Residues Asp164 and Glu165 at the substrate entryway function potently in substrate orientation of alanine racemase from E. coli: Enzymatic characterization with crystal structure analysis

Protein Science

Volumn 17, Issue 6, 2008, Pages 1066-1076

  Wu, Dalei ^a   Hu, Tiancen ^a   Zhang, Liang ^a   Chen, Jing ^a   Du, Jiamu ^b   Ding, Jianping ^b   Jiang, Hualiang ^a   Shen, Xu ^a  

^a SHANGHAI INSTITUTE OF MATERIA MEDICA   (China)

^b INSTITUTE OF BIOCHEMISTRY AND CELL BIOLOGY   (China)

Author keywords

Alanine racemase; Charged residues; Crystal structure; Escherichia coli; Pyridoxal 5 phosphate; Substrate entryway

Indexed keywords

ALANINE RACEMASE; ASPARTIC ACID; BACTERIAL ENZYME; CYCLOSERINE; GLUTAMIC ACID; LYSINE; MONOMER; MUTANT PROTEIN; PROLINE;

ARTICLE; BINDING AFFINITY; CATABOLISM; CONTROLLED STUDY; CRYSTAL STRUCTURE; ENZYME ACTIVE SITE; ENZYME ACTIVITY; ENZYME ANALYSIS; ENZYME ASSAY; ENZYME SUBSTRATE; ESCHERICHIA COLI; MUTATION; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN FUNCTION; PROTEIN METABOLISM; PSEUDOMONAS AERUGINOSA; STRUCTURE ANALYSIS;

ALANINE RACEMASE; AMINO ACID SEQUENCE; ASPARTIC ACID; CRYSTALLOGRAPHY, X-RAY; ESCHERICHIA COLI; GLUTAMIC ACID; KINETICS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; SEQUENCE HOMOLOGY, AMINO ACID; SUBSTRATE SPECIFICITY;

ESCHERICHIA COLI; PSEUDOMONAS AERUGINOSA;

EID: 44349161779     PISSN: 09618368     EISSN: 1469896X     Source Type: Journal    
DOI: 10.1110/ps.083495908     Document Type: Article

References (35)

1. Brunger, A.T., Adams, P.D., Clore, G.M., DeLano, W.L., Gros, P., Grosse-Kunstleve, R.W., Jiang, J.S., Kuszewski, J., Nilges, M., Pannu, N.S., et al. 1998. Crystallography & NMR system: A new software suite for macromolecular structure determination. Acta Crystallogr. D Biol. Crystallogr. 54: 905-921.
2. Cheng, Y.Q. and Walton, J.D. 2000. A eukaryotic alanine racemase gene involved in cyclic peptide biosynthesis. J. Biol. Chem. 275: 4906-4911.
3. Collaborative Computational Project, Number 4. 1994. The CCP4 suite: Programs for protein crystallography. Acta Crystallogr. D Biol. Crystallogr. 50: 760-763.
4. Copie, V., Faraci, W.S., Walsh, C.T., and Griffin, R.G. 1988. Inhibition of alanine racemase by alanine phosphonate: Detection of an imine linkage to pyridoxal 5′-phosphate in the enzyme-inhibitor complex by solid-state 15N nuclear magnetic resonance. Biochemistry 27: 4966-4970.
5. Emsley, P. and Cowtan, K. 2004. Coot: Model-building tools for molecular graphics. Acta Crystallogr. D Biol. Crystallogr. 60: 2126-2132.
6. Esaki, N. and Walsh, C.T. 1986. Biosynthetic alanine racemase of Salmonella typhimurium: Purification and characterization of the enzyme encoded by the alr gene. Biochemistry 25: 3261-3267.
7. 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.
8. Gille, C., Lorenzen, S., Michalsky, E., and Frommel, C. 2003. KISS for STRAP: User extensions for a protein alignment editor. Bioinformatics 19: 2489-2491.
9. Hoffmann, K., Schneider-Scherzer, E., Kleinkauf, H., and Zocher, R. 1994. Purification and characterization of eucaryotic alanine racemase acting as key enzyme in cyclosporin biosynthesis. J. Biol. Chem. 269: 12710-12714.
10. Hols, P., Defrenne, C., Ferain, T., Derzelle, S., Delplace, B., and Delcour, J. 1997. The alanine racemase gene is essential for growth of Lactobacillus plantarum.. J. Bacteriol. 179: 3804-3807.
11. Lambert, M.P. and Neuhaus, F.C. 1972. Mechanism of D-cycloserine action: Alanine racemase from Escherichia coli W. J. Bacteriol. 110: 978-987.
12. Laskowski, R.A., MacArthur, M.W., Moss, D.S., and Thornton, J.M. 1993. PROCHECK: A program to check the stereochemical quality of protein structures. J. Appl. Crystallogr. 26: 283-291.
13. LeMagueres, P., Im, H., Dvorak, A., Strych, U., Benedik, M., and Krause, K.L. 2003. Crystal structure at 1.45 Å resolution of alanine racemase from a pathogenic bacterium, Pseudomonas aeruginosa, contains both internal and external aldimine forms. Biochemistry 42: 14752-14761.
14. LeMagueres, P., Im, H., Ebalunode, J., Strych, U., Benedik, M.J., Briggs, J.M., Kohn, H., and Krause, K.L. 2005. The 1.9 Å crystal structure of alanine racemase from Mycobacterium tuberculosis contains a conserved entryway into the active site. Biochemistry 44: 1471-1481.
15. Leslie, A.G. 1999. Integration of macromolecular diffraction data. Acta Crystallogr. D Biol. Crystallogr. 55: 1696-1702.
16. Lobocka, M., Hennig, J., Wild, J., and Klopotowski, T. 1994. Organization and expression of the Escherichia coli K-12 dad operon encoding the smaller subunit of D-amino acid dehydrogenase and the catabolic alanine racemase. J. Bacteriol. 176: 1500-1510.
17. 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.
18. Neuhaus, F.C. and Hammes, W.P. 1981. Inhibition of cell wall biosynthesis by analogues and alanine. Pharmacol. Ther. 14: 265-319.
19. Newton, R.W. 1975. Side effects of drugs used to treat tuberculosis. Scott. Med. J. 20: 47-49.
20. Noda, M., Matoba, Y., Kumagai, T., and Sugiyama, M. 2004. Structural evidence that alanine racemase from a D-cycloserine-producing microorganism exhibits resistance to its own product. J. Biol. Chem. 279: 46153-46161.
21. Noda, M., Matoba, Y., Kumagai, T., and Sugiyama, M. 2005. A novel assay method for an amino acid racemase reaction based on circular dichroism. Biochem. J. 389: 491-496.
22. Patrick, W.M., 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 3: 789-792.
23. Shaw, J.P., Petsko, G.A., and Ringe, D. 1997. Determination of the structure of alanine racemase from Bacillus stearothermophilus at 1.9 Å resolution. Biochemistry 36: 1329-1342.
24. Shindyalov, I.N. and Bourne, P.E. 1998. Protein structure alignment by incremental combinatorial extension (CE) of the optimal path. Protein Eng. 11: 739-747.
25. Stamper, 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.
26. Steen, A., Palumbo, E., Deghorain, M., Cocconcelli, P.S., Delcour, J., Kuipers, O.P., Kok, J., Buist, G., and Hols, P. 2005. Autolysis of Lactococcus lactis is increased upon D-alanine depletion of peptidoglycan and lipoteichoic acids. J. Bacteriol. 187: 114-124.
27. 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.
28. Strych, U., Penland, R.L., Jimenez, M., Krause, K.L., and Benedik, M.J. 2001. Characterization of the alanine racemases from two mycobacteria.. FEMS Microbiol. Lett. 196: 93-98.
29. Sun, S. and Toney, M.D. 1999. Evidence for a two-base mechanism involving tyrosine-265 from arginine-219 mutants of alanine racemase. Biochemistry 38: 4058-4065.
30. Tauch, A., Gotker, S., Puhler, A., Kalinowski, J., and Thierbach, G. 2002. The alanine racemase gene alr is an alternative to antibiotic resistance genes in cloning systems for industrial Corynebacterium glutamicum strains. J. Biotechnol. 99: 79-91.
31. Uo, T., Yoshimura, T., Tanaka, N., Takegawa, K., and Esaki, N. 2001. Functional characterization of alanine racemase from Schizosaccharomyces pombe: A eucaryotic counterpart to bacterial alanine racemase. J. Bacteriol. 183: 2226-2233.
32. 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.
33. Watanabe, A., Kurokawa, Y., Yoshimura, T., Kurihara, T., Soda, K., and Esaki, N. 1999a. Role of lysine 39 of alanine racemase from Bacillus stearothermophilus that binds pyridoxal 5′-phosphate. Chemical rescue studies of Lys39 → Ala mutant. J. Biol. Chem. 274: 4189-4194.
34. Watanabe, A., Yoshimura, T., Mikami, B., and Esaki, N. 1999b. Tyrosine 265 of alanine racemase serves as a base abstracting α-hydrogen from L-alanine: The counterpart residue to lysine 39 specific to D-alanine. J. Biochem. 126: 781-786.
35. Watanabe, A., Yoshimura, T., Mikami, B., Hayashi, H., Kagamiyama, H., and Esaki, N. 2002. Reaction mechanism of alanine racemase from Bacillus stearothermophilus: X-ray crystallographic studies of the enzyme bound with N-(5′-phosphopyridoxyl)alanine. J. Biol. Chem. 277: 19166-19172.