› 2pyu

X-ray diffraction
2.02Å resolution

Structure of the E. coli inosine triphosphate pyrophosphatase RgdB in complex with IMP

Released:
DOI: 10.2210/pdb2pyu/pdb
PDB entry 2pyu coloured by chain, front view.
PDB entry 2pyu coloured by chain, side view.
PDB entry 2pyu coloured by chain, top view.
Source organism: Escherichia coli K-12
Primary publication:
Molecular basis of the antimutagenic activity of the house-cleaning inosine triphosphate pyrophosphatase RdgB from Escherichia coli.
Savchenko A, Proudfoot M, Skarina T, Singer A, Litvinova O, Sanishvili R, Brown G, Chirgadze N, Yakunin AF
J Mol Biol 374 1091-103 (2007)
PMID: 17976651

Function and Biology Details

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

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-156463 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
dITP/XTP pyrophosphatase Chain: A
Molecule details ›
Chain: A
Length: 219 amino acids
Theoretical weight: 23.34 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli
UniProt:
  • Canonical: P52061 (Residues: 1-197; Coverage: 100%)
Gene names: JW2921, b2954, rdgB, yggV
Sequence domains: Ham1 family
Structure domains: Maf protein

Ligands and Environments

2 bound ligands:
Ligand IMP 1 x IMP
Ligand EDO 1 x EDO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU MICROMAX-007
Spacegroup: P43212
Unit cell:
a: 77.941Å b: 77.941Å c: 81.073Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.195 0.192 0.253
Expression system: Escherichia coli

Quick links

Citations

3 review citations

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

3 mentions without citation

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