› 3giq

X-ray diffraction
1.8Å resolution

Crystal structure of N-acyl-D-Glutamate Deacylase from Bordetella Bronchiseptica complexed with zinc and phosphonate inhibitor, a mimic of the reaction tetrahedral intermediate.

Released:
DOI: 10.2210/pdb3giq/pdb
PDB entry 3giq coloured by chain, front view.
PDB entry 3giq coloured by chain, side view.
PDB entry 3giq coloured by chain, top view.
Source organism: Bordetella bronchiseptica
Primary publication:
Annotating enzymes of uncertain function: the deacylation of D-amino acids by members of the amidohydrolase superfamily.
Cummings JA, Fedorov AA, Xu C, Brown S, Fedorov E, Babbitt PC, Almo SC, Raushel FM
Biochemistry 48 6469-81 (2009)
PMID: 19518059

Function and Biology Details

Reaction catalysed: 
N-acyl-D-glutamate + H(2)O = a carboxylate + D-glutamate
Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-102122 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Amidohydrolase 3 domain-containing protein Chains: A, B
Molecule details ›
Chains: A, B
Length: 480 amino acids
Theoretical weight: 51.18 KDa
Source organism: Bordetella bronchiseptica
Expression system: Escherichia coli
UniProt:
  • Canonical: A0A0H3LXD5 (Residues: 1-480; Coverage: 100%)
Gene name: BB3285
Sequence domains: Amidohydrolase family
Structure domains:

Ligands and Environments

2 bound ligands:
Ligand G01 2 x G01
Ligand ZN 4 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X4A
Spacegroup: P6122
Unit cell:
a: 91.291Å b: 91.291Å c: 507.584Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.183 0.183 0.207
Expression system: Escherichia coli

Quick links

Citations

1 review citation

Toward mechanistic classification of enzyme functions.
Almonacid et al. (2011)
9 other articles

1 mention without citation

Annotating enzymes of uncertain function: the deacylation of D-amino acids by members of the amidohydrolase superfamily.
Cummings et al. (2009)