› 2ex6

X-ray diffraction
1.6Å resolution

Crystal structure of penicillin binding protein 4 (dacB) from Escherichia coli, complexed with ampicillin

Released:
DOI: 10.2210/pdb2ex6/pdb
PDB entry 2ex6 coloured by chain, front view.
PDB entry 2ex6 coloured by chain, side view.
PDB entry 2ex6 coloured by chain, top view.
Source organism: Escherichia coli
Primary publication:
Crystal structure of penicillin binding protein 4 (dacB) from Escherichia coli, both in the native form and covalently linked to various antibiotics.
Kishida H, Unzai S, Roper DI, Lloyd A, Park SY, Tame JR
Biochemistry 45 783-92 (2006)
PMID: 16411754

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

Assemblies composition:
monomeric (preferred)
homo dimer
Assembly name:
PDBe Complex ID:
PDB-CPX-150177 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
D-alanyl-D-alanine carboxypeptidase DacB Chain: A
Molecule details ›
Chain: A
Length: 458 amino acids
Theoretical weight: 49.8 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P24228 (Residues: 21-477; Coverage: 100%)
Gene names: JW3149, b3182, dacB
Sequence domains: D-Ala-D-Ala carboxypeptidase 3 (S13) family
Structure domains:

Ligands and Environments

2 bound ligands:
Ligand AIX 1 x AIX
Ligand GOL 1 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE BL-5A
Spacegroup: P41212
Unit cell:
a: 95.704Å b: 95.704Å c: 115.952Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.218 0.216 0.25
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

12 review citations

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

5 mentions without citation

Antibiotics: Conventional Therapy and Natural Compounds with Antibacterial Activity-A Pharmaco-Toxicological Screening.
Pancu et al. (2021)
4 more