The basis for carbapenem hydrolysis by class a β-lactamases: A combined investigation using crystallography and simulations

Journal of the American Chemical Society

Volumn 134, Issue 44, 2012, Pages 18275-18285

  Fonseca, Fátima ^a,b   Chudyk, Ewa I ^c   Van Der Kamp, Marc W ^c   Correia, António ^b   Mulholland, Adrian J ^c   Spencer, James ^a  

^a UNIVERSITY OF BRISTOL   (United Kingdom)

^b UNIVERSITY OF AVEIRO   (Portugal)

^c UNIVERSITY OF BRISTOL   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ACTIVE SITE; ACYL-ENZYME COMPLEX; CARBAPENEMS; CLASS A; DEACYLATION; GRAM-NEGATIVE BACTERIA; KEY RESIDUES; LACTAMASES; MEROPENEM; MODE OF BINDING; MOLECULAR DYNAMICS SIMULATIONS; SERRATIA; STRUCTURAL COMPARISON; WATER MOLECULE; WILD TYPES;

BACTERIA; CRYSTALLOGRAPHY; HYDROLYSIS; MOLECULAR DYNAMICS; MOLECULES;

ENZYMES;

BETA LACTAMASE; CARBAPENEM; MEROPENEM; WATER;

ARTICLE; CRYSTAL STRUCTURE; CRYSTALLOGRAPHY; DRUG HYDROLYSIS; ENZYME BINDING; ENZYME STRUCTURE; MICHAELIS CONSTANT; MOLECULAR DYNAMICS; NONHUMAN; PROTEIN INTERACTION; SERRATIA; SIMULATION;

BETA-LACTAMASES; CARBAPENEMS; CATALYTIC DOMAIN; CRYSTALLOGRAPHY, X-RAY; HYDROLYSIS; MOLECULAR DYNAMICS SIMULATION; POINT MUTATION; SERRATIA; SERRATIA INFECTIONS;

EID: 84868571211     PISSN: 00027863     EISSN: 15205126     Source Type: Journal    
DOI: 10.1021/ja304460j     Document Type: Article

References (75)

1. Nicolau, D. P. Expert Opinion on Pharmacotherapy 2008, 9, 23
2. Papp-Wallace, K. M.; Endimiani, A.; Taracila, M. A.; Bonomo, R. A. Antimicrob. Agents Chemother. 2011, 55, 4943
3. Masterton, R. G. Int. J. Antimicrob. Agents 2009, 33, 105
4. Fisher, J. F.; Meroueh, S. O.; Mobashery, S. Chem. Rev. 2005, 105, 395
5. Pfeifer, Y.; Cullik, A.; Witte, W. Int. J. Med. Microbiol. 2010, 300, 371
6. Walsh, T. R. Int. J. Antimicrob. Agents 2010, 36, S8
7. Ambler, R. P. Philos. Trans. R. Soc. London, Ser. B: Biol. Sci. 1980, 289, 321
8. Patel, G.; Bonomo, R. A. Expert Rev. Anti Infect. Ther. 2011, 9, 555
9. Rasmussen, B. A.; Bush, K.; Keeney, D.; Yang, Y.; Hare, R.; O'Gara, C.; Medeiros, A. A. Antimicrob. Agents Chemother. 1996, 40, 2080
10. Naas, T.; Nordmann, P. Proc. Natl. Acad. Sci. U. S. A. 1994, 91, 7693
11. Mariotte-Boyer, S.; Nicolas-Chanoine, M. H.; Labia, R. FEMS Microbiol. Lett. 1996, 143, 29
12. Naas, T.; Vandel, L.; Sougakoff, W.; Livermore, D. M.; Nordmann, P. Antimicrob. Agents Chemother. 1994, 38, 1262
13. Yigit, H.; Queenan, A. M.; Anderson, G. J.; Domenech-Sanchez, A.; Biddle, J. W.; Steward, C. D.; Alberti, S.; Bush, K.; Tenover, F. C. Antimicrob. Agents Chemother. 2001, 45, 1151
14. Henriques, I.; Moura, A.; Alves, A.; M.J., S.; Correia, A. Antimicrob. Agents Chemother. 2004, 48, 2321
15. Bae, I. K.; Lee, Y. N.; Jeong, S. H.; Hong, S. G.; Lee, J. H.; Lee, S. H.; Kim, H. J.; Youn, H. Diagn. Microbiol. Infect. Dis. 2007, 58, 465
16. Bonnin, R. A.; Nordmann, P.; Potron, A.; Lecuyer, H.; Zahar, J. R.; Poirel, L. Antimicrob. Agents Chemother. 2011, 55, 349
17. Kotsakis, S. D.; Miriagou, V.; Tzelepi, E.; Tzouvelekis, L. S. Antimicrob. Agents Chemother. 2010, 54, 4864
18. Poirel, L.; Weldhagen, G. F.; Naas, T.; De Champs, C.; Dove, M. G.; Nordmann, P. Antimicrob. Agents Chemother. 2001, 45, 2598
19. Vourli, S.; Giakkoupi, P.; Miriagou, V.; Tzelepi, E.; Vatopoulos, A. C.; Tzouvelekis, L. S. FEMS Microbiol. Lett. 2004, 234, 209
20. Wachino, J.; Doi, Y.; Yamane, K.; Shibata, N.; Yagi, T.; Kubota, T.; Arakawa, Y. Antimicrob. Agents Chemother. 2004, 48, 2905
21. Nordmann, P.; Cuzon, G.; Naas, T. Lancet Infect. Dis. 2009, 9, 228
22. Perez, F.; Endimiani, A.; Hujer, K. M.; Bonomo, R. A. Curr. Opin. Pharmacol. 2007, 7, 459
23. Wang, F.; Cassidy, C.; Sacchettini, J. C. Antimicrob. Agents Chemother. 2006, 50, 2762
24. Nukaga, M.; Bethel, C. R.; Thomson, J. M.; Hujer, A. M.; Distler, A.; Anderson, V. E.; Knox, J. R.; Bonomo, R. A. J. Am. Chem. Soc. 2008, 130, 12656
25. Maveyraud, L.; Mourey, L.; Kotra, L. P.; Pedelacq, J. D.; Guillet, V.; Mobashery, S.; Samama, J. P. J. Am. Chem. Soc. 1998, 120, 9748
26. Zafaralla, G.; Mobashery, S. J. Am. Chem. Soc. 1992, 114, 1505
27. Bethel, C. R.; Taracila, M.; Shyr, T.; Thomson, J. M.; Distler, A. M.; Hujer, K. M.; Hujer, A. M.; Endimiani, A.; Papp-Wallace, K.; Bonnet, R.; Bonomo, R. A. Antimicrob. Agents Chemother. 2011, 55, 3465
28. Kalp, M.; Carey, P. R. Biochemistry 2008, 47, 11830
29. Swaren, P.; Maveyraud, L.; Raquet, X.; Cabantous, S.; Duez, C.; Pedelacq, J. D.; Mariotte-Boyer, S.; Mourey, L.; Labia, R.; Nicolas-Chanoine, M. H.; Nordmann, P.; Frere, J. M.; Samama, J. P. J. Biol. Chem. 1998, 273, 26714
30. Ke, W.; Bethel, C. R.; Thomson, J. M.; Bonomo, R. A.; van den Akker, F. Biochemistry 2007, 46, 5732
31. Sougakoff, W.; L'Hermite, G.; Pernot, L.; Naas, T.; Guillet, V.; Nordmann, P.; Jarlier, V.; Delettre, J. Acta Crystallogr., Sect. D: Biol. Crystallogr. 2002, 58, 267
32. Petrella, S.; Ziental-Gelus, N.; Mayer, C.; Renard, M.; Jarlier, V.; Sougakoff, W. Antimicrob. Agents Chemother. 2008, 52, 3725
33. Frase, H.; Shi, Q.; Testero, S. A.; Mobashery, S.; Vakulenko, S. B. J. Biol. Chem. 2009, 284, 29509
34. Majiduddin, F. K.; Palzkill, T. Antimicrob. Agents Chemother. 2003, 47, 1062
35. Majiduddin, F. K.; Palzkill, T. Antimicrob. Agents Chemother. 2005, 49, 3421
36. Papp-Wallace, K. M.; Taracila, M.; Hornick, J. M.; Hujer, A. M.; Hujer, K. M.; Distler, A. M.; Endimiani, A.; Bonomo, R. A. Antimicrob. Agents Chemother. 2010, 54, 2867
37. Papp-Wallace, K. M.; Taracila, M.; Wallace, C. J.; Hujer, K. M.; Bethel, C. R.; Hornick, J. M.; Bonomo, R. A. Protein Sci. 2010, 19, 1714
38. Pfyffer, G. E. Eur. J. Clin. Microbiol. Infect. Dis. 1992, 11, 199
39. Fonseca, F.; Sarmento, A. C.; Henriques, I.; Samyn, B.; van Beeumen, J.; Domingues, P.; Domingues, M. R.; Saavedra, M. J.; Correia, A. Antimicrob. Agents Chemother. 2007, 51, 4512
40. Saavedra, M. J.; Peixe, L.; Sousa, J. C.; Henriques, I.; Alves, A.; Correia, A. Antimicrob. Agents Chemother. 2003, 47, 2330
41. Fonseca, F.; Arthur, C. J.; Bromley, E. H.; Samyn, B.; Moerman, P.; Saavedra, M. J.; Correia, A.; Spencer, J. Antimicrob. Agents Chemother. 2011, 55, 5392
42. Fonseca, F.; Bromley, E. H.; Saavedra, M. J.; Correia, A.; Spencer, J. J. Mol. Biol. 2011, 411, 951
43. Papp-Wallace, K. M.; Bethel, C. R.; Distler, A. M.; Kasuboski, C.; Taracila, M.; Bonomo, R. A. Antimicrob. Agents Chemother. 2010, 54, 890
44. Yigit, H.; Queenan, A. M.; Rasheed, J. K.; Biddle, J. W.; Domenech-Sanchez, A.; Alberti, S.; Bush, K.; Tenover, F. C. Antimicrob. Agents Chemother. 2003, 47, 3881
45. Strynadka, N. C.; Adachi, H.; Jensen, S. E.; Johns, K.; Sielecki, A.; Betzel, C.; Sutoh, K.; James, M. N. Nature 1992, 359, 700
46. Adachi, H.; Ohta, T.; Matsuzawa, H. J. Biol. Chem. 1991, 266, 3186
47. Hermann, J. C.; Ridder, L.; Höltje, L. D.; Mulholland, A. J. Org. Biomol. Chem. 2006, 4, 206
48. Otwinowski, Z.; Minor, W. Methods Enzymol. 1997, 276, 307
49. Leslie, A. G. W. Joint CCP4 + ESF-EAMCB Newsletter on Protein Crystallography 1992, 26, 27
50. Evans, P. R. Acta Crystallogr., Sect. D: Biol. Crystallogr. 2005, 62, 72
51. McCoy, A. J.; Grosse-Kunstleve, R. W.; Adams, P. D.; Winn, M. D.; Storoni, L. C.; Read, R. J. J. Appl. Crystallogr. 2007, 40, 658
52. Emsley, P.; Lohkamp, B.; Scott, W. G.; Cowtan, K. Acta Crystallogr., Sect. D: Biol. Crystallogr. 2010, 66, 486
53. Murshudov, G. N.; Vagin, A. A.; Dodson, E. J. Acta Crystallogr., Sect. D: Biol. Crystallogr. 1997, 53, 240
54. Sheldrick, G. M. Acta Crystallogr., Sect. A 2008, 64, 112
55. Chen, V. B.; Arendall, W. B., 3rd; Headd, J. J.; Keedy, D. A.; Immormino, R. M.; Kapral, G. J.; Murray, L. W.; Richardson, J. S.; Richardson, D. C. Acta Crystallogr., Sect. D: Biol. Crystallogr. 2010, 66, 12
56. Laskowski, R. A.; MacArthur, M. W.; Moss, D. S.; Thornton, J. M. J. Appl. Crystallogr. 1993, 26, 283
57. Case, D. A.; Darden, T. A.; Cheatham, III, T. E.; Simmerling, C. L.; Wang, J.; Duke, R. E.; Luo, R.; Walker, R. C.; Zhang, W.; Merz, K. M.; Roberts, B.; Wang, B.; Hayik, S.; Roitberg, A.; Seabra, G.; Kolossváry, I.; Wong, K. F.; Paesani, F.; Vanicek, J.; Liu, J.; Wu, X.; Brozell, S. R.; Steinbrecher, T.; Gohlke, H.; Cai, Q.; Ye, X.; Wang, J.; Hsieh, M.-J.; Cui, G.; Roe, D. R.; Mathews, D. H.; Seetin, M. G.; Sagui, C.; Babin, V.; Luchko, T.; Gusarov, S.; Kovalenko, A.; Kollman, P. A.; AMBER 11; University of California, San Francisco, 2010.
58. Hornak, V.; Abel, R.; Okur, A.; Strockbine, B.; Roitberg, A.; Simmerling, C. Proteins 2006, 65, 712
59. Wang, J.; Wolf, R. M.; Caldwell, J. W.; Kollman, P. A.; Case, D. A. J. Comput. Chem. 2004, 25, 1157
60. Leyssene, D.; Delmas, J.; Robin, F.; Cougnoux, A.; Gibold, L.; Bonnet, R. Antimicrob. Agents Chemother. 2011, 55, 5660
61. Beadle, B. M.; Trehan, I.; Focia, P. J.; Shoichet, B. K. Structure 2002, 10, 413
62. Shimamura, T.; Ibuka, A.; Fushinobu, S.; Wakagi, T.; Ishiguro, M.; Ishii, Y.; Matsuzawa, H. J. Biol. Chem. 2002, 277, 46601
63. Tremblay, L. W.; Xu, H.; Blanchard, J. S. Biochemistry 2010, 49, 9685
64. Hermann, J. C.; Hensen, C.; Ridder, L.; Mulholland, A. J.; Höltje, L. D. J. Am. Chem. Soc. 2005, 127, 4454
65. Hermann, J. C.; Ridder, L.; Mulholland, A. J.; Höltje, L. D. J. Am. Chem. Soc. 2003, 125, 9590
66. Wang, X.; Minasov, G.; Shoichet, B. K. Proteins 2002, 47, 86
67. Hugonnet, J. E.; Tremblay, L. W.; Boshoff, H. I.; Barry, C. E., 3rd; Blanchard, J. S. Science 2009, 323, 1215
68. Tremblay, L. W.; Fan, F.; Blanchard, J. S. Biochemistry 2010, 49, 3766
69. Krissinel, E.; Henrick, K. Acta Crystallogr., Sect. D: Biol. Crystallogr. 2004, 60, 2256
70. Dundas, J.; Ouyang, Z.; Tseng, J.; Binkowski, A.; Turpaz, Y.; Liang, J. Nucleic Acids Res. 2006, 34, W116
71. Stec, B.; Holtz, K. M.; Wojciechowski, C. L.; Kantrowitz, E. R. Acta Crystallogr., Sect. D: Biol. Crystallogr. 2005, 61, 1072
72. Nukaga, M.; Mayama, K.; Hujer, A. M.; Bonomo, R. A.; Knox, J. R. J. Mol. Biol. 2003, 328, 289
73. Chen, Y.; Bonnet, R.; Shoichet, B. K. J. Am. Chem. Soc. 2007, 129, 5378
74. Fonze, E.; Vanhove, M.; Dive, G.; Sauvage, E.; Frere, J. M.; Charlier, P. Biochemistry 2002, 41, 1877
75. Mourey, L.; Miyashita, K.; Swaren, P.; Bulychev, A.; Samama, J. P.; Mobashery, S. J. Am. Chem. Soc. 1998, 120, 9382