› 7ca1

X-ray diffraction
3.6Å resolution

Crystal structure of dihydroorotase in complex with plumbagin from Saccharomyces cerevisiae

Released:
DOI: 10.2210/pdb7ca1/pdb
PDB entry 7ca1 coloured by chain, front view.
PDB entry 7ca1 coloured by chain, side view.
PDB entry 7ca1 coloured by chain, top view.
Source organism: Saccharomyces cerevisiae S288C
Primary publication:
Plumbagin, a Natural Product with Potent Anticancer Activities, Binds to and Inhibits Dihydroorotase, a Key Enzyme in Pyrimidine Biosynthesis.
Guan HH, Huang YH, Lin ES, Chen CJ, Huang CY
Int J Mol Sci 22 (2021)
PMID: 34202294

Function and Biology Details

Reaction catalysed: 
(S)-dihydroorotate + H(2)O = N-carbamoyl-L-aspartate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-148825 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Dihydroorotase Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 372 amino acids
Theoretical weight: 41.48 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli
UniProt:
  • Canonical: P20051 (Residues: 1-364; Coverage: 100%)
Gene names: L9931.1, URA4, YLR420W
Sequence domains: Amidohydrolase

Ligands and Environments

3 bound ligands:
Ligand LMR 2 x LMR
Ligand ZN 8 x ZN
Ligand 90R 2 x 90R
1 modified residue:
Ligand KCX 4 x KCX

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL44XU
Spacegroup: P21
Unit cell:
a: 85.24Å b: 88.36Å c: 103.42Å
α: 90° β: 95.16° γ: 90°
R-values:
R R work R free
0.263 0.261 0.309
Expression system: Escherichia coli

Quick links

Citations

2 review citations

Carnivorous Plants from Nepenthaceae and Droseraceae as a Source of Secondary Metabolites.
Wójciak et al. (2023)
1 more

3 mentions without citation

Plumbagin, a Natural Product with Potent Anticancer Activities, Binds to and Inhibits Dihydroorotase, a Key Enzyme in Pyrimidine Biosynthesis.
Guan et al. (2021)
2 more