› 2fty

X-ray diffraction
2.4Å resolution

Crystal structure of dihydropyrimidinase from Saccharomyces kluyveri

Released:
DOI: 10.2210/pdb2fty/pdb
PDB entry 2fty coloured by chain, front view.
PDB entry 2fty coloured by chain, side view.
PDB entry 2fty 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

1 bound ligand:
Ligand ZN 8 x ZN
1 modified residue:
Ligand KCX 4 x KCX

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID14-2
Spacegroup: P21
Unit cell:
a: 91.428Å b: 73.32Å c: 162.181Å
α: 90° β: 91.59° γ: 90°
R-values:
R R work R free
0.22 0.217 0.274
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

1 mention without citation

Dihydropyrimidinase from Saccharomyces kluyveri can hydrolyse polyamides.
Quartinello et al. (2023)