› 3a3d

X-ray diffraction
1.6Å resolution

Crystal structure of penicillin binding protein 4 (dacB) from Haemophilus influenzae

Released:
DOI: 10.2210/pdb3a3d/pdb
PDB entry 3a3d coloured by chain, front view.
PDB entry 3a3d coloured by chain, side view.
PDB entry 3a3d coloured by chain, top view.
Source organism: Haemophilus influenzae
Primary publication:
Crystal structures of penicillin-binding proteins 4 and 5 from Haemophilus influenzae.
Kawai F, Clarke TB, Roper DI, Han GJ, Hwang KY, Unzai S, Obayashi E, Park SY, Tame JR
J Mol Biol 396 634-45 (2010)
PMID: 19958776

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:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-155254 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
D-alanyl-D-alanine carboxypeptidase DacB Chains: A, B
Molecule details ›
Chains: A, B
Length: 453 amino acids
Theoretical weight: 49.79 KDa
Source organism: Haemophilus influenzae
Expression system: Escherichia coli
UniProt:
  • Canonical: P45161 (Residues: 28-479; Coverage: 100%)
Gene names: HI_1330, dacB
Sequence domains: D-Ala-D-Ala carboxypeptidase 3 (S13) family
Structure domains:

Ligands and Environments

1 bound ligand:
Ligand GOL 4 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE BL-5A
Spacegroup: P21
Unit cell:
a: 64.548Å b: 92.59Å c: 104.882Å
α: 90° β: 107.75° γ: 90°
R-values:
R R work R free
0.173 0.171 0.204
Expression system: Escherichia coli

Quick links

Citations

3 review citations

Bridging cell wall biosynthesis and bacterial morphogenesis.
Matteï et al. (2010)
2 more

3 mentions without citation

Cell Wall Hydrolases in Bacteria: Insight on the Diversity of Cell Wall Amidases, Glycosidases and Peptidases Toward Peptidoglycan.
Vermassen et al. (2019)
2 more