Conformational changes observed in enzyme crystal structures upon substrate binding

Journal of Molecular Biology

Volumn 346, Issue 1, 2005, Pages 21-28

  Gutteridge, Alex ^a   Thornton, Janet ^a  

^a WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

Author keywords

catalysis; conformational change; enzymes; structural bioinformatics; substrate binding

Indexed keywords

ARTICLE; CONFORMATION; CRYSTAL STRUCTURE; ENZYME ACTIVE SITE; ENZYME MECHANISM; ENZYME STRUCTURE; ENZYME SUBSTRATE COMPLEX; PRIORITY JOURNAL;

EID: 12344307441     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2004.11.013     Document Type: Article

References (24)

1. D. Koshland Correlation of structure and function in enzyme action Science 142 1963 1533 1541
2. G. Hammes Multiple conformational changes in enzyme catalysis Biochemistry 41 2002 8221 8228
3. N. Echols, D. Milburn, and M. Gerstein MolMovDB: analysis and visualization of conformational change and structural flexibility Nucl. Acids Res. 31 2003 478 482
4. M. Gerstein, and W. Krebs A database of macromolecular motions Nucl. Acids Res. 26 1998 4280 4290
5. D. Joseph, G. Petsko, and M. Karplus Anatomy of a conformational change: hinged "lid" motion of the triosephosphate isomerase loop Science 249 1990 1425 1428
6. C. Anderson, F. Zucker, and T. Steitz Space-filling models of kinase clefts and conformation changes Science 204 1979 375 380
7. C. McPhalen, M. Vincent, D. Picot, J. Jansonius, A. Lesk, and C. Chothia Domain closure in mitochondrial aspartate aminotransferase J. Mol. Biol. 227 1992 197 213
8. M. Sawaya, and J. Kraut Loop and subdomain movements in the mechanism of Escherichia coli dihydrofolate reductase: crystallographic evidence Biochemistry 36 1997 586 603
9. J. Taylor, F. Takusagawa, and G. Markham The active site loop of S-adenosylmethionine synthetase modulates catalytic efficiency Biochemistry 41 2002 9358 9369
10. B. Shoichet, S. McGovern, B. Wei, and J. Irwin Lead discovery using molecular docking Curr. Opin. Chem. Biol. 6 2002 439 446
11. S. Teague Implications of protein flexibility for drug discovery Nature Rev. Drug Discov. 2 2003 527 541
12. S.K. Burley, S.C. Almo, J.B. Bonanno, M. Capel, M.R. Chance, and T. Gaasterland Structural genomics: beyond the human genome project Nature Genet. 23 1999 151 157
13. L. Shapiro, and T. Harris Finding function through structural genomics Curr. Opin. Biotechnol. 11 2000 31 35
14. A.C. Wallace, R.A. Laskowski, and J.M. Thornton Derivation of 3d coordinate templates for searching structural databases: application to Ser-His-Asp catalytic triads in the serine proteinases and lipases Protein Sci. 5 1996 1001 1013
15. J. Barker, and J. Thornton An algorithm for constraint-based structural template matching: application to 3d templates with statistical analysis Bioinformatics 19 2003 1644 1649
16. C. Porter, G. Bartlett, and J. Thornton The catalytic site atlas: a resource of catalytic sites and residues identified in enzymes using structural data Nucl. Acids Res. 32 2004 D129 D133
17. H.M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T.N. Bhat, and H. Weissig The protein data bank Nucl. Acids Res. 28 2000 235 242
18. F.M. Pearl, D. Lee, J.E. Bray, I. Sillitoe, A.E. Todd, and A.P. Harrison Assigning genomic sequences to cath Nucl. Acids Res. 28 2000 277 282
19. A. Gutteridge, and J. Thornton Conformational change in substrate binding, catalysis and product release: an open and shut case? FEBS Letters 567 2004 67 73
20. G.J. Bartlett, C.T. Porter, N. Borkakoti, and J.M. Thornton Analysis of catalytic residues in enzyme active sites J. Mol. Biol. 324 2002 105 121
21. D. Koshland Conformational changes: how small is big enough? Nature Med. 4 1998 1112 1114
22. A. Mesecar, B. Stoddard, and D. Koshland Orbital steering in the catalytic power of enzymes: small structural changes with large catalytic consequences Science 277 1997 202 206
23. T. Skarzynski, A. Mistry, A. Wonacott, S. Hutchinson, V. Kelly, and K. Duncan Structure of UDP-N-acetylglucosamine enolpyruvyl transferase, an enzyme essential for the synthesis of bacterial peptidoglycan, complexed with substrate UDP-N-acetylglucosamine and the drug fosfomycin Structure 4 1996 1465 1474
24. S. Eschenburg, and E. Schaunbrunn Comparative X-ray analysis of the un-liganded fosfomycin-target mura Proteins: Struct. Funct. Genet. 40 2000 290 298