Note_ProteinModifications – ProteinModifications

WID Note_ProteinModifications
Name ProteinModifications
Comments Stable protein modifications were compiled from several sources: a-L-glutamate ligation – NCBI Structure reports that RimK adds 4 additional Glu residues to the native E. coli Glu-Glu C-terminus of ribosomal protein S6 [PUB_0110]. Lipoate ligation – Stephens et al observed lipoate ligation sites in E. coli [PUB_0288]. The kinetic rate of lipoate ligation was measured by Morris et al [PUB_0290]. Phosphorylation – Su, Hutchison, and Giddings identified phosphorylated protein residues on a genome scale by mass-spec in M. genitalium and M. pneumoniae [PUB_0094]. For cases where multiple phosphorylations were consistent with the same mass-spec data, we assigned the phosphorylation to the most conserved residue as determined by ClustalW multiple sequence alignment. Kinetic rate of protein phosphorylation was measured by Fan, Fromm, and Bobik [PUB_0289]. Additionally we considered including modifications reported by the following sources: Computational prediction of phosphorylations by NetPhosBac [PUB_0575]. We did not include NetPhosBac predictions because it predicted over 20000 sites, and therefore its predictions likely have low specificity. Computational prediction of modifications by dbPTM [PUB_0268]. We did not include dbPTM predictions because it predicted over 2000 modifications, and therefore its predictions likely have low specificity. Additionally enzymes have not been identified in M. genitalium which generate many of the predicted modifications. Gupta et al performed a whole proteome analysis of post-translational modifications in Shewanella oneidensis MR-1[PUB_0280]. We excluded this study because it was of unclear relevance to M. genitalium. For example the study did not identify any phosphorylations, which we expected is a major form of protein modification in M. genitalium. Peril catalogued ribosomal proteins modifications including methylations and acetylations [PUB_0105]. We did not include these modifications because no enzymes have been identified in M. genitalium which generate these modifications. Hesketh et al catalogued modifications in Streptomyces coelicolor [PUB_0276]. We did not include this data because Hesketh et al did not ascertain the specific chemical composition of each modification. Krebes et al [PUB_0277], Demina et al [PUB_0282], and Macek et al [PUB_0283] identified phosphosites in Mycoplasma pneumoniae, Mycoplasma gallisepticum, and Bacillus subtilis on a genome scale. We excluded these modifications because they had no overlap with sites identified in the Su, Hutchison, and Giddings whole proteome screen [PUB_0094]. Phospho.ELM database of protein modifications [PUB_0278]. We did not include Phospo.ELM results because they are based on data from distantly related species. UniProt Unstable or transient protein modifications such as disulfide bonds were reconstructed from computational prediction and the primary literature. See Note_DisulfideBonds for a discussion of the reconstruction of disulfide bonds. Additional sources: [PUB_0281, PUB_0672, PUB_0673, PUB_0674].
  1. Chen J, Anderson JB, DeWeese-Scott C, Fedorova ND, Geer LY, He S, Hurwitz DI, Jackson JD, Jacobs AR, Lanczycki CJ, Liebert CA, Liu C, Madej T, Marchler-Bauer A, Marchler GH, Mazumder R, Nikolskaya AN, Rao BS, Panchenko AR, Shoemaker BA, Simonyan V, Song JS, Thiessen PA, Vasudevan S, Wang Y, Yamashita RA, Yin JJ, Bryant SH. MMDB: Entrez's 3D-structure database. Nucleic Acids Res 31, 474-7 (2003). WholeCell: PUB_0110, PubMed: 12520055, URL:

  2. Demina IA, Serebryakova MV, Ladygina VG, Rogova MA, Zgoda VG, Korzhenevskyi DA, Govorun VM. Proteome of the bacterium Mycoplasma gallisepticum. Biochemistry (Mosc) 74, 165-74 (2009). WholeCell: PUB_0282, PubMed: 19267672

  3. Diella F, Gould CM, Chica C, Via A, Gibson TJ. Phospho.ELM: a database of phosphorylation sites--update 2008. Nucleic Acids Res 36, D240-4 (2008). WholeCell: PUB_0278, PubMed: 17962309, URL:

  4. Fan C, Fromm HJ, Bobik TA. Kinetic and functional analysis of L-threonine kinase, the PduX enzyme of Salmonella enterica. J Biol Chem 284, 20240-8 (2009). WholeCell: PUB_0289, PubMed: 19509296

  5. Green DE, Morris TW, Green J, Cronan JE Jr, Guest JR. Purification and properties of the lipoate protein ligase of Escherichia coli. Biochem J 309 ( Pt 3), 853-62 (1995). WholeCell: PUB_0290, PubMed: 7639702

  6. ... 13 more

  7. Gupta N, Tanner S, Jaitly N, Adkins JN, Lipton M, Edwards R, Romine M, Osterman A, Bafna V, Smith RD, Pevzner PA. Whole proteome analysis of post-translational modifications: applications of mass-spectrometry for proteogenomic annotation. Genome Res 17, 1362-77 (2007). WholeCell: PUB_0280, PubMed: 17690205

  8. Hesketh AR, Chandra G, Shaw AD, Rowland JJ, Kell DB, Bibb MJ, Chater KF. Primary and secondary metabolism, and post-translational protein modifications, as portrayed by proteomic analysis of Streptomyces coelicolor. Mol Microbiol 46, 917-32 (2002). WholeCell: PUB_0276, PubMed: 12421300

  9. Jaffe JD, Berg HC, Church GM. Proteogenomic mapping as a complementary method to perform genome annotation. Proteomics 4, 59-77 (2004). WholeCell: PUB_0672, PubMed: 14730672

  10. Jaffe JD, Stange-Thomann N, Smith C, DeCaprio D, Fisher S, Butler J, Calvo S, Elkins T, FitzGerald MG, Hafez N, Kodira CD, Major J, Wang S, Wilkinson J, Nicol R, Nusbaum C, Birren B, Berg HC, Church GM. The complete genome and proteome of Mycoplasma mobile. Genome Res 14, 1447-61 (2004). WholeCell: PUB_0673, PubMed: 15289470

  11. Krebes KA, Dirksen LB, Krause DC. Phosphorylation of Mycoplasma pneumoniae cytadherence-accessory proteins in cell extracts. J Bacteriol 177, 4571-4 (1995). WholeCell: PUB_0277, PubMed: 7635846

  12. Lee TY, Huang HD, Hung JH, Huang HY, Yang YS, Wang TH. dbPTM: an information repository of protein post-translational modification. Nucleic Acids Res 34, D622-7 (2006). WholeCell: PUB_0268, PubMed: 16381945, URL:

  13. Macek B, Mijakovic I, Olsen JV, Gnad F, Kumar C, Jensen PR, Mann M. The serine/threonine/tyrosine phosphoproteome of the model bacterium Bacillus subtilis. Mol Cell Proteomics 6, 697-707 (2007). WholeCell: PUB_0283, PubMed: 17218307

  14. Miller ML, Soufi B, Jers C, Blom N, Macek B, Mijakovic I. NetPhosBac - a predictor for Ser/Thr phosphorylation sites in bacterial proteins. Proteomics 9, 116-25 (2009). WholeCell: PUB_0575, PubMed: 19053140, URL:

  15. Peil L. Ribosome assembly factors in Escherichia coli. Tartu University (2009). WholeCell: PUB_0105, URL:

  16. Peters EC, Brock A, Ficarro SB. Exploring the phosphoproteome with mass spectrometry. Mini Rev Med Chem 4, 313-24 (2004). WholeCell: PUB_0674, PubMed: 15032677

  17. Stephens PE, Darlison MG, Lewis HM, Guest JR. The pyruvate dehydrogenase complex of Escherichia coli K12. Nucleotide sequence encoding the dihydrolipoamide acetyltransferase component. Eur J Biochem 133, 481-9 (1983). WholeCell: PUB_0288, PubMed: 6345153

  18. Su HC, Hutchison CA 3rd, Giddings MC. Mapping phosphoproteins in Mycoplasma genitalium and Mycoplasma pneumoniae. BMC Microbiol 7, 63 (2007). WholeCell: PUB_0094, PubMed: 17605819

  19. Walsh CT, Garneau-Tsodikova S, Gatto GJ Jr. Protein posttranslational modifications: the chemistry of proteome diversifications. Angew Chem Int Ed Engl 44, 7342-72 (2005). WholeCell: PUB_0281, PubMed: 16267872

Created 2012-10-01 15:07:34
Last updated 2012-10-01 15:13:58