› 2qcd

X-ray diffraction
2.03Å resolution

Crystal structure of the orotidine-5'-monophosphate decarboxylase domain of human UMP synthase bound to UMP

Released:
DOI: 10.2210/pdb2qcd/pdb
PDB entry 2qcd coloured by chain, front view.
PDB entry 2qcd coloured by chain, side view.
PDB entry 2qcd coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structures of the human orotidine-5'-monophosphate decarboxylase support a covalent mechanism and provide a framework for drug design.
Wittmann JG, Heinrich D, Gasow K, Frey A, Diederichsen U, Rudolph MG
Structure 16 82-92 (2008)
PMID: 18184586

Function and Biology Details

Reactions catalysed: 
Orotidine 5'-phosphate + diphosphate = orotate + 5-phospho-alpha-D-ribose 1-diphosphate
Orotidine 5'-phosphate = UMP + CO(2)
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-145692 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Uridine 5'-monophosphate synthase Chain: A
Molecule details ›
Chain: A
Length: 260 amino acids
Theoretical weight: 28.33 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P11172 (Residues: 224-480; Coverage: 54%)
Gene names: OK/SW-cl.21, UMPS
Sequence domains: Orotidine 5'-phosphate decarboxylase / HUMPS family
Structure domains: Aldolase class I
Uridine 5'-monophosphate synthase Chain: B
Molecule details ›
Chain: B
Length: 260 amino acids
Theoretical weight: 28.3 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P11172 (Residues: 224-480; Coverage: 54%)
Gene names: OK/SW-cl.21, UMPS
Sequence domains: Orotidine 5'-phosphate decarboxylase / HUMPS family
Structure domains: Aldolase class I

Ligands and Environments

1 bound ligand:
Ligand U5P 2 x U5P
1 modified residue:
Ligand CSS 1 x CSS

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU MICROMAX-007
Spacegroup: P21
Unit cell:
a: 69.394Å b: 61.643Å c: 69.97Å
α: 90° β: 112.71° γ: 90°
R-values:
R R work R free
0.152 0.149 0.195
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

6 review citations

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

3 mentions without citation

Proton transfer from C-6 of uridine 5'-monophosphate catalyzed by orotidine 5'-monophosphate decarboxylase: formation and stability of a vinyl carbanion intermediate and the effect of a 5-fluoro substituent.
Tsang et al. (2012)
2 more