› 2dvn

X-ray diffraction
1.6Å resolution

Structure of PH1917 protein with the complex of IMP from Pyrococcus horikoshii

Released:
DOI: 10.2210/pdb2dvn/pdb
PDB entry 2dvn coloured by chain, front view.
PDB entry 2dvn coloured by chain, side view.
PDB entry 2dvn coloured by chain, top view.
Source organism: Pyrococcus horikoshii
Primary publication:
Structures of dimeric nonstandard nucleotide triphosphate pyrophosphatase from Pyrococcus horikoshii OT3: functional significance of interprotomer conformational changes.
Lokanath NK, Pampa KJ, Takio K, Kunishima N
J Mol Biol 375 1013-25 (2008)
PMID: 18062990

Function and Biology Details

Reaction catalysed: 
ITP + H(2)O = IMP + diphosphate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:
Structure domain:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-129876 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
dITP/XTP pyrophosphatase Chains: A, B
Molecule details ›
Chains: A, B
Length: 186 amino acids
Theoretical weight: 21.23 KDa
Source organism: Pyrococcus horikoshii
Expression system: Escherichia coli
UniProt:
  • Canonical: O59580 (Residues: 1-186; Coverage: 100%)
Gene name: PH1917
Sequence domains: Ham1 family
Structure domains: Maf protein

Ligands and Environments

3 bound ligands:
Ligand SO4 13 x SO4
Ligand IMP 2 x IMP
Ligand GOL 3 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL26B1
Spacegroup: P41212
Unit cell:
a: 80.295Å b: 80.295Å c: 162.367Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.183 0.183 0.188
Expression system: Escherichia coli

Quick links

Citations

1 review citation

Preventive DNA repair by sanitizing the cellular (deoxy)nucleoside triphosphate pool.
Nagy et al. (2014)
2 other articles

2 mentions without citation

ITPA (inosine triphosphate pyrophosphatase): from surveillance of nucleotide pools to human disease and pharmacogenetics.
Simone et al. (2013)
1 more