DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: Molecular Basis for the Catalytic Specificity of the CTX-M Extended-Spectrum β-Lactamases

Abstract

We report that extended-spectrum β-lactamases (ESBLs) pose a threat to public health because of their ability to confer resistance to extended-spectrum cephalosporins such as cefotaxime. The CTX-M β-lactamases are the most widespread ESBL enzymes among antibiotic resistant bacteria. Many of the active site residues are conserved between the CTX-M family and non-ESBL β-lactamases such as TEM-1, but the residues Ser237 and Arg276 are specific to the CTX-M family, suggesting that they may help to define the increased specificity for cefotaxime hydrolysis. To test this hypothesis, site-directed mutagenesis of these positions was performed in the CTX-M-14 β-lactamase. Substitutions of Ser237 and Arg276 with their TEM-1 counterparts, Ala237 and Asn276, had a modest effect on cefotaxime hydrolysis, as did removal of the Arg276 side chain in an R276A mutant. The S237A:R276N and S237A:R276A double mutants, however, exhibited 29- and 14-fold losses in catalytic efficiency for cefotaxime hydrolysis, respectively, while the catalytic efficiency for benzylpenicillin hydrolysis was unchanged. Therefore, together, the Ser237 and Arg276 residues are important contributors to the cefotaximase substrate profile of the enzyme. High-resolution crystal structures of the CTX-M-14 S70G, S70G:S237A, and S70G:S237A:R276A variants alone and in complex with cefotaxime show that residues Ser237 and Arg276 in the wild-type enzymemore » promote the expansion of the active site to accommodate cefotaxime and favor a conformation of cefotaxime that allows optimal contacts between the enzyme and substrate. In conclusion, the conservation of these residues, linked to their effects on structure and catalysis, imply that their coevolution is an important specificity determinant in the CTX-M family.« less

Authors:
 [1];  [2];  [1];  [3];  [4];  [5];  [1];  [6]
  1. Baylor College of Medicine, Houston, TX (United States). Verna and Marrs McLean Department of Biochemistry and Molecular Biology
  2. Baylor College of Medicine, Houston, TX (United States). Department of Molecular Virology and Microbiology
  3. Baylor College of Medicine, Houston, TX (United States). Department of Molecular Virology and Microbiology
  4. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
  5. Baylor College of Medicine, Houston, TX (United States). Verna and Marrs McLean Department of Biochemistry and Molecular Biology; Baylor College of Medicine, Houston, TX (United States). Department of Molecular Virology and Microbiology
  6. Baylor College of Medicine, Houston, TX (United States). Verna and Marrs McLean Dept. of Biochemistry and Molecular Biology; Baylor College of Medicine, Houston, TX (United States). Dept. of Molecular Virology and Microbiology; Baylor College of Medicine, Houston, TX (United States). Dept. of Pharmacology
Publication Date:
Research Org.:
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Basic Energy Sciences (BES)
OSTI Identifier:
1257352
Grant/Contract Number:  
AC02- 05CH11231; AI32956; Q1279; 1 R90 DA023418-03
Resource Type:
Accepted Manuscript
Journal Name:
Biochemistry
Additional Journal Information:
Journal Volume: 54; Journal Issue: 2; Journal ID: ISSN 0006-2960
Publisher:
American Chemical Society (ACS)
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Adamski, Carolyn J., Cardenas, Ana Maria, Brown, Nicholas G., Horton, Lori B., Sankaran, Banumathi, Prasad, B. V. Venkataram, Gilbert, Hiram F., and Palzkill, Timothy. Molecular Basis for the Catalytic Specificity of the CTX-M Extended-Spectrum β-Lactamases. United States: N. p., 2014. Web. doi:10.1021/bi501195g.
Adamski, Carolyn J., Cardenas, Ana Maria, Brown, Nicholas G., Horton, Lori B., Sankaran, Banumathi, Prasad, B. V. Venkataram, Gilbert, Hiram F., & Palzkill, Timothy. Molecular Basis for the Catalytic Specificity of the CTX-M Extended-Spectrum β-Lactamases. United States. https://doi.org/10.1021/bi501195g
Adamski, Carolyn J., Cardenas, Ana Maria, Brown, Nicholas G., Horton, Lori B., Sankaran, Banumathi, Prasad, B. V. Venkataram, Gilbert, Hiram F., and Palzkill, Timothy. Tue . "Molecular Basis for the Catalytic Specificity of the CTX-M Extended-Spectrum β-Lactamases". United States. https://doi.org/10.1021/bi501195g. https://www.osti.gov/servlets/purl/1257352.
@article{osti_1257352,
title = {Molecular Basis for the Catalytic Specificity of the CTX-M Extended-Spectrum β-Lactamases},
author = {Adamski, Carolyn J. and Cardenas, Ana Maria and Brown, Nicholas G. and Horton, Lori B. and Sankaran, Banumathi and Prasad, B. V. Venkataram and Gilbert, Hiram F. and Palzkill, Timothy},
abstractNote = {We report that extended-spectrum β-lactamases (ESBLs) pose a threat to public health because of their ability to confer resistance to extended-spectrum cephalosporins such as cefotaxime. The CTX-M β-lactamases are the most widespread ESBL enzymes among antibiotic resistant bacteria. Many of the active site residues are conserved between the CTX-M family and non-ESBL β-lactamases such as TEM-1, but the residues Ser237 and Arg276 are specific to the CTX-M family, suggesting that they may help to define the increased specificity for cefotaxime hydrolysis. To test this hypothesis, site-directed mutagenesis of these positions was performed in the CTX-M-14 β-lactamase. Substitutions of Ser237 and Arg276 with their TEM-1 counterparts, Ala237 and Asn276, had a modest effect on cefotaxime hydrolysis, as did removal of the Arg276 side chain in an R276A mutant. The S237A:R276N and S237A:R276A double mutants, however, exhibited 29- and 14-fold losses in catalytic efficiency for cefotaxime hydrolysis, respectively, while the catalytic efficiency for benzylpenicillin hydrolysis was unchanged. Therefore, together, the Ser237 and Arg276 residues are important contributors to the cefotaximase substrate profile of the enzyme. High-resolution crystal structures of the CTX-M-14 S70G, S70G:S237A, and S70G:S237A:R276A variants alone and in complex with cefotaxime show that residues Ser237 and Arg276 in the wild-type enzyme promote the expansion of the active site to accommodate cefotaxime and favor a conformation of cefotaxime that allows optimal contacts between the enzyme and substrate. In conclusion, the conservation of these residues, linked to their effects on structure and catalysis, imply that their coevolution is an important specificity determinant in the CTX-M family.},
doi = {10.1021/bi501195g},
journal = {Biochemistry},
number = 2,
volume = 54,
place = {United States},
year = {Tue Dec 09 00:00:00 EST 2014},
month = {Tue Dec 09 00:00:00 EST 2014}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record

Citation Metrics:
Cited by: 42 works
Citation information provided by
Web of Science

Save / Share:

Works referenced in this record:

Bacterial Resistance to β-Lactam Antibiotics:  Compelling Opportunism, Compelling Opportunity
journal, February 2005

  • Fisher, Jed F.; Meroueh, Samy O.; Mobashery, Shahriar
  • Chemical Reviews, Vol. 105, Issue 2
  • DOI: 10.1021/cr030102i

A standard numbering scheme for the class A β-lactamases
journal, May 1991

  • Ambler, R. P.; Coulson, A. F. W.; Frère, J. M.
  • Biochemical Journal, Vol. 276, Issue 1
  • DOI: 10.1042/bj2760269

Epidemiological Expansion, Structural Studies, and Clinical Challenges of New β-Lactamases from Gram-Negative Bacteria
journal, October 2011


Growing Group of Extended-Spectrum  -Lactamases: the CTX-M Enzymes
journal, December 2003


Atomic Resolution Structures of CTX-M β-Lactamases: Extended Spectrum Activities from Increased Mobility and Decreased Stability
journal, April 2005


CTX-M Enzymes: Origin and Diffusion
journal, January 2012

  • Cantón, Rafael; González-Alba, José María; Galán, Juan Carlos
  • Frontiers in Microbiology, Vol. 3
  • DOI: 10.3389/fmicb.2012.00110

Crystal structure of the E166A mutant of extended-spectrum β-lactamase toho-1 at 1.8 Å resolution 1 1Edited by R. Huber
journal, February 1999

  • Ibuka, Akiko; Taguchi, Ayako; Ishiguro, Masaji
  • Journal of Molecular Biology, Vol. 285, Issue 5
  • DOI: 10.1006/jmbi.1998.2432

Structural Insights into Substrate Recognition and Product Expulsion in CTX-M Enzymes
journal, July 2010

  • Delmas, Julien; Leyssene, David; Dubois, Damien
  • Journal of Molecular Biology, Vol. 400, Issue 1
  • DOI: 10.1016/j.jmb.2010.04.062

Structure and Dynamics of CTX-M Enzymes Reveal Insights into Substrate Accommodation by Extended-spectrum β-Lactamases
journal, January 2008


Structure-function studies of arginine at position 276 in CTX-M  -lactamases
journal, February 2008

  • Perez-Llarena, F. J.; Cartelle, M.; Mallo, S.
  • Journal of Antimicrobial Chemotherapy, Vol. 61, Issue 4
  • DOI: 10.1093/jac/dkn031

Analysis of the plasticity of location of the Arg244 positive charge within the active site of the TEM-1 β-lactamase
journal, October 2009

  • Marciano, David C.; Brown, Nicholas G.; Palzkill, Timothy
  • Protein Science, Vol. 18, Issue 10
  • DOI: 10.1002/pro.220

Molecular structure of the acyl-enzyme intermediate in β-lactam hydrolysis at 1.7 Å resolution
journal, October 1992

  • Strynadka, Natalie C. J.; Adachi, Hiroyuki; Jensen, Susan E.
  • Nature, Vol. 359, Issue 6397
  • DOI: 10.1038/359700a0

Elucidation of the role of arginine-224 in the turnover processes of class A .beta.-lactamases
journal, April 1992

  • Zafaralla, Glenn; Manavathu, Elias K.; Lerner, Stephen A.
  • Biochemistry, Vol. 31, Issue 15
  • DOI: 10.1021/bi00130a016

iMOSFLM : a new graphical interface for diffraction-image processing with MOSFLM
journal, March 2011

  • Battye, T. Geoff G.; Kontogiannis, Luke; Johnson, Owen
  • Acta Crystallographica Section D Biological Crystallography, Vol. 67, Issue 4
  • DOI: 10.1107/S0907444910048675

The CCP4 suite programs for protein crystallography
journal, September 1994


MOLREP an Automated Program for Molecular Replacement
journal, December 1997


Phaser crystallographic software
journal, July 2007

  • McCoy, Airlie J.; Grosse-Kunstleve, Ralf W.; Adams, Paul D.
  • Journal of Applied Crystallography, Vol. 40, Issue 4
  • DOI: 10.1107/S0021889807021206

[20] Processing of X-ray diffraction data collected in oscillation mode
book, January 1997


Coot model-building tools for molecular graphics
journal, November 2004

  • Emsley, Paul; Cowtan, Kevin
  • Acta Crystallographica Section D Biological Crystallography, Vol. 60, Issue 12, p. 2126-2132
  • DOI: 10.1107/S0907444904019158

LigPlot+: Multiple Ligand–Protein Interaction Diagrams for Drug Discovery
journal, October 2011

  • Laskowski, Roman A.; Swindells, Mark B.
  • Journal of Chemical Information and Modeling, Vol. 51, Issue 10
  • DOI: 10.1021/ci200227u

UCSF Chimera?A visualization system for exploratory research and analysis
journal, January 2004

  • Pettersen, Eric F.; Goddard, Thomas D.; Huang, Conrad C.
  • Journal of Computational Chemistry, Vol. 25, Issue 13
  • DOI: 10.1002/jcc.20084

Additivity of mutational effects in proteins
journal, September 1990


UCSF Chimera?A visualization system for exploratory research and analysis
journal, January 2004

  • Pettersen, Eric F.; Goddard, Thomas D.; Huang, Conrad C.
  • Journal of Computational Chemistry, Vol. 25, Issue 13
  • DOI: 10.1002/jcc.20084

Atomic Resolution Structures of CTX-M β-Lactamases: Extended Spectrum Activities from Increased Mobility and Decreased Stability
journal, April 2005


Structure and Dynamics of CTX-M Enzymes Reveal Insights into Substrate Accommodation by Extended-spectrum β-Lactamases
journal, January 2008


Evolution of an Antibiotic Resistance Enzyme Constrained by Stability and Activity Trade-offs
journal, June 2002


Additivity of mutational effects in proteins
journal, September 1990


LigPlot+: Multiple Ligand–Protein Interaction Diagrams for Drug Discovery
journal, October 2011

  • Laskowski, Roman A.; Swindells, Mark B.
  • Journal of Chemical Information and Modeling, Vol. 51, Issue 10
  • DOI: 10.1021/ci200227u

Bacterial Resistance to β-Lactam Antibiotics:  Compelling Opportunism, Compelling Opportunity
journal, February 2005

  • Fisher, Jed F.; Meroueh, Samy O.; Mobashery, Shahriar
  • Chemical Reviews, Vol. 105, Issue 2
  • DOI: 10.1021/cr030102i

Identification of the β-Lactamase Inhibitor Protein-II (BLIP-II) Interface Residues Essential for Binding Affinity and Specificity for Class A β-Lactamases
journal, June 2013

  • Brown, Nicholas G.; Chow, Dar-Chone; Ruprecht, Kevin E.
  • Journal of Biological Chemistry, Vol. 288, Issue 24
  • DOI: 10.1074/jbc.m113.463521

The Structural Bases of Antibiotic Resistance in the Clinically Derived Mutant β-Lactamases TEM-30, TEM-32, and TEM-34
journal, August 2002

  • Wang, Xiaojun; Minasov, George; Shoichet, Brian K.
  • Journal of Biological Chemistry, Vol. 277, Issue 35
  • DOI: 10.1074/jbc.m204212200

Structure-function studies of arginine at position 276 in CTX-M  -lactamases
journal, February 2008

  • Perez-Llarena, F. J.; Cartelle, M.; Mallo, S.
  • Journal of Antimicrobial Chemotherapy, Vol. 61, Issue 4
  • DOI: 10.1093/jac/dkn031

Effect of substitution of Asn for Arg-276 in the cefotaxime-hydrolyzing class A β-lactamase CTX-M-4
journal, December 1998


Sequence of the Gene Encoding a Plasmid-Mediated Cefotaxime-Hydrolyzing Class A β-Lactamase (CTX-M-4): Involvement of Serine 237 in Cephalosporin Hydrolysis
journal, May 1998

  • Gazouli, Maria; Tzelepi, Eva; Sidorenko, Sergei V.
  • Antimicrobial Agents and Chemotherapy, Vol. 42, Issue 5
  • DOI: 10.1128/aac.42.5.1259

Epidemiological Expansion, Structural Studies, and Clinical Challenges of New β-Lactamases from Gram-Negative Bacteria
journal, October 2011


Works referencing / citing this record:

Crystallographic Snapshots of Class A β-Lactamase Catalysis Reveal Structural Changes That Facilitate β-Lactam Hydrolysis
journal, January 2017

  • Pan, Xuehua; He, Yunjiao; Lei, Jinping
  • Journal of Biological Chemistry, Vol. 292, Issue 10
  • DOI: 10.1074/jbc.m116.764340

Emergence of NDM-1- and CTX-M-3-Producing Raoultella ornithinolytica in Human Gut Microbiota
journal, November 2019


Structural Insights into the TLA-3 Extended-Spectrum β-Lactamase and Its Inhibition by Avibactam and OP0595
journal, July 2017

  • Jin, Wanchun; Wachino, Jun-ichi; Yamaguchi, Yoshihiro
  • Antimicrobial Agents and Chemotherapy, Vol. 61, Issue 10
  • DOI: 10.1128/aac.00501-17

Defining Substrate Specificity in the CTX-M Family: the Role of Asp240 in Ceftazidime Hydrolysis
journal, April 2018

  • Ghiglione, Barbara; Rodríguez, María Margarita; Curto, Lucrecia
  • Antimicrobial Agents and Chemotherapy, Vol. 62, Issue 6
  • DOI: 10.1128/aac.00116-18

Designing of inhibitors against CTX-M-15 type β-lactamase: potential drug candidate against β-lactamases-producing multi-drug-resistant bacteria
journal, June 2017


Prevalence and antibiotic susceptibility pattern of CTX-M type extended-spectrum β-lactamases among clinical isolates of gram-negative bacilli in Jimma, Ethiopia
journal, October 2018

  • Zeynudin, Ahmed; Pritsch, Michael; Schubert, Sören
  • BMC Infectious Diseases, Vol. 18, Issue 1
  • DOI: 10.1186/s12879-018-3436-7