› 2fvm

X-ray diffraction
2.45Å resolution

Crystal structure of dihydropyrimidinase from Saccharomyces kluyveri in complex with the reaction product N-carbamyl-beta-alanine

Released:
DOI: 10.2210/pdb2fvm/pdb
PDB entry 2fvm coloured by chain, front view.
PDB entry 2fvm coloured by chain, side view.
PDB entry 2fvm 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 URP 2 x URP
1 modified residue:
Ligand KCX 4 x KCX

Experiments and Validation Details

Entry percentile scores
X-ray source: EMBL/DESY, HAMBURG BEAMLINE BW7B
Spacegroup: P21
Unit cell:
a: 91.141Å b: 73.027Å c: 164.105Å
α: 90° β: 91.98° γ: 90°
R-values:
R R work R free
0.185 0.182 0.237
Expression system: Escherichia coli BL21

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Citations

3 review citations

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