› 1w5d

X-ray diffraction
2.1Å resolution

Crystal structure of PBP4a from Bacillus subtilis

Released:
DOI: 10.2210/pdb1w5d/pdb
PDB 1w5d coloured by chain and viewed from the front.
PDB 1w5d coloured by chain and viewed from the side.
PDB 1w5d coloured by chain and viewed from the top.
Source organism: Bacillus subtilis
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)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
D-alanyl-D-alanine carboxypeptidase DacC Chain: A
Molecule details ›
Chain: A
Length: 462 amino acids
Theoretical weight: 49.76 KDa
Source organism: Bacillus subtilis
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

1 bound ligand:
Ligand CA 3 x CA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID29
Spacegroup: P3212
Unit cell:
a: 67.411Å b: 67.411Å c: 228.464Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.224 0.224 0.268

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Citations

7 review citations

Chemical Reporters for Bacterial Glycans: Development and Applications.
Banahene et al. (2022)
6 more

2 mentions without citation

Antimicrobial action of methanolic seed extracts of Syzygium cumini Linn. on Bacillus subtilis.
Yadav et al. (2017)
1 more