› 1rn8

X-ray diffraction
1.93Å resolution

Crystal structure of dUTPase complexed with substrate analogue imido-dUTP

Released:
DOI: 10.2210/pdb1rn8/pdb
PDB entry 1rn8 coloured by chain, front view.
PDB entry 1rn8 coloured by chain, side view.
PDB entry 1rn8 coloured by chain, top view.
Source organism: Escherichia coli
Primary publication:
Structural insights into the catalytic mechanism of phosphate ester hydrolysis by dUTPase.
Barabás O, Pongrácz V, Kovári J, Wilmanns M, Vértessy BG
J Biol Chem 279 42907-15 (2004)
PMID: 15208312

Function and Biology Details

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

Structure analysis Details

Assembly composition:
homo trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-139313 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Deoxyuridine 5'-triphosphate nucleotidohydrolase Chain: A
Molecule details ›
Chain: A
Length: 152 amino acids
Theoretical weight: 16.3 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P06968 (Residues: 1-152; Coverage: 100%)
Gene names: JW3615, b3640, dnaS, dut, sof
Sequence domains: dUTPase
Structure domains: Deoxyuridine 5'-Triphosphate Nucleotidohydrolase; Chain A

Ligands and Environments

4 bound ligands:
Ligand MG 1 x MG
Ligand ACT 1 x ACT
Ligand DUP 1 x DUP
Ligand TRS 1 x TRS
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: EMBL/DESY, HAMBURG BEAMLINE X11
Spacegroup: P6322
Unit cell:
a: 74.618Å b: 74.618Å c: 99.58Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.164 0.137 0.18
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

2 review citations

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

4 mentions without citation

The flexible motif V of Epstein-Barr virus deoxyuridine 5'-triphosphate pyrophosphatase is essential for catalysis.
Freeman et al. (2009)
3 more