› 3v39

X-ray diffraction
1.45Å resolution

Bd3459, A Predatory Peptidoglycan Endopeptidase from Bdellovibrio bacteriovorus

Released:
DOI: 10.2210/pdb3v39/pdb
PDB entry 3v39 coloured by chain, front view.
PDB entry 3v39 coloured by chain, side view.
PDB entry 3v39 coloured by chain, top view.
Source organism: Bdellovibrio bacteriovorus
Primary publication:
Specialized peptidoglycan hydrolases sculpt the intra-bacterial niche of predatory Bdellovibrio and increase population fitness.
Lerner TR, Lovering AL, Bui NK, Uchida K, Aizawa S, Vollmer W, Sockett RE
PLoS Pathog 8 e1002524 (2012)
PMID: 22346754

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:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-179886 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
D-alanyl-D-alanine carboxypeptidase Chain: A
Molecule details ›
Chain: A
Length: 418 amino acids
Theoretical weight: 46.51 KDa
Source organism: Bdellovibrio bacteriovorus
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: Q6MHT0 (Residues: 37-446; Coverage: 92%)
Gene name: Bd3459
Sequence domains: D-Ala-D-Ala carboxypeptidase 3 (S13) family
Structure domains:

Ligands and Environments

3 bound ligands:
Ligand TAU 1 x TAU
Ligand SO4 3 x SO4
Ligand PGE 1 x PGE
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID23-1
Spacegroup: P3121
Unit cell:
a: 125.24Å b: 125.24Å c: 81.37Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.167 0.166 0.182
Expression system: Escherichia coli BL21

Quick links

Citations

10 review citations

Multifaceted Interfaces of Bacterial Competition.
Stubbendieck et al. (2016)
9 more

2 mentions without citation

Specialized peptidoglycan hydrolases sculpt the intra-bacterial niche of predatory Bdellovibrio and increase population fitness.
Lerner et al. (2012)
1 more