[en] Two laboratory mutants of NDM-1 were generated by replacing the isoleucine at position 35 with threonine and serine residues: the NDM-1(I35T)and NDM-1(I35S)enzymes. These mutants were well characterized, and their kinetic parameters were compared with those of the NDM-1 wild type. Thekcat,Km, andkcat/Kmvalues calculated for the two mutants were slightly different from those of the wild-type enzyme. Interestingly, thekcat/Kmof NDM-1(I35S)for loracarbef was about 14-fold higher than that of NDM-1. Far-UV circular dichroism (CD) spectra of NDM-1 and NDM-1(I35T)and NDM-1(I35S)enzymes suggest local structural rearrangements in the secondary structure with a marked reduction of alpha-helix content in the mutants.
Disciplines :
Biochemistry, biophysics & molecular biology
Author, co-author :
Marcoccia, Francesca
Bottoni, Carlo
Sabatini, Alessia
Colapietro, Martina
Mercuri, Paola ; Université de Liège > Département des sciences de la vie > Macromolécules biologiques
Galleni, Moreno ; Université de Liège > Département des sciences de la vie > Macromolécules biologiques
Kerff, Frédéric ; Université de Liège > Département des sciences de la vie > Centre d'ingénierie des protéines
Matagne, André ; Université de Liège > Département des sciences de la vie > Enzymologie et repliement des protéines
Celenza, Giuseppe
Amicosante, Gianfranco
Perilli, Mariagrazia
Language :
English
Title :
Kinetic Study of Laboratory Mutants of NDM-1 Metallo-beta-Lactamase and the Importance of an Isoleucine at Position 35.
Publication date :
2016
Journal title :
Antimicrobial Agents and Chemotherapy
ISSN :
0066-4804
eISSN :
1098-6596
Publisher :
American Society for Microbiology, Washington, United States - District of Columbia
Volume :
60
Issue :
4
Pages :
2366-72
Peer reviewed :
Peer Reviewed verified by ORBi
Commentary :
Copyright (c) 2016, American Society for Microbiology. All Rights Reserved.
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.
Carattoli A, Fortini D, Galetti R, Garcia-Fernandez A, Nardi G, Orazi D, Capone A, Majolino I, Proia A, Mariani B, Petrosillo N. 2013. Isolation of NDM-1-producing Pseudomonas aeruginosa sequence type ST235 from a stem cell transplant patient in Italy, May 2013. Euro Surveill 18: pii20633. http://dx.doi.org/10.2807/1560-7917. ES2013.18.46.20633.
Sartor AL, Raza MW, Abbasi SA, Day KM, Perry JD, Paterson DL, Sidjabat HE. 2014. Molecular epidemiology of NDM-1-producing Enterobacteriaceae and Acinetobacter baumannii isolates from Pakistan. Antimicrob Agents Chemother 58:5589-5593. http://dx.doi.org/10.1128/AAC.02425-14.
Olaitan AO, Diene SM, Gupta SK, Adler A, Assous MV, Rolain JM. 2014. Genome analysis of NDM-1 producing Morganella morganii clinical isolate. Expert Rev Anti Infect Ther 12:1297-1305. http://dx.doi.org/10.1586/14787210.2014.944504.
Berrazeg M, Diene S, Medjahed L, Parola P, Drissi M, Raoult D, Rolain J. 2014. New Delhi metallo-β-lactamase around the world: an eReview using Google maps. Euro Surveill 22: pii20809. http://dx.doi.org/10.280 7/1560-7917. ES2014.19.20.20809.
Johnson AP, Woodford N. 2013. Global spread of antibiotic resistance: the example of New Delhi metallo-β-lactamase (NDM)-mediated carbapenem resistance. J Med Microbiol 62:499-513. http://dx.doi.org/10.1099/jmm.0.052555-0.
Kutumbaka KK, Hans S, Mategko J, Nadala C, Buser GL, Cassidy MP, Beldavs ZG, Weissman SJ, Morey KE, Vega R, Samadpour M. 2014. Draft genome sequence of blaNDM-1-positive Escherichia coli O25b-ST131 clone isolated from an environmental sample. Genome Announc 2: pii:e00462-14. http://dx.doi.org/10.1128/genomeA.00462-14.
Bonnin RA, Poirel L, Carattoli A, Nordmann P. 2012. Characterization of an IncFII plasmid encoding NDM-1 from Escherichia coli ST131. PloS One 7:e34752. http://dx.doi.org/10.1371/journal.pone.0034752.
Dolejska M, Villa L, Poirel L, Nordmann P, Carattoli A. 2013. Complete sequencing of an IncHI1 plasmid encoding the carbapenemase NDM-1, the ArmA 16S RNA methylase and a resistance-nodulation-cell division/multidrug efflux pump. J Antimicrob Chemother 68:34-39. http://dx.doi.org/10.1093/jac/dks357.
Page MI, Badarau A. 2008. The mechanisms of catalysis by metallo betalactamases. Bioinorg Chem Appl 2008:576297. http://dx.doi.org/10.1155/2008/576297.
Thomas PW, Zheng M, Wu S, Guo H, Liu D, Xu D, Fast W. 2011. Characterization of purified New Delhi metallo-β-lactamase-1. Biochemistry 50:10102-10113. http://dx.doi.org/10.1021/bi201449r.
King D, Strynadka N. 2011. Crystal structure of New Delhi metallo-β-lactamase reveals molecular basis for antibiotic resistance. Protein Sci 20:1484-1491. http://dx.doi.org/10.1002/pro.697.
Zhang HO, Hau 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.
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.
Meini MR, Llarrull LI, Vila AJ. 2014. Evolution of metallo-betalactamases: trends revealed by natural diversity and in vitro evolution. Antibiotics 3:285-316. http://dx.doi.org/10.3390/antibiotics3030285.
Ho SN, Hunt HD, Horton RM, Pullen JK, Pease LR. 1989. Site-directed mutagenesis by overlap extension using a polymerase chain reaction. Gene 77:51-59. http://dx.doi.org/10.1016/0378-1119 (89) 90358-2.
Clinical and Laboratory Standards Institute. 2006. Methods for dilution antimicrobial susceptibility tests for bacteria that grow aerobically; approved standard.. Seventh edition. Document M7-A7, 26 (2). CLSI, Wayne, PA, USA.
Laemmli UK. 1970. Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature 227:680-685. http://dx.doi.org/10.1038/227680a0.
Bradford MM. 1976. A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal Biochem 72:248-254. http://dx.doi.org/10.1016/0003-2697 (76) 90527-3.
Segel IH. 1976. Biochemical calculations, 2nd ed, p 236-241. John Wiley & Sons, New York, NY.
De Meester F, Joris B, Reckinger G. 1987. Automated analysis of enzyme inactivation phenomena. Application to β-lactamases and DDpeptidases. Biochem Pharmacol 36:2393-2403.
Manavalan P, Johnson WC, Jr. 1987. Variable selection method improves the prediction of protein secondary structure from circular dichroism spectra. Anal Biochem 167:76-85. http://dx.doi.org/10.1016/0003-2697 (87) 90135-7.
Sreerama N, Woody RW. 2000. Estimation of protein secondary structure from circular dichroism spectra: comparison of CONTIN, SELCON, and CDSSTR methods with an expanded reference set. Anal Biochem 287:252-260. http://dx.doi.org/10.1006/abio.2000.4880.
Provencher SW, Glöckner J. 1981. Estimation of globular protein secondary structure from circular dichroism. Biochemistry 20:33-37. http://dx.doi.org/10.1021/bi00504a006.
Van Stokkum IH, Spoelder HJ, Bloemendal M, Van Grondelle R, Groen FC. 1990. Estimation of protein secondary structure and error analysis from circular dichroism spectra. Anal Biochem 191:110-118. http://dx.doi.org/10.1016/0003-2697 (90) 90396-Q.
Sreerama N, Woody RW. 1993. A self-consistent method for the analysis of protein secondary structure from circular dichroism. Anal Biochem 209:32-44. http://dx.doi.org/10.1006/abio.1993.1079.
Sreerama N, Venyaminov SY, Woody RW. 1999. Estimation of the number of alpha-helical and beta-strand segments in proteins using circular dichroism spectroscopy. Protein Sci 8:370-380.
Whitmore L, Wallace BA. 2004. DICHROWEB, an online server for protein secondary structure analyses from circular dichroism spectroscopic data. Nucleic Acids Res 32:W668-W673. http://dx.doi.org/10.1093/nar/gkh371.
Whitmore L, Wallace BA. 2008. Protein secondary structure analyses from circular dichroism spectroscopy: methods and reference databases. Biopolymers 89:392-400. http://dx.doi.org/10.1002/bip. 20853.
Feng H, Ding J, Zhu D, Liu X, Xu X, Zhang Y, 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.
Krieger E, Darden T, Nabuurs SB, Finkelstein A, Vriend G. 2004. Making optimal use of empirical energy functions: force-field parameterization in crystal space. Proteins 57:678-683. http://dx.doi.org/10.1002/prot.20251.
Krieger E, Joo K, Lee J, Raman S, Thompson J, Tyka M, Baker D, Karplus K. 2009. Improving physical realism, stereochemistry, and side-chain accuracy in homology modeling: four approaches that performed well in CASP8. Proteins 77:114-122. http://dx.doi.org/10.1002/prot.22570.
Essmann U, Perera L, Berkowitz ML, Darden T, Lee H, Pedersen LG. 1995. A smooth particle mesh Ewald method. J Chem Phys 103:8577. http://dx.doi.org/10.1063/1.470117.
Kim Y, Tesar C, Mire J, Jedrzejczak R, Binkowski A, Babnigg G, Sacchettini J, Joachimiak A. 2011. Structure of apo-and monometalated forms of NDM-1-A highly potent carbapenem-hydrolyzing metallo-β-lactamase. PloS One 6:e24621. http://dx.doi.org/10.1371/journal.pone.0024621.
