Role of non-active-site residue Trp-93 in the function and stability of New Delhi metallo-β-lactamase 1

Antimicrobial Agents and Chemotherapy

Volumn 60, Issue 1, 2016, Pages 356-360

  Khan, Asad U ^a   Rehman, M Tabish ^a  

^a ALIGARH MUSLIM UNIVERSITY   (India)

Author keywords

[No Author keywords available]

Indexed keywords

ALANINE; AMINO ACID; AMPICILLIN; ASPARTIC ACID; AZTREONAM; CEFOTAXIME; CEFOXITIN; CEFTAZIDIME; GLUTAMINE; HYDROGEN; IMIPENEM; LEUCINE; MEROPENEM; METALLO BETA LACTAMASE; NEW DELHI METALLO BETA LACTAMASE 1; NITROCEFIN; SERINE; TRYPTOPHAN; UNCLASSIFIED DRUG; VALINE; ANTIINFECTIVE AGENT; BETA LACTAM; BETA LACTAMASE; BETA-LACTAMASE NDM-1; RECOMBINANT PROTEIN;

AFFINITY CHROMATOGRAPHY; ALPHA HELIX; AMINO ACID SUBSTITUTION; ANIMAL CELL; ARTICLE; BACTERIAL STRAIN; BIOCHEMICAL ANALYSIS; CATALYTIC EFFICIENCY; CIRCULAR DICHROISM; CONTROLLED STUDY; DENATURATION; DRUG DETERMINATION; ENTEROBACTER CLOACAE; GENE MUTATION; HEAT; HYDROGEN BOND; HYDROLYSIS; HYDROPHOBICITY; MICROBIOLOGICAL EXAMINATION; MINIMUM INHIBITORY CONCENTRATION; MUTANT; NONHUMAN; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; PROTEIN EXPRESSION; PROTEIN FUNCTION; PROTEIN STABILITY; PROTEIN STRUCTURE; SITE DIRECTED MUTAGENESIS; THERMOSTABILITY; ULTRAVIOLET SPECTROSCOPY; WILD TYPE; BIOCATALYSIS; CHEMICAL PHENOMENA; CHEMISTRY; ENZYME STABILITY; ENZYMOLOGY; ESCHERICHIA COLI; GENE EXPRESSION; GENETICS; KINETICS; METABOLISM; MOLECULAR CLONING; MOLECULAR MODEL; MUTATION; PROTEIN SECONDARY STRUCTURE; PROTEIN TERTIARY STRUCTURE; STRUCTURE ACTIVITY RELATION; THERMODYNAMICS;

ALANINE; ANTI-BACTERIAL AGENTS; BETA-LACTAMASES; BETA-LACTAMS; BIOCATALYSIS; CLONING, MOLECULAR; ENTEROBACTER CLOACAE; ENZYME STABILITY; ESCHERICHIA COLI; GENE EXPRESSION; HYDROGEN BONDING; HYDROLYSIS; HYDROPHOBIC AND HYDROPHILIC INTERACTIONS; KINETICS; MODELS, MOLECULAR; MUTATION; PROTEIN STRUCTURE, SECONDARY; PROTEIN STRUCTURE, TERTIARY; RECOMBINANT PROTEINS; STRUCTURE-ACTIVITY RELATIONSHIP; THERMODYNAMICS; TRYPTOPHAN;

EID: 84957885866     PISSN: 00664804     EISSN: 10986596     Source Type: Journal    
DOI: 10.1128/AAC.01194-15     Document Type: Article

References (26)

1. Khan AU, Nordmann P. 2012. NDM-1-producing Enterobacter cloacae and Klebsiella pneumoniae from diabetic foot ulcers in India. J Med Microbiol 61:454-456. http://dx.doi.org/10.1099/jmm.0.039008-0.
2. Yong D, Toleman MA, Giske CG, Cho HS, Sundman K, Lee K, Walsh TR. 2009. Characterization of a new metallo-β-lactamase gene, blaNDM-1 , and a novel erythromycin esterase gene carried on a unique genetic structure in Klebsiella pneumoniae sequence type 14 from India. Antimicrob Agents Chemother 53:5046-5054. http://dx.doi.org/10.1128/AAC.00774-09.
3. Patel G, Bonomo RA. 2013. "Stormy waters ahead": global emergence of carbapenemases. Front Microbiol 4:48.
4. Ambler RP, Coulson AF, Frere JM, Ghuysen JM, Joris B, Forsman M, Levesque RC, Tiraby G, Waley SG. 1991. A standard numbering scheme for the class A β-lactamases. Biochem J 276:269-270.
5. Bush K, Jacoby GA, Medeiros AA. 1995. A functional classification scheme for beta-lactamases and its correlation with molecular structure. Antimicrob Agents Chemother 39:1211-1233. http://dx.doi.org/10.1128/AAC.39.6.1211.
6. Green VL, Verma A, Owens RJ, Phillips SE, Carr SB. 2011. Structure of New Delhi metallo-β-lactamase 1 (NDM-1). Acta Crystallogr Sect F 67: 1160-1164. http://dx.doi.org/10.1107/S1744309111029654.
7. Kim Y, Cunningham MA, Mire J, Tesar C, Sacchettini J, Joachimiak A. 2013. NDM-1, the ultimate promiscuous enzyme: substrate recognition and catalytic mechanism. FASEB J 27:1917-1927. http://dx.doi.org/10.1096/fj.12-224014.
8. Chen J, Chen H, Shi Y, Hu F, Lao X, Gao X, Zheng H, Yao W. 2013. Probing the effect of the non-active site mutation Y229W in New Delhi metallo-β-lactamase by site-directed mutagenesis, kinetic studies, and molecular dynamics simulation. PLoS One 8:e82080. http://dx.doi.org/10.1371/journal.pone.0082080.
9. Bebrone C, Delbruck H, Kupper MB, Schlomer P, Willmann C, Frere JM, Fischer R, Galleni M, Hoffmann KMV. 2009. The structure of the di-zinc subclass B2 metallo-β-lactamase CphA reveals that the second inhibitory zinc ion binds in the histidine site. Antimicrob Agents Chemother 53:4464-4471. http://dx.doi.org/10.1128/AAC.00288-09.
10. Shakil S, Khan AU. 2010. Infected foot ulcers in male and female diabetic patients: a clinico-bioinformative study. Ann Clin Microbiol Antimicrob 9:2. http://dx.doi.org/10.1186/1476-0711-9-2.
11. Shakil S, Akram M, Ali SM, Khan AU. 2010. Acquisition of extended-spectrum beta-lactamase producing Escherichia coli strains in male and female infants admitted to a neonatal intensive care unit: molecular epidemiology and analysis of risk factors. J Med Microbiol 59:948-954. http://dx.doi.org/10.1099/jmm.0.020214-0.
12. Shen B, Yu Y, Chen H, Cao X, Lao X, Fang Y, Shi Y, Chen J, Zheng H. 2013. Inhibitor discovery of full-length New Delhi metallo-β-lactamase-1 (NDM-1). PLoS One 8:e62955. http://dx.doi.org/10.1371/journal.pone.0062955.
13. Hunt JB, Neece SH, Ginsburg A. 1985. The use of 4-(2-pyridylazo) resorcinol in studies of zinc release from Escherichia coli aspartate transcarbamoylase. Anal Biochem 146:150-157. http://dx.doi.org/10.1016/0003-2697(85)90409-9.
14. Clinical and Laboratory Standards Institute. 2014. Performance standards for antimicrobial susceptibility testing: 21st informational supplement. M100-S24. CLSI, Wayne, PA.
15. Andrews JM. 2001. Determination of minimum inhibitory concentrations. J Antimicrob Chemother 48(Suppl 1):5-16. http://dx.doi.org/10.1093/jac/48.suppl-1.5.
16. Makena A, Brem J, Pfeffer I, Geffen RE, Wilkins SE, Tarhonskaya H, Flashman E, Phee LM, Wareham DW, Schofield CJ. 2015. Biochemical characterization of New Delhi metallo-β-lactamase variants reveals differences in protein stability. J Antimicrob Chemother 70:463-469. http://dx.doi.org/10.1093/jac/dku403.
17. Chen YH, Yang JT, Martinez HM. 1972. Determination of the secondary structures of proteins by circular dichroism and optical rotatory dispersion. Biochemistry 11:4120-4131. http://dx.doi.org/10.1021/bi00772a015.
18. Kather I, Jakob RP, Dobbek H, Schmid FX. 2008. Increased folding stability of TEM-1 β-lactamase by in vitro selection. J Mol Biol 383:238-251. http://dx.doi.org/10.1016/j.jmb.2008.07.082.
19. Robertson AD, Murphy KP. 1997. Protein structure and the energetics of protein stability. Chem Rev 97:1251-1267. http://dx.doi.org/10.1021/cr960383c.
20. Yadav S, Ahmad F. 2000. A new method for the determination of stability parameters of proteins from their heat-induced denaturation curves. Anal Biochem 283:207-213. http://dx.doi.org/10.1006/abio.2000.4641.
21. Zhu K, Lu J, Liang Z, Kong X, Ye F, Jin L, Geng H, Chen Y, Zheng M, Jiang H, Li JQ, Luo C. 2013. A quantum mechanics/molecular mechanics study on the hydrolysis mechanism of New Delhi metallo-β-lactamase-1. J Comput Aid Mol Des 27:247-256. http://dx.doi.org/10.1007/s10822-012-9630-6.
22. Nordmann P, Baulanger AE, Poirel L. 2012. NDM-4 metallo-βlactamase with increased carbapenemase activity from Escherichia coli. Antimicrob Agents Chemother 56:2184-2186. http://dx.doi.org/10.1128/AAC.05961-11.
23. Hornsey M, Phee L, Warcham DW. 2011. A novel variant, NDM-5, of the New Delhi metallo-β-lactamase in a multidrug-resistant Escherichia coli ST648 isolate recovered from a patient in the United Kingdom. Antimicrob Agents Chemother 55:5952-5954. http://dx.doi.org/10.1128/AAC.05108-11.
24. Zhang HM, Hao Q. 2011. Crystal structure of NDM-1 reveals a common β-lactam hydrolysis mechanism. FASEB J 25:2574-2582. http://dx.doi.org/10.1096/fj.11-184036.
25. King DT, Worrall LJ, Gruninger R, Strynadka NCJ. 2012. New Delhi metallo-β-lactamase: structural insights into β-lactam recognition and inhibition. J Am Chem Soc 134:11362-11365. http://dx.doi.org/10.1021/ja303579d.
26. Feng H, Ding J, Zhu D, Liu X, Xu X, Zhang Y, Zang S, Wang DC, Liu W. 2014. Structural and mechanistic insights into NDM-1 catalyzed hydrolysis of cephalosporins. J Am Chem Soc 136:14694-14697. http://dx.doi.org/10.1021/ja508388e.