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Specificity Determinants for Lysine Incorporation in Staphylococcus aureus Peptidoglycan as Revealed by the Structure of a MurE Ternary Complex

DOI: 10.1074/jbc.M113.508135 DOI Help
PMID: 24064214 PMID Help

Authors: Karen Ruane (University of Warwick) , A. J. Lloyd (University of Warwick) , Vilmos Fulop (Department of Biological Sciences, University of Warwick) , Christopher G. Dowson (University of Warwick) , Helene Barreteau (University Paris-Sud) , Audrey Boniface (University Paris-Sud) , Sebastien Dementin (University Paris-Sud) , Didier Blanot (University Paris-Sud) , Dominique Mengin-lecreulx (University Paris-Sud) , Stanislav Gobec (University of Ljubljana) , Andrea Dessen (Université Grenoble I) , David Roper (University of Warwick)
Co-authored by industrial partner: No

Type: Journal Paper
Journal: Journal Of Biological Chemistry

State: Published (Approved)
Published: September 2013
Diamond Proposal Number(s): 8359

Open Access Open Access

Abstract: Formation of the peptidoglycan stem pentapeptide requires the insertion of both l and d amino acids by the ATP-dependent ligase enzymes MurC, -D, -E, and -F. The stereochemical control of the third position amino acid in the pentapeptide is crucial to maintain the fidelity of later biosynthetic steps contributing to cell morphology, antibiotic resistance, and pathogenesis. Here we determined the x-ray crystal structure of Staphylococcus aureus MurE UDP-N-acetylmuramoyl-l-alanyl-d-glutamate:meso-2,6-diaminopimelate ligase (MurE) (E.C. at 1.8 Ã… resolution in the presence of ADP and the reaction product, UDP-MurNAc-l-Ala-?-d-Glu-l-Lys. This structure provides for the first time a molecular understanding of how this Gram-positive enzyme discriminates between l-lysine and d,l-diaminopimelic acid, the predominant amino acid that replaces l-lysine in Gram-negative peptidoglycan. Despite the presence of a consensus sequence previously implicated in the selection of the third position residue in the stem pentapeptide in S. aureus MurE, the structure shows that only part of this sequence is involved in the selection of l-lysine. Instead, other parts of the protein contribute substrate-selecting residues, resulting in a lysine-binding pocket based on charge characteristics. Despite the absolute specificity for l-lysine, S. aureus MurE binds this substrate relatively poorly. In vivo analysis and metabolomic data reveal that this is compensated for by high cytoplasmic l-lysine concentrations. Therefore, both metabolic and structural constraints maintain the structural integrity of the staphylococcal peptidoglycan. This study provides a novel focus for S. aureus-directed antimicrobials based on dual targeting of essential amino acid biogenesis and its linkage to cell wall assembly.

Journal Keywords: Cell; Crystallography; X-Ray; Lysine; Metabolomics; Peptide; Peptidoglycan; Protein; Tertiary; Staphylococcus aureus

Subject Areas: Biology and Bio-materials

Instruments: I02-Macromolecular Crystallography

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