› 2pz0

X-ray diffraction
1.91Å resolution

Crystal structure of Glycerophosphodiester Phosphodiesterase (GDPD) from T. tengcongensis

Released:
DOI: 10.2210/pdb2pz0/pdb
PDB entry 2pz0 coloured by chain, front view.
PDB entry 2pz0 coloured by chain, side view.
PDB entry 2pz0 coloured by chain, top view.
Source organism: Caldanaerobacter subterraneus subsp. tengcongensis MB4
Primary publication:
Crystal structure of glycerophosphodiester phosphodiesterase (GDPD) from Thermoanaerobacter tengcongensis, a metal ion-dependent enzyme: insight into the catalytic mechanism.
Shi L, Liu JF, An XM, Liang DC
Proteins 72 280-8 (2008)
PMID: 18214974

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 analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-185945 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Glycerophosphodiester phosphodiesterase Chains: A, B
Molecule details ›
Chains: A, B
Length: 252 amino acids
Theoretical weight: 28.78 KDa
Source organism: Caldanaerobacter subterraneus subsp. tengcongensis MB4
Expression system: Escherichia coli
UniProt:
  • Canonical: Q8RB32 (Residues: 1-243; Coverage: 100%)
Gene names: TTE0993, UgpQ
Sequence domains: Glycerophosphoryl diester phosphodiesterase family
Structure domains: Phosphatidylinositol (PI) phosphodiesterase

Ligands and Environments

2 bound ligands:
Ligand CA 2 x CA
Ligand GOL 2 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU
Spacegroup: P21
Unit cell:
a: 49.401Å b: 53.608Å c: 110.885Å
α: 90° β: 97.91° γ: 90°
R-values:
R R work R free
0.229 0.229 0.236
Expression system: Escherichia coli

Quick links

Citations

2 review citations

The emerging physiological roles of the glycerophosphodiesterase family.
Corda et al. (2014)
1 more

6 mentions without citation

Crystal structure of glycerophosphodiester phosphodiesterase (GDPD) from Thermoanaerobacter tengcongensis, a metal ion-dependent enzyme: insight into the catalytic mechanism.
Shi et al. (2008)
5 more