› 2fvk

X-ray diffraction
2.4Å resolution

Crystal structure of dihydropyrimidinase from Saccharomyces kluyveri in complex with the substrate dihydrouracil

Released:
DOI: 10.2210/pdb2fvk/pdb
PDB entry 2fvk coloured by chain, front view.
PDB entry 2fvk coloured by chain, side view.
PDB entry 2fvk coloured by chain, top view.
Source organism: Lachancea kluyveri
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:
  • not assigned
Cellular component:
Sequence domains:
Structure domains:

Structure analysis Details

Assembly composition:
homo tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-192874 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Dihydropyrimidinase Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 559 amino acids
Theoretical weight: 62.33 KDa
Source organism: Lachancea kluyveri
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: Q9P903 (Residues: 2-542; Coverage: 100%)
Gene name: PYD2
Sequence domains: Amidohydrolase family
Structure domains:

Ligands and Environments

2 bound ligands:
Ligand ZN 8 x ZN
Ligand DUC 4 x DUC
1 modified residue:
Ligand KCX 4 x KCX

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID14-3
Spacegroup: P21
Unit cell:
a: 90.13Å b: 71.6Å c: 161.89Å
α: 90° β: 91.4° γ: 90°
R-values:
R R work R free
0.181 0.178 0.234
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

Inhibition of a Putative Dihydropyrimidinase from Pseudomonas aeruginosa PAO1 by Flavonoids and Substrates of Cyclic Amidohydrolases.
Huang CY. (2015)
2 more