Structure of the extended-spectrum class C β-lactamase ADC-1 from Acinetobacter baumannii

Acta Crystallographica Section D: Biological Crystallography

Volumn 70, Issue 3, 2014, Pages 760-771

  Bhattacharya, Monolekha ^a   Toth, Marta ^a   Antunes, Nuno Tiago ^a   Smith, Clyde A ^b   Vakulenko, Sergei B ^a  

^a UNIVERSITY OF NOTRE DAME   (United States)

^b SLAC NATIONAL ACCELERATOR LABORATORY   (United States)

Author keywords

Apoenzymes; Class C lactamases

Indexed keywords

AMPC BETA LACTAMASES; AMPC BETA-LACTAMASES; APOENZYME; BACTERIAL PROTEIN; BETA LACTAMASE; BETA LACTAMASE TEM 1; BETA-LACTAMASE TEM-1; CEPHALOSPORIN DERIVATIVE;

ACINETOBACTER BAUMANNII; ACINETOBACTER INFECTION; ARTICLE; CHEMISTRY; CLASS C Β-LACTAMASES; CLASSIFICATION; COMPARATIVE STUDY; DRUG EFFECT; ENZYME ACTIVE SITE; ENZYME SPECIFICITY; ENZYMOLOGY; GENETICS; METABOLISM; MICROBIOLOGY; MULTIGENE FAMILY;

APOENZYMES; CLASS C Β-LACTAMASES;

ACINETOBACTER BAUMANNII; ACINETOBACTER INFECTIONS; APOENZYMES; BACTERIAL PROTEINS; BETA-LACTAMASES; CATALYTIC DOMAIN; CEPHALOSPORINS; MULTIGENE FAMILY; SUBSTRATE SPECIFICITY;

EID: 84896779935     PISSN: 09074449     EISSN: 13990047     Source Type: Journal    
DOI: 10.1107/S1399004713033014     Document Type: Article

References (61)

1. Adams, P. D. et al. (2010). Acta Cryst. D66, 213-221.
2. Altschul, S. F., Gish, W., Miller, W., Myers, E. W. & Lipman, D. J. (1990). J. Mol. Biol. 215, 403-410.
3. Altschul, S. F., Madden, T. L., Schäffer, A. A., Zhang, J., Zhang, Z., Miller,W. & Lipman, D. J. (1997). Nucleic Acids Res. 25, 3389-3402.
4. Ambler, R. P., Coulson, A. F. W., Frère, J.-M., Ghuysen, J.-M., Joris, B., Forsman, M., Levesque, R. C., Tiraby, G. & Waley, S. G. (1991). Biochem. J. 276, 269-270.
5. Antunes, N. T., Frase, H., Toth, M., Mobashery, S. & Vakulenko, S. B. (2011). Biochemistry, 50, 6387-6395.
6. Banerjee, S., Pieper, U., Kapadia, G., Pannell, L. K. & Herzberg, O. (1998). Biochemistry, 37, 3286-3296.
7. Beadle, B. M. & Shoichet, B. K. (2002). Antimicrob. Agents Chemother. 46, 3978-3980.
8. Beadle, B. M., Trehan, I., Focia, P. J. & Shoichet, B. K. (2002). Structure, 10, 413-424.
9. Berman, H. M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T. N., Weissig, H., Shindyalov, I. N. & Bourne, P. E. (2000). Nucleic Acids Res. 28, 235-242.
10. Blizzard, T. A. et al. (2010). Bioorg. Med. Chem. Lett. 20, 918-921.
11. Bogaerts, P., Cuzon, G., Naas, T., Bauraing, C., Deplano, A., Lissoir, B., Nordmann, P. & Glupczynski, Y. (2008). Antimicrob. Agents Chemother. 52, 4205-4206.
12. Bou, G., Cerveró , G., Domínguez, M. A., Quereda, C. & Martínez- Beltrá n, J. (2000). J. Clin. Microbiol. 38, 3299-3305.
13. Bou, G. & Martínez-Beltrá n, J. (2000). Antimicrob. Agents Chemother. 44, 428-432.
14. Brown, S. & Amyes, S. (2006). J. Antimicrob. Chemother. 57, 1-3.
15. Chen, H. et al. (2011). Bioorg. Med. Chem. Lett. 21, 4267-4270.
16. Chen, V. B., Arendall, W. B., Headd, J. J., Keedy, D. A., Immormino, R. M., Kapral, G. J., Murray, L. W., Richardson, J. S. & Richardson, D. C. (2010). Acta Cryst. D66, 12-21.
17. Chen, Y., McReynolds, A. & Shoichet, B. K. (2009). Protein Sci. 18, 662-669.
18. Clark, R. B. (1996). J. Antimicrob. Chemother. 45, 245-251.
19. Clinical and Laboratory Standards Institute (2009). Methods for Dilution Antimicrobial Susceptibility Tests for Bacteria That Grow Aerobically; Approved Standard - Eighth Edition,M07-A8.Wayne: Clinical and Laboratory Standards Institute.
20. Coelho, J., Woodford, N., Turton, J. & Livermore, D. M. (2004). J. Hosp. Infect. 58, 167-169.
21. Crichlow, G. V., Kuzin, A. P., Nukaga, M., Mayama, K., Sawai, T. & Knox, J. R. (1999). Biochemistry, 38, 10256-10261.
22. Crichlow, G. V., Nukaga, M., Doppalapudi, V. R., Buynak, J. D. & Knox, J. R. (2001). Biochemistry, 40, 6233-6239.
23. DeLano, W. L. (2002). PyMOL. http://www.pymol.org.
24. Dubus, A., Ledent, P., Lamotte-Brasseur, J. & Frère, J.-M. (1996). Proteins, 25, 473-485.
25. Emsley, P. & Cowtan, K. (2004). Acta Cryst. D60, 2126-2132.
26. Evans, P. (2006). Acta Cryst. D62, 72-82.
27. Fernández-Cuenca, F., Martínez-Martínez, L., Conejo, M. C., Ayala, J. A., Perea, E. J. & Pascual, A. (2003). J. Antimicrob. Chemother. 51, 565-574.
28. Frase, H., Shi, Q., Testero, S. A., Mobashery, S. & Vakulenko, S. B. (2009). J. Biol. Chem. 284, 29509-29513.
29. Gasteiger, E., Gattiker, A., Hoogland, C., Ivanyi, I., Appel, R. D. & Bairoch, A. (2003). Nucleic Acids Res. 31, 3784-3788.
30. Golemi, D., Maveyraud, L., Vakulenko, S., Samama, J.-P. & Mobashery, S. (2001). Proc. Natl Acad. Sci. USA, 98, 14280-14285.
31. Hujer, K. M., Hamza, N. S., Hujer, A. M., Perez, F., Helfand, M. S., Bethel, C. R., Thomson, J. M., Anderson, V. E., Barlow, M., Rice, L. B., Tenover, F. C. & Bonomo, R. A. (2005). Antimicrob. Agents Chemother. 49, 2941-2948.
32. Jacoby, G. A. (2009). Clin. Microbiol. Rev. 22, 161-182.
33. Kabsch, W. (2010). Acta Cryst. D66, 125-132.
34. Kim, J. Y., Jung, H. I., An, Y. J., Lee, J. H., Kim, S. J., Jeong, S. H., Lee, K. J., Suh, P.-G., Lee, H.-S., Lee, S. H. & Cha, S.-S. (2006). Mol. Microbiol. 60, 907-916.
35. Knox, J. R., Moews, P. C. & Frere, J.-M. (1996). Chem. Biol. 3, 937-947.
36. Krissinel, E. & Henrick, K. (2004). Acta Cryst. D60, 2256-2268.
37. Lahiri, S. D., Mangani, S., Durand-Reville, T., Benvenuti, M., De Luca, F., Sanyal, G. & Docquier, J.-D. (2013). Antimicrob. Agents Chemother. 57, 2496-2505.
38. Laskowski, R. A., MacArthur, M. W., Moss, D. S. & Thornton, J. M. (1993). J. Appl. Cryst. 26, 283-291.
39. Lobkovsky, E., Billings, E. M., Moews, P. C., Rahil, J., Pratt, R. F. & Knox, J. R. (1994). Biochemistry, 33, 6762-6772.
40. Lee, S.-H., Lee, J.-J., Lee, J.-J., Wu, X., Selenge, B. & Kwon, D. B. (2013). ICAAC 2013 Abstracts, Abstract C1-1585. Washington: American Society for Microbiology.
41. Matthews, B. W. (1968). J. Mol. Biol. 33, 491-497.
42. Michaux, C., Massant, J., Kerff, F., Frère, J.-M., Docquier, J.-D., Vandenberghe, I., Samyn, B., Pierrard, A., Feller, G., Charlier, P., Van Beeumen, J. & Wouters, J. (2008). FEBS J. 275, 1687-1697.
43. Murshudov, G. N., Skubá k, P., Lebedev, A. A., Pannu, N. S., Steiner, R. A., Nicholls, R. A., Winn, M. D., Long, F. & Vagin, A. A. (2011). Acta Cryst. D67, 355-367.
44. Nukaga, M., Abe, T., Venkatesan, A. M., Mansour, T. S., Bonomo, R. A. & Knox, J. R. (2003). Biochemistry, 42, 13152-13159.
45. Nukaga, M., Kumar, S., Nukaga, K., Pratt, R. F. & Knox, J. R. (2004). J. Biol. Chem. 279, 9344-9352.
46. Oefner, C., D'Arcy, A., Daly, J. J., Gubernator, K., Charnas, R. L., Heinze, I., Hubschwerlen, C. & Winkler, F. K. (1990). Nature (London), 343, 284-288.
47. Park, Y. K., Choi, J. Y., Jung, S.-I., Park, K.-H., Lee, H., Jung, D. S., Heo, S. T., Kim, S.-W., Chang, H.-H., Cheong, H. S., Chung, D. R., Peck, K. R., Song, J. H. & Ko, K.-S. (2009). Diagn. Microbiol. Infect. Dis. 64, 389-395.
48. Peleg, A. Y., Seifert, H. & Paterson, D. L. (2008). Clin. Microbiol. Rev. 21, 538-582.
49. Perez, F., Hujer, A. M., Hujer, K. M., Decker, B. K., Rather, P. N. & Bonomo, R. A. (2007). Antimicrob. Agents Chemother. 51, 3471-3484.
50. Poirel, L. & Nordmann, P. (2006). Clin. Microbiol. Infect. 12, 826-836.
51. Rodríguez-Martínez, J. M., Nordmann, P., Ronco, E. & Poirel, L. (2010). Antimicrob. Agents Chemother. 54, 3484-3488.
52. Schneider, K. D., Karpen, M. E., Bonomo, R. A., Leonard, D. A. & Powers, R. A. (2009). Biochemistry, 48, 11840-11847.
53. Smith, C. A., Antunes, N. T., Stewart, N. K., Toth, M., Kumarasiri, M., Chang, M., Mobashery, S. & Vakulenko, S. B. (2013). Chem. Biol. 20, 1107-1115.
54. Stein, N. (2008). J. Appl. Cryst. 41, 641-643.
55. Szarecka, A., Lesnock, K. R., Ramirez-Mondragon, C. A., Nicholas, H. B. Jr & Wymore, T. (2011). Protein Eng. Des. Sel. 24, 801-809.
56. Thomas, V. L., McReynolds, A. C. & Shoichet, B. K. (2010). J. Mol. Biol. 396, 47-59.
57. Tian, G.-B., Adams-Haduch, J. M., Taracila, M., Bonomo, R. A., Wang, H.-N. & Doi, Y. (2011). Antimicrob. Agents Chemother. 55, 4922-4925.
58. Tripathi, R. & Nair, N. N. (2013). J. Am. Chem. Soc. 135, 14679-14690.
59. Usher, K. C., Blaszczak, L. C., Weston, G. S., Shoichet, B. K. & Remington, S. J. (1998). Biochemistry, 37, 16082-16092.
60. Winn, M. D. et al. (2011). Acta Cryst. D67, 235-242.
61. Zhao, W.-H. & Hu, Z.-Q. (2012). Crit. Rev. Microbiol. 38, 30-51.