› 3p48

X-ray diffraction
1.67Å resolution

Structure of the yeast dUTPase DUT1 in complex with dUMPNPP

Released:
DOI: 10.2210/pdb3p48/pdb
PDB entry 3p48 coloured by chain, front view.
PDB entry 3p48 coloured by chain, side view.
PDB entry 3p48 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: 147 amino acids
Theoretical weight: 15.32 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

2 bound ligands:
Ligand DUP 3 x DUP
Ligand MG 3 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 19-ID
Spacegroup: P212121
Unit cell:
a: 51.784Å b: 58.868Å c: 112.381Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.156 0.154 0.193
Expression system: Escherichia coli BL21(DE3)

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Citations

1 review citation

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

5 mentions without citation

Mechanism of sodium channel block by local anesthetics, antiarrhythmics, and anticonvulsants.
Tikhonov et al. (2017)
4 more