› 4ao5

X-ray diffraction
1.6Å resolution

B. subtilis prophage dUTPase YosS in complex with dUMP

Released:
DOI: 10.2210/pdb4ao5/pdb
PDB entry 4ao5 coloured by chain, front view.
PDB entry 4ao5 coloured by chain, side view.
PDB entry 4ao5 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:
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: 145 amino acids
Theoretical weight: 16.4 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

2 bound ligands:
Ligand UMP 6 x UMP
Ligand NA 5 x NA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I04-1
Spacegroup: P212121
Unit cell:
a: 99.82Å b: 100.01Å c: 99.51Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.153 0.15 0.214
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