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Title: Subfamily-specific adaptations in the structures of two penicillin-binding proteins from Mycobacterium tuberculosis

Abstract

Beta-lactam antibiotics target penicillin-binding proteins including several enzyme classes essential for bacterial cell-wall homeostasis. To better understand the functional and inhibitor-binding specificities of penicillin-binding proteins from the pathogen, Mycobacterium tuberculosis, we carried out structural and phylogenetic analysis of two predicted D,D-carboxypeptidases, Rv2911 and Rv3330. Optimization of Rv2911 for crystallization using directed evolution and the GFP folding reporter method yielded a soluble quadruple mutant. Structures of optimized Rv2911 bound to phenylmethylsulfonyl fluoride and Rv3330 bound to meropenem show that, in contrast to the nonspecific inhibitor, meropenem forms an extended interaction with the enzyme along a conserved surface. Phylogenetic analysis shows that Rv2911 and Rv3330 belong to different clades that emerged in Actinobacteria and are not represented in model organisms such as Escherichia coli and Bacillus subtilis. Clade-specific adaptations allow these enzymes to fulfill distinct physiological roles despite strict conservation of core catalytic residues. The characteristic differences include potential protein-protein interaction surfaces and specificity-determining residues surrounding the catalytic site. Overall, these structural insights lay the groundwork to develop improved beta-lactam therapeutics for tuberculosis.

Authors:
 [1];  [2];  [1];  [1];  [1];  [1];  [3];  [1];  [1];  [4]
  1. Univ. of California, Berkeley, CA (United States)
  2. Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Texas A & M Univ., College Station, TX (United States)
  3. Texas A & M Univ., College Station, TX (United States)
  4. Institut Pasteur, Paris (France)
Publication Date:
Research Org.:
Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
Sponsoring Org.:
USDOE
OSTI Identifier:
1201462
Grant/Contract Number:  
AC02-05CH11231
Resource Type:
Journal Article: Accepted Manuscript
Journal Name:
PLoS ONE
Additional Journal Information:
Journal Volume: 9; Journal Issue: 12; Journal ID: ISSN 1932-6203
Publisher:
Public Library of Science
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Prigozhin, Daniil M., Krieger, Inna V., Huizar, John P., Mavrici, Daniela, Waldo, Geoffrey S., Hung, Li -Wei, Sacchettini, James C., Terwilliger, Thomas C., Alber, Tom, and Mayer, Claudine. Subfamily-specific adaptations in the structures of two penicillin-binding proteins from Mycobacterium tuberculosis. United States: N. p., 2014. Web. doi:10.1371/journal.pone.0116249.
Prigozhin, Daniil M., Krieger, Inna V., Huizar, John P., Mavrici, Daniela, Waldo, Geoffrey S., Hung, Li -Wei, Sacchettini, James C., Terwilliger, Thomas C., Alber, Tom, & Mayer, Claudine. Subfamily-specific adaptations in the structures of two penicillin-binding proteins from Mycobacterium tuberculosis. United States. doi:10.1371/journal.pone.0116249.
Prigozhin, Daniil M., Krieger, Inna V., Huizar, John P., Mavrici, Daniela, Waldo, Geoffrey S., Hung, Li -Wei, Sacchettini, James C., Terwilliger, Thomas C., Alber, Tom, and Mayer, Claudine. Wed . "Subfamily-specific adaptations in the structures of two penicillin-binding proteins from Mycobacterium tuberculosis". United States. doi:10.1371/journal.pone.0116249. https://www.osti.gov/servlets/purl/1201462.
@article{osti_1201462,
title = {Subfamily-specific adaptations in the structures of two penicillin-binding proteins from Mycobacterium tuberculosis},
author = {Prigozhin, Daniil M. and Krieger, Inna V. and Huizar, John P. and Mavrici, Daniela and Waldo, Geoffrey S. and Hung, Li -Wei and Sacchettini, James C. and Terwilliger, Thomas C. and Alber, Tom and Mayer, Claudine},
abstractNote = {Beta-lactam antibiotics target penicillin-binding proteins including several enzyme classes essential for bacterial cell-wall homeostasis. To better understand the functional and inhibitor-binding specificities of penicillin-binding proteins from the pathogen, Mycobacterium tuberculosis, we carried out structural and phylogenetic analysis of two predicted D,D-carboxypeptidases, Rv2911 and Rv3330. Optimization of Rv2911 for crystallization using directed evolution and the GFP folding reporter method yielded a soluble quadruple mutant. Structures of optimized Rv2911 bound to phenylmethylsulfonyl fluoride and Rv3330 bound to meropenem show that, in contrast to the nonspecific inhibitor, meropenem forms an extended interaction with the enzyme along a conserved surface. Phylogenetic analysis shows that Rv2911 and Rv3330 belong to different clades that emerged in Actinobacteria and are not represented in model organisms such as Escherichia coli and Bacillus subtilis. Clade-specific adaptations allow these enzymes to fulfill distinct physiological roles despite strict conservation of core catalytic residues. The characteristic differences include potential protein-protein interaction surfaces and specificity-determining residues surrounding the catalytic site. Overall, these structural insights lay the groundwork to develop improved beta-lactam therapeutics for tuberculosis.},
doi = {10.1371/journal.pone.0116249},
journal = {PLoS ONE},
number = 12,
volume = 9,
place = {United States},
year = {Wed Dec 31 00:00:00 EST 2014},
month = {Wed Dec 31 00:00:00 EST 2014}
}

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Cited by: 1 work
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