› 3d03

X-ray diffraction
1.9Å resolution

1.9A structure of Glycerophoshphodiesterase (GpdQ) from Enterobacter aerogenes

Released:
DOI: 10.2210/pdb3d03/pdb
Model geometry
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PDB entry 3d03 coloured by chain, front view.
PDB entry 3d03 coloured by chain, side view.
PDB entry 3d03 coloured by chain, top view.
Source organism: Klebsiella aerogenes
Primary publication:
Substrate-promoted formation of a catalytically competent binuclear center and regulation of reactivity in a glycerophosphodiesterase from Enterobacter aerogenes.
Hadler KS, Tanifum EA, Yip SH, Mitić N, Guddat LW, Jackson CJ, Gahan LR, Nguyen K, Carr PD, Ollis DL, Hengge AC, Larrabee JA, Schenk G
J Am Chem Soc 130 14129-38 (2008)
PMID: 18831553

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, C, D, E, F
Molecule details ›
Chains: A, B, C, D, E, F
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

1 bound ligand:
Ligand CO 12 x CO
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: AUSTRALIAN SYNCHROTRON BEAMLINE MX1
Spacegroup: P212121
Unit cell:
a: 94.967Å b: 133.842Å c: 168.941Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.186 0.184 0.223
Expression system: Escherichia coli

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Citations

4 review citations

Metallophosphoesterases: structural fidelity with functional promiscuity.
Matange et al. (2015)
3 more

7 mentions without citation

Structural characterization of anti-inflammatory immunoglobulin G Fc proteins.
Ahmed et al. (2014)
6 more

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