3N8D

Crystal structure of Staphylococcus aureus VRSA-9 D-Ala:D-Ala ligase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.204 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

Molecular basis of vancomycin dependence in VanA-type Staphylococcus aureus VRSA-9.

Meziane-Cherif, D.Saul, F.A.Moubareck, C.Weber, P.Haouz, A.Courvalin, P.Perichon, B.

(2010) J Bacteriol 192: 5465-5471

  • DOI: https://doi.org/10.1128/JB.00613-10
  • Primary Citation of Related Structures:  
    3N8D

  • PubMed Abstract: 

    The vancomycin-resistant Staphylococcus aureus VRSA-9 clinical isolate was partially dependent on glycopeptide for growth. The responsible vanA operon had the same organization as that of Tn1546 and was located on a plasmid. The chromosomal D-Ala:D-Ala ligase (ddl) gene had two point mutations that led to Q260K and A283E substitutions, resulting in a 200-fold decrease in enzymatic activity compared to that of the wild-type strain VRSA-6. To gain insight into the mechanism of enzyme impairment, we determined the crystal structure of VRSA-9 Ddl and showed that the A283E mutation induces new ion pair/hydrogen bond interactions, leading to an asymmetric rearrangement of side chains in the dimer interface. The Q260K substitution is located in an exposed external loop and did not induce any significant conformational change. The VRSA-9 strain was susceptible to oxacillin due to synthesis of pentadepsipeptide precursors ending in D-alanyl-D-lactate which are not substrates for the β-lactam-resistant penicillin binding protein PBP2'. Comparison with the partially vancomycin-dependent VRSA-7, whose Ddl is 5-fold less efficient than that of VRSA-9, indicated that the levels of vancomycin dependence and susceptibility to β-lactams correlate with the degree of Ddl impairment. Ddl drug targeting could therefore be an effective strategy against vancomycin-resistant S. aureus.


  • Organizational Affiliation

    Institut Pasteur, Unité des Agents Antibactériens, CNRS-URA 2185, 25 rue du Docteur Roux, 75724 Paris Cedex 15, France.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
D-alanine--D-alanine ligase
A, B
364Staphylococcus aureusMutation(s): 2 
Gene Names: ddl
EC: 6.3.2.4
UniProt
Find proteins for Q5HEB7 (Staphylococcus aureus (strain COL))
Explore Q5HEB7 
Go to UniProtKB:  Q5HEB7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5HEB7
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.204 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.374α = 90
b = 87.271β = 90
c = 91.789γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
PHASERphasing
REFMACrefinement
XDSdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-10-13
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description