› 2j9p

X-ray diffraction
2.8Å resolution

Crystal structure of the Bacillus subtilis PBP4a, and its complex with a peptidoglycan mimetic peptide.

Released:
DOI: 10.2210/pdb2j9p/pdb
PDB entry 2j9p coloured by chain, front view.
PDB entry 2j9p coloured by chain, side view.
PDB entry 2j9p coloured by chain, top view.
Source organism: Bacillus subtilis subsp. subtilis str. 168
Primary publication:
Crystal structure of the Bacillus subtilis penicillin-binding protein 4a, and its complex with a peptidoglycan mimetic peptide.
Sauvage E, Duez C, Herman R, Kerff F, Petrella S, Anderson JW, Adediran SA, Pratt RF, Frère JM, Charlier P
J Mol Biol 371 528-39 (2007)
PMID: 17582436

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 domain:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-153966 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
D-alanyl-D-alanine carboxypeptidase DacC Chains: A, B
Molecule details ›
Chains: A, B
Length: 462 amino acids
Theoretical weight: 49.76 KDa
Source organism: Bacillus subtilis subsp. subtilis str. 168
Expression system: Escherichia coli
UniProt:
  • Canonical: P39844 (Residues: 30-491; Coverage: 100%)
Gene names: BSU18350, dacC, pbp
Sequence domains: D-Ala-D-Ala carboxypeptidase 3 (S13) family
Structure domains:

Ligands and Environments

2 bound ligands:
Ligand REZ 2 x REZ
Ligand DAL 2 x DAL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE BM30A
Spacegroup: P212121
Unit cell:
a: 73.859Å b: 77.586Å c: 164.739Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.208 0.208 0.29
Expression system: Escherichia coli

Quick links

Citations

7 review citations

The penicillin-binding proteins: structure and role in peptidoglycan biosynthesis.
Sauvage et al. (2008)
6 more

7 mentions without citation

Structural Insights for β-Lactam Antibiotics.
Kim et al. (2023)
6 more