Finding functional sites in structural genomics proteins

Structure

Volumn 12, Issue 8, 2004, Pages 1405-1412

  Stark, Alexander ^a   Shkumatov, Alexander ^a   Russell, Robert B ^a  

^a EUROPEAN MOLECULAR BIOLOGY LABORATORY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ARCHAEAL PROTEIN; ISOMERASE; PHOSPHOTYROSINE; RIBOSE;

ARTICLE; BINDING SITE; COMPARATIVE STUDY; CORRELATION FUNCTION; GENOMICS; PRIORITY JOURNAL; PROTEIN STRUCTURE; TECHNIQUE;

ALGORITHMS; ARCHAEAL PROTEINS; BINDING SITES; COMPUTATIONAL BIOLOGY; GENOMICS; MODELS, MOLECULAR; PHOSPHOTYROSINE; PROTEINS;

ARCHAEA;

EID: 4143145197     PISSN: 09692126     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.str.2004.05.012     Document Type: Article

References (47)

1. Altschul S.F., Madden T.L., Schaffer A.A., Zhang J., Zhang Z., Miller W., Lipman D.J. Gapped BLAST and PSI-BLAST. a new generation of protein database search programs Nucleic Acids Res. 25:1997;3389-3402
2. Artymiuk P.J., Poirrette A.R., Grindley H.M., Rice D.W., Willett P. A graph-theoretic approach to the identification of three-dimensional patterns of amino acid side-chains in protein structures. J. Mol. Biol. 243:1994;327-344. a
3. Artymiuk P.J., Rice D.W., Poirrette A.R., Willet P. A tale of two synthetases. Nat. Struct. Biol. 1:1994;758-760. b
4. Artymiuk P.J., Rice D.W., Poirrette A.R., Willett P. β- glucosyltransferase and phosphorylase reveal their common theme. Nat. Struct. Biol. 2:1995;117-120
5. Artymiuk P.J., Poirrette A.R., Rice D.W., Willett P. A polymerase I palm in adenylyl cyclase? Nature. 388:1997;33-34
6. Babbitt P.C. Definitions of enzyme function for the structural genomics era. Curr. Opin. Chem. Biol. 7:2003;230-237
7. Bakal C.J., Davies J.E. No longer an exclusive club. eukaryotic signalling domains in bacteria Trends Cell Biol. 10:2000;32-38
8. Bartlett G.J., Porter C.T., Borkakoti N., Thornton J.M. Analysis of catalytic residues in enzyme active sites. J. Mol. Biol. 324:2002;105-121
9. Berman H.M., Westbrook J., Feng Z., Gilliland G., Bhat T.N., Weissig H., Shindyalov I.N., Bourne P.E. The Protein Data Bank. Nucleic Acids Res. 28:2000;235-242
10. Burley S.K. An overview of structural genomics. Nat. Struct. Biol. Suppl. 7:2000;932-934
11. Dietmann S., Holm L. Identification of homology in protein structure classification. Nat. Struct. Biol. 8:2001;953-957
12. Gibrat J.F., Madej T., Bryant S.H. Surprising similarities in structure comparison. Curr. Opin. Struct. Biol. 6:1996;377-385
13. Hobohm U., Sander C. Enlarged representative set of protein structures. Protein Sci. 3:1994;522-524
14. Holm L., Sander C. Globin fold in a bacterial toxin. Nature. 361:1993;309. a
15. Holm L., Sander C. Protein structure comparison by alignment of distance matrices. J. Mol. Biol. 233:1993;123-138. b
16. Holm L., Sander C. Dali. a network tool for protein structure comparison Trends Biochem. Sci. 20:1995;478-480
17. Holm L., Sander C. Decision support system for the evolutionary classification of protein structures. Proc. Int. Conf. Intell. Syst. Mol. Biol. 5:1997;140-146
18. Kennelly P.J. Protein kinases and protein phosphatases in prokaryotes. a genomic perspective FEMS Microbiol. Lett. 206:2002;1-8
19. Kennelly P.J. Archaeal protein kinases and protein phosphatases. insights from genomics and biochemistry Biochem. J. 370:2003;373-389
20. Kim S.H., Shin D.H., Choi I.G., Schulze-Gahmen U., Chen S., Kim R. Structure-based functional inference in structural genomics. J. Struct. Funct. Genomics. 4:2003;129-135
21. Kleywegt G.J. Recognition of spatial motifs in protein structures. J. Mol. Biol. 285:1999;1887-1897
22. Kraulis P.J. Molscript. a program to produce both detailed and schematic plots of protein structures J. Appl. Crystallogr. 24:1991;946-950
23. 8 barrel proteins. J. Biol. Chem. 278:2003;47253-47260
24. Merritt E.A., Murphy M.E.P. Raster3D version 2.0. A program for photorealistic molecular graphics. Acta Crystallogr D Biol. Crystallogr. 50:1994;869-873
25. Mura C., Katz J.E., Clarke S.G., Eisenberg D. Structure and function of an archaeal homolog of survival protein E (SurEα). an acid phosphatase with purine nucleotide specificity J. Mol. Biol. 326:2003;1559-1575
26. Novotny M., Madsen D., Kleywegt G.J. Evaluation of protein fold comparison servers. Proteins. 54:2004;260-270
27. Oganesyan V., Busso D., Brandsen J., Chen S., Jancarik J., Kim R., Kim S.H. Structure of the hypothetical protein AQ-1354 from Aquifex aeolicus. Acta Crystallogr. D Biol. Crystallogr. 59:2003;1219-1223
28. Orengo C.A., Taylor W.R. Ssap. sequential structure alignment program for protein structure comparison Methods Enzymol. 266:1996;617-635
29. Porter C.T., Bartlett G.J., Thornton J.M. The Catalytic Site Atlas. a resource of catalytic sites and residues identified in enzymes using structural data Nucleic Acids Res. 32:2004;D129-D133
30. Rigden D.J., Lamani E., Mello L.V., Littlejohn J.E., Jedrzejas M.J. Insights into the catalytic mechanism of cofactor-independent phosphoglycerate mutase from X-ray crystallography, simulated dynamics and molecular modeling. J. Mol. Biol. 328:2003;909-920
31. Rost B. Enzyme function less conserved than anticipated. J. Mol. Biol. 318:2002;595-608
32. Russell R.B. Detection of protein three-dimensional side-chain patterns. new examples of convergent evolution J. Mol. Biol. 279:1998;1211-1227
33. Russell R.B., Barton G.J. Multiple protein sequence alignment from tertiary structure comparison. assignment of global and residue confidence levels Proteins. 14:1992;309-323
34. Russell R.B., Barton G.J. An SH2-SH3 domain hybrid. Nature. 364:1993;765
35. Sanishvili R., Yakunin A.F., Laskowski R.A., Skarina T., Evdokimova E., Doherty-Kirby A., Lajoie G.A., Thornton J.M., Arrowsmith C.H., Savchenko A., et al. Integrating structure, bioinformatics, and enzymology to discover function. BioH, a new carboxylesterase from Escherichia coli J. Biol. Chem. 278:2003;26039-26045
36. Shi L., Potts M., Kennelly P.J. The serine, threonine, and/or tyrosine-specific protein kinases and protein phosphatases of prokaryotic organisms. a family portrait FEMS Microbiol. Rev. 22:1998;229-253
37. Stark A., Russell R.B. Annotation in three dimensions. PINTS. Patterns in Non-homologous Tertiary Structures Nucleic Acids Res. 31:2003;3341-3344
38. Stark A., Sunyaev S., Russell R.B. A model for statistical significance of local similarities in structure. J. Mol. Biol. 326:2003;1307-1316
39. Swindells M.B., Orengo C.A., Jones D.T., Pearl L.H., Thornton J.M. Recurrence of a binding motif? Nature. 362:1993;299
40. Tao X., Khayat R., Christendat D., Savchenko A., Xu X., Goldsmith-Fischman S., Honig B., Edwards A., Arrowsmith C.H., Tong L. Crystal structures of MTH1187 and its yeast ortholog YBL001c. Proteins. 52:2003;478-480
41. Teplyakov A., Obmolova G., Tordova M., Thanki N., Bonander N., Eisenstein E., Howard A.J., Gilliland G.L. Crystal structure of the YjeE protein from Haemophilus influenzae. a putative Atpase involved in cell wall synthesis Proteins. 48:2002;220-226
42. Tian W., Skolnick J. How well is enzyme function conserved as a function of pairwise sequence identity? J. Mol. Biol. 333:2003;863-882
43. Todd A.E., Orengo C.A., Thornton J.M. Evolution of function in protein superfamilies, from a structural perspective. J. Mol. Biol. 307:2001;1113-1143
44. Wallace A.C., Borkakoti N., Thornton J.M. Tess. a geometric hashing algorithm for deriving 3D coordinate templates for searching structural databases. application to enzyme active sites Protein Sci. 6:1997;2308-2323
45. Wilson R.A., Maughan W.N., Kremer L., Besra G.S., Futterer K. The structure of Mycobacterium tuberculosis MPT51 (FbpC1) defines a new family of non-catalytic alpha/beta hydrolases. J. Mol. Biol. 335:2004;519-530
46. Zhang C., Kim S.H. Overview of structural genomics. from structure to function Curr. Opin. Chem. Biol. 7:2003;28-32
47. Zhang R.G., Andersson C.E., Skarina T., Evdokimova E., Edwards A.M., Joachimiak A., Savchenko A., Mowbray S.L. The 2.2 A resolution structure of RpiB/AlsB from Escherichia coli illustrates a new approach to the ribose-5-phosphate isomerase reaction. J. Mol. Biol. 332:2003;1083-1094