Supra-domains: Evolutionary Units Larger than Single Protein Domains

Journal of Molecular Biology

Volumn 336, Issue 3, 2004, Pages 809-823

  Vogel, Christine ^a   Berzuini, Carlo ^b,c   Bashton, Matthew ^a   Gough, Julian ^d,e   Teichmann, Sarah A ^a  

^a MRC LABORATORY OF MOLECULAR BIOLOGY   (United Kingdom)

^b UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^c UNIVERSITY OF PAVIA   (Italy)

^d RIKEN YOKOHAMA INSTITUTE   (Japan)

^e STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

Domain architecture; Domain combination; Functional annotation; Multi domain protein; Protein family

Indexed keywords

ISOPROTEIN;

AMINO ACID SEQUENCE; EVOLUTION; GENOME; GEOMETRY; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN STRUCTURE; REVIEW; STATISTICAL SIGNIFICANCE;

EID: 0842268045     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2003.12.026     Document Type: Article

References (36)

1. Murzin A.G., Brenner S.E., Hubbard T., Chothia C. SCOP: a structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol. 247:1995;536-540.
2. Teichmann S.A., Park J., Chothia C. Structural assignments to the Mycoplasma genitalium proteins show extensive gene duplications and domain rearrangements. Proc. Natl Acad. Sci. USA. 95:1998;14658-14663.
3. Gerstein M. How representative are the known structures of the proteins in a complete genome? A comprehensive structural census. Fold. Des. 3:1998;497-512.
4. Park J., Lappe M., Teichmann S.A. Mapping protein family interactions: intramolecular and intermolecular protein family interaction repertoires in the PDB and yeast. J. Mol. Biol. 307:2001;929-938.
5. Apic G., Gough J., Teichmann S.A. Domain combinations in archaeal, eubacterial and eukaryotic proteomes. J. Mol. Biol. 310:2001;311-325.
6. Wuchty S. Scale-free behavior in protein domain networks. Mol. Biol. Evol. 18:2001;1694-1702.
7. Apic G., Huber W., Teichmann S.A. Multi-domain protein families and domain pairs: comparison with known structures and a random model of domain recombination. J. Struct. Funct. Genomics. 4:2003;67-78.
8. Harrison S.C. Variation on an Src-like theme. Cell. 112:2003;737-740.
9. Bashton M., Chothia C. The geometry of domain combination in proteins. J. Mol. Biol. 315:2002;927-939.
10. Hegyi H., Gerstein M. Annotation transfer for genomics: measuring functional divergence in multi-domain proteins. Genome Res. 11:2001;1632-1640.
11. Wilson C.A., Kreychman J., Gerstein M. Assessing annotation transfer for genomics: quantifying the relations between protein sequence, structure and function through traditional and probabilistic scores. J. Mol. Biol. 297:2000;233-249.
12. Mott R., Schultz J., Bork P., Ponting C.P. Predicting protein cellular localization using a domain projection method. Genome Res. 12:2002;1168-1174.
13. Gough J. The SUPERFAMILY database in structural genomics. Acta Crystallog. sect. D. 58:2002;1897-1900.
14. Westbrook J., Feng Z., Chen L., Yang H., Berman H.M. The Protein Data Bank and structural genomics. Nucl. Acids Res. 31:2003;489-491.
15. Geer L.Y., Domrachev M., Lipman D.J., Bryant S.H. CDART: protein homology by domain architecture. Conserved domain architecture retrieval tool. Genome Res. 12:2003;1619-1623.
16. Marchler-Bauer A., Panchenko A.R., Shoemaker B.A., Thiessen P.A., Geer L.Y., Bryant S.H. CDD: a database of conserved domain alignments with links to domain three-dimensional structure. Nucl. Acids Res. 30:2002;281-283.
17. Letunic I., Goodstadt L., Dickens N.J., Doerks T., Schultz J., Mott R., et al. Recent improvements to the SMART domain-based sequence annotation resource. Nucl. Acids Res. 30:2002;242-244.
18. Bateman A., Birney E., Cerruti L., Durbin R., Etwiller L., Eddy S.R., et al. The Pfam protein families database. Nucl. Acids Res. 30:2002;276-280.
19. Coin L., Bateman A., Durbin R. Enhanced protein domain discovery by using language modeling techniques from speech recognition. Proc. Natl Acad. Sci. USA. 100:2003;4516-4520.
20. Benjamini Y., Hochberg Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. R. Stat. Soc. ser. B. 57:1995;289-300.
21. Tatusov R.L., Fedorova N.D., Jackson J.D., Jacobs A.R., Kiryutin B., Koonin E.V., et al. The COG database: an updated version includes eukaryotes. BMC Bioinformatics. 4:2003;41.
22. al-Karadaghi S., Aevarsson A., Garber M., Zheltonosova J., Liljas A. The structure of elongation factor G in complex with GDP: conformational flexibility and nucleotide exchange. Structure. 4:1996;455.
23. Ingelman M., Bianchi V., Eklund H. The three-dimensional structure of flavodoxin reductase from Escherichia coli at 1.7 Å resolution. J. Mol. Biol. 268:1997;147-157.
24. Teplyakov A., Obmolova G., Badet B., Badet-Denisot M. Channeling of ammonia in glucosamine-6-phosphate synthase. J. Mol. Biol. 313:2001;1093-1102.
25. Ogiso H., Ishitani R., Nureki O., Fukai S., Yamanaka M., Kim J.H., et al. Crystal structure of the complex of human epidermal growth factor and receptor extracellular domains. Cell. 110:2002;775-787.
26. Lawrence C.M., Ray S., Babyonyshev M., Galluser R., Borhani D.W., Harrison S.C. Crystal structure of the ectodomain of human transferrin receptor. Science. 286:1999;779-782.
27. Vitagliano L., Masullo M., Sica F., Zagari A., Bocchini V. Crystal structure of Sulfolobus solfataricus elongation factor 1 alpha in omplex with GDP. EMBO J. 20:2001;5305.
28. Bilwes A.M., Alex L.A., Crane B.R., Simon M.I. Structure of CheA, a signal-transducing histidine kinase. Cell. 96:1999;131-141.
29. Battaile K.P., Molin-Case J., Paschke R., Want M., Bennett D., Vockley J., Lim J.-J.P. Crystal structure of rat short chain acyl-coA dehydrogenase complexed with acetoacetyl-coA. J. Mol. Chem. 277:2002;12200-12207.
30. Davis G.J., Bosron W.F., Stone C.L., Owusu-Dekyi K., Hurley T.D. X-ray structure of human beta3beta3 alcohol dehydrogenase. The contribution of ionic interactions to coenzyme binding. J. Biol. Chem. 271:1996;17057-17061.
31. Song H., Parsons M.R., Rowsell S., Leonard G., Phillips S.E. Crystal structure of intact elongation factor EF-Tu from Escherichia coli in GDP conformation at 2.05 Å resolution. J. Mol. Biol. 285:1999;1245-1256.
32. Roll-Mecak A., Shin B.S., Dever T.E., Burley S.K. Engaging the ribosome: universal IFs of translation. Trends Biochem. Sci. 26:2001;705-709.
33. Doublie S., Sawaya M.R., Ellenberger T. An open and closed case for all polymerases. Structure. 7:1999;R31-R35.
34. Thomazeau K., Dumas R., Halgand F., Forest E., Douce R., Biou V. Structure of spinach acetohydroxyacid isomeroreductase complexed with its reaction product dihydroxymethylvalerate, manganese and (phospho)-ADP-ribose. Acta Crystallog. sect. D. 56:2000;389-397.
35. Thoden J.B., Kappock J., Stubbe H., Holden H.M. Three-dimensional structure of N5-carboxyaminoimidazole ribonucleotide synthetase: a member of the ATP grasp protein superfamily. Biochemistry. 38:1999;15480-15492.
36. Sun X., Cross J.A., Bognar A.L., Baker E.N., Smith C.A. Folate-binding triggers the activation of folylpolyglutamate synthase. J. Mol. Biol. 310:2001;1067-1078.