› 1dqx

X-ray diffraction
2.4Å resolution

CRYSTAL STRUCTURE OF OROTIDINE 5'-PHOSPHATE DECARBOXYLASE COMPLEXED TO 6-HYDROXYURIDINE 5'-PHOSPHATE (BMP)

Released:
DOI: 10.2210/pdb1dqx/pdb
PDB entry 1dqx coloured by chain, front view.
PDB entry 1dqx coloured by chain, side view.
PDB entry 1dqx coloured by chain, top view.
Source organism: Saccharomyces cerevisiae
Primary publication:
Anatomy of a proficient enzyme: the structure of orotidine 5'-monophosphate decarboxylase in the presence and absence of a potential transition state analog.
Miller BG, Hassell AM, Wolfenden R, Milburn MV, Short SA
Proc Natl Acad Sci U S A 97 2011-6 (2000)
PMID: 10681417

Function and Biology Details

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

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: 29.35 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 BMP 4 x BMP
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU RU200
Spacegroup: P21
Unit cell:
a: 79.89Å b: 79.97Å c: 98.19Å
α: 90° β: 108.59° γ: 90°
R-values:
R R work R free
0.224 0.213 0.258
Expression system: Escherichia coli

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Citations

19 review citations

Divergent evolution of enzymatic function: mechanistically diverse superfamilies and functionally distinct suprafamilies.
Gerlt et al. (2001)
18 more

32 mentions without citation

Specificity in transition state binding: the Pauling model revisited.
Amyes et al. (2013)
31 more