Substrate-induced conformational changes in Bacillus subtilis glutamate racemase and their implications for drug discovery

Structure

Volumn 13, Issue 11, 2005, Pages 1707-1713

  Ruzheinikov, Sergey N ^a   Taal, Makie A ^a   Sedelnikova, Svetlana E ^a   Baker, Patrick J ^a   Rice, David W ^a  

^a UNIVERSITY OF SHEFFIELD   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL ENZYME; ENZYME INHIBITOR; GLUTAMATE RACEMASE INHIBITOR; RACEMASE; UNCLASSIFIED DRUG;

ANTIBACTERIAL ACTIVITY; ARTICLE; BACILLUS SUBTILIS; CATALYSIS; CONFORMATIONAL TRANSITION; DRUG DESIGN; ENZYME ACTIVITY; ENZYME BINDING; ENZYME INDUCTION; ENZYME LOCALIZATION; ENZYME MECHANISM; ENZYME STRUCTURE; ENZYME SUBSTRATE; GENE DUPLICATION; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN FOLDING; STRUCTURAL HOMOLOGY;

AMINO ACID ISOMERASES; AMINO ACID SEQUENCE; BACILLUS SUBTILIS; BACTERIAL PROTEINS; BINDING SITES; CATALYTIC DOMAIN; CRYSTALLOGRAPHY, X-RAY; DRUG DESIGN; MOLECULAR SEQUENCE DATA; PROTEIN BINDING; PROTEIN CONFORMATION; SEQUENCE ALIGNMENT; SUBSTRATE SPECIFICITY;

BACILLUS SUBTILIS; BACTERIA (MICROORGANISMS);

EID: 27644453362     PISSN: 09692126     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.str.2005.07.024     Document Type: Article

References (35)

1. Baltz, R.H., Hoskins, J.A., Solenberg, P.J., and Treadway, P.J. November 1999. U.S. patent 5,981,281.
2. A.T. Brunger, P.D. Adams, G.M. Clore, W.L. DeLano, P. Gros, R.W. Grosse-Kunstleve, J.S. Jiang, J. Kuszewski, M. Nilges, and N.S. Pannu Crystallography & NMR system: a new software suite for macromolecular structure determination Acta Crystallogr. D Biol. Crystallogr. 54 1998 905 921
3. T.D.H. Bugg, and C.T. Walsh Intracellular steps of bacterial cell wall peptidoglycan biosynthesis: enzymology, antibiotics, and antibiotic resistance Nat. Prod. Rep. 9 1992 199 215
4. CCP4 (Collaborative Computational Project, Number 4) The CCP4 suite: programs for protein crystallography Acta Crystallogr D Biol. Crystallogr. 50 1994 760 763
5. D.T.W. Chu, J.J. Plattner, and L. Katz New directions in antibacterial research J. Med. Chem. 39 1996 3853 3871
6. K. Cowtan 'dm': an automated procedure for phase improvement by density modification Joint CCP4 Study Weekend and ESF-EACBM Newsletter on Protein Crystallography 31 1994 34 38
7. A. de Dios, L. Prieto, J.A. Martin, A. Rubio, J. Ezquerra, M. Tebbe, B. Lopez de Uralde, J. Martin, A. Sanchez, and D.L. LeTourneau 4-Substituted D-glutamic acid analogues: the first potent inhibitors of glutamate racemase (MurI) enzyme with antibacterial activity J. Med. Chem. 45 2002 4559 4570
8. P. Doublet, J. van Heijenoort, and D. Mengin-Lecreulx Identification of the Escherichia coli murI gene, which is required for the biosynthesis of D-glutamic acid, a specific component of bacterial peptidoglycan J. Bacteriol. 174 1992 5772 5779
9. P. Doublet, J. van Heijenoort, J.P. Bohin, and D. Mengin-Lecreulx The murI gene of Escherichia coli is an essential gene that encodes a glutamate racemase activity J. Bacteriol. 175 1993 2970 2979
10. K.A. Gallo, and J.R. Knowles Purification, cloning, and cofactor independence of glutamate racemase from Lactobacillus Biochemistry 32 1993 3981 3990
11. S. Glavas, and M.E. Tanner The inhibition of glutamate racemase by D-N-hydroxyglutamate Bioorg. Med. Chem. Lett. 7 1997 2265 2270
12. S. Glavas, and M.E. Tanner Catalytic acid/base residues of glutamate racemase Biochemistry 38 1999 4106 4113
13. S. Glavas, and M.E. Tanner Active site residues of glutamate racemase Biochemistry 40 2001 6199 6204
14. N. Guex, and M.C. Peitsch SWISS-MODEL and Swiss-PdbViewer: an environment for comparative protein modeling Electrophoresis 18 1997 2714 2723
15. W.G.J. Hol, P.T. van Duijnen, and H.J.C. Berendsen The α-helix dipole and the properties of proteins Nature 273 1978 443 446
16. L. Holm, and C. Sander Dali: a network tool for protein structure comparison Trends Biochem. Sci. 20 1995 478 480
17. K.Y. Hwang, C.-S. Cho, S.S. Kim, H.-C. Sung, Y.G. Yu, and Y. Cho Structure and mechanism of glutamate racemase from Aquifex pyrophilus Nat. Struct. Biol. 6 1999 422 426
18. J.-S. Jiang, and A.T. Brünger Protein hydration observed by X-ray diffraction: solvation properties of penicillopopsin and neuraminidase crystal structures J. Mol. Biol. 243 1994 100 115
19. S. Jones, and J.M. Thornton Protein-protein interactions: a review of protein dimer structures Prog. Biophys. Mol. Biol. 63 1995 31 65
20. G.J. Kleywegt, and T.A. Jones Databases in protein crystallography Acta Crystallogr. D Biol. Crystallogr. 54 1998 1119 1131
21. K. Kobayashi, S.D. Ehrlich, A. Albertini, G. Amati, K.K. Andersen, M. Arnaud, K. Asai, S. Ashikaga, S. Aymerich, and P. Bessieres Essential Bacillus subtilis genes Proc. Natl. Acad. Sci. USA 100 2003 4678 4683
22. 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. Crystallogr. 26 1993 283 291
23. B. Lee, and F.M. Richards The interpretation of protein structures: estimation of static accessibility J. Mol. Biol. 55 1971 379 400
24. S.B. Levy The challenge of antibiotic resistance Sci. Am. 278 1998 46 53
25. L. Liu, K. Iwata, A. Kita, Y. Kawarabayasi, M. Yohda, and K. Miki Crystal structure of aspartate racemase from Pyrococcus horikoshii OT3 and its implications for molecular mechanism of PLP-independent racemization J. Mol. Biol. 319 2002 479 489
26. Z. Otwinowski Maximum likelihood refinement of heavy atom parameters W. Wolf P.R. Evans A.G.W. Leslie Isomorphous Replacement and Anomalous Scattering 1991 SERC Daresbury Laboratory Warrington, UK 80 86
27. Z. Otwinowski, and W. Minor Processing of X-ray diffraction data collected in oscillation mode Methods Enzymol. 276 1997 307 326
28. G. Parkinson, J. Vojtechovsky, L. Clowney, A.T. Brünger, and H.M. Berman New parameters for the refinement of nucleic acid-containing structures Acta Crystallogr. D Biol. Crystallogr. 52 1996 57 64
29. M.J. Pucci, J.A. Thanassi, H.-T. Ho, P.J. Falk, and T.J. Dougherty Staphylococcus haemolyticus contains two D-glutamic acid biosynthetic activities, a glutamate racemase and a D-amino acid transaminase J. Bacteriol. 177 1995 336 342
30. A. Roussel, and C. Cambillau TURBO-FRODO Manual 1996 AFMB-CNRS Marseille, France
31. G.M. Sheldrick SHELX: applications to macromolecules S. Fortier Direct Methods for Solving Macromolecular Structures 1998 Kluwer Academic Publishers Dordrecht, The Netherlands 401 411
32. M.A. Taal, S.E. Sedelnikova, S.N. Ruzheinikov, P.J. Baker, and D.W. Rice Expression, purification and preliminary X-ray analysis of crystals of Bacillus subtilis glutamate racemase Acta Crystallogr. D Biol. Crystallogr. 60 2004 2031 2034
33. M.E. Tanner, and S. Miao The synthesis and stability of aziridino-glutamate, an irreversible inhibitor of glutamate racemase Tetrahedron Lett. 35 1994 4073 4076
34. C.T. Walsh Enzymes in the D-alanine branch of bacterial cell wall peptidoglycan assembly J. Biol. Chem. 264 1989 2393 2396
35. T. Yoshimura, M. Ashiuchi, N. Esaki, C. Kobatake, S.Y. Choi, and K. Soda Expression of glr (murI, dga) gene encoding glutamate racemase in Escherichia coli J. Biol. Chem. 268 1993 24242 24246