› 2y59

X-ray diffraction
2.5Å resolution

Unexpected tricovalent binding mode of boronic acids within the active site of a penicillin binding protein

Released:
DOI: 10.2210/pdb2y59/pdb
PDB entry 2y59 coloured by chain, front view.
PDB entry 2y59 coloured by chain, side view.
PDB entry 2y59 coloured by chain, top view.
Source organism: Actinomadura sp. R39
Primary publication:
Unexpected tricovalent binding mode of boronic acids within the active site of a penicillin-binding protein.
Zervosen A, Herman R, Kerff F, Herman A, Bouillez A, Prati F, Pratt RF, Frère JM, Joris B, Luxen A, Charlier P, Sauvage E
J Am Chem Soc 133 10839-48 (2011)
PMID: 21574608

Function and Biology Details

Reaction catalysed: 
Preferential cleavage: (Ac)(2)-L-Lys-D-Ala-|-D-Ala. Also transpeptidation of peptidyl-alanyl moieties that are N-acyl substituents of D-alanine.
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-153809 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
D-alanyl-D-alanine carboxypeptidase Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 466 amino acids
Theoretical weight: 47.65 KDa
Source organism: Actinomadura sp. R39
UniProt:
  • Canonical: P39045 (Residues: 50-515; Coverage: 95%)
Gene name: dac
Sequence domains: D-Ala-D-Ala carboxypeptidase 3 (S13) family
Structure domains:

Ligands and Environments

3 bound ligands:
Ligand ZA3 4 x ZA3
Ligand SO4 21 x SO4
Ligand MG 4 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE BM30A
Spacegroup: P21
Unit cell:
a: 103.88Å b: 91.353Å c: 106.919Å
α: 90° β: 94.27° γ: 90°
R-values:
R R work R free
0.198 0.195 0.254

Quick links

Citations

7 review citations

Resistance to antibiotics targeted to the bacterial cell wall.
Nikolaidis et al. (2014)
6 more