› 5f9k

X-ray diffraction
2.18Å resolution

Dictyostelium discoideum dUTPase at 2.2 Angstrom

Released:
DOI: 10.2210/pdb5f9k/pdb
PDB entry 5f9k coloured by chain, front view.
PDB entry 5f9k coloured by chain, side view.
PDB entry 5f9k coloured by chain, top view.
Source organism: Dictyostelium discoideum
Primary publication:
Mitochondrial localization of Dictyostelium discoideum dUTPase mediated by its N-terminus.
Chia CP, Inoguchi N, Varon KC, Bartholomai BM, Moriyama H
BMC Res Notes 13 16 (2020)
PMID: 31910901

Function and Biology Details

Reaction catalysed: 
dUTP + H(2)O = dUMP + diphosphate
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-176242 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Deoxyuridine 5'-triphosphate nucleotidohydrolase, mitochondrial Chains: A, B, C
Molecule details ›
Chains: A, B, C
Length: 146 amino acids
Theoretical weight: 15.54 KDa
Source organism: Dictyostelium discoideum
Expression system: Escherichia coli
UniProt:
  • Canonical: Q54BW5 (Residues: 38-179; Coverage: 79%)
Gene names: DDB_G0293374, dut
Sequence domains: dUTPase
Structure domains: Deoxyuridine 5'-Triphosphate Nucleotidohydrolase; Chain A

Ligands and Environments

3 bound ligands:
Ligand DUP 3 x DUP
Ligand MG 5 x MG
Ligand SO4 1 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 14-BM-C
Spacegroup: P212121
Unit cell:
a: 71.633Å b: 72.458Å c: 75.158Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.213 0.209 0.251
Expression system: Escherichia coli

Quick links

Citations

2 citation in other articles

Discovery of two new isoforms of the human DUT gene.
Rácz et al. (2023)
1 more

1 mention without citation

Mitochondrial localization of Dictyostelium discoideum dUTPase mediated by its N-terminus.
Chia et al. (2020)