Crystallographic Study of Peptidoglycan Biosynthesis Enzyme MurD: Domain Movement Revisited

PLoS One. 2016 Mar 31;11(3):e0152075. doi: 10.1371/journal.pone.0152075. eCollection 2016.

Abstract

The biosynthetic pathway of peptidoglycan, an essential component of bacterial cell wall, is a well-recognized target for antibiotic development. Peptidoglycan precursors are synthesized in the bacterial cytosol by various enzymes including the ATP-hydrolyzing Mur ligases, which catalyze the stepwise addition of amino acids to a UDP-MurNAc precursor to yield UDP-MurNAc-pentapeptide. MurD catalyzes the addition of D-glutamic acid to UDP-MurNAc-L-Ala in the presence of ATP; structural and biochemical studies have suggested the binding of the substrates with an ordered kinetic mechanism in which ligand binding inevitably closes the active site. In this work, we challenge this assumption by reporting the crystal structures of intermediate forms of MurD either in the absence of ligands or in the presence of small molecules. A detailed analysis provides insight into the events that lead to the closure of MurD and reveals that minor structural modifications contribute to major overall conformation alterations. These novel insights will be instrumental in the development of new potential antibiotics designed to target the peptidoglycan biosynthetic pathway.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Crystallography, X-Ray
  • Escherichia coli / enzymology*
  • Peptide Synthases / chemistry*
  • Peptide Synthases / metabolism
  • Peptidoglycan / biosynthesis
  • Peptidoglycan / chemistry
  • Protein Structure, Tertiary

Substances

  • Peptidoglycan
  • Peptide Synthases
  • UDP-N-acetylmuramoylalanine-D-glutamate ligase

Grant support

This work was financially supported by the European Union FP6 Integrated Project EURINTAFAR (project no. LSHM-CT-2004-512138; http://www.eur-intafar.ulg.ac.be/usefulllinks/index.html); the Slovenian Research Agency (grant no. L1-6745; https://www.arrs.gov.si/en/novo.asp); the Proteus program (project 31185YL; http://www.campusfrance.org/fr/proteus) and the Institut Français Charles Nodier. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. This work used the platforms of the Grenoble Instruct centre (ISBG; UMS 3518 CNRS-CEA-UJF-EMBL) with support from FRISBI (ANR-10-INSB-05-02) and GRAL (ANR-10-LABX-49-01) within the Grenoble Partnership for Structural Biology (PSB)[Lek Pharmaceuticals d.d. http://www.lek.si]. The funder provided support in the form of salaries for MK, but did not have any additional role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript.