Cocrystal structures of diaminopimelate decarboxylase: Mechanism, evolution, and inhibition of an antibiotic resistance accessory factor

Structure

Volumn 10, Issue 11, 2002, Pages 1499-1508

  Ray, Soumya S ^a   Bonanno, Jeffrey B ^a   Rajashankar, K R ^a   Pinho, Mariana G ^a   He, Guoshun ^a   De Lencastre, Herminia ^a   Tomasz, Alexander ^a   Burley, Stephen K ^a  

^a ROCKEFELLER UNIVERSITY   (United States)

Author keywords

Antibiotic resistance; Diaminopimalate decarboxylase; Lysine biosynthesis; Structural genomics; X ray crystallography

Indexed keywords

AZELAIC ACID; BETA LACTAM; CARBOXYLYASE; DIAMINOPIMELATE DECARBOXYLASE; LYSINE; UNCLASSIFIED DRUG; ANTIINFECTIVE AGENT; BACTERIAL PROTEIN; LYSA PROTEIN, BACTERIA;

ANTIBIOTIC RESISTANCE; ARTICLE; BIOSYNTHESIS; CHEMICAL BOND; CHIRALITY; CRYSTAL STRUCTURE; ENZYME ACTIVE SITE; ENZYME ACTIVITY; ENZYME ASSAY; ENZYME SPECIFICITY; ESCHERICHIA COLI; EVOLUTION; INHIBITION KINETICS; MEASUREMENT; METHANOCOCCUS JANNASCHII; PRIORITY JOURNAL; R FACTOR; SEQUENCE ALIGNMENT; STAPHYLOCOCCUS AUREUS; AMINO ACID SEQUENCE; BINDING SITE; CHEMICAL MODEL; CHEMICAL STRUCTURE; CHEMISTRY; DIMERIZATION; DRUG RESISTANCE; ENZYMOLOGY; KINETICS; METABOLISM; METHANOCOCCUS; MOLECULAR GENETICS; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN SECONDARY STRUCTURE; SEQUENCE HOMOLOGY; X RAY CRYSTALLOGRAPHY;

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI; METHANOCALDOCOCCUS JANNASCHII; METHANOCOCCUS; STAPHYLOCOCCUS; STAPHYLOCOCCUS AUREUS;

AMINO ACID SEQUENCE; ANTI-BACTERIAL AGENTS; BACTERIAL PROTEINS; BINDING SITES; CARBOXY-LYASES; CRYSTALLOGRAPHY, X-RAY; DIMERIZATION; DRUG RESISTANCE; KINETICS; METHANOCOCCUS; MODELS, CHEMICAL; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN STRUCTURE, SECONDARY; SEQUENCE HOMOLOGY, AMINO ACID; STAPHYLOCOCCUS AUREUS;

EID: 0036848911     PISSN: 09692126     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0969-2126(02)00880-8     Document Type: Article

References (42)

1. Expert Committee W.H.O. The use of essential drugs. World Health Organ. Tech. Rep. Ser. 895:2000;1-61.
2. Tenover F.C., Gaynes R.P. The epidemiology of Staphylococcus infections. Fischetti V.A., Novick R.P., Ferreri J.J., Portnoy D.A., Rood J.I. Gram-Positive Pathogens. 2000;ASM Press, Washington, DC. 414-421.pp.
3. Oliveira D.C., Tomasz A., de Lencastre H. The secrets of success of a human pathogen. molecular evolution of pandemic clones of methicillin-resistant Staphylococcus aureus Lancet. Infect. Dis. in press:2002.
4. Crisostomo M.I., Westh H., Tomasz A., Chung M., Oliveira D.C., de Lencastre H. The evolution of methicillin resistance in Staphylococcus aureus. similarity of genetic backgrounds in historically early methicillin-susceptible and -resistant isolates and contemporary epidemic clones Proc. Natl. Acad. Sci. USA. 98:2001;9865-9870.
5. Tomasz A. Multiple-antibiotic-resistant pathogenic bacteria. A report on the Rockefeller University Workshop. N. Engl. J. Med. 330:1994;1247-1251.
6. Hiramatsu K., Aritaka N., Hanaki H., Kawasaki S., Hosoda Y., Hori S., Fukuchi Y., Kobayashi I. Dissemination in Japanese hospitals of strains of Staphylococcus aureus heterogeneously resistant to vancomycin. Lancet. 350:1997;1670-1673.
7. Sieradzki K., Roberts R.B., Haber S.W., Tomasz A. The development of vancomycin resistance in a patient with methicillin-resistant Staphylococcus aureus infection. N. Engl. J. Med. 340:1999;517-523.
8. Linares J. The VISA/GISA problem. therapeutic implications Clin. Microbiol. Infect. 7:2001;8-15.
9. Hartman B.J., Tomasz A. Low-affinity penicillin-binding protein associated with beta-lactam resistance in Staphylococcus aureus. J. Bacteriol. 158:1984;513-516.
10. Reynolds P.E., Brown D.F. Penicillin-binding proteins of beta-lactam-resistant strains of Staphylococcus aureus. FEBS Lett. 192:1985;28-32.
11. Utsui Y., Yokota T. Role of an altered penicillin-binding protein in methicillin- and cephem-resistant Staphylococcus aureus. Antimicrob. Agents Chemother. 28:1985;397-403.
12. Song M.D., Wachi M., Doi M., Ishino F., Matsuhashi M. Evolution of an inducible penicillin-target protein in methicillin-resistant Staphylococcus aureus by gene fusion. FEBS Lett. 221:1987;167-171.
13. Matthews P.R., Reed K.C., Stewart P.R. The cloning of chromosomal DNA associated with methicillin and other resistances in Staphylococcus aureus. J. Gen. Microbiol. 133:1987;1919-1929.
14. Hartman B.J., Tomasz A. Expression of methicillin resistance in heterogeneous strains of Staphylococcus aureus. Antimicrob. Agents Chemother. 29:1986;85-92.
15. De Lencastre H., Tomasz A. Reassessment of the number of auxiliary genes essential for expression of high-level methicillin resistance in Staphylococcus aureus. Antimicrob. Agents Chemother. 38:1994;2590-2598.
16. De Lencastre H., Wu S.W., Pinho M.G., Ludovice A.M., Filipe S., Gardete S., Sobral R., Gill S., Chung M., Tomasz A. Antibiotic resistance as a stress response. complete sequencing of a large number of chromosomal loci in Staphylococcus aureus strain COL that impact on the expression of resistance to methicillin Microb. Drug Resist. 5:1999;163-175.
17. Born T.L., Blanchard J.S. Structure/function studies on enzymes in the diaminopimelate pathway of bacterial cell wall biosynthesis. Curr. Opin. Chem. Biol. 3:1999;607-613.
18. Grishin N.V., Osterman A.L., Brooks H.B., Phillips M.A., Goldsmith E.J. X-ray structure of ornithine decarboxylase from Trypanosoma brucei. the native structure and the structure in complex with alpha-difluoromethylornithine Biochemistry. 38:1999;15174-15184.
19. Sander C., Schneider R. Database of homology-derived protein structures and structural meaning of sequence alignment. Proteins. 9:1991;56-68.
20. Burley S.K., Wang A.H., Votano J.R., Rich A. Antigelling and antisickling bisphenyl oligopeptides and peptide analogues have similar structural features. Biochemistry. 26:1987;5091-5099.
21. Morollo A.A., Petsko G.A., Ringe D. Structure of a Michaelis complex analogue. propionate binds in the substrate carboxylate site of alanine racemase Biochemistry. 38:1999;3293-3301.
22. Jackson L.K., Brooks H.B., Osterman A.L., Goldsmith E.J., Phillips M.A. Altering the reaction specificity of eukaryotic ornithine decarboxylase. Biochemistry. 39:2000;11247-11257.
23. Swanson T., Brooks H.B., Osterman A.L., O'Leary M.H., Phillips M.A. Carbon-13 isotope effect studies of Trypanosoma brucei ornithine decarboxylase. Biochemistry. 37:1998;14943-14947.
24. Rosner A. Control of lysine biosynthesis in Bacillus subtilis. inhibition of diaminopimelate decarboxylase by lysine J. Bacteriol. 121:1975;20-28.
25. Velazquez-Campoy A., Todd M.J., Freire E. HIV-1 protease inhibitors. enthalpic versus entropic optimization of the binding affinity Biochemistry. 39:2000;2201-2207.
26. Tsukamoto T., Haile W.H., McGuire J.J., Coward J.K. Synthesis and biological evaluation of N alpha-(4-amino-4-deoxy-10-methylpteroyl)-DL-4,4-difluoroornithine. J. Med. Chem. 39:1996;2536-2540.
27. Petru A.M., Azimi P.H., Cummins S.K., Sjoerdsma A. African sleeping sickness in the United States. Successful treatment with eflornithine. Am. J. Dis. Child. 142:1988;224-228.
28. Kelland J.G., Arnold L.D., Palcic M.M., Pickard M.A., Vederas J.C. Analogs of diaminopimelic acid as inhibitors of meso-diaminopimelate decarboxylase from Bacillus sphaericus and wheat germ. J. Biol. Chem. 261:1986;13216-13223.
29. Cirilli M., Scapin G., Sutherland A., Vederas J.C., Blanchard J.S. The three-dimensional structure of the ternary complex of Corynebacterium glutamicum diaminopimelate dehydrogenase-NADPH-L-2-amino-6-methylene-pimelate. Protein Sci. 9:2000;2034-2037.
30. Caplan J.F., Zheng R., Blanchard J.S., Vederas J.C. Vinylogous amide analogues of diaminopimelic acid (DAP) as inhibitors of enzymes involved in bacterial lysine biosynthesis. Org. Lett. 2:2000;3857-3860.
31. Auger G., van Heijenoort J., Vederas J.C., Blanot D. Effect of analogues of diaminopimelic acid on the meso-diaminopimelate-adding enzyme from Escherichia coli. FEBS Lett. 391:1996;171-174.
32. Scapin G., Cirilli M., Reddy S.G., Gao Y., Vederas J.C., Blanchard J.S. Substrate and inhibitor binding sites in Corynebacterium glutamicum diaminopimelate dehydrogenase. Biochemistry. 37:1998;3278-3285.
33. Otwinowski Z., Minor W. Processing of X-ray diffraction data collected in oscillation mode. Carter C.W. Jr., Sweet R.M. Methods in Enzymology, Volume 276. 1997;Academic Press, San Diego, CA. 307-326.pp.
34. Weeks C., Miller R. The design and implementation of SnBv2.0. J. Appl. Crystallogr. 32:1999;120-124.
35. de La Fortelle E., Bricogne G. Maximum-likelihood heavy atom parameter refinement for multiple isomorphous replacement and multiwavelength anomalous diffraction methods. Carter C.W. Jr., Sweet R.M. Methods in Enzymology, Volume 276. 1997;Academic Press, San Diego, CA. 472-494.pp.
36. Kleywegt G.J., Read R.J. Not your average density. Structure. 5:1997;1557-1569.
37. Dodson E.J., Winn M., Ralph A. Collaborative computational project number 8. providing programs for protein crystallography Methods Enzymol. 277:1997;620-633.
38. Brünger 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. Crystallography and NMR system. a new software suite for macromolecular structure determination Acta Crystallogr. D Biol. Crystallogr. 54:1998;905-921.
39. Navaza J. AMoRe. an automated package for molecular replacement Acta Crystallogr. A. 50:1994;157-163.
40. Laskowski R.A., MacArthur M.W., Moss D.S., Thornton J.M. Procheck. a program to check the stereochemical quality of protein structures J. Appl. Crystallogr. 26:1993;283-291.
41. Pankuch G.A., Jacobs M.R., Appelbaum P.C. Comparative activity of ampicillin, amoxycillin, amoxycillin/clavulanate and cefotaxime against 189 penicillin-susceptible and -resistant pneumococci. J. Antimicrob. Chemother. 35:1995;883-888.
42. Nicholls A., Sharp K., Honig B. Protein folding and association. insights from the interfacial and thermodynamic properties of hydrocarbons Proteins. 11:1991;281-296.