Preferred in vivo ubiquitination sites

Bioinformatics

Volumn 20, Issue 18, 2004, Pages 3302-3307

  Catic, André ^a   Collins, Cal ^b   Church, George M ^a   Ploegh, Hidde L ^a  

^a HARVARD MEDICAL SCHOOL   (United States)

^b Akaza Research Inc ^*  (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ASPARTIC ACID; CYSTEINE; GLUTAMIC ACID; LIGASE; LYSINE; MEMBRANE PROTEIN; NUCLEAR PROTEIN; SERINE; SUMO PROTEIN; THREONINE; TYROSINE; UBIQUITIN; UBIQUITIN CONJUGATING ENZYME; UBIQUITIN PROTEIN LIGASE E3;

AMINO ACID SEQUENCE; ANIMAL CELL; ARTICLE; CELL COMPARTMENTALIZATION; CELLULAR DISTRIBUTION; CONJUGATION; CONTROLLED STUDY; ENZYME MECHANISM; ENZYME SUBSTRATE; GENETIC ANALYSIS; IN VIVO STUDY; LIGATION; NONHUMAN; PREDICTION; PRIORITY JOURNAL; PROTEIN MOTIF; PROTEIN STRUCTURE; PROTEIN TARGETING; SACCHAROMYCES CEREVISIAE; SEQUENCE ANALYSIS; STRUCTURE ACTIVITY RELATION; STRUCTURE ANALYSIS; UBIQUITINATION;

SACCHAROMYCES; SACCHAROMYCES CEREVISIAE;

EID: 12344310195     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/bth407     Document Type: Article

References (27)

1. Altschul,S.F., Gish,W., Miller,W., Myers,E.W. and Lipman,D.J. (1990) Basic local alignment search tool. J. Mol. Biol., 215, 403-410.
2. Berman,H.M., Westbrook,J., Feng,Z., Gilliland,G., Bhat,T.N., Weissig,H., Shindyalov,I.N. and Bourna,P.E. (2000) The Protein Data Bank. Nucleic Acids Res., 28, 235-242.
3. Bernier-Villamor,V., Sampson,D.A., Matunis,M.J. and Lima,C.D. (2002) Structural basis for E2-mediated SUMO conjugation revealed by a complex between ubiquitin-conjugating enzyme Ubc9 and RanGAP1. Cell 108, 345-356.
4. Blom,N., Gammeltoft,S. and Brunak,S. (1999) Sequence and structure-based prediction of eukaryotic protein phosphorylation sites. J. Mol. Biol., 294, 1351-1362.
5. Cook,W.J., Jeffrey,L.C., Xu,Y. and Chau,V. (1993) Tertiary structures of class I ubiquitin-conjugating enzymes are highly conserved: crystal structure of yeast Ubc4. Biochemistry (Washington), 32 13809-13817.
6. Fischle,W., Wang,Y. and Allis,C.D. (2003) Binary switches and modification cassettes in histone biology and beyond. Nature, 425, 475-479.
7. Guex,N. and Peitsch,M.C. (1997) SWISS-MODEL and the Swiss-Pdb Viewer: an environment for comparative protein modeling. Electrophoresis, 18, 2714-2723.
8. Haas,A.L. and Siepmann,T.J. (1997) Pathways of ubiquitin conjugation. FASEB J., 11, 1257-1268.
9. Hirokawa,T., Boon-Chieng,S. and Mitaku,S. (1998) SOSUI: classification and secondary structure prediction system for membrane proteins. Bioinformatics, 14, 378-379.
10. Hitchcock,A.L., Auld,K., Gygi,S.P. and Silver,P.A. (2003) A subset of membrane-associated proteins is ubiquitinated in response to mutations in the endoplasmic reticulum degradation machinery. Proc. Natl Acad. Sci. USA, 100, 12735-12740.
11. Hoege,C., Pfander,B., Moldovan,G.L., Pyrowolakis,G. and Jentsch,S. (2002) RAD6-dependent DNA repair is linked to modification of PCNA by ubiquitin and SUMO. Nature, 419, 135-141.
12. Horton,P. and Nakai,K. (1997) Better prediction of protein cellular localization sites with the κ-nearest neighbors classifier. Proc. Int. Conf. Intell. Syst. Mol. Biol., 5, 147-152.
13. Huh,W.K., Falvo,J.V., Gerke,L.C., Carroll,A.S., Howson,R.W., Weisman,J.S. and O'Shea,E.K. (2003) Global analysis of protein localization in budding yeast. Nature, 425, 686-691.
14. Jonassen,I., Collins,J.F. and Higgins,D.G. (1995) Finding flexible patterns in unaligned protein sequences. Protein Sci., 4, 1587-1595.
15. Kolling,R. (2002) Mutations affecting the phosphorylation, ubiquitination and turnover of the ABC-transporter Ste6. FEBS Lett. 531, 548-552.
16. Lin,D., Tabb,D.L. and Yates, J.R., III (2003) Large-scale protein identification using mass spectrometry. Biochim. Biophys. Acta 1646, 1-10.
17. Nash,P., Tang,X., Orlicky,S., Chen,Q., Gertler,F.B., Mendenhall,M.D., Sicheri,F., Pawson,T. and Tyers,M. (2001) Multisite phosphorylation of a CDK inhibitor sets a threshold for the onset of DNA replication. Nature, 414, 514-521.
18. Peng,J., Schwartz,D., Elias,J.E., Thoreen,C.C., Cheng,D., Marsischky,G., Roelofs,J., Finley,D. and Gygi,S.P. (2003) A proteomics approach to understanding protein ubiquitination. Nat. Biotechnol., 21, 921-926.
19. Petroski,M.D. and Deshaies,R.J. (2003) Context of multiubiquitin chain attachment influences the rate of Sic1 degradation. Mol. Cell, 11, 1435-1444.
20. Pickart,C.M. (2001) Mechanisms underlying ubiquitination. Annu. Rev. Biochem., 70, 503-533.
21. Santos,J.L. and Shiozaki,K. (2001) Fungal histidine kinases. Sci. STKE, 98, RE1.
22. Soetens,O., DeCraene,J.O. and Andre,B. (2001) Ubiquitin is required for sorting to the vacuole of the yeast general amino acid permease, Gap1. J. Biol. Chem., 276, 43949-43957.
23. Thompson,J.D., Higgins,D.G. and Gibson,T.J. (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res., 22, 4673-4680.
24. Weissman,A.M. (2001) Themes and variations on ubiquitylation. Nat. Rev. Mol. Cell Biol., 2, 169-178.
25. Williams,R.W., Chang,A., Juretic,D. and Loughran,S. (1987) Secondary structure predictions and medium range interactions. Biochim. Biophys. Acta, 916, 200-204.
26. Wilmot,C.M. and Thornton,J.M. (1988) Analysis and prediction of the different types of beta-turn in proteins. J. Mol. Biol., 203, 221-232.
27. Zhou,H., Watts,J.D. and Aebersold,R. (2001) A systematic approach to the analysis of protein phosphorylation. Nat. Biotechnol. 19, 375-378.