› 2py4

X-ray diffraction
1.49Å resolution

Full length structure of the Mycobacterium tuberculosis dUTPase complexed with magnesium and alpha,beta-imido-dUTP.

Released:
DOI: 10.2210/pdb2py4/pdb
PDB entry 2py4 coloured by chain, front view.
PDB entry 2py4 coloured by chain, side view.
PDB entry 2py4 coloured by chain, top view.
Source organism: Mycobacterium tuberculosis
Primary publication:
Active site of mycobacterial dUTPase: structural characteristics and a built-in sensor.
Varga B, Barabás O, Takács E, Nagy N, Nagy P, Vértessy BG
Biochem Biophys Res Commun 373 8-13 (2008)
PMID: 18519027

Function and Biology Details

Reaction catalysed: 
dUTP + H(2)O = dUMP + diphosphate
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:
Structure domain:

Structure analysis Details

Assembly composition:
homo trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-161882 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Deoxyuridine 5'-triphosphate nucleotidohydrolase Chain: A
Molecule details ›
Chain: A
Length: 174 amino acids
Theoretical weight: 17.99 KDa
Source organism: Mycobacterium tuberculosis
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P9WNS5 (Residues: 1-154; Coverage: 100%)
Gene names: MTCY05A6.18c, Rv2697c, dut
Sequence domains: dUTPase
Structure domains: Deoxyuridine 5'-Triphosphate Nucleotidohydrolase; Chain A

Ligands and Environments

3 bound ligands:
Ligand MG 1 x MG
Ligand DUP 1 x DUP
Ligand TRS 1 x TRS
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU
Spacegroup: P63
Unit cell:
a: 54.591Å b: 54.591Å c: 83.051Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.146 0.144 0.17
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

1 review citation

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

12 mentions without citation

Aromatic stacking between nucleobase and enzyme promotes phosphate ester hydrolysis in dUTPase.
Pecsi et al. (2010)
11 more