201029-Oct-2010O-(ADP-ribosyl)-L-threonineO3-(ADP-ribosyl)-L-threonineO3-alpha-D-ribofuranosyl-L-threonine 5'->5'-ester with adenosine 5'-(trihydrogen diphosphate)O3-[alpha-D-ribofuranoside 5'->5'-ester with adenosine 5'-(trihydrogen diphosphate)]-L-threonine(S)-2-amino-3-([adenosine 5'-(trihydrogen diphosphate) 5'->5'-ester with alpha-D-ribofuranosyl]oxy)-butanoic acidC 19 H 28 N 6 O 15 P 2642.41642.108787C 15 H 21 N 5 O 13 P 2541.30541.061109Lang, A.E.Schmidt, G.Schlosser, A.Hey, T.D.Larrinua, I.M.Sheets, J.J.Mannherz, H.G.Aktories, K.Science 327, 1139-1142, 2010Photorhabdus luminescens toxins ADP-ribosylate actin and RhoA to force actin clustering.DOI:10.1126/science.1184557PMID:20185726It is not known whether Photorhabdus luminescens toxin catalyzes formation of the alpha or beta isomer. The alpha form is presented.The keyword "phosphoprotein" is not used with toxin modification.NAD(P)+--threonine ADP-ribosyltransferase TccC3 (EC 2.4.2.-)TPSI-MOD:01663*phosphoproteinNot availablethis modification is not annotated in UniProt featuresAA052031-Mar-201031-Mar-201031-Mar-20107'-hydroxy-L-tryptophan7-hydroxy-L-tryptophan(2S)-2-amino-3-(7-hydroxy-1H-indol-3-yl)propanoic acidPDBHET:0AFC 11 H 10 N 2 O 2202.21202.074228C 0 H 0 N 0 O 116.0015.994915Jensen, L.M.Sanishvili, R.Davidson, V.L.Wilmot, C.M.Science 327, 1392-1394, 2010In crystallo posttranslational modification within a MauG/pre-methylamine dehydrogenase complex.DOI:10.1126/science.1182492PMID:20223990X-ray diffraction, 2.1 angstromsJensen, L.M.Wilmot, C.M.submitted to the Protein Data Bank, December 2009Crystal structure of the MauG/pre-methylamine dehydrogenase complex.PDB:3L4MX-ray diffraction, 2.1 angstroms; this previously modified tryptophan is one of the two substrate residues of the enzymeThis modification without secondary glycosylation (see RESID:AA0506) has only been observed as the first precursor form of 4'-(L-tryptophan)-L-tryptophyl quinone (see RESID:AA0149).peptidyl-tryptophan 7-oxygenase MauX (EC 1.-.-.-)WPSI-MOD:01664hydroxylationMOD_RES 7'-hydroxytryptophanthis modification does not occur in UniProt features without secondary modificationsAA052131-Mar-201031-Mar-201030-Sep-2010N-(DNA-1',2'-dideoxyribos-1'-ylidene)-L-valineDNA glycosylase valine Schiff base intermediate(2S)-2-[(3R,4R)-3,4-dihydroxy-5-(phosphonooxy)pentylidene]amino-3-methylbutanoic acidC 10 H 17 N 1 O 6 P 1278.22278.079349C 5 H 7 N 0 O 5 P 1178.08178.003110Liu, M.Bandaru, V.Bond, J.P.Jaruga, P.Zhao, X.Christov, P.P.Burrows, C.J.Rizzo, C.J.Dizdaroglu, M.Wallace, S.S.Proc. Natl. Acad. Sci. U.S.A. 107, 4925-4930, 2010The mouse ortholog of NEIL3 is a functional DNA glycosylase in vitro and in vivo.DOI:10.1073/pnas.0908307107PMID:20185759chemical evidence of N-terminal valine linkage to DNAThe model has three open valences, one on the valine carboxyl group and two in the DNA nucleotide segment on the 5'-phosphate and the 3'-hydroxyl.The keyword "phosphoprotein" is not used with polynucleotide-linked intermediate modifications.DNA glycosylase (EC 3.2.2.-)Vamino-terminalPSI-MOD:01665*phosphoproteinblocked amino endACT_SITE Schiff-base intermediate with DNA; via amino nitrogenAA052230-Apr-201030-Apr-201030-Apr-2010O4-(8alpha-FAD)-L-aspartate8alpha-[(4-aspartyl)oxy]FAD(2S)-2-amino-4-oxo-4-[8alpha-riboflavin 5'-(trihydrogen diphosphate) 5'->5'-ester with adenosine]oxybutanoic acidPDBHET:FADC 31 H 36 N 10 O 18 P 2898.63898.168428C 27 H 31 N 9 O 15 P 2783.54783.141485Podzelinska, K.Latimer, R.Bhattacharya, A.Vining, L.C.Zechel, D.L.Jia, Z.J. Mol. Biol. 397, 316-331, 2010Chloramphenicol biosynthesis: the structure of CmlS, a flavin-dependent halogenase showing a covalent flavin-aspartate bond.DOI:10.1016/j.jmb.2010.01.020PMID:20080101X-ray diffraction, 2.20 angstromsPodzelinska, K.Soares, A.Jia, Z.submitted to the Protein Data Bank, June 2009Crystal structure of CmlS, a flavin-dependent halogenase.PDB:3I3LX-ray diffraction, 2.20 angstromsautocatalyticDPSI-MOD:01668*phosphoproteinFADflavoproteinNot availablethis modification is not annotated in UniProt featuresAA052330-Apr-201030-Apr-201031-May-2018N(omega)-,N(omega)-,N(omega')-trimethyl-L-arginine(2S)-2-amino-5-([(dimethylamino)(methylimino)methyl]amino)pentanoic acid2-[(4S)-4-amino-5-oxopentyl]-1,1,3-trimethylguanidineN(G)-trimethylarginineN5-[(dimethylamino)(imino)methyl]ornithine(2S)-2-amino-5-([(dimethylamino)(methylamino)methylidene]amino)pentanoic acidC 9 H 18 N 4 O 1198.27198.148061C 3 H 6 N 0 O 042.0842.046950Patthy, A.Bajusz, S.Patthy, L.Acta Biochim. Biophys. Acad. Sci. Hung. 12, 191-196, 1977Preparation and characterization of N(G)-mono-, di- and trimethylated arginines.PMID:602668chemical synthesis; chromatographic detection; the free amino acid was not found in human urinePelletier, M.Xu, Y.Wang, X.Zahariev, S.Pongor, S.Aletta, J.M.Read, L.K.Mol. Biochem. Parasitol. 118, 49-59, 2001Arginine methylation of a mitochondrial guide RNA binding protein from Trypanosoma brucei.DOI:10.1016/S0166-6851(01)00367-XPMID:11704273mass spectrometric detection reported in one tryptic peptide of RNA-binding protein 16; the mass difference is reported as 42.981 Da, measured from the neutral parent, spectral data not shown; subsequently, it has not been confirmed or characterized, or detected in other proteins (Laurie K. Read, private communication, 2010)No enzyme activities capable of producing this modification under physiological conditions have been reported.RPSI-MOD:01669methylated amino acidNot availablethis modification is not annotated in UniProt featuresAA052430-Apr-201030-Apr-201030-Apr-2010N6-chloro-L-lysineepsilon-chlorolysinelysine chloramineN(zeta)-chlorolysine(2S)-2-amino-6-(chloroamino)hexanoic acidC 6 Cl 1 H 11 N 2 O 1162.62162.055991C 0 Cl 1 H -1 N 0 O 034.4433.961028Peng, D.Q.Wu, Z.Brubaker, G.Zheng, L.Settle, M.Gross, E.Kinter, M.Hazen, S.L.Smith, J.D.J. Biol. Chem. 280, 33775-33784, 2005Tyrosine modification is not required for myeloperoxidase-induced loss of apolipoprotein A-I functional activities.DOI:10.1074/jbc.M504092200PMID:16091367conversion of lysine residues to chlorolysine by myeloperoxidase is assayed with 5-thio-2-nitrobenzoic acid (TNB)Dong, C.Flecks, S.Unversucht, S.Haupt, C.van Pée, K.H.Naismith, J.H.Science 309, 2216-2219, 2005Tryptophan 7-halogenase (PrnA) structure suggests a mechanism for regioselective chlorination.DOI:10.1126/science.1116510PMID:16195462X-ray diffraction, 1.95 angstroms; proposal for a mechanism with hypochlorite bound between lysine and glutamateYeh, E.Blasiak, L.C.Koglin, A.Drennan, C.L.Walsh, C.T.Biochemistry 46, 1284-1292, 2007Chlorination by a long-lived intermediate in the mechanism of flavin-dependent halogenases.DOI:10.1021/bi0621213PMID:17260957X-ray diffraction, 2.08 angstroms; proposal for the formation of lysine chloramine as an intermediate based on the persistence of chlorinating activity after dialysis removal of flavin and chloride; the proposed intermediate is not modeled in the deposited structuresIn tryptophan 7-halogenase (EC 1.14.14.7), the modification is formed by autocatalysis as an intermediate in the catalytic cycle. The formation by myeloperoxidase (EC 1.11.1.7) is probably not a normal metabolic process.autocatalyticmyeloperoxidase (EC 1.11.1.7)KPSI-MOD:01670chlorineNot availablethis modification is not annotated in UniProt featuresAA052530-Apr-201030-Apr-201031-May-2018O-(L-isoaspartyl)-L-threonine(2S,3R)-2-amino-3-([(4S)-3-amino-3-carboxypropanoyl]oxy)propanoic acidO(beta)-(beta-aspartyl)threonineO3-(isoaspartyl)-threonine(2S)-2-amino-4-([(1S,2R)-1-amino-1-carboxypropan-2-yl]oxy)-4-oxobutanoic acidPDBHET:AEIC 8 H 10 N 2 O 4198.18198.064057C 8 H 12 N 2 O 5216.19216.074621C 0 H -2 N 0 O -1-18.02-18.010565C 4 H 5 N 1 O 3115.09115.026943Ishitsuka, M.O.Kusumi, T.Kakisawa, H.Kaya, K.Watanabe, M.M.J. Am. Chem. Soc. 112, 8180-8182, 1990Microviridin. A novel tricyclic depsipeptide from the toxic cyanobacterium Microcystis viridis.DOI:10.1021/ja00178a060amino acid composition; (1)H-NMR and (13)C-NMR identification; chemical characterization of the ester cross-linksPalm, G.J.Lubkowski, J.Derst, C.Schleper, S.Röhm, K.H.Wlodawer, A.FEBS Lett. 390, 211-216, 1996A covalently bound catalytic intermediate in Escherichia coli asparaginase: crystal structure of a Thr-89-Val mutant.DOI:10.1016/0014-5793(96)00660-6PMID:8706862X-ray diffraction, 2.20 angstroms; a Thr-89-Val mutant has a trapped covalent intermediatePalm, G.J.Lubkowski, J.Derst, C.Wlodawer, A.submitted to the Protein Data Bank, February 1997Asparaginase from E. coli, mutant T89V with covalently bound aspartate.PDB:4ECAX-ray diffraction, 2.20 angstromsWang, Y.Guo, H.C.J. Mol. Biol. 366, 82-92, 2007Crystallographic snapshot of a productive glycosylasparaginase-substrate complex.DOI:10.1016/j.jmb.2006.09.051PMID:17157318X-ray diffraction, 2.00 angstromsWang, Y.Guo, H.C.submitted to the Protein Data Bank, April 2006Crystal structure of glycosylasparaginase-substrate complex.PDB:2GL9X-ray diffraction, 2.00 angstromsPhilmus, B.Christiansen, G.Yoshida, W.Y.Hemscheidt, T.K.Chembiochem 9, 3066-3073, 2008Post-translational modification in microviridin biosynthesis.DOI:10.1002/cbic.200800560PMID:19035375(1)H-NMR and (13)C-NMR analysis; mass spectrometric and chemical characterization; directed mutation analysis; gene sequence for the encoded peptideThe formula and records labeled "TDX" refers to O3-(isoaspartyl)-threonine produced as an ester cross-link of a peptidyl threonine residue and a peptidyl aspartic acid residue. The ester cross-link is formed by an RimK related enzyme using ATP.The formula and records labeled "THR" refers to O3-(isoaspartyl)-threonine produced as peptidyl threonine residue ester bonded to a free asparagine with the release of ammonia. The isoaspartylation modification of threonine by asparagine is produced by autocatalysis as an intermediate in the catalytic cycle of asparginase.peptidyl-threonine--peptidyl-aspartate ligase MvdD (EC 6.1.2.-)autocatalyticD, Tcross-link 2PSI-MOD:01947TPSI-MOD:01671ACT_SITE O-isoaspartyl threonine intermediateCROSSLNK isoaspartyl threonine ester (Thr-Asp)ACT_SITE Acyl-ester intermediatethis ambiguous form is used for enzymes with glutaminase-asparaginase activityAA052628-May-201028-May-201031-Dec-2012S-(coelenterazin-3a-yl)-L-cysteinedehydrocoelenterazine cysteine adductsymplectin chromophore(2R)-2-amino-3-([(4-hydroxyphenyl)(8-benzyl-3-oxo-6-[4-hydroxyphenyl]-3,7-dihydroimidazo[1,2-a]pyrazin-2-yl)methyl]sulfanyl)propanoic acidCAS:55779-48-1ChEBI:2311C 29 H 24 N 4 O 4 S 1524.60524.151826C 26 H 19 N 3 O 3 S 0421.46421.142641Isobe, M.Kuse, M.Tani, N.Fujii, T.Matsuda, T.Proc. Jpn. Acad., Ser. B, Phys. Biol. Sci. 84, 386-392, 2008Cysteine-390 is the binding site of luminous substance with symplectin, a photoprotein from Okinawan squid, Symplectoteuthis oualaniensis.DOI:10.2183/pjab/84.386PMID:18997450Coelenterazine is one of the four major marine luciferins, being used by various bioluminescent species in at least eight phyla. Coelenterazine may result from modification of a phenylalanyl-tyrosyl-tyrosine peptide produced by an unidentified endosymbiotic organism. See RESID:AA0595.The chirality of the cysteine adduct has not been determined.This entry presents coelenterazine as a heterogen cross-linked to a cysteine. For coelenterazine as a modification produced by the cross-linking of a tripeptide precursor see RESID:AA0595.autocatalyticCPSI-MOD:01694chromoproteinMOD_RES S-(coelenterazin-3a-yl)cysteineAA052730-Jun-201030-Jun-201031-May-2018N6-octanoyl-L-lysineepsilon-octanoyllysineN(zeta)-octanoyllysineN6-(1-oxooctyl)-L-lysine(2S)-2-amino-6-(octanoylamino)hexanoic acidCAS:23735-96-8ChEBI:78809C 14 H 26 N 2 O 2254.37254.199428C 8 H 14 N 0 O 1126.20126.104465Ali, S.T.Moir, A.J.Ashton, P.R.Engel, P.C.Guest, J.R.Mol. Microbiol. 4, 943-950, 1990Octanoylation of the lipoyl domains of the pyruvate dehydrogenase complex in a lipoyl-deficient strain of Escherichia coli.DOI:10.1111/j.1365-2958.1990.tb00667.xPMID:2215217mass spectrometric detection at the same site as lipoic acid modification in dihydrolipoamide acetyltransferase when it is over-expressedJordan, S.W.Cronan Jr., J.E.J. Bacteriol. 185, 1582-1589, 2003The Escherichia coli lipB gene encodes lipoyl (octanoyl)-acyl carrier protein:protein transferase.DOI:10.1128/JB.185.5.1582-1589.2003PMID:12591875identification of enzyme activity for the modificationThe metabolic role of this modification is uncertain.octanoyltransferase (EC 2.3.1.181)KPSI-MOD:01774lipoproteinNot availablethis modification is not annotated in UniProt featuresAA052830-Jun-201030-Jun-201031-May-20135-glutamyl serotoninN2-(gamma-glutamyl)-5-hydoxytryptamineN5-[2-(5-hydroxy-3-indolyl)ethyl]glutamine(2S)-2-amino-5-([2-(5-hydroxy-1H-indol-3-yl)ethyl]amino)-5-oxopentanoic acidCAS:61059-62-9C 15 H 17 N 3 O 3287.32287.126991C 10 H 9 N 1 O 1159.19159.068414Dale, G.L.Friese, P.Batar, P.Hamilton, S.F.Reed, G.L.Jackson, K.W.Clemetson, K.J.Alberio, L.Nature 415, 175-179, 2002Stimulated platelets use serotonin to enhance their retention of procoagulant proteins on the cell surface.DOI:10.1038/415175aPMID:11805836chromatographic detection on COAT-platelet alpha-granule proteins after hydrolysisWalther, D.J.Peter, J.U.Winter, S.Höltje, M.Paulmann, N.Grohmann, M.Vowinckel, J.Alamo-Bethencourt, V.Wilhelm, C.S.Ahnert-Hilger, G.Bader, M.Cell 115, 851-862, 2003Serotonylation of small GTPases is a signal transduction pathway that triggers platelet alpha-granule release.DOI:10.1016/S0092-8674(03)01014-6PMID:14697203radiolabeling demonstrates serotonin transamidation to RhoA and small GTPases during activation; glutamine-63 is suggested, but not demonstrated, to be transamidated by serotoninLin, J.C.Chou, C.C.Gao, S.Wu, S.C.Khoo, K.H.Lin, C.H.Chembiochem 14, 813-817, 2013An in Vivo Tagging Method Reveals that Ras Undergoes Sustained Activation upon Transglutaminase-Mediated Protein Serotonylation.DOI:10.1002/cbic.201300050PMID:23592595chemical derivatization; mass spectrometric identification and localizationThe structure shown in PubChem for this name is incorrect being instead alpha-glutamyl serotonin, which is not the product of transamidation.protein-glutamine gamma-glutamyltransferase (EC 2.3.2.13)QPSI-MOD:01775serotonylationNot availablethis modification is not annotated in UniProt featuresAA052930-Sep-201030-Sep-201030-Sep-2011N-(glycyl)-L-cysteineN-(2-amino-1-oxoethyl)cysteine(2R)-2-[(aminoacetyl)amino]-3-sulfanylpropanoic acidC 5 H 9 N 2 O 3 S 1177.20177.033388C 3 H 5 N 1 O 1 S 1103.14103.009185Ågren, D.Schnell, R.Oehlmann, W.Singh, M.Schneider, G.J. Biol. Chem. 283, 31567-31574, 2008Cysteine synthase (CysM) of Mycobacterium tuberculosis is an O-phosphoserine sulfhydrylase: evidence for an alternative cysteine biosynthesis pathway in mycobacteria.DOI:10.1074/jbc.M804877200PMID:18799456the encoding of an author's name in the PubMed citation is corrected to UTF8Jurgenson, C.T.Burns, K.E.Begley, T.P.Ealick, S.E.Biochemistry 47, 10354-10364, 2008Crystal structure of a sulfur carrier protein complex found in the cysteine biosynthetic pathway of Mycobacterium tuberculosis.DOI:10.1021/bi800915jPMID:18771296O'Leary, S.E.Jurgenson, C.T.Ealick, S.E.Begley, T.P.Biochemistry 47, 11606-11615, 2008O-phospho-L-serine and the thiocarboxylated sulfur carrier protein CysO-COSH are substrates for CysM, a cysteine synthase from Mycobacterium tuberculosis.DOI:10.1021/bi8013664PMID:18842002cysteine thioester linked to a carboxyl terminal glycine is formed by condensation of a carboxyl terminal thioglycine with free phosphoserineThis modified carboxyl end glycine residue is produced by transamidation of S-(glycyl)-L-cysteine (see RESID:AA0206) transiently forming a peptide bond to a free cysteine before the cysteine is released by a peptidase activity.Gcarboxyl-terminalPSI-MOD:01778blocked carboxyl endMOD_RES CysO-cysteine adductAA053030-Sep-201030-Sep-201001-Mar-2013N6-(L-lysyl)-L-lysineN6-(alpha-lysyl)-lysine(2S)-2-amino-6-([(2S)-2,6-diaminohexanoyl]amino)hexanoic acidC 12 H 24 N 4 O 2256.35256.189926C 6 H 12 N 2 O 1128.18128.094963Aoki, H.Xu, J.Emili, A.Chosay, J.G.Golshani, A.Ganoza, M.C.FEBS J. 275, 671-681, 2008Interactions of elongation factor EF-P with the Escherichia coli ribosome.DOI:10.1111/j.1742-4658.2007.06228.xPMID:18201202mass spectrometric detection of a modification with a change in mass of 143.8 Da probably at Lys-34; proposed to be a spermidine derivativeYanagisawa, T.Sumida, T.Ishii, R.Takemoto, C.Yokoyama, S.Nature Struct. Mol. Biol. 17, 1136-1143, 2010A paralog of lysyl-tRNA synthetase aminoacylates a conserved lysine residue in translation elongation factor P.DOI:10.1038/nsmb.1889PMID:20729861mass spectrometric detection of a modification with a change in mass of 127.7 Da at Lys-34; identified as probably being N6-(L-lysyl)-L-lysine produced by enzymatic transfer from lysyl-tRNAThis modification occurs transiently in prokaryotic elogation factor P during production of the mature protein. For the mature form of the EF-P modification, see RESID:AA0531.The modified lysine residue is homologous to the lysine modified to hypusine (see RESID:AA0116) in eukaryotic and archaeal translation initiation factor 5A.translation elongation factor P-lysine N6-lysyltransferase YjeA (EC 2.3.2.-)KGO:0071915GO:0072580PSI-MOD:01779Not availablethis modification is not annotated in UniProt featuresAA053130-Sep-201024-Aug-201231-Dec-20135-hydroxy-N6-(beta-lysyl)-L-lysine5-hydroxy-N6-[(3R)-beta-lysyl]lysineEF-P lysine derivativelysyl spermidine derivative [misidentification]N6-[(3R)-3,6-diaminohexanoyl]-L-5-hydroxylysine(2S)-2-amino-6-([(3R)-3,6-diaminohexanoyl]amino)-5-hydroxyhexanoic acidC 12 H 24 N 4 O 3272.35272.184841C 6 H 12 N 2 O 2144.17144.089878Aoki, H.Xu, J.Emili, A.Chosay, J.G.Golshani, A.Ganoza, M.C.FEBS J. 275, 671-681, 2008Interactions of elongation factor EF-P with the Escherichia coli ribosome.DOI:10.1111/j.1742-4658.2007.06228.xPMID:18201202mass spectrometric detection of a modification with a change in mass of 143.8 Da probably at Lys-34; proposed to be a spermidine derivativeYanagisawa, T.Sumida, T.Ishii, R.Takemoto, C.Yokoyama, S.Nature Struct. Mol. Biol. 17, 1136-1143, 2010A paralog of lysyl-tRNA synthetase aminoacylates a conserved lysine residue in translation elongation factor P.DOI:10.1038/nsmb.1889PMID:20729861mass spectrometric detection of a modification with a change in mass of 127.7 Da at Lys-34; isobaric product of N6-(L-lysyl)-L-lysine produced by an enzyme similar to lysine 2,3-aminomutase.Roy, H.Zou, S.B.Bullwinkle, T.J.Wolfe, B.S.Gilreath, M.S.Forsyth, C.J.Navarre, W.W.Ibba, M.Nature Chem. Biol. 7, 667-669, 2011The tRNA synthetase paralog PoxA modifies elongation factor-P with (R)-beta-lysine.DOI:10.1038/nchembio.632PMID:21841797enzyme kinetics suggests that the preferred substrate for (3R)-beta-lysinePeil, L.Starosta, A.L..Virumäe, K.Atkinson, G.C.Tenson, T.Remme, J.Wilson, D.N.Nature Chem. Biol. 8, 695-697, 2012Lys34 of translation elongation factor EF-P is hydroxylated by YfcM.DOI:10.1038/nchembio.1001PMID:22706199mass spectrometric identification; radiolabelingUde, S.Lassak, J.Starosta, A.L.Kraxenberger, T.Wilson, D.N.Jung, K.Science 339, 82-85, 2013Translation elongation factor EF-P alleviates ribosome stalling at polyproline stretches.DOI:10.1126/science.1228985PMID:23239623determination of functionDoerfel, L.K.Wohlgemuth, I.Kothe, C.Peske, F.Urlaub, H.Rodnina, M.V.Science 339, 85-88, 2013EF-P is essential for rapid synthesis of proteins containing consecutive proline residues.DOI:10.1126/science.1229017PMID:23239624determination of functionYanagisawa, T.Sumida, T.Ishii, R.Takemoto, C.Yokoyama, S.Nature Struct. Mol. Biol. 17, 1136-1143, 2010A paralog of lysyl-tRNA synthetase aminoacylates a conserved lysine residue in translation elongation factor P.DOI:10.1038/nsmb.1889PMID:20729861mass spectrometric detectionSumida, T.Yanagisawa, T.Ishii, R.Yokoyama, S.submitted to the Protein Data Bank, August 2009Crystal Structure of Escherichia coli GenX in complex with elongation factor P.PDB:3A5ZX-ray diffraction, 2.50 angstromsThis modification is produced from N6-acylation of lysine by a lysyl-adenylate. However, evidence on whether alpha- or beta-lysyl adenylate is used, and the intermediates on the pathway appears to be in conflict (see RESID:AA0530). The modified lysine residue is homologous to the lysine modified to hypusine in eukaryotic and archaeal translation initiation factor 5A.The structure of this modification has not been established. The original proposed structure was not hydroxylated. Neither the location of the hydroxyl, shown as a 5-hydroxy, or its stereochemistry is known.translation elongation factor P-lysine 2,3-aminomutase YjeK (EC 5.4.3.-)translation elongation factor P-lysine monooxygenase YfcM (EC 1.14.99.-)KGO:0072580GO:0072581PSI-MOD:01780MOD_RES N6-(3,6-diaminohexanoyl)-5-hydroxylysineAA053230-Sep-201030-Sep-201031-Dec-2011N6-butanoyl-L-lysine(2S)-2-azanyl-6-(butanoylamino)hexanoic acid2-amino-6-butyrylaminocaproic acidepsilon-butanoyl-L-lysineepsilon-butyryl-L-lysineN(zeta)-butanoyllysineN6-(1-oxobutyl)-L-lysineN6-butyryllysine(2S)-2-amino-6-(butanoylamino)hexanoic acidPDBHET:BTKC 10 H 18 N 2 O 2198.27198.136828C 4 H 6 N 0 O 170.0970.041865Chen, Y.Sprung, R.Tang, Y.Ball, H.Sangras, B.Kim, S.C.Falck, J.R.Peng, J.Gu, W.Zhao, Y.Mol. Cell. Proteomics 6, 812-819, 2007Lysine propionylation and butyrylation are novel post-translational modifications in histones.DOI:10.1074/mcp.M700021-MCP200PMID:17267393the modification is not chemically characterized and isobaric alternatives are not eliminatedVollmuth, F.Geyer, M.Angew. Chem. Int. Ed. Engl. 49, 6768-6772, 2010Interaction of propionylated and butyrylated histone H3 lysine marks with Brd4 bromodomains.DOI:10.1002/anie.201002724PMID:20715035X-ray diffraction, 1.65 angstroms; iosthermal titration calorimetry; binding of butanoylated lysine histone peptide is found to be unspecific and too weak to be measured as compared with the corresponding acetylated peptideVollmuth, V.Geyer, M.submitted to the Protein Data Bank, May 2010Crystal structure of Brd4 bromodomain 1 with butyrylated histone H3-K(buty)14.PDB:3MULX-ray diffraction, 1.65 angstromsA metabolic source for butanoic acid in the nucleus is not evident, and a responsible generating enzyme activity is not identified.KPSI-MOD:01781lipoproteinNot availablethis modification is not annotated in UniProt featuresAA053330-Sep-201030-Sep-201031-May-2018N-methyl-L-serineN-methylserine(2S)-3-hydroxy-2-(methylamino)propanoic acidCAS:2480-26-4C 4 H 7 N 1 O 2101.10101.047678C 1 H 2 N 0 O 014.0314.015650Tooley, C.E.Petkowski, J.J.Muratore-Schroeder, T.L.Balsbaugh, J.L.Shabanowitz, J.Sabat, M.Minor, W.Hunt, D.F.Macara, I.G.Nature 466, 1125-1128, 2010NRMT is an alpha-N-methyltransferase that methylates RCC1 and retinoblastoma protein.DOI:10.1038/nature09343PMID:20668449Polypeptides with monomethylated amino terminals can undergo premature cleavage during the coupling step of an Edman degradation. This can result in "preview" with both a residue and the following residue being seen from the first step on through a sequence.N-terminal RCC1 methyltransferaseprotein N-terminal methyltransferaseS-adenosyl-L-methionine:N-terminal-(A,P,S)PK-[protein] methyltransferase (EC 2.1.1.244)protein N-terminal monomethyltransferaseS-adenosyl-L-methionine:N-terminal-(A,P,S)PK-[protein] monomethyltransferase (EC 2.1.1.299)SGO:0035570GO:0035571PSI-MOD:01782methylated amino endMOD_RES N-methylserineAA053430-Sep-201030-Sep-201031-May-2018N,N-dimethyl-L-serineN,N-dimethylserine(2S)-2-(dimethylamino)propanoic acidC 5 H 10 N 1 O 2116.14116.071154C 2 H 4 N 0 O 028.0528.031300Tooley, C.E.Petkowski, J.J.Muratore-Schroeder, T.L.Balsbaugh, J.L.Shabanowitz, J.Sabat, M.Minor, W.Hunt, D.F.Macara, I.G.Nature 466, 1125-1128, 2010NRMT is an alpha-N-methyltransferase that methylates RCC1 and retinoblastoma protein.DOI:10.1038/nature09343PMID:20668449For alpha-aino acids, both N-alpha-monomethylation, and N-alpha protonation and complete trimethylation have been observed, but incomplete dimethylation has not been reported as the end result of a natural process.N-terminal RCC1 methyltransferaseprotein N-terminal methyltransferaseS-adenosyl-L-methionine:N-terminal-(A,P,S)PK-[protein] methyltransferase (EC 2.1.1.244)Samino-terminalGO:0035570GO:0035572PSI-MOD:01783blocked amino endmethylated amino endMOD_RES N,N-dimethylserineAA053530-Sep-201030-Sep-201031-May-2018N,N,N-trimethyl-L-serine(1S)-1-carboxy-2-hydroxy-N,N,N-trimethylethanazanium(2S)-2-trimethylammonio-3-hydroxypropanoic acidN,N,N-trimethylserine cationN,N,N-trimethylserinium(1S)-1-carboxy-2-hydroxy-N,N,N-trimethylethanaminiumC 6 H 13 N 1 O 21+131.17131.094080C 3 H 7 N 0 O 01+43.0943.054227Henry, G.D.Trayer, I.P.Brewer, S.Levine, B.A.Eur. J. Biochem. 148, 75-82, 1985The widespread distribution of alpha-N-trimethylalanine as the N-terminal amino acid of light chains from vertebrate striated muscle myosins.DOI:10.1111/j.1432-1033.1985.tb08809.xPMID:3979397(1)H-NMR detection of N,N,N-trimethylated amino terminal "slightly downfield" of N,N,N-trimethylalanine in bovine cardiac myosin regulatory light chain 2, see UniProtKB:Q3SZE5Tooley, C.E.Petkowski, J.J.Muratore-Schroeder, T.L.Balsbaugh, J.L.Shabanowitz, J.Sabat, M.Minor, W.Hunt, D.F.Macara, I.G.Nature 466, 1125-1128, 2010NRMT is an alpha-N-methyltransferase that methylates RCC1 and retinoblastoma protein.DOI:10.1038/nature09343PMID:20668449Consult FAQ at http://pir.georgetown.edu/resid/faq.shtml#q12 concerning calculation of the difference formula.N-terminal RCC1 methyltransferaseprotein N-terminal methyltransferaseS-adenosyl-L-methionine:N-terminal-(A,P,S)PK-[protein] methyltransferase (EC 2.1.1.244)Samino-terminalGO:0035570GO:0035573PSI-MOD:01784blocked amino endmethylated amino endMOD_RES N,N,N-trimethylserineAA053630-Sep-201013-Sep-201331-May-2018O-(L-isoglutamyl)-L-threonine(2S,3R)-2-amino-3-([(4S)-4-amino-4-carboxybutanoyl]oxy)-propanoic acid5-(threon-O3-yl)glutamateO(beta)-(gamma-glutamyl)threonineO3-(isoglutamyl)threonine(2S)-2-amino-5-([(1S,2R)-1-amino-1-carboxypropan-2-yl]oxy)-5-oxopentanoic acidC 9 H 14 N 2 O 5230.22230.090272C 9 H 12 N 2 O 4212.20212.079707C 5 H 7 N 1 O 3129.12129.042593C 0 H -3 N -1 O 0-17.03-17.026549Palm, G.J.Lubkowski, J.Derst, C.Schleper, S.Röhm, K.H.Wlodawer, A.FEBS Lett. 390, 211-216, 1996A covalently bound catalytic intermediate in Escherichia coli asparaginase: crystal structure of a Thr-89-Val mutant.DOI:10.1016/0014-5793(96)00660-6PMID:8706862X-ray diffraction, 2.20 angstroms; a Thr-89-Val mutant has a trapped covalent intermediateInoue, M.Hiratake, J.Suzuki, H.Kumagai, H.Sakata, K.Biochemistry 39, 7764-7771, 2000Identification of catalytic nucleophile of Escherichia coli gamma-glutamyltranspeptidase by gamma-monofluorophosphono derivative of glutamic acid: N-terminal thr-391 in small subunit is the nucleophile.DOI:10.1021/bi000220pPMID:10869181mass-spectrometric analysis of chemically labeled active site; Fig. 6 sequence should read TTHYSVVDK which matches the translation and the massesOkada, T.Suzuki, H.Wada, K.Kumagai, H.Fukuyama, K.Proc. Natl. Acad. Sci. U.S.A. 103, 6471-6476, 2006Crystal structures of gamma-glutamyltranspeptidase from Escherichia coli, a key enzyme in glutathione metabolism, and its reaction intermediate.DOI:10.1073/pnas.0511020103PMID:16618936the active site threonine of gamma-glutamyltranspeptidase forms a gamma-glutamyl ester intermediateOkada, T.Wada, K.Fukuyama, K.submitted to the Protein Data Bank, December 2005Crystal structure of gamma-glutamyltranspeptidase from Escherichia coli acyl-enzyme intermediate.PDB:2DBWX-ray diffraction, 1.80 angstromsAbdul Ajees, A.Gunasekaran, K.Volanakis, J.E.Narayana, S.V.Kotwal, G.J.Murthy, H.M.Nature 444, 221-225, 2006The structure of complement C3b provides insights into complement activation and regulation.DOI:10.1038/nature05258PMID:17051152X-ray diffraction, 2.26 angstroms; N-acetyl-L-threonine is the model substrateAbdul Ajees, A.Gunasekaran, K.Volanakis, J.E.Narayana, S.V.Kotwal, G.J.Murthy, H.M.submitted to the Protein Data Bank, July 2006Structure of complement C3B: Insights into complement activation and regulation.PDB:2HR0X-ray diffraction, 2.26 angstroms; N-acetyl-L-threonine is the model substrate; Caution: structures from the laboratory of H.M. Murthy have been withdrawn at the request of the University of Alabama, and although this report has been questioned, it has not been withdrwanJanssen, B.J.Read, R.J.Brünger, A.T.Gros, P.Nature 448, E1-2; discussion E2-E1-2; discussion E3, 2007Crystallography: crystallographic evidence for deviating C3b structure.DOI:10.1038/nature06102PMID:17687277report of inconsistencies among structuresWada, K.Hiratake, J.Irie, M.Okada, T.Yamada, C.Kumagai, H.Suzuki, H.Fukuyama, K.J. Mol. Biol. 380, 361-372, 2008Crystal structures of Escherichia coli gamma-glutamyltranspeptidase in complex with azaserine and acivicin: novel mechanistic implication for inhibition by glutamine antagonists.DOI:10.1016/j.jmb.2008.05.007PMID:18555071X-ray diffraction, 1.65 angstromsThe formula and records labeled "TQX" refers to O3-(isoglutamyl)threonine produced as an ester cross-link of a peptidyl threonine residue and a peptidyl glutamic acid residue. The ester cross-link between threonine residues of target proteins and complement C3 and C4 glutamine residues occurs autocatalytically after C3 and C4 form internal intermediate thioester cross-links with the liberation of ammonia.The formula and records labeled "THR" refers to O3-(isoglutamyl)threonine produced as a peptidyl threonine residue ester bonded to a free glutamine with the release of ammonia. The isoglutamylation modification of threonine by glutamine is predicted to be produced by autocatalysis as an intermediate in the catalytic cycle of glutaminases that are homologous to asparaginase.autocatalyticTPSI-MOD:01785Q, Tcross-link 2PSI-MOD:01952Not availablethis modification is not annotated in UniProt featuresAA053730-Sep-201030-Sep-201029-Oct-20103'-nitro-L-tyrosine3-nitro-L-tyrosine3-nitrotyrosinem-nitrotyrosinemeta-nitrotyrosine(2S)-2-amino-3-(4-hydroxy-3-nitrophenyl)propanoic acidCAS:3604-79-3CAS:621-44-3ChEBI:44454PDBHET:NIYC 9 H 8 N 2 O 4208.17208.048407C 0 H -1 N 1 O 245.0044.985078Lyashenko, A.V.Bento, I.Zaitsev, V.N.Zhukhlistova, N.E.Zhukova, Y.N.Gabdoulkhakov, A.G.Morgunova, E.Y.Voelter, W.Kachalova, G.S.Stepanova, E.V.Koroleva, O.V.Lamzin, V.S.Tishkov, V.I.Betzel, C.Lindley, P.F.Mikhailov, A.M.J. Biol. Inorg. Chem. 11, 963-973, 2006X-ray structural studies of the fungal laccase from Cerrena maxima.DOI:10.1007/s00775-006-0158-xPMID:16944230X-ray diffraction, 1.9 angstroms; the sequence was modeled by homology; the protein was not artifactually exposed to peroxynitrite; no chemical evidence was obtained for this modificationLyashenko, A.V.Zhukova, Y.N.Mikhailov, A.M.submitted to the Protein Data Bank, June 2008Crystal structure studies of laccase from Cerrena maxima at 1.76 A resolution.PDB:3DIVX-ray diffraction, 1.76 angstromsThis modification is produced artifactually by treatment with peroxynitrite.YPSI-MOD:01786MOD_RES 3'-NitrotyrosineAA053829-Oct-201029-Oct-201031-May-2018N,N-dimethyl-L-leucine2-(dimethylamino)-4-methylvaleric acid2-(dimethylazanyl)-4-methylpentanoic acidN,N-dimethylleucine(2S)-2-(dimethylamino)-4-methylpentanoic acidC 8 H 16 N 1 O 1142.22142.123189C 2 H 4 N 0 O 028.0528.031300Armirotti, A.Damonte, G.Pozzolini, M.Mussino, F.Cerrano, C.Salis, A.Benatti, U.Giovine, M.J. Proteome Res. 8, 3995-4004, 2009Primary structure and post-translational modifications of silicatein beta from the marine sponge Petrosia ficiformis (Poiret, 1789).DOI:10.1021/pr900342yPMID:19522542mass spectrometric identification; the authors do not provide numeric data to support their mass-spectrometric interpretationsprotein N-terminal methyltransferase (EC 2.1.1.-)Lamino-terminalPSI-MOD:01806blocked amino endmethylated amino endMOD_RES N,N-dimethylleucineAA053929-Oct-201029-Oct-201031-Mar-2012N-formyl-L-glutamic acid2-(formylazanyl)pentanedioic acid2-formamidopentanedioic acid2-formylaminopentanedioic acid(2S)-2-(formylamino)pentanedioic acidC 6 H 8 N 1 O 4158.13158.045333C 1 H 0 N 0 O 128.0127.994915Shen, P.-T.Hsu, J.-L.Chen, S.-H.Anal. Chem. 79, 9520-9530, 2007Dimethyl isotope-coded affinity selection for the analysis of free and blocked N-termini of proteins using LC-MS/MS.DOI:10.1021/ac701678hPMID:18001127it is extremely improbable that the source tissue MCF-7, a mammary tumor cell line, produces a processed immunoglobulin, and the enzymatic origin of the modification in that tissue is not explained; authors' initials in the PubMed citation are correctedEamino-terminalPSI-MOD:01807blocked amino endformylationNot availablethis dubious modification is not currently annotated in UniProt featuresAA054029-Nov-201029-Nov-201030-Sep-2011L-cysteine 3-hydroxy-2,5-pyridinedicarboxylic acid6-[1-azanyl-2-sulfanylethyl]-3-hydroxypyridine-2,5-dicarboxylic acid6-[(1R)-1-amino-2-sulfanylethyl]-3-hydroxypyridine-2,5-dicarboxylic acidPDBHET:MH6C 9 H 7 N 2 O 3 S 1223.23223.017738C 0 H -8 N -1 O -2 S 0-54.07-54.055504Pascard, C.Ducruix, A.Lunel, J.Prangé, T.J. Am. Chem. Soc. 99, 6418-6423, 1977Highly modified cysteine-containing antibiotics. Chemical structure and configuration of nosiheptide.DOI:10.1021/ja00461a039PMID:893891X-ray diffraction; the resolution is not specified; the structure is deposited in the Cambridge Structural Database entry NOSHEP10Harms, J.M.Wilson, D.N.Schluenzen, F.Connell, S.R.Stachelhaus, T.Zaborowska, Z.Spahn, C.M.Fucini, P.Mol. Cell 30, 26-38, 2008Translational regulation via L11: molecular switches on the ribosome turned on and off by thiostrepton and micrococcin.DOI:10.1016/j.molcel.2008.01.009PMID:18406324X-ray diffraction, 2.50 angstromsHarms, J.M.Wilson, D.N.Schluenzen, F.Connell, S.R.Stachelhaus, T.Zaborowska, Z.Spahn, C.M.Fucini, P.submitted to the Protein Data Bank, March 2008Thiopeptide antibiotic nosiheptide bound to the large ribosomal subunit of Deinococcus radiodurans.PDB:2ZJPX-ray diffraction, 3.70 angstromsYu, Y.Duan, L.Zhang, Q.Liao, R.Ding, Y.Pan, H.Wendt-Pienkowski, E.Tang, G.Shen, B.Liu, W.ACS Chem. Biol. 4, 855-864, 2009Nosiheptide biosynthesis featuring a unique indole side ring formation on the characteristic thiopeptide framework.DOI:10.1021/cb900133xPMID:19678698Formed by the metathesis of two didehydroalanines made from serines, condensation with a cysteine carbonyl and dehydrogenation.This modification is currently represented in the PDB as part of the HET group for the entire molecule of nosiheptide.C, S, Scross-link 3incidental to RESID:AA0244PSI-MOD:01814pyridine ringCROSSLNK 3-hydroxypyridine-2,5-dicarboxylic acid (Ser-Ser) (with C-...)CROSSLNK 3-hydroxypyridine-2,5-dicarboxylic acid (Ser-Cys) (with S-...)AA054129-Nov-201029-Nov-201031-Dec-2011L-glutamate thiazole-4-carboxylic acid2-[-1-azanyl-3-carboxypropyl]-1,3-thiazole-4-carboxylic acid2-[(1S)-1-amino-3-carboxypropyl]-1,3-thiazole-4-carboxylic acidPDBHET:BB9C 8 H 8 N 2 O 3 S 1212.22212.025563C 0 H -4 N 0 O -1 S 0-20.03-20.026215Pascard, C.Ducruix, A.Lunel, J.Prangé, T.J. Am. Chem. Soc. 99, 6418-6423, 1977Highly modified cysteine-containing antibiotics. Chemical structure and configuration of nosiheptide.DOI:10.1021/ja00461a039PMID:893891X-ray diffractionHarms, J.M.Wilson, D.N.Schluenzen, F.Connell, S.R.Stachelhaus, T.Zaborowska, Z.Spahn, C.M.Fucini, P.Mol. Cell 30, 26-38, 2008Translational regulation via L11: molecular switches on the ribosome turned on and off by thiostrepton and micrococcin.DOI:10.1016/j.molcel.2008.01.009PMID:18406324X-ray diffraction, 2.50 angstromsHarms, J.M.Wilson, D.N.Schluenzen, F.Connell, S.R.Stachelhaus, T.Zaborowska, Z.Spahn, C.M.Fucini, P.submitted to the Protein Data Bank, March 2008Thiopeptide antibiotic nosiheptide bound to the large ribosomal subunit of Deinococcus radiodurans.PDB:2ZJPX-ray diffraction, 3.70 angstromsYu, Y.Duan, L.Zhang, Q.Liao, R.Ding, Y.Pan, H.Wendt-Pienkowski, E.Tang, G.Shen, B.Liu, W.ACS Chem. Biol. 4, 855-864, 2009Nosiheptide biosynthesis featuring a unique indole side ring formation on the characteristic thiopeptide framework.DOI:10.1021/cb900133xPMID:19678698Formed by the condensation of a cysteine thiol with the carbonyl of the preceding residue and alpha-beta dehydrogenation.This modification is currently represented in the PDB as part of the HET group for the entire molecule of nosiheptide.peptidyl-cysteine cyclase (EC 4.2.1.-)peptidyl-thiazoline dehydrogenase (EC 1.3.-.-)C, Ecross-link 1incidental to RESID:AA0487incidental to RESID:AA0488PSI-MOD:01815oxazole/thiazole ringthioether bondCROSSLNK Thiazole-4-carboxylic acid (Glu-Cys)AA054231-Dec-201031-Dec-201025-Feb-20112'-hydroxy-L-tryptophan2-azanyl-3-(2-hydroxy-1H-indol-3-yl)propanoic acid2-hydroxy-L-tryptophan2-hydroxy-tryptophan(2S)-2-amino-3-(2-hydroxy-1H-indol-3-yl)propanoic acidPDBHET:TROC 11 H 10 N 2 O 2202.21202.074228C 0 H 0 N 0 O 116.0015.994915Oubrie, A.Rozeboom, H.J.Kalk, K.H.Huizinga, E.G.Dijkstra, B.W.J. Biol. Chem. 277, 3727-3732, 2002Crystal structure of quinohemoprotein alcohol dehydrogenase from Comamonas testosteroni: structural basis for substrate oxidation and electron transfer.DOI:10.1074/jbc.M109403200PMID:11714714X-ray diffraction, 1.44 angstroms; the modification is not discussed in the paperRozeboom, H.J.Oubrie, A.submitted to the Protein Data Bank, November 2001Crystal structure of quinohemoprotein alcohol dehydrogenase from Comamonas testosteroni.PDB:1KB0X-ray diffraction, 1.44 angstroms; in the PDB entry the modification is assigned the HET group TRO and called 2-hydroxy-tryptophan; both CG and CD1 are trigonal planarThis modification may be produced artifactually.WPSI-MOD:01816hydroxylationNot availablethis modification is not annotated in UniProt featuresAA054331-Dec-201031-Dec-201025-Feb-20112'-oxo-L-tryptophan2-azanyl-3-[(3S)-2-oxo-2,3-dihydro-1H-indol-3-yl]propanoic acid2-oxo-L-tryptophan2-oxotryptophan(2S)-2-amino-3-[(3S)-2-oxo-2,3-dihydro-1H-indol-3-yl]propanoic acidPDBHET:TROC 11 H 10 N 2 O 2202.21202.074228C 0 H 0 N 0 O 116.0015.994915Lubkowski, J.Hennecke, F.Plückthun, A.Wlodawer, A.Nature Struct. Biol. 5, 140-147, 1998The structural basis of phage display elucidated by the crystal structure of the N-terminal domains of g3p.DOI:10.1038/nsb0298-140PMID:9461080X-ray diffraction, 1.46 angstroms; the authors model the modification as 2'-oxotryptophan with CD1 trigonal planar and CG tetrahedral; the modification is not chemically characterizedLubkowski, J.Hennecke, F.Pluckthun, A.Wlodawer, A.submitted to the Protein Data Bank, December 1997Crystal structure of the N-terminal domains of bacteriophage minor coat protein G3P.PDB:1G3PX-ray diffraction, 1.46 angstroms; in the PDB entry the modification is assigned the HET group TRO and called 2-hydroxy-tryptophanThis modification, which is not observed in other preparations of the same protein, is probably produced artifactually.WPSI-MOD:01817Not availablethis modification is not annotated in UniProt featuresAA054431-Dec-201031-Dec-201031-May-20181-(L-tryptophan-3-yl)-L-tryptophan(2S,2'S)-3,3'-(3'H-1,3'-biindole-3,3'-diyl)bis(2-aminopropanoic acid)2-amino-3-[2-[2-amino-3-(2-carboxyethyl)-1H-indol-4-yl]-1H-indol-3-yl]propanoic acid3-[2-azanyl-2-carboxyethyl]-3-(3-[2-azanyl-2-carboxyethyl]-1H-indol-2-yl)-1H-indoleditryptophan3-[(2S)-2-amino-2-carboxyethyl]-3-(3-[(2S)-2-amino-2-carboxyethyl]-1H-indol-2-yl)-1H-indoleC 22 H 18 N 4 O 2370.41370.142976C 0 H -2 N 0 O 0-2.02-2.015650Medinas, D.B.Gozzo, F.C.Santos, L.F.Iglesias, A.H.Augusto, O.Free Radic. Biol. Med. 49, 1046-1053, 2010A ditryptophan cross-link is responsible for the covalent dimerization of human superoxide dismutase 1 during its bicarbonate-dependent peroxidase activity.DOI:10.1016/j.freeradbiomed.2010.06.018PMID:20600836mass spectrometric and linkage analysisThe production of this cross-link during bicarbonate-dependent peroxidase catalysis may be artifactual.autocatalyticW, Wcross-link 2PSI-MOD:01818CROSSLNK 1-(tryptophan-3-yl)-tryptophan (Trp-Trp)AA054531-Dec-201031-Dec-201031-May-2018N6-succinyl-L-lysine2-azanyl-6-[(3-carboxypropanoyl)azanyl]hexanoic acid4-[[(5S)-5-amino-6-hydroxy-6-oxohexyl]amino]-4-oxobutanoateN(epsilon)-(succinyl)lysinesuccinyllysine(2S)-2-amino-6-[(3-carboxypropanoyl)amino]hexanoic acidCAS:52685-16-2C 10 H 16 N 2 O 4228.25228.111007C 4 H 4 N 0 O 3100.07100.016044Platt, T.Files, J.G.Weber, K.J. Biol. Chem. 248, 110-121, 1973Lac repressor. Specific proteolytic destruction of the NH2-terminal region and loss of the deoxyribonucleic acid-binding activity.PMID:4571224chemical synthesis and chromatographic detectionDimick, S.M.Powell, S.C.McMahon, S.A.Moothoo D.N.Naismith, J.H.Toone, E.J.J. Am. Chem. Soc. 121, 10286-10296, 1999On the Meaning of Affinity: Cluster Glycoside Effects and Concanavalin A.DOI:10.1021/ja991729eX-ray diffraction, 2.66 angstromsNaismith, J.H.submitted to the Protein Data Bank, April 1999Room temperature structure of concanavalin A complexed to bivalent ligand.PDB:1QGLX-ray diffraction, 2.66 angstroms; each subunit of a homodimer contains one succinylated lysine, but the modification can be resolved only in one subunit, and the distance from NZ to C1 is 4.44 angstromsKawai, Y.Fujii, H.Okada, M.Tsuchie, Y.Uchida, K.Osawa, T.J. Lipid Res. 47, 1386-1398, 2006Formation of Nepsilon-(succinyl)lysine in vivo: a novel marker for docosahexaenoic acid-derived protein modification.DOI:10.1194/jlr.M600091-JLR200PMID:16582421chromatographic detection; mass spectrometric identification; a major product after radical-catalyzed peroxidation of docosahexaenoic acidZhang, Z.Tan, M.Xie, Z.Dai, L.Chen, Y.Zhao, Y.Nature Chem. Biol. 7, 58-63, 2011Identification of lysine succinylation as a new post-translational modification.DOI:10.1038/nchembio.495PMID:21151122mass spectrometric detection; chromatographic and radiolabeling identificationDu, J.Zhou, Y.Su, X.Yu, J.J.Khan, S.Jiang, H.Kim, J.Woo, J.Kim, J.H.Choi, B.H.He, B.Chen, W.Zhang, S.Cerione, R.A.Auwerx, J.Hao, Q.Lin, H.Science 334, 806-809, 2011Sirt5 is a NAD-dependent protein lysine demalonylase and desuccinylase.DOI:10.1126/science.1207861PMID:22076378mass spectrometric identification in a number of mitochondrial proteins; identification of Sirt5 as a desuccinylase and increase of detectable succinylation of carbamoyl phosphate synthase 1 when Sirt5 is deletedThe responsible generating enzyme activity is not identified. This modification can be reversed by Sirt5.KPSI-MOD:01819MOD_RES N6-succinyllysineAA054625-Feb-201125-Feb-201131-Dec-2011L-allo-isoleucine2-azanyl-3-methylpentanoic acid3-methyl-norvalineallo-L-isoleucinealpha-amino-beta-methylvaleric acidL-threo-isoleucine(2S,3R)-2-amino-3-methylpentanoic acidCAS:1509-34-8ChEBI:30008C 6 H 11 N 1 O 1113.16113.084064C 0 H 0 N 0 O 00.000.000000Minami, Y.Yoshida, K.Azuma, R.Urakawa, A.Kawauchi, T.Otani, T.Komiyama, K.Omura, S.Tetrahedron Lett. 35, 8001-8004, 1994Structure of cypemycin, a new peptide antibiotic.DOI:10.1016/0040-4039(94)80033-2mass spectrometric, (1)H-NMR, and (13)C-NMR identificationClaesen, J.Bibb, M.Proc. Natl. Acad. Sci. U.S.A. 107, 16297-16302, 2010Genome mining and genetic analysis of cypemycin biosynthesis reveal an unusual class of posttranslationally modified peptides.DOI:10.1073/pnas.1008608107PMID:20805503gene sequence for the encoded peptide, biosynthesisprotein-isoleucine 3-epimerase (EC 5.1.1.-)IPSI-MOD:01840MOD_RES L-allo-isoleucineAA054725-Feb-201125-Feb-201120-May-2011(E)-dehydrobutyrine(E)-2-amino-2-butenoic acid(E)-2-aminobutenoic acid2,3-didehydrobutyrine3-methyldehydroalaninealpha,beta-dehydroaminobutyric acidanhydrothreonineDhbmethyl-dehydroalanine(2E)-2-aminobut-2-enoic acidC 4 H 5 N 1 O 183.0983.037114C 0 H -2 N 0 O -1-18.02-18.010565Piard, J.C.Kuipers, O.P.Rollema, H.S.Desmazeaud, M.J.de Vos, W.M.J. Biol. Chem. 268, 16361-16368, 1993Structure, organization, and expression of the lct gene for lacticin 481, a novel lantibiotic produced by Lactococcus lactis.PMID:8344922the E- and Z- isomers are distinguished by (1)H-NOE NMRMinami, Y.Yoshida, K.Azuma, R.Urakawa, A.Kawauchi, T.Otani, T.Komiyama, K.Omura, S.Tetrahedron Lett. 35, 8001-8004, 1994Structure of cypemycin, a new peptide antibiotic.DOI:10.1016/0040-4039(94)80033-2mass spectrometric, (1)H-NMR, and (13)C-NMR identificationClaesen, J.Bibb, M.Proc. Natl. Acad. Sci. U.S.A. 107, 16297-16302, 2010Genome mining and genetic analysis of cypemycin biosynthesis reveal an unusual class of posttranslationally modified peptides.DOI:10.1073/pnas.1008608107PMID:20805503gene sequence for the encoded peptide, biosynthesisIn some cases it has not been firmly established whether the natural form is the Z or the E isomer. For the Z isomer, see RESID:AA0182.A 2,3-didehydro amino acid blocks Edman degradation.protein-threonine dehydratase (EC 4.2.1.-)TPSI-MOD:00190PSI-MOD:01470MOD_RES (E)-2,3-didehydrobutyrineMOD_RES 2,3-didehydrobutyrinethis UniProt feature is used when the stereochemistry has not been determinedAA054825-Feb-201125-Feb-201120-May-2011S-(2-aminovinyl)-L-cysteine(R,Z)-S-(2-aminovinyl)cysteine(2R)-2-amino-3-([(Z)-2-aminoethenyl]sulfanyl)propanoic acidC 5 H 7 N 2 O 1 S 1143.18143.027909C -1 H -4 N 0 O -2 S -1-80.10-79.993200Minami, Y.Yoshida, K.Azuma, R.Urakawa, A.Kawauchi, T.Otani, T.Komiyama, K.Omura, S.Tetrahedron Lett. 35, 8001-8004, 1994Structure of cypemycin, a new peptide antibiotic.DOI:10.1016/0040-4039(94)80033-2mass spectrometric, (1)H-NMR, and (13)C-NMR identificationClaesen, J.Bibb, M.Proc. Natl. Acad. Sci. U.S.A. 107, 16297-16302, 2010Genome mining and genetic analysis of cypemycin biosynthesis reveal an unusual class of posttranslationally modified peptides.DOI:10.1073/pnas.1008608107PMID:20805503gene sequence for the encoded peptide, biosynthesis; the authors did not have enough material to determine the stereochemistry and assume that it was the D stereoisomer [private communication]This cross-link arises from the decarboxylation of the carboxyl-terminal portion of a lanthionine, either L-lanthionine (see RESID:AA0110) or meso-lanthionine (see RESID:AA0111).The stereochemistry of the (2-aminovinyl)-cysteine in cypemycin has not been determined. For the D stereoisomer, see RESID:AA0204.peptidyl-cysteine dethiolase (EC 4.4.1.-)peptidyl-cysteine dehydroalanine/dehydrobutyrine ligase (EC 6.2.-.-)C, Ccarboxyl-terminalcross-link 2PSI-MOD:01842blocked carboxyl endlanthioninethioether bondNot availablethis modification is not annotated in UniProt featuresAA054925-Feb-201125-Feb-201125-Feb-20115'-chloro-L-tryptophan(2S)-2-amino-3-(5-chloro-1H-indol-3-yl)propanoic acidCAS:33468-35-8C 11 Cl 1 H 9 N 2 O 1220.66220.040341C 0 Cl 1 H -1 N 0 O 034.4433.961028Castiglione, F.Lazzarini, A.Carrano, L.Corti, E.Ciciliato, I.Gastaldo, L.Candiani, P.Losi, D.Marinelli, F.Selva, E.Parenti, F.Chem. Biol. 15, 22-31, 2008Determining the structure and mode of action of microbisporicin, a potent lantibiotic active against multiresistant pathogens.DOI:10.1016/j.chembiol.2007.11.009PMID:18215770mass spectrometric, (1)H-NMR, and (13)C-NMR identificationWPSI-MOD:01843chlorineMOD_RES 5'-chlorotryptophanAA055031-Mar-201131-Mar-201128-Oct-20112-(3-methylbutanoyl)-5-hydroxyoxazole-4-carbothionic acid(4Z)-4-[hydroxy(sulfanyl)methylidene]-2-(3-methylbutanoyl)-1,3-oxazol-5(4H)-one [tautomer]5-hydroxy-2-(3-methylbutanoyl)-1,3-oxazole-4-carbothioic O-acidPDBHET:8LIC 9 H 10 N 1 O 3 S 1212.24212.038139C 0 H -7 N -1 O 1 S 0-5.06-5.062935Kim, H.J.Graham, D.W.DiSpirito, A.A.Alterman, M.A.Galeva, N.Larive, C.K.Asunskis, D.Sherwood, P.M.Science 305, 1612-1615, 2004Methanobactin, a copper-acquisition compound from methane-oxidizing bacteria.DOI:10.1126/science.1098322PMID:15361623mass spectrometric and chemical characterization; X-ray diffraction, 1.5 angstroms; proposed structure in Cambridge Crystallographic Data Center (241254)Behling, L.A.Hartsel, S.C.Lewis, D.E.DiSpirito, A.A.Choi, D.W.Masterson, L.R.Veglia, G.Gallagher, W.H.J. Am. Chem. Soc. 130, 12604-12605, 2008NMR, mass spectrometry and chemical evidence reveal a different chemical structure for methanobactin that contains oxazolone rings.DOI:10.1021/ja804747dPMID:18729522(1)H-NMR, (13)C-NMR and (15)N-NMR identification; structure revisionKrentz, B.D.Mulheron, H.J.Semrau, J.D.Dispirito, A.A.Bandow, N.L.Haft, D.H.Vuilleumier, S.Murrell, J.C.McEllistrem, M.T.Hartsel, S.C.Gallagher, W.H.Biochemistry 49, 10117-10130, 2010A comparison of methanobactins from Methylosinus trichosporium OB3b and Methylocystis strain Sb2 predicts methanobactins are synthesized from diverse peptide precursors modified to create a common core for binding and reducing copper ions.DOI:10.1021/bi1014375PMID:20961038(1)H-NMR, (13)C-NMR and (15)N-NMR identification; structure revision; gene sequence for the encoded peptideEl Ghazouani, A.Baslé, A.Firbank, S.J.Knapp, C.W.Gray, J.Graham, D.W.Dennison, C.Inorg. Chem. 50, 1378-1391, 2011Copper-Binding Properties and Structures of Methanobactins from Methylosinus trichosporium OB3b.DOI:10.1021/ic101965jPMID:21254756X-ray diffraction, 0.92 angstromsEl Ghazouani, A.Basle, A.Firbank, S.J.Knapp, C.W.Gray, J.Graham, D.W.Dennison, C.submitted to the Protein Data Bank, July 2010Structures and copper-binding properties of methanobactins from Methylosinus trichosporium OB3b.PDB:2XJHX-ray diffraction, 2.50 angstromsThe amino group of the following amino acid forms a thiopeptide bond. The amino(sulfanyl)methylidene tautomeric form is shown in the diagram and model.The biosynthesis of this modification from the encoded cysteine peptide has not been elaborated. C, Lamino-terminalcross-link 1PSI-MOD:01844imidazolinone/oxazolinone ringthiopeptide bondMOD_RES 2-(3-methylbutanoyl)-5-hydroxyoxazole-4-carbothionic acid (Leu-Cys)AA055131-Mar-201131-Mar-201128-Oct-2011L-proline 5-hydroxy-oxazole-4-carbothionic acid(4Z)-4-[hydroxy(sulfanyl)methylidene]-2-[(2S)-pyrrolidin-2-yl]-1,3-oxazol-5(4H)-one [tautomer]5-hydroxy-2-[(2S)-pyrrolidin-2-yl]-1,3-oxazole-4-carbothioic O-acidPDBHET:66GC 8 H 8 N 2 O 2 S 1196.22196.030649C 0 H -4 N 0 O 0 S 0-4.03-4.031300Kim, H.J.Graham, D.W.DiSpirito, A.A.Alterman, M.A.Galeva, N.Larive, C.K.Asunskis, D.Sherwood, P.M.Science 305, 1612-1615, 2004Methanobactin, a copper-acquisition compound from methane-oxidizing bacteria.DOI:10.1126/science.1098322PMID:15361623mass spectrometric and chemical characterization; X-ray diffraction, 1.5 angstroms; proposed structure in Cambridge Crystallographic Data Center (241254)Behling, L.A.Hartsel, S.C.Lewis, D.E.DiSpirito, A.A.Choi, D.W.Masterson, L.R.Veglia, G.Gallagher, W.H.J. Am. Chem. Soc. 130, 12604-12605, 2008NMR, mass spectrometry and chemical evidence reveal a different chemical structure for methanobactin that contains oxazolone rings.DOI:10.1021/ja804747dPMID:18729522(1)H-NMR, (13)C-NMR and (15)N-NMR identification; structure revisionKrentz, B.D.Mulheron, H.J.Semrau, J.D.Dispirito, A.A.Bandow, N.L.Haft, D.H.Vuilleumier, S.Murrell, J.C.McEllistrem, M.T.Hartsel, S.C.Gallagher, W.H.Biochemistry 49, 10117-10130, 2010A comparison of methanobactins from Methylosinus trichosporium OB3b and Methylocystis strain Sb2 predicts methanobactins are synthesized from diverse peptide precursors modified to create a common core for binding and reducing copper ions.DOI:10.1021/bi1014375PMID:20961038(1)H-NMR, (13)C-NMR and (15)N-NMR identification; structure revision; gene sequence for the encoded peptideEl Ghazouani, A.Baslé, A.Firbank, S.J.Knapp, C.W.Gray, J.Graham, D.W.Dennison, C.Inorg. Chem. 50, 1378-1391, 2011Copper-Binding Properties and Structures of Methanobactins from Methylosinus trichosporium OB3b.DOI:10.1021/ic101965jPMID:21254756X-ray diffraction, 0.92 angstromsEl Ghazouani, A.Basle, A.Firbank, S.J.Knapp, C.W.Gray, J.Graham, D.W.Dennison, C.submitted to the Protein Data Bank, July 2010Structures and copper-binding properties of methanobactins from Methylosinus trichosporium OB3b.PDB:2XJHX-ray diffraction, 2.50 angstromsThe amino group of the following amino acid forms a thiopeptide bond. The amino(sulfanyl)methylidene tautomeric form is shown in the diagram and model.The biosynthesis of this modification from the encoded cysteine peptide has not been elaborated. C, Pcross-link 1PSI-MOD:01845imidazolinone/oxazolinone ringthiopeptide bondCROSSLNK Proline 5-hydroxy-oxazole-4-carbothionic acid (Pro-Cys)AA055231-Mar-201128-Oct-201128-Oct-2011methanobactin OB3b copper complexbis[4-(hydroxy[sulfanyl-kappaS]methylidene)-1,3-oxazol-5(4H)-onato-kappaN]copperC 6 Cu 1 H 0 N 2 O 4 S 2291.74290.859546C 0 Cu 1 H -10 N 0 O 2 S 085.4684.841176Kim, H.J.Graham, D.W.DiSpirito, A.A.Alterman, M.A.Galeva, N.Larive, C.K.Asunskis, D.Sherwood, P.M.Science 305, 1612-1615, 2004Methanobactin, a copper-acquisition compound from methane-oxidizing bacteria.DOI:10.1126/science.1098322PMID:15361623mass spectrometric and chemical characterization; X-ray diffraction, 1.5 angstroms; proposed structure in Cambridge Crystallographic Data Center (241254)Behling, L.A.Hartsel, S.C.Lewis, D.E.DiSpirito, A.A.Choi, D.W.Masterson, L.R.Veglia, G.Gallagher, W.H.J. Am. Chem. Soc. 130, 12604-12605, 2008NMR, mass spectrometry and chemical evidence reveal a different chemical structure for methanobactin that contains oxazolone rings.DOI:10.1021/ja804747dPMID:18729522(1)H-NMR, (13)C-NMR and (15)N-NMR identification; structure revisionKrentz, B.D.Mulheron, H.J.Semrau, J.D.Dispirito, A.A.Bandow, N.L.Haft, D.H.Vuilleumier, S.Murrell, J.C.McEllistrem, M.T.Hartsel, S.C.Gallagher, W.H.Biochemistry 49, 10117-10130, 2010A comparison of methanobactins from Methylosinus trichosporium OB3b and Methylocystis strain Sb2 predicts methanobactins are synthesized from diverse peptide precursors modified to create a common core for binding and reducing copper ions.DOI:10.1021/bi1014375PMID:20961038(1)H-NMR, (13)C-NMR and (15)N-NMR identification; structure revision; gene sequence for the encoded peptideEl Ghazouani, A.Baslé, A.Firbank, S.J.Knapp, C.W.Gray, J.Graham, D.W.Dennison, C.Inorg. Chem. 50, 1378-1391, 2011Copper-Binding Properties and Structures of Methanobactins from Methylosinus trichosporium OB3b.DOI:10.1021/ic101965jPMID:21254756X-ray diffraction, 0.92 angstromsEl Ghazouani, A.Basle, A.Firbank, S.J.Knapp, C.W.Gray, J.Graham, D.W.Dennison, C.submitted to the Protein Data Bank, July 2010Structures and copper-binding properties of methanobactins from Methylosinus trichosporium OB3b.PDB:2XJHX-ray diffraction, 2.50 angstromsThis entry represents the copper binding portions of methanobactin OB3b, which are derived from cysteine residues. The modification of these cysteines, which has not been experimentally elaborated, includes crosslinking with the carboxyl group of residue N-1 to form 1,3-oxazol-5-one rings, and formation of a thiopeptide bond with the amino group of residue N+1.The modified residue N-1 is presented in a separate entry and is not included in the mass accounting of this entry. The original carboxyl atom of residue N-1, and the hydroxyl lost from thionic acid in forming the thiopeptide are shown in gray in the diagram. C, Ccross-link 2secondary to RESID:AA0550secondary to RESID:AA0551PSI-MOD:01846coppermetalloproteinMETAL copper [Cu-methanobactin OB3b complex]AA055330-Jun-201130-Jun-201128-Oct-20112-(4-guanidinobutanoyl)-5-hydroxyimidazole-4-carbothionic acid(4Z)-2-(4-guanidinobutanoyl)-5-oxo-4-(sulfanylmethylidene)-4,5-dihydro-1H-imidazole2-(4-guanidinobutanoyl)-5-hydroxy-4-thioformyl-1H-imidazole [tautomer]2-(4-guanidinobutanoyl)-5-hydroxy-1H-imidazole-4-carbothioic O-acidC 9 H 12 N 5 O 2 S 1254.29254.071171C 0 H -6 N 0 O 0 S 0-6.05-6.046950Krentz, B.D.Mulheron, H.J.Semrau, J.D.Dispirito, A.A.Bandow, N.L.Haft, D.H.Vuilleumier, S.Murrell, J.C.McEllistrem, M.T.Hartsel, S.C.Gallagher, W.H.Biochemistry 49, 10117-10130, 2010A comparison of methanobactins from Methylosinus trichosporium OB3b and Methylocystis strain Sb2 predicts methanobactins are synthesized from diverse peptide precursors modified to create a common core for binding and reducing copper ions.DOI:10.1021/bi1014375PMID:20961038(1)H-NMR, (13)C-NMR and (15)N-NMR identificationThe amino group of the following amino acid forms a thiopeptide bond. This is an amino(sulfanyl)methylidene in the tautomeric form, which is shown in the diagram and model.C, Ramino-terminalcross-link 1PSI-MOD:01877imidazolinone/oxazolinone ringthiopeptide bondCROSSLNK 2-(4-guanidinobutanoyl)-5-hydroxyimidazole-4-carbothionic acid (Arg-Cys)AA055430-Jun-201130-Jun-201128-Oct-2011L-threonine 5-hydroxy-oxazole-4-carbonthionic acid(4Z)-2-[(1S,2R)-1-amino-2-hydroxypropyl]-4-(sulfanylmethylidene)-1,3-oxazol-5(4H)-one [tautomer]2-[(1S,2R)-1-amino-2-hydroxypropyl]-5-hydroxy-1,3-oxazole-4-carbothioic O-acidC 7 H 8 N 2 O 3 S 1200.21200.025563C 0 H -4 N 0 O 0 S 0-4.03-4.031300Krentz, B.D.Mulheron, H.J.Semrau, J.D.Dispirito, A.A.Bandow, N.L.Haft, D.H.Vuilleumier, S.Murrell, J.C.McEllistrem, M.T.Hartsel, S.C.Gallagher, W.H.Biochemistry 49, 10117-10130, 2010A comparison of methanobactins from Methylosinus trichosporium OB3b and Methylocystis strain Sb2 predicts methanobactins are synthesized from diverse peptide precursors modified to create a common core for binding and reducing copper ions.DOI:10.1021/bi1014375PMID:20961038(1)H-NMR, (13)C-NMR and (15)N-NMR identificationThe amino group of the following amino acid forms a thiopeptide bond. This is an amino(sulfanyl)methylidene in the tautomeric form, which is shown in the diagram and model.C, Tcross-link 1PSI-MOD:01878imidazolinone/oxazolinone ringthiopeptide bondCROSSLNK Threonine 5-hydroxy-oxazole-4-carbonthionic acid (Thr-Cys)AA055530-Jun-201128-Oct-201131-May-2018methanobactin SB2 copper complex[5-(hydroxy[sulfanyl-kappaS]methylene)-3,5-dihydro-4H-imidazol-4-onato-kappaN1][4-(hydroxy[sulfanyl-kappaS]methylene)-1,3-oxazol-5(4H)-onato-kappaN]copperC 6 Cu 1 H 1 N 3 O 3 S 2290.76289.875530C 0 Cu 1 H -9 N 1 O 1 S 084.4883.857161Krentz, B.D.Mulheron, H.J.Semrau, J.D.Dispirito, A.A.Bandow, N.L.Haft, D.H.Vuilleumier, S.Murrell, J.C.McEllistrem, M.T.Hartsel, S.C.Gallagher, W.H.Biochemistry 49, 10117-10130, 2010A comparison of methanobactins from Methylosinus trichosporium OB3b and Methylocystis strain Sb2 predicts methanobactins are synthesized from diverse peptide precursors modified to create a common core for binding and reducing copper ions.DOI:10.1021/bi1014375PMID:20961038(1)H-NMR, (13)C-NMR and (15)N-NMR identificationC, Ccross-link 2secondary to RESID:AA0553secondary to RESID:AA0554PSI-MOD:01879copperMETAL copper [Cu-methanobactin SB2 complex]AA055631-Mar-201131-Mar-201131-Mar-2011L-cysteine sulfonic acid2-amino-2-carboxyethanesulfonic acid2-azanyl-3-sulfopropanoic acid3-sulfoalaninecysteic acidcysteine sulphonic acid(2R)-2-amino-3-sulfopropanoic acidCAS:498-40-8ChEBI:17285PDBHET:OCSC 3 H 5 N 1 O 4 S 1151.14150.993929C 0 H 0 N 0 O 3 S 048.0047.984744Armirotti, A.Damonte, G.Pozzolini, M.Mussino, F.Cerrano, C.Salis, A.Benatti, U.Giovine, M.J. Proteome Res. 8, 3995-4004, 2009Primary structure and post-translational modifications of silicatein beta from the marine sponge Petrosia ficiformis (Poiret, 1789).DOI:10.1021/pr900342yPMID:19522542mass spectrometric identification after treatment with sulfuric/nitric acid (4:1), and ammonium fluoride and hydrofluoric acid; the authors do not provide numeric data to support their mass-spectrometric interpretationsThis modification is easily produced artifactually. Cysteine sulfinic acid (see RESID:AA0262) exposed to air oxidizes to cysteic acid.CPSI-MOD:00460Not availablethis dubious modification is not currently annotated in UniProt featuresAA055731-Mar-201131-Mar-201131-Mar-2011L-cysteine sulfinyl phosphatecysteine sulfinic phosphoryl ester(2R)-2-amino-3-[(phosphonooxy)sulfinyl]propanoic acidC 3 H 6 N 1 O 6 P 1 S 1215.12214.965345C 0 H 1 N 0 O 5 P 1 S 0111.98111.956160Jeong, W.Park, S.J.Chang, T.S.Lee, D.Y.Rhee, S.G.J. Biol. Chem. 281, 14400-14407, 2006Molecular mechanism of the reduction of cysteine sulfinic acid of peroxiredoxin to cysteine by mammalian sulfiredoxin.DOI:10.1074/jbc.M511082200PMID:16565085This modification is probably produced as an intermediate during the ATP mediated reduction of cysteine sulfinic acid (see RESID:AA0262) formed in some proteins during oxidative stress.CPSI-MOD:01847phosphoproteinNot availablethis modification is not annotated in UniProt featuresAA055831-Mar-201131-Mar-201120-May-2011S-(spermidinoglutathion-S-yl)-L-cysteinecysteine glutathionylspermidine disulfideL-gamma-glutamyl-[S-(L-cystein-S-yl)]-L-cysteinyl-N-{3-[(4-aminobutyl)amino]propyl}glycinamide(2R)-2-amino-3-([(2R)-2-([(4S)-4-amino-4-carboxybutanoyl]amino)-2-([2-([3-([4-aminobutyl]amino)propyl]carbamoyl)methyl]carbamoyl)ethyl]disulfanyl)propanoic acidCAS:33932-35-3ChEBI:16613PDBHET:TS5C 20 H 37 N 7 O 6 S 2535.68535.224674C 17 H 32 N 6 O 5 S 1432.54432.215489Chiang, B.Y.Chen, T.C.Pai, C.H.Chou, C.C.Chen, H.H.Ko, T.P.Hsu, W.H.Chang, C.Y.Wu, W.F.Wang, A.H.Lin, C.H.J. Biol. Chem. 285, 25345-25353, 2010Protein S-thiolation by Glutathionylspermidine (Gsp): the role of Escherichia coli Gsp synthetASE/amidase in redox regulation.DOI:10.1074/jbc.M110.133363PMID:20530482Hofmann, B.Budde, H.Bruns, K.Guerrero, S.A.Kalisz, H.M.Menge, U.Montemartini, M.Nogoceke, E.Steinert, P.Wissing, J.B.Flohé, L.Hecht, H.J.J. Biol. Chem. 382, 459-471, 2001Structures of tryparedoxins revealing interaction with trypanothione.DOI:10.1515/BC.2001.056PMID:11347894X-ray diffraction, 1.40 angstromsHofmann, B.Budde, H.Bruns, K.Guerrero, S.A.Kalisz, H.M.Menge, U.Montemartini, M.Nogoceke, E.Steinert, P.Wissing, J.B.Flohe, L.Hecht, H.J.submitted to the Protein Data Bank, February 2001Tryparedoxin II complexed with glutathionylspermidine.PDB:1I5GX-ray diffraction, 1.40 angstromsCPSI-MOD:01848disulfide bondNot availablethis modification is not annotated in UniProt featuresAA055920-May-201120-May-201124-Aug-20122-(L-cystein-S-yl)-methionine(2R)-2-amino-2-([2-amino-2-carboxyethyl]sulfanyl)-4-(methylsulfanyl)butanoic acidC 8 H 12 N 2 O 2 S 2232.32232.034020C 0 H -2 N 0 O 0 S 0-2.02-2.015650Liu, W.T.Yang, Y.L.Xu, Y.Lamsa, A.Haste, N.M.Yang, J.Y.Ng, J.Gonzalez, D.Ellermeier, C.D.Straight, P.D.Pevzner, P.A.Pogliano, J.Nizet, V.Pogliano, K.Dorrestein, P.C.Proc. Natl. Acad. Sci. U.S.A. 107, 16286-16290, 2010Imaging mass spectrometry of intraspecies metabolic exchange revealed the cannibalistic factors of Bacillus subtilis.DOI:10.1073/pnas.1008368107PMID:20805502mass spectrometric and (1)H-NMR identification; the sterochemistry was not determinedThe stereochemistry of the methionine alpha-carbon has not been determined. The R form is shown.C, Mcross-link 2PSI-MOD:01857thioether bondCROSSLNK 2-(S-cysteinyl)-methionine (Cys-Met)AA056020-May-201120-May-201120-Apr-2012S-(N-acetylamino)glucosyl-L-cysteineS-[(N-acetylamino)glycosyl]cysteineS-[beta-D-(N-acetylamino)glucopyranosyl]cysteine(2R)-2-amino-3-(2-acetamido-2-deoxy-beta-D-glucopyranosylsulfanyl)propanoic acidCAS:10036-64-3ChEBI:61631PDBHET:NAGC 11 H 18 N 2 O 6 S 1306.33306.088557C 8 H 13 N 1 O 5 S 0203.19203.079373Stepper, J.Shastri, S.Loo, T.S.Preston, J.C.Novak, P.Man, P.Moore, C.H.Havlíček, V.Patchett, M.L.Norris, G.E.FEBS Lett. 585, 645-650, 2011Cysteine S-glycosylation, a new post-translational modification found in glycopeptide bacteriocins.DOI:10.1016/j.febslet.2011.01.023PMID:21251913mass spectrometric detectionVenugopal, H.Edwards, P.J.Schwalbe, M.Claridge, J.K.Libich, D.S.Stepper, J.Loo, T.Patchett, M.L.Norris, G.E.Pascal, S.M.Biochemistry 50, 2748-2755, 2011Structural, dynamic, and chemical characterization of a novel s-glycosylated bacteriocin.DOI:10.1021/bi200217uPMID:21395300(1)H-NMR, (13)C-NMR and (15)N-NMR identification; stereochemical determinationVenugopal, H.Edwards, P.Schwalbe, M.Claridge, J.Stepper, J.Patchett, M.Loo, T.Libich, D.Norris, G.Pascal, S.submitted to the Protein Data Bank, March 2010Structure of glycocin A.PDB:2KUYNMR structural determinationSee also RESID:AA0152 and RESID:AA0392 for other S-glycosylated cysteines.CPSI-MOD:01858glycoproteinthioether bondCARBOHYD S-linked (GlcNAc)CARBOHYD S-linked (GlcNAc...)CARBOHYD S-linked (HexNAc...)AA056130-Sep-201130-Sep-201130-Sep-2011S-(2-succinyl)-L-cysteine(2R)-2-{[(2R)-2-amino-2-carboxyethyl]sulfanyl}butanedioic acid2-((2-amino-2-carboxyethyl)thio)butanedioic acid2-amino-3-(1,2-dicarboxyethylthio)propanoic acidS-(1,2-dicarboxyethyl)cysteineS-(2-succinyl)cysteineS-[(2R)-2-succinyl]-L-cysteine(2R)-2-amino-3-([(1R)-1,2-dicarboxyethyl]sulfanyl)propanoic acidCAS:34317-60-7PDBHET:SINC 7 H 9 N 1 O 5 S 1219.21219.020143C 4 H 4 N 0 O 4 S 0116.07116.010959Alderson, N.L.Wang, Y.Blatnik, M.Frizzell, N.Walla, M.D.Lyons, T.J.Alt, N.Carson, J.A.Nagai, R.Thorpe, S.R.Baynes, J.W.Arch. Biochem. Biophys. 450, 1-8, 2006S-(2-Succinyl)cysteine: a novel chemical modification of tissue proteins by a Krebs cycle intermediate.DOI:10.1016/j.abb.2006.03.005PMID:16624247chromatographic detection; mass spectrometric identification; identified as an advanced glycation artifactBlatnik, M.Thorpe, S.R.Baynes, J.W.Ann. N. Y. Acad. Sci. 1126, 272-275, 2008Succination of proteins by fumarate: mechanism of inactivation of glyceraldehyde-3-phosphate dehydrogenase in diabetes.DOI:10.1196/annals.1433.047PMID:18448829mass spectrometric identification; identified as the active site cysteine inhibited product of glyceraldehyde-3-phosphate dehydrogenase; an artifact of diabetic stressFisch, F.Fleites, C.M.Delenne, M.Baudendistel, N.Hauer, B.Turkenburg, J.P.Hart, S.Bruce, N.C.Grogan, G.J. Am. Chem. Soc. 132, 11455-11457, 2010A covalent succinylcysteine-like intermediate in the enzyme-catalyzed transformation of maleate to fumarate by maleate isomerase.DOI:10.1021/ja1053576PMID:20677745X-ray diffraction, 1.95 angstroms; directed mutation analysis; trapping of covalent intermediateFisch, F.Martinez-Fleites, C.Baudendistel, N.Hauer, B.Turkenburg, J.P.Hart, S.Bruce, N.C.Grogan, G.submitted to the Protein Data Bank, May 2010Nocardia farcinica maleate cis-trans isomerase C194S mutant with A covalently bound succinylcysteine intermediate.PDB:2XEDX-ray diffraction, 1.95 angstromsThis modification is produced in the active site inhibition of glyceraldehyde-3-phosphate dehydrogenase by fumarate, but as the active site intermediate in maleate isomerase.autocatalyticCPSI-MOD:01889Not availablethis modification is not annotated in UniProt featuresAA056220-May-201120-May-201130-Jun-2011N,N-(L-cysteine-1,S-diyl)-L-phenylalanine2-(4-amino-3-oxo-isothiazolidin-2-yl)-3-phenylpropanoic acid4-amino-3-isothiazolidinone-L-phenylalaninecysteinyl phenylalanine sulfenamidephenylalanine-cysteine sulfenyl amide cross-linkphenylalanine-cysteine sulphenyl amide cross-link(2S)-2-[(4R)-4-amino-3-oxo-1,2-thiazolidin-2-yl]-3-phenylpropanoic acidC 12 H 12 N 2 O 2 S 1248.30248.061949C 0 H -2 N 0 O 0 S 0-2.02-2.015650Lee, J.W.Soonsanga, S.Helmann, J.D.Proc. Natl. Acad. Sci. U.S.A. 104, 8743-8748, 2007A complex thiolate switch regulates the Bacillus subtilis organic peroxide sensor OhrR.DOI:10.1073/pnas.0702081104PMID:17502599mass spectrometric detection; the modification is not chemically characterizedThis cross-link is formed by the condensation of a cysteine residue sulfhydryl with the alpha-amido of the following residue.autocatalyticC, Fcross-link 1PSI-MOD:01859isothiazole ringCROSSLNK N,N-(cysteine-1,S-diyl)phenylalanine (Cys-Phe)AA056320-May-201120-May-201130-Sep-2011L-cysteine bacillithiol disulfideBSHBSH(2S)-(2-[S-(L-cystein-S-yl)-L-cysteinyl]amino-2-deoxy-alpha-D-glucopyranosyloxy)-butanedioic acidChEBI:61338C 16 H 25 N 3 O 11 S 2499.51499.093051C 13 H 20 N 2 O 10 S 1396.37396.083866Lee, J.W.Soonsanga, S.Helmann, J.D.Proc. Natl. Acad. Sci. U.S.A. 104, 8743-8748, 2007A complex thiolate switch regulates the Bacillus subtilis organic peroxide sensor OhrR.DOI:10.1073/pnas.0702081104PMID:17502599mass spectrometric detection; the modification is not chemically characterizedNewton, G.L.Rawat, M.La Clair, J.J.Jothivasan, V.K.Budiarto, T.Hamilton, C.J.Claiborne, A.Helmann, J.D.Fahey, R.C.Nature Chem. Biol. 5, 625-627, 2009Bacillithiol is an antioxidant thiol produced in Bacilli.DOI:10.1038/nchembio.189PMID:19578333mass spectrometric and (1)H-NMR identification; chemical characterization; namingautocatalyticCPSI-MOD:01860disulfide bondMOD_RES S-bacillithiol cysteine disulfideAA056430-Jun-201130-Jun-201131-May-2018L-deoxyhypusinedeoxyhypusineN6-(4-aminobutyl)lysine (2S)-2-amino-6-[(4-aminobutyl)amino]hexanoic acidCAS:82543-85-9ChEBI:91176C 10 H 21 N 3 O 1199.30199.168462C 4 H 9 N 1 O 071.1271.073499Park, M.H.J. Biochem. 139, 161-169, 2006The post-translational synthesis of a polyamine-derived amino acid, hypusine, in the eukaryotic translation initiation factor 5A (eIF5A).DOI:10.1093/jb/mvj034PMID:16452303review articleDeoxyhypusine is generated as an intermediate modification of initiation factor 5A, eIF5A, and as a modified lysine reaction intermediate in deoxyhypusine synthase before transfer of the 4-aminobutyl group.autocatalyticdeoxyhypusine synthase (EC 2.5.1.46)KGO:0034038PSI-MOD:01880Not availablethis modification is not annotated in UniProt featuresAA056530-Jun-201130-Jun-201130-Jun-20113-(L-phenylalan-2'-yl)-L-valinesymerythrin valine-phenylalanine cross-link(2S)-2-amino-4-(2-[(2S)-2-amino-2-carboxyethyl]phenyl)-3-methylbutanoic acidC 14 H 16 N 2 O 2244.29244.121178C 0 H -2 N 0 O 0-2.02-2.015650Cooley, R.B.Rhoads, T.W.Arp, D.J.Karplus, P.A.Science 332, 929, 2011A diiron protein autogenerates a valine-phenylalanine cross-link.DOI:10.1126/science.1205687PMID:21596985X-ray diffraction, 1.20 angstromsCooley, R.B.Arp, D.J.Karplus, P.A.submitted to the Protein Data Bank, January 2011Crystal structure of oxidized symerythrin from Cyanophora paradoxa.PDB:3QHBX-ray diffraction, 1.20 angstromsautocatalyticF, Vcross-link 2PSI-MOD:01881Not availablethis modification is not annotated in UniProt featuresAA056630-Sep-201130-Sep-201130-Sep-2011N-[(L-histidin-1'-yl)methyl]-L-methionine(2S)-2-([(4-[(2S)-2-amino-2-carboxyethyl]-1H-imidazol-1-yl)methyl]amino)-4-(methylsulfanyl)butanoic acidPDBHET:FMEPDBHET:HICC 12 H 17 N 4 O 2 S 1281.35281.107222C 0 H 0 N 0 O -1 S 0-16.00-15.994915C 1 H 0 N 0 O 0 S 012.0112.000000Gregory, S.T.Demirci, H.Belardinelli, R.Monshupanee, T.Gualerzi, C.Dahlberg, A.E.Jogl, G.RNA 15, 1693-1704, 2009Structural and functional studies of the Thermus thermophilus 16S rRNA methyltransferase RsmG.DOI:10.1261/rna.1652709PMID:19622680X-ray diffraction, 1.50 angstromsDemirci, H.Gregory, S.T.Belardinelli, R.Gualerzi, C.Dahlberg, A.E.Jogl, G.submitted to the Protein Data Bank, February 2009T. thermophilus 16S rRNA G527 methyltransferase in complex with AdoMet and AMP in space group P61.PDB:3G89X-ray diffraction, 1.50 angstromsThe electron density model has contradictory characteristics. The bond distances from the "formyl" carbon to the two nitrogens are in the single bond range, and the torsion angles around those bonds are not planar, suggesting that neither is a double bond. However, the bond angle between that carbon and the two nitrogens is closer to trigonal than to tetrahedral, suggesting sp2 hybridization. The modification is shown in a reduced state.Since both the source organism and the expression host encode N-formylmethionine initiator and the autocatalytic modification can occur before completion of translation, it is probable but not yet established that the modification occurs under natural conditions.autocatalyticH, Mamino-terminalcross-link 2PSI-MOD:01890H, Mamino-terminalcross-link 2PSI-MOD:01891Not availablethis modification is not annotated in UniProt featuresAA056730-Sep-201130-Sep-201131-May-2018N6-crotonyl-L-lysine(2S)-2-amino-6-[(2E)-but-2-enamido]hexanoic acid(2S)-2-azanyl-6-[(2E)-but-2-enoylazanyl]hexanoic acidN(epsilon)-crotonyllysineN6-(E)-crotonyllysineN6-crotonyllysineN6-trans-crotonyllysineN6-[(2E)-2-butenoyl]-L-lysine(2S)-2-amino-6-[(2E)-but-2-enoylamino]hexanoic acidC 10 H 16 N 2 O 2196.25196.121178C 4 H 4 N 0 O 168.0768.026215Tan, M.Luo, H.Lee, S.Jin, F.Yang, J.S.Montellier, E.Buchou, T.Cheng, Z.Rousseaux, S.Rajagopal, N.Lu, Z.Ye, Z.Zhu, Q.Wysocka, J.Ye, Y.Khochbin, S.Ren, B.Zhao, Y.Cell 146, 1016-1028, 2011Identification of 67 histone marks and histone lysine crotonylation as a new type of histone modification.DOI:10.1016/j.cell.2011.08.008PMID:21925322chromatographic and mass spectrometric identification; modification specific antibodyA metabolic source for crotonic acid or crotonyl-CoA in the nucleus is not evident, and a responsible enzyme activity is not identified.KPSI-MOD:01892MOD_RES N6-crotonyllysineAA056830-Sep-201130-Sep-201131-Dec-2011N6-malonyl-L-lysine2-azanyl-6-[(carboxyacetyl)azanyl]hexanoic acidmalonyllysineN(epsilon)-(malonyl)lysineN6-(carboxyacetyl)lysineN6-malonyllysine(2S)-2-amino-6-[(carboxyacetyl)amino]hexanoic acidC 9 H 14 N 2 O 4214.22214.095357C 3 H 2 N 0 O 386.0586.000394Dalpozzo, A.Kanai, K.Kereszturi, G.Calabrese, G.Int. J. Pept. Protein Res. 41, 561-566, 1993H-Gly-His psi (NHCO)Lys-OH, partially modified retro-inverso analogue of the growth factor glycyl-L-histidyl-L-lysine with enhanced enzymatic stability.DOI:10.1111/j.1399-3011.1993.tb00478.xPMID:8349414chemical synthesisPeng, C.Lu, Z.Xie, Z.Cheng, Z.Chen, Y.Tan, M.Luo, H.Zhang, Y.He, W.Yang, K.Zwaans, B.M.Tishkoff, D.Ho, L.Lombard, D.He, T.C.Dai, J.Verdin, E.Ye, Y.Zhao, Y.Mol. Cell. Proteomics 10, M111.012658, 2011The first identification of lysine malonylation substrates and its regulatory enzyme.DOI:10.1074/mcp.M111.012658PMID:21908771chromatographic and mass spectrometric identification; modification specific antibodyDu, J.Zhou, Y.Su, X.Yu, J.J.Khan, S.Jiang, H.Kim, J.Woo, J.Kim, J.H.Choi, B.H.He, B.Chen, W.Zhang, S.Cerione, R.A.Auwerx, J.Hao, Q.Lin, H.Science 334, 806-809, 2011Sirt5 is a NAD-dependent protein lysine demalonylase and desuccinylase.DOI:10.1126/science.1207861PMID:22076378mass spectrometric identification in a number of mitochondrial proteins; identification of Sirt5 as a demalonylaseThe responsible generating enzyme activity is not identified. This modification can be reversed by Sirt5.KGO:0044392PSI-MOD:01893MOD_RES N6-malonyllysineAA056928-Oct-201128-Oct-201131-May-2018N2,N2-dimethyl-L-arginine(2S)-5-carbamimidamido-2-(dimethylamino)pentanoic acid [tautomer]N(alpha),N(alpha)-dimethylarginineN2,N2-dimethylarginine(2S)-5-[(diaminomethylidene)amino]-2-(dimethylamino)pentanoic acidCAS:190784-00-0C 8 H 17 N 4 O 1185.25185.140236C 2 H 4 N 0 O 028.0528.031300Kalyon, B.Helaly, S.E.Scholz, R.Nachtigall, J.Vater, J.Borriss, R.Süssmuth, R.D.Org. Lett. 13, 2996-2999, 2011Plantazolicin A and B: Structure Elucidation of Ribosomally Synthesized Thiazole/Oxazole Peptides from Bacillus amyloliquefaciens FZB42.DOI:10.1021/ol200809mPMID:21568297mass spectrometric, (1)H-NMR, (13)C-NMR and (15)N-NMR identificationMolohon, K.J.Melby, J.O.Lee, J.Evans, B.S.Dunbar, K.L.Bumpus, S.B.Kelleher, N.L.Mitchell, D.A.ACS Chem. Biol. 6, 1307-1313, 2011Structure determination and interception of biosynthetic intermediates for the plantazolicin class of highly discriminating antibiotics.DOI:10.1021/cb200339dPMID:21950656mass spectrometric, (1)H-NMR and (13)C-NMR identificationThis modification should not be confused with omega-N,omega-N'-dimethyl-L-arginine (see RESID:AA0067) or omega-N,omega-N-dimethyl-L-arginine (see RESID:AA0068).protein N-terminal methyltransferase (EC 2.1.1.-)Ramino-terminalPSI-MOD:01898blocked amino endmethylated amino endMOD_RES N2,N2-dimethylarginineAA057028-Oct-201128-Oct-201131-Dec-2011L-arginine thiazole-4-carboxylic acid2-[(1S)-1-amino-4-([diaminomethylidene]amino)butyl]-1,3-thiazole-4-carboxylic acidC 9 H 13 N 5 O 1 S 1239.30239.084081C 0 H -4 N 0 O -1 S 0-20.03-20.026215Kalyon, B.Helaly, S.E.Scholz, R.Nachtigall, J.Vater, J.Borriss, R.Süssmuth, R.D.Org. Lett. 13, 2996-2999, 2011Plantazolicin A and B: Structure Elucidation of Ribosomally Synthesized Thiazole/Oxazole Peptides from Bacillus amyloliquefaciens FZB42.DOI:10.1021/ol200809mPMID:21568297mass spectrometric, (1)H-NMR, (13)C-NMR and (15)N-NMR identificationMolohon, K.J.Melby, J.O.Lee, J.Evans, B.S.Dunbar, K.L.Bumpus, S.B.Kelleher, N.L.Mitchell, D.A.ACS Chem. Biol. 6, 1307-1313, 2011Structure determination and interception of biosynthetic intermediates for the plantazolicin class of highly discriminating antibiotics.DOI:10.1021/cb200339dPMID:21950656mass spectrometric, (1)H-NMR and (13)C-NMR identificationFormed by the condensation of a cysteine thiol with the carbonyl of the preceding residue and alpha-beta dehydrogenation.peptidyl-cysteine cyclase (EC 4.2.1.-)peptidyl-thiazoline dehydrogenase (EC 1.3.-.-)C, Rcross-link 1PSI-MOD:01899oxazole/thiazole ringthioether bondCROSSLNK Thiazole-4-carboxylic acid (Arg-Cys)AA057128-Oct-201128-Oct-201131-Dec-2011L-cysteine 5-methyloxazole-4-carboxylic acid2-[(1R)-1-azanyl-2-sulfanylethyl]-5-methyl-1,3-oxazole-4-carboxylic acid2-[(1R)-1-amino-2-sulfanylethyl]-5-methyl-1,3-oxazole-4-carboxylic acidC 7 H 8 N 2 O 2 S 1184.21184.030649C 0 H -4 N 0 O -1 S 0-20.03-20.026215Kalyon, B.Helaly, S.E.Scholz, R.Nachtigall, J.Vater, J.Borriss, R.Süssmuth, R.D.Org. Lett. 13, 2996-2999, 2011Plantazolicin A and B: Structure Elucidation of Ribosomally Synthesized Thiazole/Oxazole Peptides from Bacillus amyloliquefaciens FZB42.DOI:10.1021/ol200809mPMID:21568297mass spectrometric, (1)H-NMR, (13)C-NMR and (15)N-NMR identificationMolohon, K.J.Melby, J.O.Lee, J.Evans, B.S.Dunbar, K.L.Bumpus, S.B.Kelleher, N.L.Mitchell, D.A.ACS Chem. Biol. 6, 1307-1313, 2011Structure determination and interception of biosynthetic intermediates for the plantazolicin class of highly discriminating antibiotics.DOI:10.1021/cb200339dPMID:21950656mass spectrometric, (1)H-NMR and (13)C-NMR identificationFormed by the condensation of a cysteine thiol with the carbonyl of the preceding residue and alpha-beta dehydrogenation.peptidyl-threonine cyclase (EC 4.2.1.-)peptidyl-oxazoline dehydrogenase (EC 1.3.-.-)C, Tcross-link 1PSI-MOD:01900oxazole/thiazole ringCROSSLNK 5-methyloxazole-4-carboxylic acid (Cys-Thr)AA057228-Oct-201128-Oct-201131-Dec-2011L-threonine 5-methyloxazole-4-carboxylic acid2-[(1S,2R)-1-azanyl-2-hydroxypropyl]-5-methyl-1,3-oxazole-4-carboxylic acid2-[(1S,2R)-1-amino-2-hydroxypropyl]-5-methyl-1,3-oxazole-4-carboxylic acidC 8 H 10 N 2 O 3182.18182.069142C 0 H -4 N 0 O -1-20.03-20.026215Kalyon, B.Helaly, S.E.Scholz, R.Nachtigall, J.Vater, J.Borriss, R.Süssmuth, R.D.Org. Lett. 13, 2996-2999, 2011Plantazolicin A and B: Structure Elucidation of Ribosomally Synthesized Thiazole/Oxazole Peptides from Bacillus amyloliquefaciens FZB42.DOI:10.1021/ol200809mPMID:21568297mass spectrometric, (1)H-NMR, (13)C-NMR and (15)N-NMR identificationMolohon, K.J.Melby, J.O.Lee, J.Evans, B.S.Dunbar, K.L.Bumpus, S.B.Kelleher, N.L.Mitchell, D.A.ACS Chem. Biol. 6, 1307-1313, 2011Structure determination and interception of biosynthetic intermediates for the plantazolicin class of highly discriminating antibiotics.DOI:10.1021/cb200339dPMID:21950656mass spectrometric, (1)H-NMR and (13)C-NMR identificationFormed by the condensation of a cysteine thiol with the carbonyl of the preceding residue and alpha-beta dehydrogenation.peptidyl-threonine cyclase (EC 4.2.1.-)peptidyl-oxazoline dehydrogenase (EC 1.3.-.-)T, Tcross-link 1PSI-MOD:01901oxazole/thiazole ringCROSSLNK 5-methyloxazole-4-carboxylic acid (Thr-Thr)AA057328-Oct-201128-Oct-201131-Dec-2011L-isoleucine oxazole-4-carboxylic acid2-[(1S,2S)-1-azanyl-2-methylbutyl]-1,3-oxazole-4-carboxylic acid2-[(1S,2S)-1-amino-2-methylbutyl]-1,3-oxazole-4-carboxylic acid C 9 H 12 N 2 O 2180.21180.089878C 0 H -4 N 0 O -1-20.03-20.026215Kalyon, B.Helaly, S.E.Scholz, R.Nachtigall, J.Vater, J.Borriss, R.Süssmuth, R.D.Org. Lett. 13, 2996-2999, 2011Plantazolicin A and B: Structure Elucidation of Ribosomally Synthesized Thiazole/Oxazole Peptides from Bacillus amyloliquefaciens FZB42.DOI:10.1021/ol200809mPMID:21568297mass spectrometric, (1)H-NMR, (13)C-NMR and (15)N-NMR identificationMolohon, K.J.Melby, J.O.Lee, J.Evans, B.S.Dunbar, K.L.Bumpus, S.B.Kelleher, N.L.Mitchell, D.A.ACS Chem. Biol. 6, 1307-1313, 2011Structure determination and interception of biosynthetic intermediates for the plantazolicin class of highly discriminating antibiotics.DOI:10.1021/cb200339dPMID:21950656mass spectrometric, (1)H-NMR and (13)C-NMR identificationFormed by the condensation of a cysteine thiol with the carbonyl of the preceding residue and alpha-beta dehydrogenation.peptidyl-serine cyclase (EC 4.2.1.-)peptidyl-oxazoline dehydrogenase (EC 1.3.-.-)I, Scross-link 1PSI-MOD:01902oxazole/thiazole ringCROSSLNK Oxazole-4-carboxylic acid (Ile-Ser)AA057428-Oct-201128-Oct-201131-Dec-2011L-serine oxazole-4-carboxylic acid2-[(1S)-1-azanyl-2-hydroxyethyl]-1,3-oxazole-4-carboxylic acid 2-[(1S)-1-amino-2-hydroxyethyl]-1,3-oxazole-4-carboxylic acidC 6 H 6 N 2 O 3154.13154.037842C 0 H -4 N 0 O -1-20.03-20.026215Kalyon, B.Helaly, S.E.Scholz, R.Nachtigall, J.Vater, J.Borriss, R.Süssmuth, R.D.Org. Lett. 13, 2996-2999, 2011Plantazolicin A and B: Structure Elucidation of Ribosomally Synthesized Thiazole/Oxazole Peptides from Bacillus amyloliquefaciens FZB42.DOI:10.1021/ol200809mPMID:21568297mass spectrometric, (1)H-NMR, (13)C-NMR and (15)N-NMR identificationMolohon, K.J.Melby, J.O.Lee, J.Evans, B.S.Dunbar, K.L.Bumpus, S.B.Kelleher, N.L.Mitchell, D.A.ACS Chem. Biol. 6, 1307-1313, 2011Structure determination and interception of biosynthetic intermediates for the plantazolicin class of highly discriminating antibiotics.DOI:10.1021/cb200339dPMID:21950656mass spectrometric, (1)H-NMR and (13)C-NMR identificationFormed by the condensation of a cysteine thiol with the carbonyl of the preceding residue and alpha-beta dehydrogenation.peptidyl-serine cyclase (EC 4.2.1.-)peptidyl-oxazoline dehydrogenase (EC 1.3.-.-)S, Scross-link 1PSI-MOD:01903oxazole/thiazole ringCROSSLNK Oxazole-4-carboxylic acid (Ser-Ser)AA057528-Oct-201128-Oct-201131-Dec-2011L-serine 5-methyloxazoline-4-carboxylic acid2-[(1S)-1-amino-2-hydroxyethyl]-5-methyl-1,3-oxazoline-4-carboxylic acid2-[(1S)-1-azanyl-2-hydroxyethyl]-5-methyl-4,5-dihydro-1,3-oxazole-4-carboxylic acid2-[(1S)-1-amino-2-hydroxyethyl]-5-methyl-4,5-dihydro-1,3-oxazole-4-carboxylic acidC 7 H 10 N 2 O 3170.17170.069142C 0 H -2 N 0 O -1-18.02-18.010565Kalyon, B.Helaly, S.E.Scholz, R.Nachtigall, J.Vater, J.Borriss, R.Süssmuth, R.D.Org. Lett. 13, 2996-2999, 2011Plantazolicin A and B: Structure Elucidation of Ribosomally Synthesized Thiazole/Oxazole Peptides from Bacillus amyloliquefaciens FZB42.DOI:10.1021/ol200809mPMID:21568297mass spectrometric, (1)H-NMR, (13)C-NMR and (15)N-NMR identificationMolohon, K.J.Melby, J.O.Lee, J.Evans, B.S.Dunbar, K.L.Bumpus, S.B.Kelleher, N.L.Mitchell, D.A.ACS Chem. Biol. 6, 1307-1313, 2011Structure determination and interception of biosynthetic intermediates for the plantazolicin class of highly discriminating antibiotics.DOI:10.1021/cb200339dPMID:21950656mass spectrometric, (1)H-NMR and (13)C-NMR identificationFormed by the condensation of a cysteine thiol with the carbonyl of the preceding residue and alpha-beta dehydrogenation.peptidyl-threonine cyclase (EC 4.2.1.-)S, Tcross-link 1PSI-MOD:01904oxazole/thiazole ringCROSSLNK 5-methyloxazoline-4-carboxylic acid (Ser-Thr)AA057631-Dec-201131-Dec-201131-Dec-2011N-formyl-L-alanine2-formamidopropanoic acid2-formamidopropionic acid(2S)-2-(formylamino)propanoic acidCAS:10512-86-4PDBHET:FORC 4 H 6 N 1 O 2100.10100.039853C 1 H 0 N 0 O 128.0127.994915Transue, T.R.Smith, A.K.Mo, H.Goldstein, I.J.Saper, M.A.Nature Struct. Biol. 4, 779-783, 1997Structure of benzyl T-antigen disaccharide bound to Amaranthus caudatus agglutinin.DOI:10.1038/nsb1097-779PMID:9334739X-ray diffraction, 2.20 angstroms; the amino-terminal is blocked; there is no chemical evidence for the identity of the blocking group; a formyl group fits the electron densityTransue, T.R.Smith, A.K.Mo, H.Goldstein, I.J.Saper, M.A.submitted to the Protein Data Bank, July 1997Crystal structure of Amaranthus caudatus agglutinin.PDB:1JLYX-ray diffraction, 2.20 angstromsAamino-terminalPSI-MOD:01915blocked amino endformylationNot availablethis modification is not annotated in UniProt featuresAA057731-Dec-201131-Dec-201131-May-2018O4'-(N-acetylamino)galactosyl-L-tyrosinemucin type O-glycosyltyrosineO4'-(N-acetylgalactosaminyl)tyrosineO4'-glycosyl-L-tyrosine(2S)-2-amino-3-[4-(2-acetamido-2-deoxy-beta-D-galactopyranosyloxy)phenyl]propanoic acidC 17 H 22 N 2 O 7 +366.37 +366.142701 +C 8 H 13 N 1 O 5 +203.19 +203.079373 +Halim, A.Brinkmalm, G.Rüetschi, U.Westman-Brinkmalm, A.Portelius, E.Zetterberg, H.Blennow, K.Larson, G.Nilsson, J.Proc. Natl. Acad. Sci. U.S.A. 108, 11848-11853, 2011Site-specific characterization of threonine, serine, and tyrosine glycosylations of amyloid precursor protein/amyloid beta-peptides in human cerebrospinal fluid.DOI:10.1073/pnas.1102664108PMID:21712440mass spectrometric detectionSteentoft, C.Vakhrushev, S.Y.Vester-Christensen, M.B.Schjoldager, K.T.Kong, Y.Bennett, E.P.Mandel, U.Wandall, H.Levery, S.B.Clausen, H.Nature Methods 8, 977-982, 2011Mining the O-glycoproteome using zinc-finger nuclease-glycoengineered SimpleCell lines.DOI:10.1038/nmeth.1731PMID:21983924mass spectrometric detection; assumed to be (N-acetylamino)galactose in alpha linkage because of the disialylated core structureThe alpha anomeric form is shown.See also RESID:AA0157 for other O-glycosylated tyrosines.polypeptide N-acetylgalactosaminyltransferase (EC 2.4.1.-)YPSI-MOD:01916glycoproteinCARBOHYD O-linked (GalNAc) tyrosineCARBOHYD O-linked (GalNAc...) tyrosineCARBOHYD O-linked (HexNAc...) tyrosinethis UniProt feature is used when the identity of the sugar has not been determinedAA057831-Mar-201231-Mar-201231-Mar-2012(2S,5S)-5-hydroxylysine2,6-bisazanyl-5-hydroxyhexanoic acid2,6-diamino-2,3,4,6-tetradeoxyhexonic acidalpha,epsilon-diamino-delta-hydroxycaproic acidL-allo-delta-hydroxylysineL-threo-delta-hydroxylysine(2S,5S)-2,6-diamino-5-hydroxyhexanoic acidCAS:18899-29-1C 6 H 12 N 2 O 2144.17144.089878C 0 H 0 N 0 O 116.0015.994915Webby, C.J.Wolf, A.Gromak, N.Dreger, M.Kramer, H.Kessler, B.Nielsen, M.L.Schmitz, C.Butler, D.S.Yates 3rd, J.R.Delahunty, C.M.Hahn, P.Lengeling, A.Mann, M.Proudfoot, N.J.Schofield, C.J.Böttger, A.Science 325, 90-93, 2009Jmjd6 Catalyses Lysyl-Hydroxylation of U2AF65, a Protein Associated with RNA Splicing.DOI:10.1126/science.1175865PMID:19574390identification of JMJD6 (Jumonji domain-6) protein as a lysyl-5-hydroxylase acting on U2AF65; JMJD6 had earlier been identified as an iron and 2-oxoglutarate-dependent oxygenase acting as a histone arginine demethylaseMantri, M.Loik, N.D.Hamed, R.B.Claridge, T.D.McCullagh, J.S.Schofield, C.J.Chembiochem 12, 531-534, 2011The 2-Oxoglutarate-Dependent Oxygenase JMJD6 Catalyses Oxidation of Lysine Residues to give 5S-Hydroxylysine Residues.DOI:10.1002/cbic.201000641PMID:22238144synthesis of diastereomers, and (1)H-NMR identificationThis diastereomeric form has been found in some splicing regulatory proteins. For the (2S,5R)-diastereomer, see RESID:AA0028.The Enzyme Commission has not yet distinguished the different stereospecific enzyme activities.peptide-lysine 5-dioxygenase JMJD6 (EC 1.14.11.-)KPSI-MOD:01918hydroxylationMOD_RES (5S)-5-hydroxylysineMOD_RES 5-hydroxylysinethis UniProt feature is used when the stereochemistry has not been determinedAA057931-Mar-201231-Mar-201201-Mar-2013(2S,3S)-3-hydroxyaspartic acid(3S)-3-hydroxy-L-aspartic acid2-amino-3-hydroxysuccinic acid2-azanyl-3-hydroxybutanedioic acid3-hydroxyaspartic acidL-threo-3-hydroxyaspartic acidL-threo-beta-hydroxyaspartic acid(2S,3S)-2-amino-3-hydroxybutanedioic acidCAS:7298-99-9ChEBI:10696PDBHET:BHDC 4 H 5 N 1 O 4131.09131.021858C 0 H 0 N 0 O 116.0015.994915Yang, M.Ge, W.Chowdhury, R.Claridge, T.D.Kramer, H.B.Schmierer, B.McDonough, M.A.Gong, L.Kessler, B.M.Ratcliffe, P.J.Coleman, M.L.Schofield, C.J.J. Biol. Chem. 286, 7648-7660, 2011Asparagine and aspartate hydroxylation of the cytoskeletal ankyrin family is catalyzed by factor-inhibiting hypoxia-inducible factor.DOI:10.1074/jbc.M110.193540PMID:21177872mass spectrometric detection; (1)H-NMR and (13)C-NMR identification; X-ray diffraction, 2.20 angstromsYang, M.Ge, W.Chowdhury, R.McDonough, M.A.Schofield, C.J.submitted to the Protein Data Bank, October 2010Factor-inhibiting HIF (FIH) Q239H mutant in complex with Zn(II), NOG and Asp-substrate peptide (20-mer).PDB:2XUMX-ray diffraction, 2.20 angstromsThis diastereomeric form has been found in the ankyrin repeat domain of many proteins. For the (2S,3R)-diastereomer, see RESID:AA0027.hypoxia-inducible factor-asparagine dioxygenase (EC 1.14.11.30)DPSI-MOD:01919hydroxylationMOD_RES (3S)-3-hydroxyaspartateAA058031-Mar-201231-Mar-201220-Apr-20123-hydroxy-L-histidine(2S)-2-amino-3-hydroxy-3-(1H-imidazol-4-yl)propanoic acidC 6 H 7 N 3 O 2153.14153.053826C 0 H 0 N 0 O 116.0015.994915Yang, M.Chowdhury, R.Ge, W.Hamed, R.B.McDonough, M.A.Claridge, T.D.Kessler, B.M.Cockman, M.E.Ratcliffe, P.J.Schofield, C.J.FEBS J. 278, 1086-1097, 2011Factor-inhibiting hypoxia-inducible factor (FIH) catalyses the post-translational hydroxylation of histidinyl residues within ankyrin repeat domains.DOI:10.1111/j.1742-4658.2011.08022.xPMID:21251231mass spectrometric detection; (1)H-NMR identification; X-ray diffraction, 2.28 angstroms; the unmodified peptide was used in the crystallographic workChowdhury, R.McDonough, M.A.Schofield, C.J.submitted to the Protein Data Bank, December 2010Factor-inhibiting HIF-1 alpha in complex with tankyrase-2 (TNKS2) fragment peptide (21-mer).PDB:2Y0IX-ray diffraction, 2.28 angstromsThis modified histidine has been found in an ankyrin repeat domain in a position occupied by asparagine in homologous sequences. The diastereomeric form has not been determined.peptide-histidine beta-dioxygenase (EC 1.14.11.-)HPSI-MOD:01920hydroxylationMOD_RES 3-hydroxyhistidineAA058131-Mar-201213-Sep-201331-May-2018L-methionine (R)-sulfoxideL-methionine (R)-S-oxide(2S)-2-amino-4-[(R)-methylsulfinyl]butanoic acid CAS:3226-66-2ChEBI:45764PDBHET:SMEC 5 H 9 N 1 O 2 S 1147.19147.035400C 0 H 0 N 0 O 1 S 016.0015.994915Ghesquière, B.Jonckheere, V.Colaert, N.Van Durme, J.Timmerman, E.Goethals, M.Schymkowitz, J.Rousseau, F.Vandekerckhove, J.Gevaert, K.Mol. Cell. Proteomics 10, M110.006866, 2011Redox proteomics of protein-bound methionine oxidation.DOI:10.1074/mcp.M110.006866PMID:21406390mass spectrometric and enzymatic analysisHung, R.J.Pak, C.W.Terman, J.R.Science 334, 1710-1713, 2011Direct redox regulation of F-actin assembly and disassembly by Mical.DOI:10.1126/science.1211956PMID:22116028mass spectrometric detection; directed mutation analysis; the stereochemistry was not determined; observation of a 64 Da neutral loss in the dioxidized peptide indicates that at least one of the methionine residues was probably an S-oxideLee, B.C.Péterfi, Z.Hoffmann, F.W.Moore, R.E.Kaya, A.Avanesov, A.Tarrago, L.Zhou, Y.Weerapana, E.Fomenko, D.E.Hoffmann, P.R.Gladyshev, V.N.Mol. Cell 51, 397-404, 2013MsrB1 and MICALs Regulate Actin Assembly and Macrophage Function via Reversible Stereoselective Methionine Oxidation.DOI:10.1016/j.molcel.2013.06.019PMID:23911929it is established that the methionine sulfoxide residues of oxidized, and depolymerized, actin are stereoselctively reduced to methionine by the selenoenzyme methionine-R-sulfoxide reductase B1, and thus that the modified form is methionine (R)-sulfoxideGruez, A.Libiad, M.Boschi-Muller, S.Branlant, G.submitted to the Protein Data Bank, April 2010X-ray structure of free methionine-R-sulfoxide reductase from Neisseria meningitidis in complex with its substrate.PDB:3MMHX-ray diffraction, 1.25 angstroms; the free amino acid is modeled in the active site of the stereospecific methionine (R)-sulfoxide MsrB reductaseThe S-oxide of methionine is a chiral center. The oxidized methionine in actin has been determined to be the (R)-sulfoxide.The methionine (R)-sulfoxides in actin can be reduced to methionine by methionine-R-sulfoxide reductase B1, MsrB1 (EC 1.8.4.12).[F-actin]-L-methionine,NADPH:O2 S-oxidoreductase (EC 1.14.13.225)MPSI-MOD:00721thioether bondMOD_RES Methionine (R)-sulfoxideMOD_RES Methionine sulfoxidethis UniProt feature is used when the stereochemistry has not been determinedAA058231-Mar-201231-Mar-201231-Mar-20123-methoxydehydroalanine3-methoxydidehydroalanine2-amino-3-methoxyprop-2-enoic acidC 4 H 5 N 1 O 299.0999.032028C 1 H 0 N 0 O 012.0112.000000Mukai, A.Fukai, T.Hoshino, Y.Yazawa, K.Harada, K.-I.Mikami, Y.J. Antibiot. 62, 613-619, 2009Nocardithiocin, a novel thiopeptide antibiotic, produced by pathogenic Nocardia pseudobrasiliensis IFM 0757.DOI:10.1038/ja.2009.90PMID:19745839the initials of K.-I. Harada in the PubMed citation are correctedIt has not been established whether the natural form is the Z or the E isomer. The Z isomer is shown.Sincidental to RESID:AA0242PSI-MOD:01922methylated amino acidNot availablethis modification is not annotated in UniProt featuresAA058331-Mar-201231-Mar-201231-Dec-2012N6-(L-aspartyl)-L-lysinealpha-(N6-lysyl)aspartyl acidaspartyl N6-lysineN(epsilon)-(alpha-aspartyl)lysine(2S)-2-amino-6-([(2S)-2-amino-3-carboxypropanoyl]amino)hexanoic acidC 10 H 16 N 3 O 4242.26242.114081C 0 H -2 N 0 O -1-18.02-18.010565Osička, R.Procházková, K.Šulc, M.Linhartová, I.Havlíček, V.Šebo, P.J. Biol. Chem. 279, 24944-24956, 2004A novel "clip-and-link" activity of repeat in toxin (RTX) proteins from gram-negative pathogens. Covalent protein cross-linking by an Asp-Lys isopeptide bond upon calcium-dependent processing at an Asp-Pro bond.DOI:10.1074/jbc.M314013200PMID:15044436chemical characterization and mass spectrometric identification; directed mutation analysis; it was not determined whether the cross-link was through the aspartyl C1 or C4 carboxyl, and both are probably formed, see also RESID:AA0294; the encoding of an author's name in the PubMed citation is corrected to UTF8Osipiuk, J.Mulligan, R.Bargassa, M.Hamilton, J.E.Cunningham, M.A.Joachimiak, A.J. Biol. Chem. 287, 19452-19461, 2012Characterization of member of DUF1888 protein family, self-cleaving and self-assembling endopeptidase.DOI:10.1074/jbc.M112.358069PMID:22493430X-ray diffraction, 1.57 angstroms; the cross-link is discussed and is annotated in the revised PDB entryOsipiuk, J.Mulligan, R.Collart, A.Joachimiak, A.submitted to the Protein Data Bank, May 2010SO1698 protein, an aspartic peptidase from Shewanella oneidensis.PDB:3N55X-ray diffraction, 1.57 angstromsD, Kcarboxyl-terminalcross-link 2PSI-MOD:01923blocked carboxyl endisopeptide bondCROSSLNK Aspartyl lysine isopeptide (Asp-Lys) (interchain with K-...)CROSSLNK Aspartyl lysine isopeptide (Lys-Asp) (interchain with D-...)AA058431-Mar-201231-Mar-201231-Mar-2012S-octanoyl-L-cysteine2-amino-3-(octanoylthio)propanoic acidcysteine octanoate thioester(2S)-2-amino-3-(octanoylsulfanyl)propanoic acidC 11 H 19 N 1 O 2 S 1229.34229.113650C 8 H 14 N 0 O 1 S 0126.20126.104465Jordan, S.W.Cronan Jr., J.E.J. Bacteriol. 185, 1582-1589, 2003The Escherichia coli lipB gene encodes lipoyl (octanoyl)-acyl carrier protein:protein transferase.DOI:10.1128/JB.185.5.1582-1589.2003PMID:12591875identification of enzyme activity for the modificationZhao, X.Miller, J.R.Cronan, J.E.Biochemistry 44, 16737-16746, 2005The reaction of LipB, the octanoyl-[acyl carrier protein]:protein N-octanoyltransferase of lipoic acid synthesis, proceeds through an acyl-enzyme intermediate.DOI:10.1021/bi051865yPMID:16342964chemical characterization and mass spectrometric identification; directed mutation analysisautocatalyticCPSI-MOD:01924lipoproteinthioester bondACT_SITE Acyl-thioester intermediateAA058530-Jun-201230-Jun-201230-Jun-2012N6-phospho-L-lysine(2S)-2-azanyl-6-(phosphonoamino)hexanoic acid6-phospholysineN(6)-phosphonolysineN(epsilon)-phospholysineN(epsilon)-phosphonolysineN(epsilon)-phosphonyllysineN(epsilon)-phosphoryllysine(2S)-2-amino-6-(phosphonoamino)hexanoic acidCAS:14721-74-5C 6 H 13 N 2 O 4 P 1208.15208.061294C 0 H 1 N 0 O 3 P 179.9879.966331Kowalewska, K.Stefanowicz, P.Ruman, T.Fraczyk, T.Rode, W.Szewczuk, Z.Biosci. Rep. 30, 433-443, 2010Electron capture dissociation mass spectrometric analysis of lysine-phosphorylated peptides.DOI:10.1042/BSR20090167PMID:20144148mass spectrometric and (1)H-NMR analysis; chemical stabilityN6-phospho-L-lysine hydrolyzes rapidly at acidic pH, but is more stable at neutral pH and below freezing.Although N6-phospho-L-lysine has been proposed to occur in histone H1, its occurrence has not been reported in a sequenced peptide.KPSI-MOD:01931phosphoproteinNot availablethis modification is not annotated in UniProt featuresAA058630-Jun-201230-Jun-201201-Mar-2013L-lysinonorleucine(2S,2'S)-6,6'-iminobis(2-aminohexanoic acid)6-(N6-L-lysino)-L-norleucinelysinonorleucinelysinorleucine [misspelling]lysylnorleucineN6-[(5S)-5-amino-5-carboxypentyl]-L-lysine(2S)-2-amino-6-([(5S)-5-amino-5-carboxypentyl]amino)hexanoic acidCAS:25612-46-8C 12 H 21 N 3 O 2239.32239.163377C 0 H -3 N -1 O 0-17.03-17.026549Franzblau, C.Sinex, F.M.Faris, B.Lampidis, R.Biochem. Biophys. Res. Commun. 21, 575-581, 1965Identification of a new crosslinking amino acid in elastin.DOI:10.1016/0006-291X(65)90524-3PMID:5879466isolation of reduced form; chemical characterization and naming of lysinonorleucineFranzblau, C.Faris, B.Papaioannou, R.Biochemistry 8, 2833-2837, 1969Lysinonorleucine. A new amino acid from hydrolysates of elastin.DOI:10.1021/bi00835a021PMID:5817620mass spectrometric and chemical characterization of the reduced form; stereochemical determinationLent, R.Franzblau, C.Biochem. Biophys. Res. Commun. 26, 43-50, 1967Studies on the reduction of bovine elastin: evidence for the presence of Delta-6,7-dehydrolysinonorleucine.DOI:10.1016/0006-291X(67)90250-1PMID:6030254observation of the aldimine formBailey, A.J.Peach, C.M.Biochem. J. 121, 257-259, 1971The chemistry of the collagen cross-links. The absence of reduction of dehydrolysinonorleucine and dehydrohydroxylysinonorleucine in vivo.PMID:5117030the non-reduced aldimine form is the predominant form in collagen, and in insoluble collagens there is less hydroxylation; the predominant form in elastin is the reduced lysinonorleucineAfter the oxidation of a lysine to allysine (see RESID:AA0121), this cross-link forms spontaneously with a Schiff-base reaction. In this aleatoric modification two peptide chains may be crosslinked with the peptides contributing a lysine in either biosynthetic position.The lysines forming the cross-link may also be hydroxylated and glycosylated (see RESID:AA0028 and RESID:AA0153).lysyl oxidase (EC 1.4.3.13)K, Kcross-link 2incidental to RESID:AA0028secondary to RESID:AA0121PSI-MOD:01932aleatoric crosslinkNot availablethis modification is not annotated in UniProt featuresAA058730-Jun-201230-Jun-201201-Mar-2013desmosine6-[4-(4-amino-4-carboxybutyl)-3,5-bis(3-amino-3-carboxypropyl)pyridinio]norleucine4-[(4S)-4-amino-4-carboxybutyl]-1-[(5S)-5-amino-5-carboxypentyl]-3,5-bis[(3S)-3-amino-3-carboxypropyl]pyridiniumCAS:11003-57-9ChEBI:37629C 24 H 32 N 5 O 41+454.55454.244881C 0 H -16 N -3 O 01+-58.15-58.134971Partridge, S.M.Elsden, D.F.Thomas, J.Nature 197, 1297-1298, 1963Constitution of the cross-linkages in elastin.DOI:10.1038/1971297a0PMID:13941623isolation; chemical characterization; determination of molecular weight and elemental composition; spectrographic characterizationThomas, J.Elsden, D.F.Partridge, S.M.Nature 200, 651-652, 1963Partial structure of two major degradation products from the cross-linkages in elastin.DOI:10.1038/200651a0PMID:14109938determination of molecular weight and elemental compositionBedford, G.R.Katritzky, A.R.Nature 200, 652, 1963Proton magnetic resonance spectra of degradation products from elastin.DOI:10.1038/200652a0PMID:14109939(1)H-NMR identificationPartridge, S.M.Elsden, D.F.Thomas, J.Dorfman, A.Telser, A.Ho, P.L.Biochem. J. 93, 30C-33C, 1964Biosynthesis of the desmosine and isodesmosine cross-bridges in elastin.PMID:5839176determination of molecular structure; radiolabeling; biosynthesis; the initials of P.-L. Ho in the PubMed citation are correctedAfter the oxidation of three of the four lysines to allysine (see RESID:AA0121), this cross-link forms spontaneously with a Schiff-base reaction, and a series of one aldimine and two aldol condensation reactions. In this aleatoric modification up to four peptide chains may be crosslinked, with each peptide contributing a lysine potentially in any of the four biosynthetic positions. Isodesmosine is a structural isomer (see RESID:AA0588).Up to two of the lysines forming the cross-link may also be hydroxylated and glycosylated (see RESID:AA0028 and RESID:AA0153).lysyl oxidase (EC 1.4.3.13)K, K, K, Kcross-link 4incidental to RESID:AA0028secondary to RESID:AA0121PSI-MOD:01933aleatoric crosslinkpyridine ringNot availablethis modification is not annotated in UniProt featuresAA058830-Jun-201230-Jun-201201-Mar-2013isodesmosine6-[2-(4-amino-4-carboxybutyl)-3,5-bis(3-amino-3-carboxypropyl)pyridinio]norleucine2-[(4S)-4-amino-4-carboxybutyl]-1-[(5S)-5-amino-5-carboxypentyl]-3,5-bis[(3S)-3-amino-3-carboxypropyl]pyridiniumCAS:991-01-5ChEBI:64366C 24 H 32 N 5 O 41+454.55454.244881C 0 H -16 N -3 O 01+-58.15-58.134971Partridge, S.M.Elsden, D.F.Thomas, J.Nature 197, 1297-1298, 1963Constitution of the cross-linkages in elastin.DOI:10.1038/1971297a0PMID:13941623isolation; chemical characterization; determination of molecular weight and elemental composition; spectrographic characterizationThomas, J.Elsden, D.F.Partridge, S.M.Nature 200, 651-652, 1963Partial structure of two major degradation products from the cross-linkages in elastin.DOI:10.1038/200651a0PMID:14109938determination of molecular weight and elemental compositionBedford, G.R.Katritzky, A.R.Nature 200, 652, 1963Proton magnetic resonance spectra of degradation products from elastin.DOI:10.1038/200652a0PMID:14109939(1)H-NMR identificationPartridge, S.M.Elsden, D.F.Thomas, J.Dorfman, A.Telser, A.Ho, P.L.Biochem. J. 93, 30C-33C, 1964Biosynthesis of the desmosine and isodesmosine cross-bridges in elastin.PMID:5839176determination of molecular structure; radiolabeling; biosynthesis; the initials of P.-L. Ho in the PubMed citation are correctedAfter the oxidation of three of the four lysines to allysine (see RESID:AA0121), this cross-link forms spontaneously with a Schiff-base reaction, and a series of one aldimine and two aldol condensation reactions. In this aleatoric modification up to four peptide chains may be crosslinked, with each peptide contributing a lysine potentially in any of the four biosynthetic positions. Desmosine is a structural isomer (see RESID:AA0587).Up to two of the lysines forming the cross-link may also be hydroxylated and glycosylated (see RESID:AA0028 and RESID:AA0153).lysyl oxidase (EC 1.4.3.13)K, K, K, Kcross-link 4incidental to RESID:AA0028secondary to RESID:AA0121PSI-MOD:01934aleatoric crosslinkpyridine ringNot availablethis modification is not annotated in UniProt featuresAA058930-Jun-201230-Jun-201230-Jun-2012O-glucosyl-L-hydroxylysine(D-glucopyranosyl)oxy-L-lysineC 12 H 22 N 2 O 7306.32306.142701C 6 H 10 N 0 O 6178.14178.047738Luther, K.B.Hülsmeier, A.J.Schegg, B.Deuber, S.A.Raoult, D.Hennet, T.J. Biol. Chem. 286, 43701-43709, 2011Mimivirus collagen is modified by bifunctional lysyl hydroxylase and glycosyltransferase enzyme.DOI:10.1074/jbc.M111.309096PMID:22045808biosynthesis; cloning, expression and directed mutation analysis of the enzymeThe mimivirus enzyme is bifunctional and carries out both hydroxylation and glucosylation. Neither the regiospecificity nor stereospecificity of the hydroxylation, nor the anomeric specificity of the glucosylation have been determined.The 5-hydroxy, beta anomeric form is shown.lysine dioxygenase (EC 1.14.11.-)hydroxylysine glucosyltransferase (EC 2.4.1.-)KPSI-MOD:01935glycoproteinhydroxylationNot availablethis modification is not annotated in UniProt featuresAA059030-Jun-201230-Jun-201230-Jun-2012N6-oleoyl-L-lysineN6-[(9Z)-1-oxo-9-octadecenyl]lysine(2S)-2-amino-6-([(9Z)-octadec-9-enoyl]amino)hexanoic acidCAS:23499-75-4C 24 H 44 N 2 O 2392.63392.340279C 18 H 32 N 0 O 1264.45264.245316Schey, K.L.Gutierrez, D.B.Wang, Z.Wei, J.Grey, A.C.Biochemistry 49, 9858-9865, 2010Novel fatty acid acylation of lens integral membrane protein aquaporin-0.DOI:10.1021/bi101415wPMID:20942504mass spectrometric detectionpeptidyl-lysine N6-oleoyltransferase (EC 2.3.1.-)KPSI-MOD:01936lipoproteinNot availablethis modification is not annotated in UniProt featuresAA059130-Jun-201230-Jun-201230-Jun-2012N-palmitoyl-L-methionine2-(hexadecanamido)-4-(methylsulfanyl)butanoic acidN-(1-oxohexadecyl)methionine(2S)-2-(hexadecanoylamino)-4-(methylsulfanyl)butanoic acidCAS:36416-81-6C 21 H 40 N 1 O 2 S 1370.62370.277976C 16 H 30 N 0 O 1 S 0238.41238.229666Schey, K.L.Gutierrez, D.B.Wang, Z.Wei, J.Grey, A.C.Biochemistry 49, 9858-9865, 2010Novel fatty acid acylation of lens integral membrane protein aquaporin-0.DOI:10.1021/bi101415wPMID:20942504mass spectrometric detectionmethionylpeptide N-palmitoyltransferase (EC 2.3.1.-)Mamino-terminalPSI-MOD:01937blocked amino endlipoproteinpalmitoylationLIPID N-palmitoyl methionineAA059230-Jun-201230-Jun-201230-Jun-20122-(2-aminosuccinimidyl)-3-sulfanylpropanoic acidaspartimide cysteine(2R)-2-[(3S)-3-amino-2,5-dioxopyrrolidin-1-yl]-3-sulfanylpropanoic acidPDBHET:SICPDBHET:SNNC 7 H 8 N 2 O 3 S 1200.21200.025563C 0 H -3 N -1 O 0 S 0-17.03-17.026549C 0 H -2 N 0 O -1 S 0-18.02-18.010565Bonanno, J.B.Freeman, J.Bain, K.T.Zhang, F.Ozyurt, S.Smith, D.Wasserman, S.Sauder, J.M.Burley, S.K.Almo, S.C.submitted to the Protein Data Bank, June 2008Crystal structure of an enolase protein from the environmental genome shotgun sequencing of the Sargasso Sea.PDB:3DIPX-ray diffraction, 2.50 angstromsVetting, M.W.Bouvier, J.T.Toro, R.Bhosle, R.Al Obaidi, N.F.Morisco, L.L.Wasserman, S.R.Sojitra, S.Imker, H.J.Gerlt, J.A.Almo, S.C.submitted to the Protein Data Bank, February 2012Crystal structure of an enolase (Mandelate racemase subgroup, Target EFI-502086) from Agrobacterium tumefaciens, with a succinimide residue.PDB:4DX3X-ray diffraction, 1.65 angstromsVetting, M.W.Bouvier, J.T.Toro, R.Bhosle, R.Al Obaidi, N.F.Morisco, L.L.Wasserman, S.R.Sojitra, S.Imker, H.J.Gerlt, J.A.Almo, S.C.submitted to the Protein Data Bank, February 2012Crystal structure of an enolase (Mandelate racemase subgroup, target EFI-502086) from Agrobacterium tumefaciens, with a succinimide residue, Na and phosphate.PDB:4DXKX-ray diffraction, 1.25 angstromsThis cross-link is formed by the condensation of an aspartic acid or asparagine residue with the alpha-amido of the following residue.autocatalyticC, Ncross-link 1PSI-MOD:01938C, Dcross-link 1PSI-MOD:01939succinimide ringNot availablethis modification is not annotated in UniProt featuresAA059330-Jun-201230-Jun-201230-Jun-20122-(2-aminosuccinimidyl)pentanedioic acidaspartimide glutamic acid(4S)-4-[(3S)-3-amino-2,5-dioxopyrrolidin-1-yl]-5-oxopentanoic acidPDBHET:SNNC 9 H 10 N 2 O 5226.19226.058971C 0 H -3 N -1 O 0-17.03-17.026549C 0 H -2 N 0 O -1-18.02-18.010565Lokanath, N.K.Kunishima, N.submitted to the Protein Data Bank, June 2004Crystal structure of PH1346 protein from Pyrococcus horikoshii.PDB:1WL8X-ray diffraction, 1.45 angstromsThis cross-link is formed by the condensation of an aspartic acid or asparagine residue with the alpha-amido of the following residue.autocatalyticE, Ncross-link 1PSI-MOD:01940D, Ecross-link 1PSI-MOD:01941succinimide ringNot availablethis modification is not annotated in UniProt featuresAA059424-Aug-201224-Aug-201231-May-2013labionin(2S,4S,8R)-2,4,8-triamino-4-carboxy-6-thianonanedioic acid(2S,4S,8R)-labionin(2S,4S)-2,4-diamino-2-[([(2R)-2-amino-2-carboxyethyl]sulfanyl)methyl]pentanedioic acidC 9 H 11 N 3 O 3 S 1241.26241.052112C 0 H -4 N 0 O -2 S 0-36.03-36.021129Meindl, K.Schmiederer, T.Schneider, K.Reicke, A.Butz, D.Keller, S.Gühring, H.Vértesy, L.Wink, J.Hoffmann, H.Brönstrup, M.Sheldrick, G.M.Süssmuth, R.D.Angew. Chem. Int. Ed. Engl. 49, 1151-1154, 2010Labyrinthopeptins: a new class of carbacyclic lantibiotics.DOI:10.1002/anie.200905773PMID:20082397mass spectrometric characterization and chemical characterization; gene sequence for the encoded peptide; X-ray diffraction, 1.0 angstroms; structure in Cambridge Crystallographic Data Center (721326); namingPesic, A.Henkel, M.Süssmuth, R.D.Chem. Commun. (Camb.) 47, 7401-7403, 2011Identification of the amino acid labionin and its desulfurised derivative in the type-III lantibiotic LabA2 by means of GC/MS.DOI:10.1039/c1cc11573aPMID:21603709mass spectrometric identificationThis three residue cross-link modification includes both a thioether bond and an alpha-linked carbon-carbon bond.C, S, Scross-link 3PSI-MOD:01948lanthioninethioether bondCROSSLNK Labionin (Ser-Ser) (with C-...)CROSSLNK Labionin (Ser-Cys) (with S-...)AA059524-Aug-201224-Aug-201231-May-2018coelenterazineOplophorus luciferin8-benzyl-2-(4-hydroxybenzyl)-6-(4-hydroxyphenyl)imidazo[1,2-a]pyrazin-3(7H)-oneCAS:55779-48-1ChEBI:2311C 26 H 21 N 3 O 3423.47423.158292C -1 H -8 N 0 O -3-68.07-68.047344Ward, W.W.Chalfie, M.submitted to the United States Patent Office, 21 April 1998Expression of a gene for a modified green-fluorescent protein.USPTO:US5741668a claim of autocatalytic production of coelenterazine from a green fluorescent protein with a modified FYYG sequence has not been confirmed in a subsequent publicationHead, J.F.Inouye, S.Teranishi, K.Shimomura, O.Nature 405, 372-376, 2000The crystal structure of the photoprotein aequorin at 2.3 A resolution.DOI:10.1038/35012659PMID:10830969X-ray diffraction, 2.3 angstroms; contains the activated form colenterazine-2-hydroperoxideHead, J.F.Inouye, S.Teranishi, K.Shimomura, O.submitted to the Protein Data Bank, February 2000Crystal structure of aequorin.PDB:1EJ3X-ray diffraction, 2.3 angstroms; contains the activated form colenterazine-2-hydroperoxideHaddock, S.H.Rivers, T.J.Robison, B.H.Proc. Natl. Acad. Sci. U.S.A. 98, 11148-11151, 2001Can coelenterates make coelenterazine? Dietary requirement for luciferin in cnidarian bioluminescence.DOI:10.1073/pnas.201329798PMID:11572972coelenterates cannot biosynthesize coelenterazine and acquire it by dietary intakeOba, Y.Kato, S.Ojika, M.Inouye, S.Biochem. Biophys. Res. Commun. 390, 684-688, 2009Biosynthesis of coelenterazine in the deep-sea copepod, Metridia pacifica.DOI:10.1016/j.bbrc.2009.10.028PMID:19833098radiolabeling experiments establish that the coelenterazine is constucted from one molecule of phenylalanine and two of tyrosineFrancis, W.R.Shaner, N.C.Christianson, L.M.Powers, M.L.Haddock, S.H.PLoS ONE 10, e0128742, 2015Occurrence of Isopenicillin-N-Synthase Homologs in Bioluminescent Ctenophores and Implications for Coelenterazine Biosynthesis.DOI:10.1371/journal.pone.0128742PMID:26125183candidate genes for coelenterazine precursors, found in luminous ctenophore species and not in non-luminous species, have Phe-Tyr-Tyr at their C-terminus and are conserved non-heme iron oxidases similar to isopenicillin-N-synthaseThe structure of the amino acid components of coelenterazine suggest that it is biosynthesized from a phenylalanyl-tyrosyl-tyrosine peptide.This entry presents coelenterazine as a modification produced by the cross-linking of a tripeptide precursor. For coelenterazine as a heterogen cross-linked to a cysteine see RESID:AA0526.F, Y, Yamino-terminalcarboxyl-terminalcross-link 3PSI-MOD:01949blocked amino endblocked carboxyl endNot availablethis modification is not annotated in UniProt featuresAA059631-Dec-201231-Dec-201231-Dec-2012L-isoglutamyl histamine(gamma-glutamyl)histamine(2S)-2-amino-5-([2-(1H-imidazol-5-yl)ethyl]amino)-5-oxopentanoic acidC 10 H 14 N 4 O 2222.25222.111676C 5 H 6 N 2 O 094.1294.053098Vowinckel, J.Stahlberg, S.Paulmann, N.Bluemlein, K.Grohmann, M.Ralser, M.Walther, D.J.FEBS Lett. 586, 3819-3824, 2012Histaminylation of glutamine residues is a novel posttranslational modification implicated in G-protein signaling.DOI:10.1016/j.febslet.2012.09.027PMID:23022564mass spectrometric identificationprotein-glutamine gamma-glutamyltransferase (EC 2.3.2.13)QPSI-MOD:01950Not availablethis modification is not annotated in UniProt featuresAA059731-Dec-201231-Dec-201231-May-2013O-(L-isoglutamyl)-L-serineO(beta)-(gamma-glutamyl)serineO3-(isoglutamyl)-serine(2S)-2-amino-5-[(2S)-2-amino-2-carboxyethoxy]-5-oxopentanoic acidC 8 H 10 N 2 O 4198.18198.064057C 0 H -2 N 0 O -1-18.02-18.010565C 0 H -3 N -1 O 0-17.03-17.026549Ishitsuka, M.O.Kusumi, T.Kakisawa, H.Kaya, K.Watanabe, M.M.J. Am. Chem. Soc. 112, 8180-8182, 1990Microviridin. A novel tricyclic depsipeptide from the toxic cyanobacterium Microcystis viridis.DOI:10.1021/ja00178a060amino acid composition; (1)H-NMR and (13)C-NMR identification; chemical characterization of the ester cross-linksPhilmus, B.Christiansen, G.Yoshida, W.Y.Hemscheidt, T.K.Chembiochem 9, 3066-3073, 2008Post-translational modification in microviridin biosynthesis.DOI:10.1002/cbic.200800560PMID:19035375(1)H-NMR and (13)C-NMR analysis; mass spectrometric and chemical characterization; directed mutation analysis; gene sequence for the encoded peptideAbdul Ajees, A.Gunasekaran, K.Volanakis, J.E.Narayana, S.V.Kotwal, G.J.Murthy, H.M.Nature 444, 221-225, 2006The structure of complement C3b provides insights into complement activation and regulation.DOI:10.1038/nature05258PMID:17051152X-ray diffraction, 2.26 angstroms; N-acetyl-L-threonine is the model substrateAbdul Ajees, A.Gunasekaran, K.Volanakis, J.E.Narayana, S.V.Kotwal, G.J.Murthy, H.M.submitted to the Protein Data Bank, July 2006Structure of complement C3B: Insights into complement activation and regulation.PDB:2HR0X-ray diffraction, 2.26 angstroms; N-acetyl-L-threonine is the model substrateThe ester cross-link of glutamate with serine is formed by an RimK related enzyme using ATP.The formation of an ester cross-link between serine residues of target proteins and complement C3 and C4 glutamine residues occurs autocatalytically after C3 and C4 form internal intermediate thioester cross-links with the liberation of ammonia.peptidyl-threonine--peptidyl-aspartate ligase MvdD (EC 6.1.2.-)autocatalyticE, Scross-link 2PSI-MOD:00953Q, Scross-link 2PSI-MOD:01951CROSSLNK isoglutamyl serine ester (Ser-Glu)AA059931-Dec-201231-Dec-201231-Mar-2013tetrakis-L-cysteinyl tetrairon octanitrosyltetrakis(mu3-cysteinato-kappa(3)S)-octanitrosyl-1kappa(2)N,2kappa(2)N,3kappa(2),4kappa(2)N-tetrahedro-tetraironC 12 Fe 4 H 16 N 12 O 12 S 4871.95871.729098C 0 Fe 4 H -4 N 8 O 8 S 0459.40459.692359Crack, J.C.Smith, L.J.Stapleton, M.R.Peck, J.Watmough, N.J.Buttner, M.J.Buxton, R.S.Green, J.Oganesyan, V.S.Thomson, A.J.Le Brun, N.E.J. Am. Chem. Soc. 133, 1112-1121, 2011Mechanistic insight into the nitrosylation of the [4Fe-4S] cluster of WhiB-like proteins.DOI:10.1021/ja109581tPMID:21182249spectrographic characterizationIt has been proposed that in the WhiD protein of Streptomyces coelicolor and Mycobacterium this cluster is rapidly and specifically produced by nitrosylation of a tetrakis-L-cysteinyl tetrairon tetrasulfide cluster. See RESID:AA0140.autocatalyticC, C, C, Ccross-link 4PSI-MOD:01953ironmetalloproteinNot availablethis modification is not annotated in UniProt featuresAA060001-Mar-201301-Mar-201301-Mar-2013L-alaninato bis-L-aspartato tris-L-glutamato L-histidino calcium tetramanganese pentoxide4Mn-Ca-5O clusterphotosystem II catalytic clustermu2-alaninato-1kappaO(1),3kappaO(1')-mu2-aspartato-1kappaO(4),5kappaO(4')-mu2-aspartato-2kappaO(4),3kappaO(4')-mu2-glutamato-3kappaO(5),4kappaO(5')-mu2-glutamato-4kappaO(5),5kappaO(5')-mu-glutamato-2kappaO(5)-mu-histidino-2kappaN(tau)-mu4-oxido-1:2:4:5kappa(4)O-tri-mu3-oxido-1:2:3kappa(3)O;1:3:4kappa(3)O;2:3:4kappa(3)O;mu-oxido-4:5kappa(2)O-calciumtetramanganesePDBHET:OEXC 32 Ca 1 H 38 Mn 4 N 9 O 231176.531175.922825C 0 Ca 1 H -6 Mn 4 N 0 O 5333.78333.642394Umena, Y.Kawakami, K.Shen, J.R.Kamiya, N.Nature 473, 55-60, 2011Crystal structure of oxygen-evolving photosystem II at a resolution of 1.9 Å.DOI:10.1038/nature09913PMID:21499260X-ray diffraction, 1.9 angstromsUmena, Y.Kawakami, K.Shen, J.-R.Kamiya, N.submitted to the Protein Data Bank, October 2012Crystal structure of oxygen-evolving photosystem II at 1.9 angstrom resolution.PDB:3ARCX-ray diffraction, 1.90 angstromsThe metal cluster consists of a three-manganese, one-calcium, four-oxygen cubane with a cubane oxygen that ligates the calcium also ligating a fourth manganese, and a fifth oxygen that ligates the fourth manganese and a cubane manganese. Additionally but not shown in the model, one omega amino group of an arginine donates hydrogen bonds to two cubane oxygens, and the tele-nitrogen of a histidine donates a hydrogen bond to another cubane oxygen.The reactive center for converting several water molecules to dioxygen may be between the calcium and the fourth manganese where electron density was modeled as bicarbonate and chloride ions.The formal charge is uncertain.A, D, D, E, E, E, Hcarboxyl-terminalcross-link 7PSI-MOD:01955calciummanganesemetalloproteinNot availablethis modification is not annotated in UniProt featuresAA060101-Mar-201301-Mar-201331-May-2018(3R)-3-hydroxy-L-arginine2-amino-5-(carbamimidamido)-3-hydroxypentanoic acid [tautomer]2-amino-5-guanidino-3-hydroxypentanoic acid2-amino-5-[(aminoiminomethyl)amino]-3-hydroxypentanoic acid [tautomer]beta-hydroxyarginineC(beta)-hydroxyarginine(2S,3R)-2-amino-5-[(diaminomethylidene)amino]-3-hydroxypentanoic acidChEBI:29965C 6 H 12 N 4 O 2172.19172.096026C 0 H 0 N 0 O 116.0015.994915Brosius, J.Chen, R.FEBS Lett. 68, 105-109, 1976The primary structure of protein L16 located at the peptidyltransferase center of Escherichia coli ribosomes.DOI:10.1016/0014-5793(76)80415-2PMID:786730modified arginine observed in Escherichia coli ribosomal protein L16Arnold, R.J.Reilly, J.P.Anal. Biochem. 269, 105-112, 1999Observation of Escherichia coli ribosomal proteins and their posttranslational modifications by mass spectrometry.DOI:10.1006/abio.1998.3077PMID:10094780top-down mass-spectrometry; in a private communication from J. Brosius the modification was identified as a probable hydroxyarginineGe, W.Wolf, A.Feng, T.Ho, C.H.Sekirnik, R.Zayer, A.Granatino, N.Cockman, M.E.Loenarz, C.Loik, N.D.Hardy, A.P.Claridge, T.D.Hamed, R.B.Chowdhury, R.Gong, L.Robinson, C.V.Trudgian, D.C.Jiang, M.Mackeen, M.M.McCullagh, J.S.Gordiyenko, Y.Thalhammer, A.Yamamoto, A.Yang, M.Liu-Yi, P.Zhang, Z.Schmidt-Zachmann, M.Kessler, B.M.Ratcliffe, P.J.Preston, G.M.Coleman, M.L.Schofield, C.J.Nature Chem. Biol. 8, 960-962, 2012Oxygenase-catalyzed ribosome hydroxylation occurs in prokaryotes and humans.DOI:10.1038/nchembio.1093PMID:23103944mass spectrometry; NMR; radiolabeling; amino acid analysis indicate that the modification is the (2S,3R) diastereomer, by comparison with the synthetic diastereomersvan Staalduinen, L.M.Novakowski, S.K.Jia, Z.J. Mol. Biol. 426, 1898-1910, 2014Structure and functional analysis of YcfD, a novel 2-oxoglutarate/Fe²⁺-dependent oxygenase involved in translational regulation in Escherichia coli.DOI:10.1016/j.jmb.2014.02.008PMID:24530688Jumonji C-domain-containing protein ycfD modifies E.coli ribosomal protein L16 arginine-81 to (3R)-3-hydroxy-L-arginineThe diastereomer (2S,3S)-3-hydroxyarginine is produced in non-ribosomal antibiotic peptides of Streptomyces vinaceus.ribosomal protein L16 arginine hydroxylase ycfD50S ribosomal protein L16 3-hydroxylase[50S ribosomal protein L16]-L-Arg81,2-oxoglutarate:oxygen oxidoreductase (3-hydroxylating) (EC 1.14.11.47)RPSI-MOD:01956hydroxylationMOD_RES (3R)-3-hydroxyarginineAA060201-Mar-201301-Mar-201330-Jun-20132-hydroxyproline2-oxidanylpyrrolidine-2-carboxylic acidalpha-hydroxyproline(2R)-2-hydroxypyrrolidine-2-carboxylic acidPDBHET:PXUC 5 H 7 N 1 O 2113.12113.047678C 0 H 0 N 0 O 116.0015.994915Fadouloglou, V.E.Kapanidou, M.Agiomirgianaki, A.Arnaouteli, S.Bouriotis, V.Glykos, N.M.Kokkinidis, M.Acta Crystallogr. D Biol. Crystallogr. 69, 276-283, 2013Structure determination through homology modelling and torsion-angle simulated annealing: application to a polysaccharide deacetylase from Bacillus cereus.DOI:10.1107/S0907444912045829PMID:23385463X-ray diffraction, 2.50 angstroms; electron density of a first row element appears to replace the alpha-carbon hydrogen in the neighborhood of a bound zinc atom; it is modeled as an alpha-hydroxyl group; there is no supporting chemical or mass-spectrometic evidenceFadouloglou, V.E.Kokkinidis, M.Glykos, N.M.submitted to the Protein Data Bank, October 2012Crystal structure of BC0361, a polysaccharide deacetylase from Bacillus cereus.PDB:4HD5X-ray diffraction, 2.50 angstromsThe chemical stability of this modification has been questioned. However, a similar modification in an homologous enzyme has apparently been observed by another group in work that has not yet been published.autocatalyticPPSI-MOD:01957hydroxylationNot availablethis modification is not annotated in UniProt featuresAA060331-Mar-201331-Mar-201331-Mar-2013bis-L-cysteinyl bisglutathion-S-yl diiron disulfidemitochondrial glutaredoxin 2 dimer iron-sulfur clusterplant glutaredoxin C1 dimer iron-sulfur clusterdi-mu-sulfido-bis(cysteinato)-1kappaS,2kappaS-bis(glutathionato)-1kappaS,2kappaS-diironPDBHET:FESC 26 Fe 2 H 40 N 8 O 14 S 6992.70991.968699C 20 Fe 2 H 30 N 6 O 12 S 4786.42785.950329Johansson, C.Kavanagh, K.L.Gileadi, O.Oppermann, U.J. Biol. Chem. 282, 3077-3082, 2007Reversible sequestration of active site cysteines in a 2Fe-2S-bridged dimer provides a mechanism for glutaredoxin 2 regulation in human mitochondria.DOI:10.1074/jbc.M608179200PMID:17121859X-ray diffraction, 1.90 angstromsJohansson, C.Smee, C.Kavanagh, K.L.Debreczeni, J.Von Delft, F.Gileadi, O.Arrowsmith, C.Weigelt, J.Edwards, A.Sundstrom, M.Oppermann, U.submitted to the Protein Data Bank, August 1996The structure of dimeric human glutaredoxin 2.PDB:2HT9X-ray diffraction, 1.90 angstromsThe iron-sulfur cluster binding, dimeric form is described as "quiescent", and the reactivity is regulated by the relative redox potential determined by the GSH/GSSG ratio and the concentration of Fe(2+).autocatalyticC, Ccross-link 2PSI-MOD:019582Fe-2Siron-sulfur proteinmetalloproteinNot availablethis modification is not annotated in UniProt featuresAA060431-Mar-201331-Mar-201331-Mar-2013tris-L-cysteinyl L-glutamato tetrairon tetrasulfidetris-mu3-sulfido-tris(cysteinato)-1kappaS,2kappaS,3kappaS-glutamato-4kappaO(5),4kappaO(5')-tetraironPDBHET:SF4C 14 Fe 4 H 18 N 4 O 6 S 7786.12785.666881C 0 Fe 4 H -4 N 0 O 0 S 4347.59347.596734Rekittke, I.Nonaka, T.Wiesner, J.Demmer, U.Warkentin, E.Jomaa, H.Ermler, U.FEBS Lett. 585, 447-451, 2011Structure of the E-1-hydroxy-2-methyl-but-2-enyl-4-diphosphate synthase (GcpE) from Thermus thermophilus.DOI:10.1016/j.febslet.2010.12.012PMID:21167158X-ray diffraction, 2.50 angstromsRekittke, I.Nonaka, T.Wiesner, J.Demmer, U.Warkentin, E.Jomaa, H.Ermler, U.submitted to the Protein Data Bank, December 2010Structure of GcpE (IspG) from Thermus thermophilus HB27.PDB:2Y0FX-ray diffraction, 2.50 angstromsBoth mono- and bidentate ligation by the glutamate were observed. Bidentate ligation is shown.The glutamate ligation is weak and is preferentially displaced by the substrate.C, C, C, Ecross-link 4PSI-MOD:019594Fe-4Siron-sulfur proteinmetalloproteinNot availablethis modification is not annotated in UniProt featuresAA060531-Mar-201331-Mar-201331-Dec-2013tris-L-cysteinyl L-glutamin-O6-yl tetrairon tetrasulfidetris-mu3-sulfido-tris(cysteinato)-1kappaS,2kappaS,3kappaS-glutaminato-4kappaN(5)-tetraironPDBHET:SF4C 14 Fe 4 H 19 N 5 O 5 S 7785.14784.682866C 0 Fe 4 H -4 N 0 O 0 S 4347.59347.596734Dobritzsch, D.Ricagno, S.Schneider, G.Schnackerz, K.D.Lindqvist, Y.J. Biol. Chem. 277, 13155-13166, 2002Crystal structure of the productive ternary complex of dihydropyrimidine dehydrogenase with NADPH and 5-iodouracil. Implications for mechanism of inhibition and electron transfer.DOI:10.1074/jbc.M111877200PMID:11796730X-ray diffraction, 1.65 angstromsDobritzsch, D.Ricagno, S.Schneider, G.Schnackerz, K.D.Lindqvist, Y.submitted to the Protein Data Bank, January 2002Dihydropyrimidine dehydrogenase (DPD) from pig, binaty complex with 5-iodouracil.PDB:1GTEX-ray diffraction, 1.65 angstromsThe glutamine ligation could be by either O(5) or N(5), and could not be distinguished at this resolution. The ligation was modeled as O(5) and that is the tautomeric form that is shown.C, C, C, Qcross-link 4PSI-MOD:019604Fe-4Siron-sulfur proteinmetalloproteinMETAL Iron-sulfur (4Fe-4S)AA060631-May-201331-May-201330-Jun-2013N4-(2,4-diacetamido-2,4,6-trideoxy-D-glucosyl)-L-asparagineDABADATDHDiNAcBacN4-[2,4-bis(acetylamino)-2,4,6-trideoxy-beta-D-glucopyranosyl]-L-asparagineN4-[N,N-diacetylbacillosaminyl]asparagineN4-[N2,N4-diacetylbacillosaminyl]asparagine(2S)-2-amino-4-[(2,4-diacetylamino-2,4,6-trideoxy-beta-D-glucopyranosyl)amino]-4-oxobutanoic acidPDBHET:B6DC 14 H 22 N 4 O 6342.35342.153934C 10 H 16 N 2 O 4228.25228.111007Young, N.M.Brisson, J.R.Kelly, J.Watson, D.C.Tessier, L.Lanthier, P.H.Jarrell, H.C.Cadotte, N.St. Michael, F.Aberg, E.Szymanski, C.M.J. Biol. Chem. 277, 42530-42539, 2002Structure of the N-linked glycan present on multiple glycoproteins in the Gram-negative bacterium, Campylobacter jejuni.DOI:10.1074/jbc.M206114200PMID:12186869mass spectrometric identification and (1)H-NMR characterization; large scale proteomic analysis; the spelling of St. Michael in the PubMed citation is correctedMin, T.Vedadi, M.Watson, D.C.Wasney, G.A.Munger, C.Cygler, M.Matte, A.Young, N.M.Biochemistry 48, 3057-3067, 2009Specificity of Campylobacter jejuni adhesin PEB3 for phosphates and structural differences among its ligand complexes.DOI:10.1021/bi802195dPMID:19236052X-ray diffraction, 2.00 angstromsMin, T.Matte, A.Cygler, M.submitted to the Protein Data Bank, December 2008Crystal structure of glycosylated K135E PEB3.PDB:3FIRX-ray diffraction, 2.00 angstromsBacillosamine is a trivial name formed by modification of a non-standard monosaccharide parent name, and is not recommended by the IUPAC Nomenclature Committee. Some authors use bacillosamine to refer to the diacetylated form, rather than the unacetylated form.NPSI-MOD:01962glycoproteinNot availablethis modification is not annotated in UniProt featuresAA060731-May-201331-May-201330-Jun-2013O-(2,4-diacetamido-2,4,6-trideoxy-D-glucosyl)-L-serineDABADATDHDiNAcBacO-[2,4-bis(acetylamino)-2,4,6-trideoxy-beta-D-glucopyranosyl]-L-serineO-[N,N-diacetylbacillosaminyl]serineO-[N2,N4-diacetylbacillosaminyl]serine(2S)-2-amino-4-[(2,4-diacetamido-2,4,6-trideoxy-beta-D-glucopyranosyl)oxy]propanoic acidC 13 H 21 N 3 O 6315.33315.143035C 10 H 16 N 2 O 4228.25228.111007Anonsen, J.H.Vik, Å.Egge-Jacobsen, W.Koomey, M.J. Proteome Res. 11, 5781-5793, 2012An extended spectrum of target proteins and modification sites in the general O-linked protein glycosylation system in Neisseria gonorrhoeae.DOI:10.1021/pr300584xPMID:23030644mass spectrometric identification; large scale proteomic analysisBacillosamine is a trivial name formed by modification of a non-standard monosaccharide parent name, and is not recommended by the IUPAC Nomenclature Committee. Some authors use bacillosamine to refer to the diacetylated form, rather than the unacetylated form.For O-(2,4-diacetamido-2,4-dideoxy-D-glucosyl)-L-serine, see RESID:AA0499.SPSI-MOD:01963glycoproteinNot availablethis modification is not annotated in UniProt featuresAA060831-May-201331-May-201330-Jun-2013O-(2-acetamido-4-glyceramido-2,4,6-trideoxy-D-glucosyl)-L-serineGATDHO-(2-acetamido-4-glyceramido-2,4,6-trideoxy-D-glucopyranosyl)-L-serineO-(N2-acetyl-N4-glycerylbacillosaminyl)-L-serine(2S)-2-amino-3-[(2-acetamido-4-glycerylamino-2,4,6-trideoxy-D-glucopyranosyl)oxy]propanoic acidC 14 H 23 N 3 O 8361.35361.148515C 11 H 18 N 2 O 6274.27274.116486Chamot-Rooke, J.Rousseau, B.Lanternier, F.Mikaty, G.Mairey, E.Malosse, C.Bouchoux, G.Pelicic, V.Camoin, L.Nassif, X.Duménil, G.Proc. Natl. Acad. Sci. U.S.A. 104, 14783-14788, 2007Alternative Neisseria spp. type IV pilin glycosylation with a glyceramido acetamido trideoxyhexose residue.DOI:10.1073/pnas.0705335104PMID:17804791mass spectrometric identification; the identity of the sugar is inferred by genomic analysisThe stereochemical identity of the sugar and the glyceryl group have not been established by chemical methods.SPSI-MOD:01964glycoproteinNot availablethis modification is not annotated in UniProt featuresAA060913-Sep-201313-Sep-201331-May-2018N(omega)-(N-acetylamino)glucosyl-L-arginineN(omega)-(2-acetamido-2-deoxy-D-glucopyranosyl)-L-arginineN(omega)-(2-acetylamino-2-deoxy-D-glucopyranosyl)-L-arginineN(omega)-(2-N-acetylaminoglucosyl)arginineNG-(2-acetamido-2-deoxy-D-glucopyranosyl)-L-arginineNG-(2-acetylamino-2-deoxy-D-glucopyranosyl)-L-arginineNG-(2-N-acetylaminoglucosyl)arginineomega-N-(2-acetamido-2-deoxy-D-glucopyranosyl)-L-arginineomega-N-(2-acetylamino-2-deoxy-D-glucopyranosyl)-L-arginineomega-N-(2-N-acetylaminoglucosyl)arginine(2S)-2-amino-5-[(amino[(2-N-acetylamino-2-deoxy-D-glucopyranosyl)amino]methylidene)amino]pentanoic acidC 14 H 25 N 5 O 6359.38359.180484C 8 H 13 N 1 O 5203.19203.079373Li, S.Zhang, L.Yao, Q.Li, L.Dong, N.Rong, J.Gao, W.Ding, X.Sun, L.Chen, X.Chen, S.Shao, F.Nature 501, 242-246, 2013Pathogen blocks host death receptor signalling by arginine GlcNAcylation of death domains.DOI:10.1038/nature12436PMID:23955153chromatographic and mass spectrometric identification; biosynthesis; the anomeric stereochemistry was not determinedThis modification is produced in host proteins by a secretion system effector of some enteropathogenic bacteria. The anomeric form of the product has not been characterized; the beta form is presented.[protein]-L-arginine N-acetyl-D-glucosaminyl-transferase NleB (EC 2.4.1.-)RPSI-MOD:01967glycoproteinNot availablethis modification is not annotated in UniProt featuresAA061013-Sep-201313-Sep-201331-May-2018(2R,3R,2'R)-3-methyllanthionine(2R,3R,2'R)-2-amino-3-[(2-amino-2-carboxyethyl)thio]butanoic acid(2R,3R,6R)-2,6-diamino-3-methyl-4-thiaheptanedioic acid(2R,3R,6R)-3-methyllanthionine2-azanyl-3-[(2-azanyl-2-carboxyethyl)sulfanyl]butanoic acid3-methyl-L,L-lanthioninecysteine-3-L-butyrine thioether(2R,3R)-2-amino-3-([(2R)-2-amino-2-carboxyethyl]sulfanyl)butanoic acidC 7 H 10 N 2 O 2 S 1186.23186.046299C 0 H -2 N 0 O -1 S 0-18.02-18.010565Tang, W.van der Donk, W.A.Nature Chem. Biol. 9, 157-159, 2013The sequence of the enterococcal cytolysin imparts unusual lanthionine stereochemistry.DOI:10.1038/nchembio.1162PMID:23314913chiral gas chromatographic and mass spectrometric identificationThere are 3 chiral centers, so there are 8 possible stereoisomers. Bacterial peptidyl-cysteine dehydroalanine/dehydrobutyrine ligase and peptide conformation preferentially produce the (2S,3S,2'R) diastereomer. The cysteine maintains its L configuration (R chirality), while the threonine 2-aminobutanoate skeleton loses and then regains an L configuration (R chirality). For the (2S,3S,2'R), see RESID:AA0112.peptidyl-phosphoserine/phosphothreonine dehydratase (EC 4.2.1.-)peptidyl-cysteine dehydroalanine/dehydrobutyrine ligase (EC 6.2.-.-)C, Tcross-link 2PSI-MOD:01968lanthioninethioether bondNot availablethis modification is not annotated in UniProt featuresAA061113-Sep-201313-Sep-201313-Sep-2013S-(gamma-glutamyl-cysteinyl-glycyl)-cysteineS-(glutathion-1-yl)-L-cysteine(2S)-2-amino-5-([(2R)-1-([2-([(2R)-2-amino-2-carboxyethyl]sulfanyl)-2-oxoethyl]amino)-1-oxo-3-sulfanylpropan-2-yl]amino)-5-oxopentanoic acidC 13 H 20 N 4 O 6 S 2392.44392.082426C 10 H 15 N 3 O 5 S 1289.31289.073242Lin, C.H.Kwon, D.S.Bollinger Jr., J.M.Walsh, C.T.Biochemistry 36, 14930-14938, 1997Evidence for a glutathionyl-enzyme intermediate in the amidase activity of the bifunctional glutathionylspermidine synthetase/amidase from Escherichia coli.DOI:10.1021/bi9714464PMID:9398217chemical characterization; directed mutation analysisautocatalyticCPSI-MOD:01969glutathionethioester bondACT_SITE S-(gamma-glutamyl-cysteinyl-glycyl)-cysteine intermediateAA061213-Sep-201313-Sep-201330-Sep-20135-glutamyl glutamic acid(2S)-2-[(4S)-4-amino-4-carboxybutanamido]pentanedioic acid2-([4-azanyl-4-carboxybutanoyl]azanyl)pentanedioic acidgamma-glutamylglutamateisoglutamyl glutamic acidisoglutamyl monoglutamic acidN-(gamma-L-glutamyl)-L-glutamic acid(2S)-2-([(4S)-4-amino-4-carboxybutanoyl]amino)pentanedioic acidCAS:1116-22-9C 10 H 14 N 2 O 6258.23258.085186C 5 H 7 N 1 O 3129.12129.042593Ouchi, T.Tomita, T.Horie, A.Yoshida, A.Takahashi, K.Nishida, H.Lassak, K.Taka, H.Mineki, R.Fujimura, T.Kosono, S.Nishiyama, C.Masui, R.Kuramitsu, S.Albers, S.V.Kuzuyama, T.Nishiyama, M.Nature Chem. Biol. 9, 277-283, 2013Lysine and arginine biosyntheses mediated by a common carrier protein in Sulfolobus.DOI:10.1038/nchembio.1200PMID:23434852biosynthesis; mass spectrometric detectionThis entry is for isoglutamyl glutamic acid where there is a single glutamic acid attached to a peptide glutamyl residue by an isopeptide bond. For L-isoglutamyl-polyglutamic acid where there are 2 to 6 alpha-peptide linked glutamic acid residues attached to a peptide glutamyl residue by an isopeptide bond, see RESID:AA0202.glutamate--LysW ligase, ArgX (EC 6.3.2.-)EPSI-MOD:01970isopeptide bondMOD_RES 5-glutamyl glutamateAA061313-Sep-201313-Sep-201313-Sep-20135-glutamyl N2-ornithine(2S)-5-amino-2-([(4S)-4-amino-4-carboxybutanoyl]amino)pentanoic acid4-amino-5-[(4-amino-1-carboxy-butyl)amino]-5-ketovaleric acid4-amino-5-[(4-amino-1-carboxy-butyl)amino]-5-oxopentanoic acidgamma-glutamylornithineN2-(gamma-glutamyl)ornithineN2-(L-isoglutamyl)-L-ornithine(2S)-5-amino-2-[(4S)-4-amino-4-carboxybutanamido]pentanoic acidCAS:56523-61-6C 10 H 17 N 3 O 4243.26243.121906C 5 H 10 N 2 O 1114.15114.079313Ouchi, T.Tomita, T.Horie, A.Yoshida, A.Takahashi, K.Nishida, H.Lassak, K.Taka, H.Mineki, R.Fujimura, T.Kosono, S.Nishiyama, C.Masui, R.Kuramitsu, S.Albers, S.V.Kuzuyama, T.Nishiyama, M.Nature Chem. Biol. 9, 277-283, 2013Lysine and arginine biosyntheses mediated by a common carrier protein in Sulfolobus.DOI:10.1038/nchembio.1200PMID:23434852biosynthesis; this intermediate product was not directly observed but was inferredThis modification is probably produced on the C-terminal glutamic acid of a carrier protein as one of a series of intermediates.EPSI-MOD:01971isopeptide bondMOD_RES 5-glutamyl N2-ornithineAA061413-Sep-201313-Sep-201330-Sep-20135-glutamyl coenzyme A thioester(2S)-2-amino-5-(2-[([3-([(2R)-2-hydroxy-3,3-dimethyl-4-([3'-phospho-adenosyl-5'-diphosphoryl]-oxy)-butanoyl]-amino)-propanoyl]-amino)-ethyl]-sulfanyl)-5-oxopentanoic acid5-glutamyl 4-[(3'-phospho-adenosyl-5'-diphosphoryl)oxy]pantetheine thioester(2S)-2-amino-5-([2-(3-[(2R)-2-hydroxy-3,3-dimethyl-4-([3'-phospho-adenosyl-5'-diphosphoryl]-oxy)-butanamido]-propanamido)-ethyl]-sulfanyl)-5-oxopentanoic acidC 26 H 41 N 8 O 18 P 3 S 1878.63878.147237C 21 H 34 N 7 O 15 P 3 S 1749.52749.104644Rochet, J.C.Bridger, W.A.Protein Sci. 3, 975-981, 1994Identification of glutamate 344 as the catalytic residue in the active site of pig heart CoA transferase.DOI:10.1002/pro.5560030613PMID:7915164mass spectrometric identificationFraser, M.E.Hayakawa, K.Brown, W.D.Biochemistry 49, 10319-10328, 2010Catalytic role of the conformational change in succinyl-CoA:3-oxoacid CoA transferase on binding CoA.DOI:10.1021/bi100659sPMID:20977214X-ray diffraction, 2.30 angstromsFraser, M.E.submitted to the Protein Data Bank, September 2010Succinyl-CoA:3-ketoacid CoA transferase from pig heart covalently bound to CoA.PDB:3OXOX-ray diffraction, 2.30 angstromsRangarajan, E.S.Li, Y.Ajamian, E.Iannuzzi, P.Kernaghan, S.D.Fraser, M.E.Cygler, M.Matte, A.J. Biol. Chem. 280, 42919-42928, 2005Crystallographic trapping of the glutamyl-CoA thioester intermediate of family I CoA transferases.DOI:10.1074/jbc.M510522200PMID:16253988X-ray diffraction, 2.00 angstromsRangarajan, E.S.Li, Y.Ajamian, E.Iannuzzi, P.Kernaghan, S.D.Fraser, M.E.Cygler, M.Matte, A.submitted to the Protein Data Bank, July 2005Crystal structure of acyl-CoA transferase from E. coli O157:H7 (YdiF)- thioester complex with CoA- 1.PDB:2AHVX-ray diffraction, 2.00 angstromsautocatalyticEPSI-MOD:01972coenzyme Athioester bond5-glutamyl coenzyme A thioester intermediateAA061513-Sep-201313-Sep-201313-Sep-2013N6-(3-phosphoglyceryl)-L-lysine(2S)-2-amino-6-([(2R)-2-hydroxy-3-(phosphonooxy)propanoyl]amino)hexanoic acid3-phosphoglyceryl-lysine(2S)-2-amino-6-[(2R)-2-hydroxy-3-(phosphonooxy)propanamido]hexanoic acidC 9 H 17 N 2 O 7 P 1296.22296.077338C 3 H 5 N 0 O 6 P 1168.04167.982375Moellering, R.E.Cravatt, B.F.Science 341, 549-553, 2013Functional lysine modification by an intrinsically reactive primary glycolytic metabolite.DOI:10.1126/science.1238327PMID:23908237mass-spectrometic detection; radiolabelingautocatalyticKPSI-MOD:01973phosphoproteinNot availablethis modification is not annotated in UniProt featuresAA061613-Sep-201313-Sep-201313-Sep-2013S-methyl-L-methionine(2S)-2-amino-4-(dimethylsulfonio)butanoateS-methylmethionineS-methylmethioniniumvitamin U[(3S)-3-amino-3-carboxypropyl](dimethyl)sulfonium(3S)-(3-amino-3-carboxypropyl)dimethylsulfaniumCAS:4727-40-6ChEBI:17728C 6 H 12 N 1 O 1 S 11+146.23146.063411C 1 H 3 N 0 O 0 S 01+15.0315.022927Patananan, A.N.Palmer, J.M.Garvey, G.S.Keller, N.P.Clarke, S.G.J. Biol. Chem. 288, 14032-14045, 2013A novel automethylation reaction in the Aspergillus nidulans LaeA protein generates S-methylmethionine.DOI:10.1074/jbc.M113.465765PMID:23532849radiolabeling detection; chromatographic identification; no protein was detected as a methylation target other than the LaeA protein itself, but the modified methionine was not required for transcription regulating activityautocatalyticMPSI-MOD:01974methylated amino acidNot availablethis modification is not annotated in UniProt featuresAA061730-Sep-201330-Sep-201331-Dec-2013S-poly(3-hydroxybutyrate)-L-cysteineS-poly(3-hydroxybutanoate)cysteineS-poly(3-hydroxybutanoic acid)cysteineS-poly(3-hydroxybutyrate)cysteineS-poly(3-hydroxybutyric acid)cysteineS-poly(beta-hydroxybutyrate)cysteineS-poly[(R)-3-hydroxybutyrate]cysteine(alpha)-([(2R)-2-amino-2-carboxyethyl]sulfanyl)-(omega)-[(3R)-3-hydroxybutanoyl]-poly([(3R)-3-methyl-1-oxopropane-1,3-diyl]oxy)CAS:29435-48-1C 11 H 17 N 1 O 5 S 1275.32275.082744C 8 H 12 N 0 O 4 S 0172.18172.073559Müh, U.Sinskey, A.J.Kirby, D.P.Lane, W.S.Stubbe, J.Biochemistry 38, 826-837, 1999PHA synthase from chromatium vinosum: cysteine 149 is involved in covalent catalysis.DOI:10.1021/bi9818319PMID:9888824biosynthesis; chromatographic and mass spectrometric identification; radiolabeling; directed mutation analysis; the production of poly-3-hydroxybutyrate by Escherichia coli polyhydroxybutyrate synthase requires Cys-149Li, P.Chakraborty, S.Stubbe, J.Biochemistry 48, 9202-9211, 2009Detection of covalent and noncovalent intermediates in the polymerization reaction catalyzed by a C149S class III polyhydroxybutyrate synthase.DOI:10.1021/bi901329bPMID:19711985biosynthesis; chromatographic and mass spectrometric identification; radiolabeling; directed mutation analysis; the autocatalytic covalent modification by polymeric 3-hydroxybutyrate of Cys-149 in Escherichia coli polyhydroxybutyrate synthase is demonstratedThe mechanism of biosynthesis may involve transfer of the polymer to and from a noncovalently bound coenzyme A.The intermediate modification with two polymeric units is presented.autocatalyticCPSI-MOD:01975Not availablethis modification is not annotated in UniProt featuresAA061830-Sep-201330-Sep-201330-Sep-2013O3-(poly-3-hydroxybutyrate)-L-serineO3-poly(3-hydroxybutanoate)serineO3-poly(3-hydroxybutanoic acid)serineO3-poly(3-hydroxybutyrate)serineO3-poly(3-hydroxybutyric acid)serineO3-poly(beta-hydroxybutyrate)serineO3-poly[(R)-3-hydroxybutyrate]serine(2S)-2-amino-3-[([(3R)-3-hydroxybutanoyl]oxy)-poly([(3R)-3-methyl-1-oxopropane-1,3-diyl]oxy)]propanoic acidCAS:29435-48-1C 11 H 17 N 1 O 6259.26259.105587C 8 H 12 N 0 O 4172.18172.073559Xian, M.Fuerst, M.M.Shabalin, Y.Reusch, R.N.Biochim. Biophys. Acta 1768, 2660-2666, 2007Sorting signal of Escherichia coli OmpA is modified by oligo-(R)-3-hydroxybutyrate.DOI:10.1016/j.bbamem.2007.06.019PMID:17659252chromatographic and mass spectrometric identification; directed mutation analysis; probably both Ser-184 and Ser-188 of E.coli OmpA (UniProt:P0A910) are modified by a polymer of 6-10 units, but degradation during isolation was possibleNegoda, A.Negoda, E.Reusch, R.N.Biochim. Biophys. Acta 1798, 1480-1484, 2010Oligo-(R)-3-hydroxybutyrate modification of sorting signal enables pore formation by Escherichia coli OmpA.DOI:10.1016/j.bbamem.2009.11.023PMID:20004640modification of OmpA is necessary for targeting to membrane and pore formationThe mechanism for transfer of the polymer from the synthase is uncertain.The modification with two polymeric units is presented.SPSI-MOD:01976Not availablethis modification is not annotated in UniProt featuresAA061931-Dec-201331-Dec-201331-May-2018N,N,N-trimethylglycine(trimethylammonio)ethanoic acid1-carboxy-N,N,N-trimethylmethanazanium2-trimethylammonioacetatebetainecarboxymethyl-trimethylazaniumglycine betaineN,N,N-trimethylglycine cationN,N,N-trimethylglyciniumcarboxy-N,N,N-trimethylmethanaminiumCAS:107-43-7ChEBI:17750C 5 H 11 N 1 O 11+101.15101.083515C 3 H 7 N 0 O 01+43.0943.054227Bailey, A.O.Panchenko, T.Sathyan, K.M.Petkowski, J.J.Pai, P.J.Bai, D.L.Russell, D.H.Macara, I.G.Shabanowitz, J.Hunt, D.F.Black, B.E.Foltz, D.R.Proc. Natl. Acad. Sci. U.S.A. 110, 11827-11832, 2013Posttranslational modification of CENP-A influences the conformation of centromeric chromatin.DOI:10.1073/pnas.1300325110PMID:23818633mass spectrometric identificationDai, X.Otake, K.You, C.Cai, Q.Wang, Z.Masumoto, H.Wang, Y.J. Proteome Res. 12, 4167-4175, 2013Identification of novel α-n-methylation of CENP-B that regulates its binding to the centromeric DNA.DOI:10.1021/pr400498yPMID:23978223mass spectrometric identificationThis modification is the major post-translational modification in the methylation of N-terminal glycine. See also RESID:AA0063 and RESID:AA0620.Consult FAQ at http://pir.georgetown.edu/resid/faq.shtml#q12 concerning calculation of the difference formula.It is not clear whether the N-terminal methyltransferase responsible for methylating N-terminal glycine is distinguishable from the enzyme activities of EC 2.1.1.244 or EC 2.1.1.299.protein N-terminal methyltransferase (EC 2.1.1.-)Gamino-terminalPSI-MOD:01982blocked amino endmethylated amino endMOD_RES N,N,N-trimethylglycineAA062031-Dec-201331-Dec-201331-May-2018N,N-dimethylglycine1-carboxy-N,N-dimethylaminomethane2-(dimethylamino)acetic acidvitamin B16(dimethylamino)ethanoic acidCAS:1118-68-9ChEBI:17724PDBHET:DMGC 4 H 8 N 1 O 186.1186.060589C 2 H 4 N 0 O 028.0528.031300Bailey, A.O.Panchenko, T.Sathyan, K.M.Petkowski, J.J.Pai, P.J.Bai, D.L.Russell, D.H.Macara, I.G.Shabanowitz, J.Hunt, D.F.Black, B.E.Foltz, D.R.Proc. Natl. Acad. Sci. U.S.A. 110, 11827-11832, 2013Posttranslational modification of CENP-A influences the conformation of centromeric chromatin.DOI:10.1073/pnas.1300325110PMID:23818633mass spectrometric identificationDai, X.Otake, K.You, C.Cai, Q.Wang, Z.Masumoto, H.Wang, Y.J. Proteome Res. 12, 4167-4175, 2013Identification of novel α-n-methylation of CENP-B that regulates its binding to the centromeric DNA.DOI:10.1021/pr400498yPMID:23978223mass spectrometric identificationThis modification is a minor post-translational modification in the incomplete trimethylation of N-terminal glycine. See also RESID:AA0063 and RESID:AA0619.This modification is readily formed artifactually from N-terminal glycine by reductive methylation using formaldehyde.It is not clear whether the N-terminal methyltransferase responsible for methylating N-terminal glycine is distinguishable from the enzyme activities of EC 2.1.1.244 or EC 2.1.1.299.protein N-terminal methyltransferase (EC 2.1.1.-)Gamino-terminalPSI-MOD:01983blocked amino endmethylated amino endMOD_RES N,N-dimethylglycineAA062131-Dec-201331-Dec-201331-Dec-20132-(L-cystein-S-yl)-L-alanine(2R,5R)-2,5-diamino-5-methyl-4-thiahexanedioic acidalpha-(L-cystein-S-yl)-L-alanine(2R)-2-amino-2-[(2R)-2-amino-2-carboxyethyl]sulfanyl-3-hydroxybutanoic acidC 6 H 8 N 2 O 2 S 1172.20172.030649C 0 H -2 N 0 O 0 S 0-2.02-2.015650Sit, C.S.McKay, R.T.Hill, C.Ross, R.P.Vederas, J.C.J. Am. Chem. Soc. 133, 7680-7683, 2011The 3D structure of thuricin CD, a two-component bacteriocin with cysteine sulfur to α-carbon cross-links.DOI:10.1021/ja201802fPMID:21526839(1)H-NMR, (13)C-NMR and (15)N-NMR geometry constraint modeling; stereochemical determinationSit, C.S.McKay, R.T.Hill, C.Ross, R.P.Vederas, J.C.submitted to the Protein Data Bank, February 2011Trn- peptide of the two-component bacteriocin thuricin CD.PDB:2LA0this is Trn-beta peptide; (1)H-NMR, (13)C-NMR and (15)N-NMR geometry constraint modeling; stereochemical determinationA, Ccross-link 2PSI-MOD:01984thioether bondNot availablethis modification is not annotated in UniProt featuresAA062231-Dec-201331-Dec-201331-Dec-20132-(L-cystein-S-yl)-D-asparaginealpha-(L-cystein-S-yl)-D-asparagine(2S)-2,4-diamino-2-([(2R)-2-amino-2-carboxyethyl]sulfanyl)-4-oxobutanoic acidPDBHET:DSGC 7 H 9 N 3 O 3 S 1215.23215.036462C 0 H -2 N 0 O 0 S 0-2.02-2.015650Sit, C.S.van Belkum, M.J.McKay, R.T.Worobo, R.W.Vederas, J.C.Angew. Chem. Int. Ed. Engl. 50, 8718-8721, 2011The 3D solution structure of thurincin H, a bacteriocin with four sulfur to α-carbon crosslinks.DOI:10.1002/anie.201102527PMID:21786372mass spectrometric, (1)H-NMR, (13)C-NMR and (15)N-NMR identificationSit, C.S.van Belkum, M.J.McKay, R.T.Worobo, R.W.Vederas, J.C.submitted to the Protein Data Bank, April 2011Thurincin H.PDB:2LBZ(1)H-NMR, (13)C-NMR and (15)N-NMR geometry constraint modeling; stereochemical determinationC, Ncross-link 2PSI-MOD:01985D-amino acidthioether bondNot availablethis modification is not annotated in UniProt featuresAA062331-Dec-201331-Dec-201331-Dec-20132-(L-cystein-S-yl)-L-serine(2R,5R)-2,5-diamino-5-carboxy-6-hydroxy-4-thiahexanoic acid(2R)-2-amino-2-([(2R)-2-amino-2-carboxyethyl]sulfanyl)-3-hydroxypropanoic acidC 6 H 8 N 2 O 3 S 1188.20188.025563C 0 H -2 N 0 O 0 S 0-2.02-2.015650Sit, C.S.McKay, R.T.Hill, C.Ross, R.P.Vederas, J.C.J. Am. Chem. Soc. 133, 7680-7683, 2011The 3D structure of thuricin CD, a two-component bacteriocin with cysteine sulfur to α-carbon cross-links.DOI:10.1021/ja201802fPMID:21526839(1)H-NMR, (13)C-NMR and (15)N-NMR identificationSit, C.S.McKay, R.T.Hill, C.Ross, R.P.Vederas, J.C.submitted to the Protein Data Bank, February 2011Thurincin H.PDB:2L9X(1)H-NMR, (13)C-NMR and (15)N-NMR geometry constraint modeling; stereochemical determinationC, Scross-link 2PSI-MOD:01986thioether bondNot availablethis modification is not annotated in UniProt featuresAA062431-Dec-201331-Dec-201331-Dec-20132-(L-cystein-S-yl)-D-serine(2R,5S)-2,5-diamino-5-carboxy-6-hydroxy-4-thiahexanoic acid(2S)-2-amino-2-([(2R)-2-amino-2-carboxyethyl]sulfanyl)-3-hydroxypropanoic acidPDBHET:DSNC 6 H 8 N 2 O 3 S 1188.20188.025563C 0 H -2 N 0 O 0 S 0-2.02-2.015650Sit, C.S.van Belkum, M.J.McKay, R.T.Worobo, R.W.Vederas, J.C.Angew. Chem. Int. Ed. Engl. 50, 8718-8721, 2011The 3D solution structure of thurincin H, a bacteriocin with four sulfur to α-carbon crosslinks.DOI:10.1002/anie.201102527PMID:21786372mass spectrometric, (1)H-NMR, (13)C-NMR and (15)N-NMR identificationSit, C.S.van Belkum, M.J.McKay, R.T.Worobo, R.W.Vederas, J.C.submitted to the Protein Data Bank, April 2011Thurincin H.PDB:2LBZ(1)H-NMR, (13)C-NMR and (15)N-NMR geometry constraint modeling; stereochemical determinationC, Scross-link 2PSI-MOD:01987D-amino acidthioether bondNot availablethis modification is not annotated in UniProt featuresAA062531-Dec-201331-Dec-201331-Dec-20132-(L-cystein-S-yl)-L-threonine(2R,5R,6R)-2,5-diamino-5-carboxy-6-hydroxy-4-thiaheptanoic acidalpha-(L-cystein-S-yl)-L-threonine(2R,3R)-2-amino-2-[(2R)-2-amino-2-carboxyethyl]sulfanyl-3-hydroxybutanoic acidC 7 H 10 N 2 O 3 S 1202.23202.041213C 0 H -2 N 0 O 0 S 0-2.02-2.015650Sit, C.S.McKay, R.T.Hill, C.Ross, R.P.Vederas, J.C.J. Am. Chem. Soc. 133, 7680-7683, 2011The 3D structure of thuricin CD, a two-component bacteriocin with cysteine sulfur to α-carbon cross-links.DOI:10.1021/ja201802fPMID:21526839(1)H-NMR, (13)C-NMR and (15)N-NMR geometry constraint modeling; stereochemical determinationSit, C.S.McKay, R.T.Hill, C.Ross, R.P.Vederas, J.C.submitted to the Protein Data Bank, February 2011Trn- peptide of the two-component bacteriocin thuricin CD.PDB:2LBXthis is Trn-alpha peptide; (1)H-NMR, (13)C-NMR and (15)N-NMR geometry constraint modeling; stereochemical determinationSit, C.S.McKay, R.T.Hill, C.Ross, R.P.Vederas, J.C.submitted to the Protein Data Bank, February 2011Trn- peptide of the two-component bacteriocin thuricin CD.PDB:2LA0this is Trn-beta peptide; (1)H-NMR, (13)C-NMR and (15)N-NMR geometry constraint modeling; stereochemical determinationC, Tcross-link 2PSI-MOD:01988thioether bondNot availablethis modification is not annotated in UniProt featuresAA062631-Dec-201331-Dec-201331-Dec-20132-(L-cystein-S-yl)-D-tyrosine(2R,5S)-2,5-diamino-5-carboxyl-6-(hydroxyphenyl)-4-thiahexanoic acidalpha-(L-cystein-S-yl)-D-tyrosine(2S)-2-amino-2-([(2R)-2-amino-2-carboxyethyl]sulfanyl)-3-(4-hydroxyphenyl)propanoic acidC 12 H 12 N 2 O 3 S 1264.30264.056863C 0 H -2 N 0 O 0 S 0-2.02-2.015650Sit, C.S.McKay, R.T.Hill, C.Ross, R.P.Vederas, J.C.J. Am. Chem. Soc. 133, 7680-7683, 2011The 3D structure of thuricin CD, a two-component bacteriocin with cysteine sulfur to α-carbon cross-links.DOI:10.1021/ja201802fPMID:21526839(1)H-NMR, (13)C-NMR and (15)N-NMR geometry constraint modeling; stereochemical determinationSit, C.S.McKay, R.T.Hill, C.Ross, R.P.Vederas, J.C.submitted to the Protein Data Bank, February 2011Trn- peptide of the two-component bacteriocin thuricin CD.PDB:2LA0this is Trn-beta peptide; (1)H-NMR, (13)C-NMR and (15)N-NMR geometry constraint modeling; stereochemical determinationC, Ycross-link 2PSI-MOD:01989thioether bondNot availablethis modification is not annotated in UniProt features