› 1pkk

X-ray diffraction
1.77Å resolution

Structural basis for recognition and catalysis by the bifunctional dCTP deaminase and dUTPase from Methanococcus jannaschii

Released:
DOI: 10.2210/pdb1pkk/pdb
PDB entry 1pkk coloured by chain, front view.
PDB entry 1pkk coloured by chain, side view.
PDB entry 1pkk coloured by chain, top view.
Source organism: Methanocaldococcus jannaschii
Primary publication:
Structural basis for recognition and catalysis by the bifunctional dCTP deaminase and dUTPase from Methanococcus jannaschii.
Huffman JL, Li H, White RH, Tainer JA
J Mol Biol 331 885-96 (2003)
PMID: 12909016

Function and Biology Details

Reaction catalysed: 
dCTP + 2 H(2)O = dUMP + diphosphate + NH(3)
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:
Structure domain:

Structure analysis Details

Assemblies composition:
homo hexamer (preferred)
homo trimer
Assembly name:
PDBe Complex ID:
PDB-CPX-176494 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
dCTP deaminase, dUMP-forming Chains: A, B
Molecule details ›
Chains: A, B
Length: 204 amino acids
Theoretical weight: 23.46 KDa
Source organism: Methanocaldococcus jannaschii
Expression system: Escherichia coli
UniProt:
  • Canonical: Q57872 (Residues: 1-204; Coverage: 100%)
Gene names: MJ0430, dcd
Sequence domains: dUTPase
Structure domains: Deoxyuridine 5'-Triphosphate Nucleotidohydrolase; Chain A

Ligands and Environments

2 bound ligands:
Ligand EDO 7 x EDO
Ligand DCP 1 x DCP
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRL BEAMLINE BL9-2
Spacegroup: P213
Unit cell:
a: 110.576Å b: 110.576Å c: 110.576Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.197 0.197 0.219
Expression system: Escherichia coli

Quick links

Citations

3 review citations

DNA base damage recognition and removal: new twists and grooves.
Huffman et al. (2005)
2 more

1 mention without citation

Purification, crystallization and preliminary crystallographic analysis of deoxyuridine triphosphate nucleotidohydrolase from Arabidopsis thaliana.
Bajaj et al. (2007)