› 2ftw

X-ray diffraction
2.05Å resolution

Crystal structure of dihydropyrimidinase from dictyostelium discoideum

Released:
DOI: 10.2210/pdb2ftw/pdb
PDB entry 2ftw coloured by chain, front view.
PDB entry 2ftw coloured by chain, side view.
PDB entry 2ftw coloured by chain, top view.
Source organism: Dictyostelium discoideum
Primary publication:
The crystal structures of dihydropyrimidinases reaffirm the close relationship between cyclic amidohydrolases and explain their substrate specificity.
Lohkamp B, Andersen B, Piškur J, Dobritzsch D
J Biol Chem 281 13762-13776 (2006)
PMID: 16517602

Function and Biology Details

Reaction catalysed: 
5,6-dihydrouracil + H(2)O = 3-ureidopropanoate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:
Structure domains:

Structure analysis Details

Assembly composition:
homo tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-560603 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Dihydropyrimidinase Chain: A
Molecule details ›
Chain: A
Length: 521 amino acids
Theoretical weight: 58.34 KDa
Source organism: Dictyostelium discoideum
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: Q55DL0 (Residues: 1-503; Coverage: 100%)
Gene names: DDB_G0269246, pyd2
Sequence domains: Amidohydrolase family
Structure domains: Metal-dependent hydrolases

Ligands and Environments

2 bound ligands:
Ligand ZN 2 x ZN
Ligand MLI 1 x MLI
1 modified residue:
Ligand KCX 1 x KCX

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID14-4
Spacegroup: I222
Unit cell:
a: 84.6Å b: 89.599Å c: 134.953Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.207 0.204 0.252
Expression system: Escherichia coli BL21

Quick links

Citations

3 review citations

Saccharomyces kluyveri as a model organism to study pyrimidine degradation.
Beck et al. (2008)
2 more

3 mentions without citation

The crystal structure of Escherichia coli TdcF, a member of the highly conserved YjgF/YER057c/UK114 family.
Burman et al. (2007)
2 more