› 4aoz

X-ray diffraction
2.05Å resolution

B. subtilis dUTPase YncF in complex with dU, PPi and Mg (P212121)

Released:
DOI: 10.2210/pdb4aoz/pdb
PDB entry 4aoz coloured by chain, front view.
PDB entry 4aoz coloured by chain, side view.
PDB entry 4aoz coloured by chain, top view.
Source organism: Bacillus subtilis
Primary publication:
Tying down the arm in Bacillus dUTPase: structure and mechanism.
García-Nafría J, Timm J, Harrison C, Turkenburg JP, Wilson KS
Acta Crystallogr D Biol Crystallogr 69 1367-80 (2013)
PMID: 23897460

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-128374 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Deoxyuridine 5'-triphosphate nucleotidohydrolase YncF Chains: A, B, C
Molecule details ›
Chains: A, B, C
Length: 144 amino acids
Theoretical weight: 16.43 KDa
Source organism: Bacillus subtilis
Expression system: Escherichia coli
UniProt:
  • Canonical: O31801 (Residues: 1-144; Coverage: 100%)
Gene names: BSU17660, yncF
Sequence domains: dUTPase
Structure domains: Deoxyuridine 5'-Triphosphate Nucleotidohydrolase; Chain A

Ligands and Environments

5 bound ligands:
Ligand DUR 3 x DUR
Ligand POP 2 x POP
Ligand MG 2 x MG
Ligand ACT 2 x ACT
Ligand CL 1 x CL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I04-1
Spacegroup: P212121
Unit cell:
a: 70.27Å b: 71.534Å c: 92.299Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.162 0.159 0.213
Expression system: Escherichia coli

Quick links

Citations

5 citation in other articles

Catalytic mechanism of α-phosphate attack in dUTPase is revealed by X-ray crystallographic snapshots of distinct intermediates, 31P-NMR spectroscopy and reaction path modelling.
Barabás et al. (2013)
4 more