› 2xy3

X-ray diffraction
2.55Å resolution

Structure of the Bacillus subtilis prophage dUTPase with dUpNHpp

Released:
DOI: 10.2210/pdb2xy3/pdb
PDB entry 2xy3 coloured by chain, front view.
PDB entry 2xy3 coloured by chain, side view.
PDB entry 2xy3 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 BL21
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

2 bound ligands:
Ligand DUP 6 x DUP
Ligand MG 3 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I02
Spacegroup: P212121
Unit cell:
a: 98.474Å b: 98.4Å c: 97.993Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.197 0.194 0.251
Expression system: Escherichia coli BL21

Quick links

Citations

1 review citation

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