› 1gth

X-ray diffraction
2.25Å resolution

DIHYDROPYRIMIDINE DEHYDROGENASE (DPD) FROM PIG, TERNARY COMPLEX WITH NADPH AND 5-IODOURACIL

Released:
DOI: 10.2210/pdb1gth/pdb
PDB entry 1gth coloured by chain, front view.
PDB entry 1gth coloured by chain, side view.
PDB entry 1gth coloured by chain, top view.
Source organism: Sus scrofa
Primary publication:
Crystal structure of the productive ternary complex of dihydropyrimidine dehydrogenase with NADPH and 5-iodouracil. Implications for mechanism of inhibition and electron transfer.
Dobritzsch D, Ricagno S, Schneider G, Schnackerz KD, Lindqvist Y
J Biol Chem 277 13155-66 (2002)
PMID: 11796730

Function and Biology Details

Reaction catalysed: 
5,6-dihydrouracil + NADP(+) = uracil + NADPH
Biochemical function:
Biological process:
Cellular component:
Sequence domains:
Structure domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-173320 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Dihydropyrimidine dehydrogenase [NADP(+)] Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 1025 amino acids
Theoretical weight: 111.6 KDa
Source organism: Sus scrofa
Expression system: Escherichia coli DH5[alpha]
UniProt:
  • Canonical: Q28943 (Residues: 1-1025; Coverage: 100%)
Gene name: DPYD
Sequence domains:
Structure domains:

Ligands and Environments


Cofactor: Ligand FAD 4 x FAD

Cofactor: Ligand FMN 4 x FMN

Cofactor: Ligand NDP 4 x NDP
4 bound ligands:
Ligand SF4 16 x SF4
Ligand IDH 2 x IDH
Ligand IUR 1 x IUR
Ligand URA 1 x URA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID14-3
Spacegroup: P21
Unit cell:
a: 82.21Å b: 159.69Å c: 167.59Å
α: 90° β: 97.11° γ: 90°
R-values:
R R work R free
0.177 0.177 0.209
Expression system: Escherichia coli DH5[alpha]

Quick links

Citations

4 review citations

Dihydropyrimidine dehydrogenase deficiency, a pharmacogenetic syndrome associated with potentially life-threatening toxicity following 5-fluorouracil administration.
Ezzeldin et al. (2004)
3 more

5 mentions without citation

Comparative functional analysis of DPYD variants of potential clinical relevance to dihydropyrimidine dehydrogenase activity.
Offer et al. (2014)
4 more