› 3n8d

X-ray diffraction
2.3Å resolution

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

Released:
DOI: 10.2210/pdb3n8d/pdb
PDB entry 3n8d coloured by chain, front view.
PDB entry 3n8d coloured by chain, side view.
PDB entry 3n8d coloured by chain, top view.
Source organism: Staphylococcus aureus
Primary publication:
Molecular basis of vancomycin dependence in VanA-type Staphylococcus aureus VRSA-9.
Meziane-Cherif D, Saul FA, Moubareck C, Weber P, Haouz A, Courvalin P, Périchon B
J Bacteriol 192 5465-71 (2010)
PMID: 20729361

Function and Biology Details

Reaction catalysed: 
ATP + 2 D-alanine = ADP + phosphate + D-alanyl-D-alanine
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-177181 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
D-alanine--D-alanine ligase Chains: A, B
Molecule details ›
Chains: A, B
Length: 364 amino acids
Theoretical weight: 41.41 KDa
Source organism: Staphylococcus aureus
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q5HEB7 (Residues: 1-356; Coverage: 100%)
Gene names: SACOL2074, ddl
Sequence domains:
Structure domains:

Ligands and Environments

3 bound ligands:
Ligand ANP 2 x ANP
Ligand SO4 2 x SO4
Ligand CL 1 x CL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SOLEIL BEAMLINE PROXIMA 1
Spacegroup: P212121
Unit cell:
a: 84.374Å b: 87.271Å c: 91.789Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.204 0.2 0.276
Expression system: Escherichia coli BL21(DE3)

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Citations

1 review citation

Fierce poison to others: the phenomenon of bacterial dependence on antibiotics.
Paredes-Amaya et al. (2023)
6 other articles

1 mention without citation

Molecular basis of vancomycin dependence in VanA-type Staphylococcus aureus VRSA-9.
Meziane-Cherif et al. (2010)