› 1v8m

X-ray diffraction
1.8Å resolution

Crystal structure analysis of ADP-ribose pyrophosphatase complexed with ADP-ribose and Gd

Released:
DOI: 10.2210/pdb1v8m/pdb
PDB entry 1v8m coloured by chain, front view.
PDB entry 1v8m coloured by chain, side view.
PDB entry 1v8m coloured by chain, top view.
Source organism: Thermus thermophilus
Primary publication:
Structural insights into the Thermus thermophilus ADP-ribose pyrophosphatase mechanism via crystal structures with the bound substrate and metal.
Yoshiba S, Ooga T, Nakagawa N, Shibata T, Inoue Y, Yokoyama S, Kuramitsu S, Masui R
J Biol Chem 279 37163-74 (2004)
PMID: 15210687

Function and Biology Details

Reaction catalysed: 
ADP-D-ribose + H(2)O = AMP + D-ribose 5-phosphate
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-183026 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Nudix hydrolase domain-containing protein Chain: A
Molecule details ›
Chain: A
Length: 170 amino acids
Theoretical weight: 19.29 KDa
Source organism: Thermus thermophilus
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q84CU3 (Residues: 1-170; Coverage: 100%)
Gene name: ndx4
Sequence domains: NUDIX domain
Structure domains: Nucleoside Triphosphate Pyrophosphohydrolase

Ligands and Environments

2 bound ligands:
Ligand APR 1 x APR
Ligand GD 4 x GD
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL44B2
Spacegroup: P3221
Unit cell:
a: 49.61Å b: 49.61Å c: 119.87Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.22 0.22 0.244
Expression system: Escherichia coli BL21(DE3)

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Citations

1 review citation

Structures and mechanisms of Nudix hydrolases.
Mildvan et al. (2005)
17 other articles

2 mentions without citation

The evolution of function within the Nudix homology clan.
Srouji et al. (2017)
1 more