› 3gdt

X-ray diffraction
1.6Å resolution

Crystal structure of the D91N mutant of the orotidine 5'-monophosphate decarboxylase from Saccharomyces cerevisiae complexed with 6-azauridine 5'-monophosphate

Released:
DOI: 10.2210/pdb3gdt/pdb
PDB entry 3gdt coloured by chain, front view.
PDB entry 3gdt coloured by chain, side view.
PDB entry 3gdt coloured by chain, top view.
Source organism: Saccharomyces cerevisiae
Primary publication:
Mechanism of the orotidine 5'-monophosphate decarboxylase-catalyzed reaction: evidence for substrate destabilization.
Chan KK, Wood BM, Fedorov AA, Fedorov EV, Imker HJ, Amyes TL, Richard JP, Almo SC, Gerlt JA
Biochemistry 48 5518-31 (2009)
PMID: 19435314

Function and Biology Details

Reaction catalysed: 
Orotidine 5'-phosphate = UMP + CO(2)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-137303 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Orotidine 5'-phosphate decarboxylase Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 267 amino acids
Theoretical weight: 29.28 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Escherichia coli
UniProt:
  • Canonical: P03962 (Residues: 1-267; Coverage: 100%)
Gene names: URA3, YEL021W
Sequence domains: Orotidine 5'-phosphate decarboxylase / HUMPS family
Structure domains: Aldolase class I

Ligands and Environments

1 bound ligand:
Ligand UP6 4 x UP6
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X4A
Spacegroup: P212121
Unit cell:
a: 84.351Å b: 99.14Å c: 126.307Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.237 0.236 0.257
Expression system: Escherichia coli

Quick links

Citations

5 review citations

Enzyme activation through the utilization of intrinsic dianion binding energy.
Amyes et al. (2017)
4 more

2 mentions without citation

Mechanism of the orotidine 5'-monophosphate decarboxylase-catalyzed reaction: evidence for substrate destabilization.
Chan et al. (2009)
1 more