› 2hr6

X-ray diffraction
1.84Å resolution

Crystal structure of dUTPase in complex with substrate analogue dUDP and manganese

Released:
DOI: 10.2210/pdb2hr6/pdb
PDB entry 2hr6 coloured by chain, front view.
PDB entry 2hr6 coloured by chain, side view.
PDB entry 2hr6 coloured by chain, top view.
Source organism: Escherichia coli
Primary publication:
Methylene substitution at the alpha-beta bridging position within the phosphate chain of dUDP profoundly perturbs ligand accommodation into the dUTPase active site.
Kovári J, Barabás O, Varga B, Békési A, Tölgyesi F, Fidy J, Nagy J, Vértessy BG
Proteins 71 308-19 (2008)
PMID: 17932923

Function and Biology Details

Reaction catalysed: 
dUTP + H(2)O = dUMP + diphosphate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:
Structure domain:

Structure analysis Details

Assembly composition:
homo trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-139313 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Deoxyuridine 5'-triphosphate nucleotidohydrolase Chain: A
Molecule details ›
Chain: A
Length: 152 amino acids
Theoretical weight: 16.3 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P06968 (Residues: 2-152; Coverage: 99%)
Gene names: JW3615, b3640, dnaS, dut, sof
Sequence domains: dUTPase
Structure domains: Deoxyuridine 5'-Triphosphate Nucleotidohydrolase; Chain A

Ligands and Environments

3 bound ligands:
Ligand MN 1 x MN
Ligand DUD 1 x DUD
Ligand EDO 1 x EDO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: EMBL/DESY, HAMBURG BEAMLINE X11
Spacegroup: P6322
Unit cell:
a: 75.049Å b: 75.049Å c: 99.936Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.152 0.151 0.173
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)
21 other articles

1 mention without citation

FERROCHELATASE: THE CONVERGENCE OF THE PORPHYRIN BIOSYNTHESIS AND IRON TRANSPORT PATHWAYS.
Hunter et al. (2011)