› 2zoa

X-ray diffraction
2.4Å resolution

Malonate-bound structure of the glycerophosphodiesterase from Enterobacter aerogenes (GpdQ) COLLECTED AT 1.280 ANGSTROM

Released:
DOI: 10.2210/pdb2zoa/pdb
PDB entry 2zoa coloured by chain, front view.
PDB entry 2zoa coloured by chain, side view.
PDB entry 2zoa coloured by chain, top view.
Source organism: Klebsiella aerogenes
Primary publication:
Malonate-bound structure of the glycerophosphodiesterase from Enterobacter aerogenes (GpdQ) and characterization of the native Fe2+ metal-ion preference.
Jackson CJ, Hadler KS, Carr PD, Oakley AJ, Yip S, Schenk G, Ollis DL
Acta Crystallogr Sect F Struct Biol Cryst Commun 64 681-5 (2008)
PMID: 18678932

Function and Biology Details

Reaction catalysed: 
A glycerophosphodiester + H(2)O = an alcohol + sn-glycerol 3-phosphate
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:
Structure domain:

Structure analysis Details

Assemblies composition:
homo hexamer
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-180519 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Glycerophosphodiester phosphodiesterase GpdQ Chains: A, B
Molecule details ›
Chains: A, B
Length: 274 amino acids
Theoretical weight: 30.77 KDa
Source organism: Klebsiella aerogenes
Expression system: Escherichia coli
UniProt:
  • Canonical: Q6XBH1 (Residues: 1-274; Coverage: 100%)
Gene names: gpdQ, ph
Sequence domains: Calcineurin-like phosphoesterase
Structure domains:

Ligands and Environments

2 bound ligands:
Ligand FE2 4 x FE2
Ligand MLI 2 x MLI
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 19-ID
Spacegroup: P213
Unit cell:
a: 164.343Å b: 164.343Å c: 164.343Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.16 0.158 0.179
Expression system: Escherichia coli

Quick links

Citations

1 review citation

The emerging physiological roles of the glycerophosphodiesterase family.
Corda et al. (2014)
4 other articles

2 mentions without citation

The non-catalytic "cap domain" of a mycobacterial metallophosphoesterase regulates its expression and localization in the cell.
Matange et al. (2014)
1 more