Computational analysis of pathogen-borne metallo β-lactamases reveals discriminating structural features between B1 types

BMC Research Notes

Volumn 5, Issue , 2012, Pages

  Cadag, Eithon ^a   Vitalis, Elizabeth ^a   Lennox, Kristin P ^a   Zhou, Carol ^a   Zemla, Adam T ^a  

^a LAWRENCE LIVERMORE NATIONAL LABORATORY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIA (MICROORGANISMS); ENTEROBACTERIACEAE;

EID: 84857023787     PISSN: None     EISSN: 17560500     Source Type: Journal    
DOI: 10.1186/1756-0500-5-96     Document Type: Article

References (50)

1. Novel acquired metallo-beta-lactamase gene, bla(sim-1), in a class 1 integron from acinetobacter baumannii clinical isolates from Korea. Lee K, Yum JH, Yong D, Lee HM, Kim HD, Docquier J-D, Rossolini GM, Chong Y, Antimicrob Agents Chemother 2005 49 11 4485 4491 10.1128/AAC.49.11.4485-4491.2005 16251286 (Pubitemid 41552576)
2. Characterization of a new metallo-beta-lactamase gene, blaNDM-1, and a novel erythromycin esterase gene carried on a unique genetic structure in Klebsiella pneumoniae sequence type 14 from India. Yong D, Toleman MA, Giske CG, Cho HS, Sundman K, Lee K, Walsh TR, Antimicrob Agents Chemother 2009 53 12 5046 5054 10.1128/AAC.00774-09 19770275
3. Carbapenem-non-susceptible enterobacteriaceae in Europe: conclusions from a meeting of national experts. Grundmann H, Livermore DM, Giske CG, Canton R, Rossolini GM, Campos J, Vatopoulos A, Gniadkowski M, Toth A, Pfeifer Y, Jarlier V, Carmeli Y, CNSE Working Group, Euro Surveill 2010 15 46 1 13
4. Emergence of a new antibiotic resistance mechanism in India, Pakistan, and the UK: a molecular, biological, and epidemiological study. Kumarasamy KK, Toleman MA, Walsh TR, Bagaria J, Butt F, Balakrishnan R, Chaudhary U, Doumith M, Giske CG, Irfan S, Krishnan P, Kumar AV, Maharjan S, Mushtaq S, Noorie T, Paterson DL, Pearson A, Perry C, Pike R, Rao B, Ray U, Sarma JB, Sharma M, Sheridan E, Thirunarayan MA, Turton J, Upadhyay S, Warner M, Welfare W, Livermore DM, Woodford N, Lancet Infect Dis 2010 10 9 597 602 10.1016/S1473-3099(10)70143-2 20705517
5. New Delhi metallo-Beta-lactamase in Klebsiella pneumoniae and Escherichia coli Canada. Mulvey MR, Grant JM, Plewes K, Roscoe D, Boyd DA, Emerg Infect Dis 2011 17 1 103 106 21192866
6. NDM-1 producing Klebsiella pneumoniae isolated in the Sultanate of Oman. Poirel L, Al∼Maskari Z, Al∼Rashdi F, Bernabeu S, Nordmann P, J Antimicrob Chemother 2010 66 2 304 306 21098539
7. Emergence of metallo-beta-lactamase NDM-1 producing multidrug-resistant escherichia coli in Australia. Poirel L, Lagrutta E, Taylor P, Pham J, Nordmann P, Antimicrob Agents Chemother 2010 54 11 4914 4916 10.1128/AAC.00878-10 20823289
8. Detection of ndm-1-producing klebsiella pneumoniae in Kenya. Poirel L, Revathi G, Bernabeu S, Nordmann P, Antimicrob Agents Chemother 2010 55 2 934 936 21115785
9. Detection of Enterobacteriaceae isolates carrying metallo-beta-lactamase - United States, 2010. CDC Morbidity and Mortality Weekly Report 2010 59 750
10. Infrastructure for the life sciences: design and implementation of the UniProt website. Jain E, Bairoch A, Duvaud S, Phan I, Redashi N, Suzek BE, Martin MJ, McGarvey P, Gasteiger E, BMC Bioinf 2009 10 136 10.1186/1471-2105-10- 136
11. Extremely drug-resistant citrobacter freundii isolate producing NDM-1 and other carbapenemases identified in a patient returning from India. Poirel L, Ros A, Carricajo A, Berthelot P, Pozzetto B, Bernabeu S, Nordmann P, Antimicrob Agents Chemother 2011 55 1 447 448 10.1128/AAC.01305-10 20974865
12. Spread of integron-associated vim-type metallo-beta-lactamase genes among imipenem-nonsusceptible pseudomonas aeruginosa strains in greek hospitals. Giakkoupi P, Petrikkos G, Tzouvelekis LS, Tsonas S, Legakis NJ, Vatopoulos AC, WHONET Greece Study Group, J Clin Microbiol 2003 41 2 822 825 10.1128/JCM.41.2.822-825.2003 12574292 (Pubitemid 36184206)
13. Vim-4 in a carbapenem-resistant strain of pseudomonas aeruginosa isolated in Sweden. Giske CG, Rylander M, Kronvall G, Antimicrob Agents Chemother 2003 47 9 3034 3035 10.1128/AAC.47.9.3034-3035.2003 12937022 (Pubitemid 37040296)
14. Metallo-beta-lactamases: the quiet before the storm? Walsh TR, Toleman MA, Poirel L, Nordmann P, Clin Microbiol Rev 2005 18 2 306 325 10.1128/CMR.18.2.306-325.2005 15831827 (Pubitemid 40548296)
15. Metallo-beta-lactamases in clinical pseudomonas isolates in Taiwan and identification of vim-3, a novel variant of the vim-2 enzyme. Yan JJ, Hsueh PR, Ko WC, Luh KT, Tsai SH, Wu HM, Wu JJ, Antimicrob Agents Chemother 2001 45 8 2224 2228 10.1128/AAC.45.8.2224-2228.2001 11451678 (Pubitemid 32664460)
16. Early dissemination of NDM-1 and OXA-181 producing Enterobacteriaceae in Indian hospitals: Report from the SENTRY antimicrobial surveillance program (2006-2007). Castanheira M, Deshpande LM, Mathai D, Bell JM, Jones RN, Mendes RE, Antimicrob Agents Chemother 2010 55 3 1274 1278 21189345
17. Update of the standard numbering scheme for class b beta-lactamases. Garau G, Garcia-Saez I, Bebrone C, Anne C, Mercuri P, Galleni M, Frere J-M, Dideberg O, Antimicrob Agents Chemother 2004 48 7 2347 2349 10.1128/AAC.48.7. 2347-2349.2004 15215079 (Pubitemid 38823395)
18. Updated functional classification of beta-lactamases. Bush K, Jacoby GA, Antimicrob Agents Chemother 2010 54 3 969 976 10.1128/AAC.01009-09 19995920
19. A functional classification scheme for beta-lactamases and its correlation with molecular structure. Bush K, Jacoby GA, Medeiros AA, Antimicrob Agents Chemother 1995 39 6 1211 1233 7574506
20. The mechanisms of catalysis by metallo beta-lactamases. Badarau A, Page M, Bioinorg Chem Appl 2008 576297 1 14
21. Metallo-beta-lactamases (classification, activity, genetic organization, structure, zinc coordination) and their superfamily. Bebrone C, Biochem Pharmacol 2007 74 12 1686 1701 10.1016/j.bcp.2007.05.021 17597585 (Pubitemid 350088675)
22. Molecular analysis of beta-lactamase structure and function. Majiduddin F, Materon I, Palzkill T, Int J Med Microb 2002 292 127 137 10.1078/1438-4221- 00198 (Pubitemid 34842183)
23. Crystal structure of NDM-1 reveals a common beta-lactamase hydrolysis mechanism. Zhang H, Hao Q, FASEB J 2011 25 8 2574 2582 10.1096/fj.11-184036 21507902
24. On the mechanism of the metallo-beta-lactamase from Bacteriodes fragilis. Wang Z, Fast W, Benkovic S, Biochemistry 1999 38 10013 10023 10.1021/bi990356r 10433708 (Pubitemid 29374954)
25. Analysis of the importance of the metallo-beta-lactamase active site loop in substrate binding and catalysis. Moali C, Anne C, Lamotte-Brasseur J, Groslambert S, Devreese B, Van Beeumen J, Galleni M, Frere JM, Chem Biol 2003 10 4 319 329 10.1016/S1074-5521(03)00070-X 12725860 (Pubitemid 36516650)
26. Role of a solvent- exposed tryptophan in the recognition and binding of antibiotic substrates for a metallo-beta-lactamase. Huntley JJA, Fast W, Benkovic SJ, Wright PE, Dyson HJ, Protein Sci 2003 12 7 1368 1375 10.1110/ps.0305303 12824483 (Pubitemid 36759341)
27. Nmr characterization of the metallo-beta-lactamase from bacteroides fragilis and its interaction with a tight-binding inhibitor: role of an active-site loop. Scrofani SD, Chung J, Huntley JJ, Benkovic SJ, Wright PE, Dyson HJ, Biochemistry 1999 38 44 14507 14514 10.1021/bi990986t 10545172 (Pubitemid 29522088)
28. Mutational analysis of vim-2 reveals an essential determinant for metallo-beta-lactamase stability and folding. Borgianni L, Vandenameele J, Matagne A, Bini L, Bonomo RA, Frere J-M, Rossolini GM, Docquier J-D, Antimicrob Agents Chemother 2010 54 8 3197 3204 10.1128/AAC.01336-09 20498317
29. A structural view of the antibiotic degradation enzyme NDM-1 from a superbug. Guo Y, Niu G, Shui W, Zhou H, Zhang Y, Yang C, Lou Z, Rao Z, Protein Cell 2011 2 5 384 394 10.1007/s13238-011-1055-9 21637961
30. Crystal structure of New Delhi metallo-beta-lactamase (NDM-1) reveals molecular basis for antibiotic resistance. King D, Strynadka N, Protein Sci 2011 20 9 1484 1491 10.1002/pro.697 21774017
31. The Protein Data Bank. Berman HM, Battistuz T, Bhat TN, Bluhm WF, Bourne PE, Burkhardt K, Feng Z, Gilliland GL, Iype L, Jain S, Fagan P, Marvin J, Padilla D, Ravichandran V, Schneider B, Thanki N, Weissig H, Westbrook JD, Zardecki C, Acta Crystallogr D: Biol Crystallogr 2002 58 Pt 6 No 1 899 907 (Pubitemid 34653017)
32. StralSV - assessment of sequence variability within similar 3D structures and application to polio RNA-dependent RNA polymerase. Zemla A, Lang D, Kostova T, Andino R, Zhou C, BMC Bioinf 2011 12 226 10.1186/1471-2105-12-226
33. LGA - A method for finding 3 d similarities in protein structures. Zemla A, Nucleic Acids Res 2003 31 13 3370 3374 10.1093/nar/gkg571 12824330 (Pubitemid 37442162)
34. Stralcp - structure alignment-based clustering of proteins. Zemla A, Geisbrecht B, Smith J, Lam M, Kirkpatrick B, Wagner M, Slezak T, Zhou CE, Nucleic Acids Res 2007 35 22 150 10.1093/nar/gkm1049 18039711
35. Clustering protein environments for function prediction: finding PROSITE motifs in 3D. Yoon S, Ebert J, Chung E, Micheli G, Altman R, BMC Bioinf 2007 8 Suppl 4 10 10.1186/1471-2105-8-S4-S10 (Pubitemid 351833827)
36. Anatomy of protein pockets and cavities: measurement of binding site geometry and implications for ligand design. Liang J, Edelsbrunner H, Woodward C, Protein Sci 1998 7 9 1884 1897 10.1002/pro.5560070905 9761470 (Pubitemid 28432430)
37. Systematic analysis of short internal indels and their impact on protein folding. Kim R, Guo J-T, BMC Struct Biol 2010 10 24 10.1186/1472-6807-10-24 20684774
38. Crystal structure of the imp-1 metallo beta-lactamase from pseudomonas aeruginosa and its complex with a mercaptocarboxylate inhibitor: binding determinants of a potent, broad-spectrum inhibitor. Concha NO, Janson CA, Rowling P, Pearson S, Cheever CA, Clarke BP, Lewis C, Galleni M, Frere JM, Payne DJ, Bateson JH, Abdel-Meguid SS, Biochemistry 2000 39 15 4288 4298 10.1021/bi992569m 10757977 (Pubitemid 30212644)
39. The PyMol molecular graphics system August 2010. Schrodinger LLC
40. Adaptive protein evolution grants organismal fitness by improving catalysis and flexibility. Tomatis P, Fabiane S, Simona F, Carloni P, Sutton B, Vila A, PNAS 2008 105 52 20605 20610 10.1073/pnas.0807989106 19098096
41. Antibiotic sensitization using biphenyl tetrazoles as potent inhibitors of Bacteroides fragilis metallo-beta-lactamse. Toney J, Fitzgerald P, Grover-Sharma N, Olson S, May W, Sundelof J, Vanderwall D, Cleary K, Grant S, Wu J, Kozarich J, Pompliano D, Hammond G, Chem Bio 1998 5 185 196 10.1016/S1074-5521(98)90632-9 (Pubitemid 28203049)
42. Crystallographic investigation of the inhibition mode of a VIM-2 metallo-beta-lactamase from Pseudomonas aeruginosa by a mercaptocarboxylate inhibitor. Yamaguchi Y, Jin W, Matsunaga K, Ikemizu S, Yamagata Y, Wachino J, Shibata N, Arakawa Y, Kurosaki H, J Med Chem 2007 50 6647 6653 10.1021/jm701031n 18052313 (Pubitemid 350309101)
43. Biochemical characterization of the Pseudomonas aeruginosa 101/1477 metallo-beta-lactamase IMP-1 produced by Escherichia coli. Laraki N, Franceschini N, Rossolini GM, Santucci P, Meunier C, de Pauw E, Amicosante G, Fre're JM, Galleni M, Antimicrob Agents Chemother 1999 43 902 906 10103197 (Pubitemid 29165755)
44. The other 90% of the protein: assessment beyond the C-alphas for CASP8 template-based and high-accuracy models. Keedy D, Williams C, Headd J, Arendall W, Chen V, Kapral G, Gillespie R, Block J, Zemla A, Richardson D, Richardson J, Prot Struct Func Bioinf 2009 77 29 49 10.1002/prot.22551
45. VMD - Visual molecular dynamics. Humphrey W, Dalke A, Schulten K, J Molec Graphics 1996 14 33 38 10.1016/0263-7855(96)00018-5 (Pubitemid 26152973)
46. Biochemical characterization of metallo-beta-lactamse VIM-11 from a Pseudomonas aeruginos clinical strain. Marchiaro P, Tomatis P, Mussi M, Pasteran A, Viale A, Limansky A, Vila A, Antimicrob Agents Chemother 2008 52 2250 2252 10.1128/AAC.01025-07 18362187 (Pubitemid 351758571)
47. Impact of remote mutations on metallo-beta-lactamase substrate specificity: implications for the evolution of antibiotic resistance. Oelschlaeger P, Mayo S, Pleiss J, Prot Sci 2005 14 3 765 774 10.1110/ps.041093405 (Pubitemid 40283915)
48. VIM-19, a metallo-beta-lactamase with increased carbapenemase activity from Escherichia coli and Klebsiella pneumoni. Rodriguez-Martinez J, Nordmann P, Fortineau N, Poirel L, Antimicrob Agents Chemother 2010 54 1 471 476 10.1128/AAC.00458-09 19917750
49. Crystal structure of pseudomonas aeruginosa spm-1 provides insights into variable zinc affinity of metallo-beta-lactamases. Murphy TA, Catto LE, Halford SE, Hadfield AT, Minor W, Walsh TR, Spencer J, J Mol Biol 2006 357 3 890 903 10.1016/j.jmb.2006.01.003 16460758
50. Bacterial resistance to beta-lactam antibiotics: compelling opportunism, compelling opportunity. Fisher J, Meroueh S, Mobashery S, Chem Rev 2005 104 2 395 424 (Pubitemid 40351628)