› 3f4f

X-ray diffraction
2Å resolution

Crystal structure of dUT1p, a dUTPase from Saccharomyces cerevisiae

Released:
DOI: 10.2210/pdb3f4f/pdb
PDB entry 3f4f coloured by chain, front view.
PDB entry 3f4f coloured by chain, side view.
PDB entry 3f4f coloured by chain, top view.
Source organism: Saccharomyces cerevisiae
Primary publication:
Structure and activity of the Saccharomyces cerevisiae dUTP pyrophosphatase DUT1, an essential housekeeping enzyme.
Tchigvintsev A, Singer AU, Flick R, Petit P, Brown G, Evdokimova E, Savchenko A, Yakunin AF
Biochem J 437 243-53 (2011)
PMID: 21548881

Function and Biology Details

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

Structure analysis Details

Assembly composition:
homo trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-152587 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Deoxyuridine 5'-triphosphate nucleotidohydrolase Chains: A, B, C
Molecule details ›
Chains: A, B, C
Length: 167 amino acids
Theoretical weight: 17.49 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P33317 (Residues: 1-147; Coverage: 100%)
Gene names: DUT1, YBR1705, YBR252W
Sequence domains: dUTPase
Structure domains: Deoxyuridine 5'-Triphosphate Nucleotidohydrolase; Chain A

Ligands and Environments

4 bound ligands:
Ligand UMP 3 x UMP
Ligand NA 1 x NA
Ligand EDO 2 x EDO
Ligand PEG 2 x PEG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU MICROMAX-007
Spacegroup: P43212
Unit cell:
a: 124.498Å b: 124.498Å c: 51.664Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.149 0.146 0.207
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

1 review citation

dUTPases, the unexplored family of signalling molecules.
Penadés et al. (2013)
15 other articles

2 mentions without citation

In situ proteolysis to generate crystals for structure determination: an update.
Wernimont et al. (2009)
1 more