› 1su2

X-ray diffraction
1.6Å resolution

CRYSTAL STRUCTURE OF THE NUDIX HYDROLASE DR1025 IN COMPLEX WITH ATP

Released:
DOI: 10.2210/pdb1su2/pdb
PDB entry 1su2 coloured by chain, front view.
PDB entry 1su2 coloured by chain, side view.
PDB entry 1su2 coloured by chain, top view.
Source organism: Deinococcus radiodurans
Primary publication:
Structural studies of the Nudix hydrolase DR1025 from Deinococcus radiodurans and its ligand complexes.
Ranatunga W, Hill EE, Mooster JL, Holbrook EL, Schulze-Gahmen U, Xu W, Bessman MJ, Brenner SE, Holbrook SR
J Mol Biol 339 103-16 (2004)
PMID: 15123424

Function and Biology Details

Reactions catalysed: 
P(1),P(4)-bis(5'-adenosyl)tetraphosphate + H(2)O = ATP + AMP
8-oxo-GTP + H(2)O = 8-oxo-GDP + phosphate
Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:
Structure domain:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-193302 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Nudix hydrolase DR_1025 Chains: A, B
Molecule details ›
Chains: A, B
Length: 159 amino acids
Theoretical weight: 17.59 KDa
Source organism: Deinococcus radiodurans
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: Q9RVK2 (Residues: 1-159; Coverage: 100%)
Gene name: DR_1025
Sequence domains: NUDIX domain
Structure domains: Nucleoside Triphosphate Pyrophosphohydrolase

Ligands and Environments

2 bound ligands:
Ligand MG 6 x MG
Ligand ATP 2 x ATP
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 5.0.2
Spacegroup: P41
Unit cell:
a: 53.232Å b: 53.232Å c: 122.362Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.206 0.204 0.225
Expression system: Escherichia coli BL21

Quick links

Citations

1 review citation

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

4 mentions without citation

Analysis of DBC1 and its homologs suggests a potential mechanism for regulation of sirtuin domain deacetylases by NAD metabolites.
Anantharaman et al. (2008)
3 more