› 2xcd

X-ray diffraction
1.84Å resolution

Structure of YncF,the genomic dUTPase from Bacillus subtilis

Released:
DOI: 10.2210/pdb2xcd/pdb
PDB entry 2xcd coloured by chain, front view.
PDB entry 2xcd coloured by chain, side view.
PDB entry 2xcd coloured by chain, top view.
Source organism: Bacillus subtilis
Primary publication:
The structure of the genomic Bacillus subtilis dUTPase: novel features in the Phe-lid.
García-Nafría J, Burchell L, Takezawa M, Rzechorzek NJ, Fogg MJ, Wilson KS
Acta Crystallogr D Biol Crystallogr 66 953-61 (2010)
PMID: 20823546

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, D, E, F
Molecule details ›
Chains: A, B, C, D, E, F
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

4 bound ligands:
Ligand MG 2 x MG
Ligand NA 6 x NA
Ligand CL 3 x CL
Ligand GOL 1 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID14-2
Spacegroup: P212121
Unit cell:
a: 98.81Å b: 98.84Å c: 99.11Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.156 0.155 0.184
Expression system: Escherichia coli

Quick links

Citations

1 review citation

Preventive DNA repair by sanitizing the cellular (deoxy)nucleoside triphosphate pool.
Nagy et al. (2014)
4 other articles

3 mentions without citation

The Blueprint of a Minimal Cell: MiniBacillus.
Reuß et al. (2016)
2 more