Crystal Structure at 1.45 Å Resolution of Alanine Racemase from a Pathogenic Bacterium, Pseudomonas aeruginosa, Contains Both Internal and External Aldimine Forms

Biochemistry

Volumn 42, Issue 50, 2003, Pages 14752-14761

  LeMagueres, Pierre ^a   Im, Hookang ^a   Dvorak, Anna ^a   Strych, Ulrich ^a   Benedik, Michael ^a   Krause, Kurt L ^a,b  

^a University of Houston   (United States)

^b BAYLOR COLLEGE OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIA; CHEMICAL BONDS; CONFORMATIONS; CRYSTAL STRUCTURE; DIMERS; MONOMERS;

DOMAIN GEOMETRY;

ENZYMES;

ALANINE RACEMASE; DIMER; PROTEIN DADX; UNCLASSIFIED DRUG;

ARTICLE; CRYSTAL STRUCTURE; ENZYME ACTIVE SITE; ENZYME CONFORMATION; ENZYME STRUCTURE; GEOBACILLUS STEAROTHERMOPHILUS; GEOMETRY; NONHUMAN; PRIORITY JOURNAL; PROTEIN DOMAIN; PSEUDOMONAS AERUGINOSA; ROTATION; STRUCTURE ANALYSIS;

ALANINE RACEMASE; AMINO ACID SEQUENCE; BACILLUS STEAROTHERMOPHILUS; BINDING SITES; CRYSTALLOGRAPHY, X-RAY; DIMERIZATION; HYDROGEN BONDING; IMINES; MOLECULAR SEQUENCE DATA; PEPTIDE FRAGMENTS; PROTEIN STRUCTURE, TERTIARY; PSEUDOMONAS AERUGINOSA; PYRIDOXAL PHOSPHATE; SEQUENCE ALIGNMENT;

BACTERIA (MICROORGANISMS); GEOBACILLUS STEAROTHERMOPHILUS; NEGIBACTERIA; PSEUDOMONAS; PSEUDOMONAS AERUGINOSA;

EID: 0345734003     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi030165v     Document Type: Article

References (48)

1. Pollack, M. (1995) Pseudomonas aeruginosa, in Principles and Practice of Infectious Diseases (Mandell, G. L., Bennett, J. E., and Dolin, R., Eds.) pp 2310-2335, Churchill Livingstone, New York.
2. Martone, W. J., and Jarvis, W. R. (1992) Predominant Pathogens in Hospital Infections, J. Antimicrob. Chemother. 19-24.
3. FitzSimmons, S. C. (1993) The Changing Epidemiology of Cystic Fibrosis, J. Pediatr. 1-9.
4. Bert, F., Maubec, E., and Bruneau, B. et al. (1998) Multi-resistant Pseudomonas aeruginosa Outbreak Associated with Contaminated Tap Water in a Neurosurgery Intensive Care Unit, J. Hops. Infect. 53-62.
5. Chen, H. Y., Yuan, M., Ibrahim-Elmagboul, I. B., and Livermore, D. M. (1995) National Survey of Susceptibility to Antimicrobials amongst Clinical Isolates of Pseudomonas aeruginosa, J. Antimicrob. Chemother. 521-534.
6. Strych, U., Huang, H. C., Krause, K. L., and Benedik, M. J. (2000) Characterization of the Alanine Racemases from Pseudomonas aeruginosa PAO1, Curr. Microbiol. 41, 290-294.
7. Wasserman, S. A., Walsh, C. T., and Botstein, D. (1983) Two Alanine Racemase Genes in Salmonella typhimurium that Differ in Structure and Function, J. Bacteriol. 153, 1439-1450.
8. Wild, J., Hennig, J., Lobocka, M., Walczak, W., and Klopotowski, T. (1985) Identification of the dadx Gene Coding for the Predominant Isozyme of Alanine Racemase in Escherichia coli K12, Mol. Gen. Genet. 198, 315-322.
9. Lambert, M. P., and Neuhaus, M. P. (1972) Mechanism of D-Cycloserine Action: Alanine Racemase from Escherichia coli, J. Bacteriol. 110, 978-987.
10. Silverman, R. B. (1988) The Potential Use of Mechanism-Based Enzyme Inactivators in Medicine, J. Enzyme Inhib. 2, 73-90.
11. 15N Nuclear Magnetic Resonance, Biochemistry 27, 4966-4970.
12. Erion, M. D., and Walsh, C. T. (1987) 1-Aminocyclopropane-phosphonate: Time-Dependent Inactivation of 1-Aminocyclopro-panecarboxylate Deaminase and Bacillus stearothermophilus Alanine Racemase by Slow dissociation Behavior, Biochemistry 26, 3417-3425.
13. Wang, E., and Walsh, C. T. (1978) Suicide Substrates for the Alanine Racemase from Escherichia coli B, Biochemistry 17, 1313-1321.
14. Neuhaus, F. C. (1967) Mechanism of Action, in Antibiotics (Gottleib, D., and Shaw, P. D., Eds.) pp 40, Springer-Verlag, New York.
15. Walsh, C. (2003) Antibiotics that Act on Cell Wall Biosynthesis, in Antibiotics-actions, origins, resistance, pp 23-49, ASM Press, Washington.
16. Weinstein, L. (1975) Antimicrobial Agents-Drugs Used in the Chemotherapy of Tuberculosis and Leprosy, in The Pharmacological Basis of Therapeutics, 5th ed. (Goodman, L. S. and Gilman, A., Eds.) pp 1202-1223, Macmillan Publishing, New York.
17. Newton, R. W. (1975) Side Effects of Drugs Used to Treat Tuberculosis, Scott. Med. J. 20, 47-49.
18. Yew, W. W., Wong, C. F., Wong, P. C., Lee, J., and Chau, C. H. (1993) Adverse Neurological Reactions in Patients with Multidrug-Resistant Pulmonary Tuberculosis after Coadministration of Cycloserine and Ofloxacin, Clin. Infect. Dis. 17, 288-289.
19. Katz, M. H. (1994) Effect of HIV Treatment on Cognition, Behavior, and Emotion, Psychiatr. Clin. North Am. 17, 227-230.
20. Shaw, J. P., Petsko, G. A., and Ringe, D. (1997) Determination of the Structure of Alanine Racemase from Bacillus stearo-thermophilus at 1.9 Å Resolution, Biochemistry 36, 1329-1342.
21. Morollo, A. A., Petsko, G. A., and Ringe, D. (1999) Structure of a Michaelis Complex Analogue: Propionate Binds in the Substrate Carboxylate Site of Alanine Racemase, Biochemistry 38, 3293-3301.
22. Stamper, C. G. F., Morollo, A. A., and Ringe D. (1998) Reaction of Alanine Racemase with 1-Aminoethylphosphonic Acid Forms a Stable External Aldimine, Biochemistry 37, 10438-10445.
23. Jansonius, J. N. (1998) Structure, Evolution and Action of Vitamin B(6) Dependent Enzymes, Curr. Opin. Struct. Biol. 8, 756-759.
24. Ondrechen, M. J., Briggs, J. M., and McCammon, J. A. (2001) A Model for Enzyme - Substrate Interaction in Alanine Racemase, J. Am. Chem. Soc. 123, 2830-2834.
25. Watanabe, A., Yoshimura, T., Mikami, B., and Esaki, N. (1999) Tyrosine 265 of Alanine Racemase Serves as a Base Abstracting a Hydrogen from L-Alanine: the Counterpart Residue to Lys39 Specific to D-Alanine, J. Biochem. 126, 781-786.
26. Fenn, T. D., Stamper, G. F., Morollo, A. A., and Ringe, D. (2003) A side Reaction of Alanine Racemase: Transamination of Cycloserine, Biochemistry 42, 5775-5783.
27. Olson, G. T., Mengmeng, F., Lau, S., Rinehart, K. L., and Silverman, R. B. (1998) An Aromatization Mechanism of Inactivation of γ-Aminobutyric Acid Aminotransferase for the Antibiotic L-Cycloseline, J. Am. Chem. Soc. 120, 2256-2267.
28. Peisach, D., Chipman, D. M., Van Ophem, P. W., Manning, J. M., and Ringe, D. (1998) D-Cycloserine Inactivation of D-Amino Acid Aminotransferase Leads to a Stable Noncovalent Protein Complex with an Aromatic Cycloserine-PLP Derivative, J. Am. Chem. Soc. 120, 2268-2274.
29. Yokoigawa, K., Okubo, Y., and Soda, K. (2003) Subunit Interaction of Monomeric Alanine Racemases from Four Shigella Species in Catalytic Reaction, FEMS Microbiol. Lett. 221, 263-267.
30. Otwinowski, Z., and Minor, W. (1997) Processing of X-ray Diffraction Data Collected in Oscillation Mode, in Methods of Enzymology (C. W. Carter, J., and Sweet, R. M., Eds.) pp 307-326, Academic Press, New York.
31. Terwilliger, T. C., and Berendzen, J. (1999) Automated Structure Solution for MIR and MAD, Acta Crystallogr. D55, 849-861.
32. Lamzin, V. S., and Wilson, K. S. (1997) Automated Refinement for Protein Crystallography, Methods Enzymol. 277, 269-305.
33. Perrakis, A., Sixma, T. K., Wilson, K. S., and Lamzin, V. S. (1997) wARP: Improvement and Extension of Crystallographic Phases by Weighted Averaging of Multiple Refined Dummy Atomic Models, Acta Crystallogr. D53, 448-455.
34. Perrakis, A., Morris, R. J., and Lamzin, V. S. (1999) Automated Protein Model Building Combined with Iterative Structure Refinement, Nat. Struct. Biol. 6, 458-463.
35. Sheldrick, G. M., and Schneider, T. R. (1997) Shelxl: High-Resolution Refinement, Methods Enzymol. 277, 319-343.
36. Jones, T. A., Zou, J. Y., Cowan, S. W., and Kjeldgaard, M. (1991) Improved Methods for Building Protein Models in Electron Density Maps and the Location of Errors in these Models, Acta Crystallogr. A47, 110-119.
37. Yano, T., Kuramiysu, S., Tanase, S., Morino, Y., and Kagamiyama, H. (1992) Role of Asp222 in the Catalytic Mechanism of Escherichia coli Aspartate Aminotransferase: The Amino Acid Residue Which Enhances the Function of the Enzyme-Bound Coenzyme Pyridoxal 5′-Phosphate, Biochemistry 31, 5878-5887.
38. Amone, A., Christen, P., Jansonius, J. N., and Metzler, D. E. (1985) in Transaminases (Christen, P., and Metzler, D. E., Eds.) pp 326-357, John Wiley and Sons, New York.
39. McPhalen, C. A., Vincent, M. G., and Jansonius, J. N. (1992) X-ray Structure Refinement and Comparison of Three Forms of Mitochondrial Aspartate Aminotransferase, J. Mol. Biol. 225, 495-517.
40. Ashley Spies, M., and Toney, M. D. (2003) Multiple Hydrogen Kinetic Isotope for Enzymes Catalyzing Exchange with Solvent: Application to Alanine Racemase, Biochemistry 42, 5099-5107.
41. Watanabe, A., Yoshimura, T., Mikami, B., Kagamiyama, H., and Esaki, N. (2002) Reaction Machanism of Alanine Racemase from Bacillus stearothermophilus, J. Biol. Chem. 277, 19166-19172.
42. Rathore, R., Lindeman, S. V., and Kochi, J. K. (1997) Charge-Transfer Probes for Molecular Recognition via Steric Hindrance in Donor-Acceptor Pairs, J. Am. Chem. Soc. 119, 9393-9404.
43. Le Magueres, P., Lindeman, S. V., and Kochi, J. K. (2000) Novel (Heteromolecular) π-Complexes of Aromatic Cation Radicals. Isolation and Structural Characterization, Org. Lett. 2, 3567-3570.
44. Wayne, M. P., Weisner, J., and Blackburn, J. M. (2002) Site-Directed Mutagenesis of Tyr354 in Geobacillus stearothermophilus Alanine Racemase Identifies a Role in Controlling Substrate Specificity and a Possible Role in the Evolution of Antibiotic Resistance, ChemBioChem 8, 789-792.
45. Mustata, G. I., and Briggs, J. M. (2002) A Structure-Based Design Approach for the Identification of Novel Inhibitors: Application to an Alanine Racemase, J. Comput.-Aided Mol. Des. 16, 935-953.
46. Boggetto, N., and Reboud-Ravaux, M. (2002) Dimeric Inhibitors of HIV-1 Protease, Biol. Chem. 383, 1321-1324.
47. Song, M., Rajesh, S., Hayashi, Y., and Kiso, Y. (2001) Design and Synthesis of New Inhibitors of HIV-1 Protease Dimerization with Conformationally Constrained Templates, Bioorg. Med. Chem. Lett. 11, 2465-2468.
48. Cochran, A. G. (2001) Protein-Protein Interfaces: Mimics and Inhibitors, Curr. Opin. Chem. Biol. 5, 654-659.