› 2y1t

X-ray diffraction
1.89Å resolution

Bacillus subtilis prophage dUTPase in complex with dUDP

Released:
DOI: 10.2210/pdb2y1t/pdb
PDB entry 2y1t coloured by chain, front view.
PDB entry 2y1t coloured by chain, side view.
PDB entry 2y1t coloured by chain, top view.
Source organism: Bacillus subtilis
Primary publication:
The structure of Bacillus subtilis SPβ prophage dUTPase and its complexes with two nucleotides.
García-Nafría J, Harkiolaki M, Persson R, Fogg MJ, Wilson KS
Acta Crystallogr D Biol Crystallogr 67 167-75 (2011)
PMID: 21358047

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-128623 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
SPbeta prophage-derived deoxyuridine 5'-triphosphate nucleotidohydrolase YosS Chains: A, B, C, D, E, F
Molecule details ›
Chains: A, B, C, D, E, F
Length: 142 amino acids
Theoretical weight: 16.17 KDa
Source organism: Bacillus subtilis
Expression system: Escherichia coli
UniProt:
  • Canonical: O34919 (Residues: 1-142; Coverage: 100%)
Gene names: BSU20020, yojU, yosS
Sequence domains: dUTPase
Structure domains: Deoxyuridine 5'-Triphosphate Nucleotidohydrolase; Chain A

Ligands and Environments

1 bound ligand:
Ligand DUD 5 x DUD
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID14-1
Spacegroup: P212121
Unit cell:
a: 99.515Å b: 99.338Å c: 99.306Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.142 0.14 0.166
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)
2 other articles

1 mention without citation

Homology-based loop modeling yields more complete crystallographic protein structures.
van Beusekom et al. (2018)