Comparison of ligand-induced conformational changes and domain closure mechanisms, between prokaryotic and eukaryotic dehydroquinate synthases

Journal of Molecular Biology

Volumn 343, Issue 3, 2004, Pages 533-546

  Nichols, C E ^a   Ren, J ^a   Leslie, K ^a   Dhaliwal, B ^a   Lockyer, M ^b   Charles, I ^b   Hawkins, A R ^c   Stammers, D K ^a  

^a UNIVERSITY OF OXFORD   (United Kingdom)

^b Britannia House   (United Kingdom)

^c School of Medical Education Development   (United Kingdom)

Author keywords

conformational changes; crystal structure; DHQS; domain closure; X ray crystallography

Indexed keywords

BACTERIAL ENZYME; FUNGAL ENZYME; SYNTHETASE;

ARTICLE; CATALYSIS; CONFORMATIONAL TRANSITION; ENZYME ANALYSIS; ENZYME STRUCTURE; EUKARYOTE; NONHUMAN; PRIORITY JOURNAL; PROKARYOTE; PROTEIN DOMAIN; PROTEIN EXPRESSION; PROTEIN STRUCTURE; STAPHYLOCOCCUS AUREUS; STATISTICAL SIGNIFICANCE; STEREOCHEMISTRY;

ASPERGILLUS; BACTERIA (MICROORGANISMS); EMERICELLA NIDULANS; EUKARYOTA; PROKARYOTA; STAPHYLOCOCCUS; STAPHYLOCOCCUS AUREUS;

EID: 4744337641     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2004.08.039     Document Type: Article

References (33)

1. R. Bentley The shikimate pathway - a metabolic tree with many branches Crit. Rev. Biochem. Mol. Biol. 25 1990 307 384
2. A. Gunel-Ozcan, K.A. Brown, A.G. Allen, and D.J. Maskell Salmonella typhimurium aroB mutants are attentuated in BALB/c mice Microb. Pathog. 23 1997 311 316
3. T. Widlanski, S.L. Bender, and J.R. Knowles Dehydroquinate synthase: the use of substrate analogues to probe the late steps of the catalyzed reaction Biochemistry 28 1989 7572 7582
4. P.R. Srinivasan, J. Rothchild, and D.B. Sprinson The enzymatic conversion of 3-deoxy-d-arabino-heptulosinic acid 7-phosphate to 5-dehydroquinate J. Biol. Chem. 238 1963 3176 3182
5. A.R. Hawkins, H.K. Lamb, J.D. Moore, I.G. Charles, and C.F. Roberts The pre-chorismate (shikimate) and quinate pathways in filamentous fungi: theoretical and practical aspects J. Gen. Microbiol. 139 1993 2891 2899
6. S.L. Bender, T. Widlanski, and J.R. Knowles Dehydroquinate synthase: the use of substrate analogues to probe the early steps of the catalyzed reaction Biochemistry 28 1989 7560 7572
7. E. Carpenter, A. Hawkins, J. Frost, and K. Brown Structure of dehydroquinate synthase reveals an active site capable of multistep catalysis Nature 394 1998 299 302
8. C.E. Nichols, J. Ren, H. Lamb, F. Haldane, A.R. Hawkins, and D.K. Stammers Identification of many crystal forms of Aspergillus nidulans dehydroquinate synthase Acta Crystallog. sect. D 57 2001 306 309
9. C.E. Nichols, J. Ren, H.K. Lamb, A.R. Hawkins, and D.K. Stammers Ligand-induced conformational changes and a mechanism for domain closure in Aspergillus nidulans dehydroquinate synthase J. Mol. Biol. 327 2003 129 144
10. K.A. Brown, E.P. Carpenter, K.A. Watson, J.R. Coggins, A.R. Hawkins, M.H. Koch, and D.I. Svergun Twists and turns: a tale of two shikimate-pathway enzymes Biochem. Soc. Trans. 31 2003 543 547
11. C. Nichols, A. Hawkins, and D. Stammers Structure of the open form of Aspergillus nidulans 3-dehydroquinate synthase, at 1.7 Å resolution, from crystals grown following enzyme turnover Acta Crystallog. sect, D 60 2004 971 973
12. P.A. Bartlett, K.L. McLaren, and M.A. Marx Divergence between the enzyme-catalysed and non-catalysed synthesis of 3-dehydroquinate J. Org. Chem. 59 1994 2082 2085
13. A.R. Hawkins The complex Arom locus of Aspergillus nidulans. Evidence for multiple gene fusions and convergent evolution Curr. Genet 11 1987 491 498
14. W. Wriggers, and K. Schulten Protein domain movements: detection of rigid domains and visualization of hinges in comparisons of atomic coordinates Proteins: Struct. Funct. Genet. 29 1997 1 14
15. A.R. Hawkins, and M. Smith Domain structure and interaction within the pentafunctional arom polypeptide Eur. J. Biochem. 196 1991 717 724
16. H.K. Lamb, J.P.T.W. van der Hombergh, G.H. Newton, J.D. Moore, C.F. Roberts, and A.R. Hawkins Differential flux through the quinate and shikimate pathways. Implications for the channelling hypothesis Biochem. J. 284 1992 181 187
17. W.H. Lee, L.A. Perles, R.A. Nagem, A.K. Shrive, A. Hawkins, L. Sawyer, and I. Polikarpov Comparison of different crystal forms of 3-dehydroquinase from Salmonella typhi and its implication for the enzyme activity Acta Crystallog. sect. D 58 2002 798 804
18. C.E. Nichols, B. Dhaliwal, M. Lockyer, A.R. Hawkins, and D.K. Stammers High-resolution structures reveal details of domain closure and "half-of-sites-reactivity" in Escherichia coli aspartate beta-semialdehyde dehydrogenase J. Mol. Biol. 341 2004 797 806
19. C.E. Nichols, M. Lockyer, A.R. Hawkins, and D.K. Stammers Crystal structures of Staphylococcus aureus type I dehydroquinase from enzyme turnover experiments Proteins: Struct. Funct. Genet. 56 2004 625 628
20. K. Harlos Microbridges for sitting drop crystallisations J. Appl. Crystllog. 25 1992 536 538
21. Z. Otwinowski, and W. Minor Processing of X-ray diffraction data collected in oscillation mode Methods Enzymol. 276 1996 307 326
22. Z. Otwinowski Data Collection and Processing 1993 Daresbury Laboratory Warrington, UK
23. A.T. Brunger, P.D. Adams, G.M. Clore, W.L. Delano, P. Gros, and K.R.W. Grosse Crystallography and NMR system: a new software suite for macromolecular structure determination Acta Crystallog. sect. D 54 1998 905 921
24. A.T. Brunger, A. Krukowski, and J. Erickson Slow-cooling protocols for crystallographic refinement by simulated annealing Acta Crystallog. sect. A 46 1990 585 593
25. A.T. Brunger Extension of molecular replacement: a new search strategy based on Patterson correlation coefficient refinement Acta Crystallog. sect. A 46 1990 46 57
26. T.A. Jones, J.Y. Zou, S.W. Cowan, and M. Kjeldgaard Improved methods for building protein models in electron density maps and the location of errors in these models Acta Crystallog. sect. A 47 1991 110 119
27. R.A. Laskowski, M.W. MacArthur, D.S. Moss, and J.M. Thornton PROCHECK: a program to check the stereochemical quality of protein structures J. Appl. Crystallog. 26 1993 283 291
28. Collaborative Computational Project Number 4 The CCP4 suite: programs for protein crystallography Acta Crystallog. sect. D 50 1994 760 763
29. X.J. Zhang, and B.W. Matthews A multi-functional tool for protein structure analysis J. Appl. Crystallog. 1995 624 630
30. D. Frishman, and P. Argos Knowledge-based protein secondary structure assignment Proteins: Struct. Funct. Genet. 23 1995 566 579
31. W. Humphrey, A. Dalke, and K. Schulten VMD: visual molecular dynamics J. Mol. Graph. 14 1996 27 28
32. M.M. Flocco, and S.L. Mowbray C alpha-based torsion angles: a simple tool to analyze protein conformational changes Protein Sci. 4 1995 2118 2122
33. A. Nicholls, R. Bharadwaj, and B. Honig GRASP: graphical representation and analysis of surface properties Biophys. J. 64 1993 166 170