› 1km4

X-ray diffraction
1.5Å resolution

crystal structure of ODCase mutant K72A complexed with UMP

Released:
DOI: 10.2210/pdb1km4/pdb
PDB entry 1km4 coloured by chain, front view.
PDB entry 1km4 coloured by chain, side view.
PDB entry 1km4 coloured by chain, top view.
Source organism: Methanothermobacter thermautotrophicus
Primary publication:
Mapping the active site-ligand interactions of orotidine 5'-monophosphate decarboxylase by crystallography.
Wu N, Gillon W, Pai EF
Biochemistry 41 4002-11 (2002)
PMID: 11900543

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-127822 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Orotidine 5'-phosphate decarboxylase Chain: A
Molecule details ›
Chain: A
Length: 247 amino acids
Theoretical weight: 26.74 KDa
Source organism: Methanothermobacter thermautotrophicus
Expression system: Escherichia coli
UniProt:
  • Canonical: O26232 (Residues: 1-228; Coverage: 100%)
Gene names: MTH_129, pyrF
Sequence domains: Orotidine 5'-phosphate decarboxylase / HUMPS family
Structure domains: Aldolase class I

Ligands and Environments

1 bound ligand:
Ligand U 1 x U
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 14-BM-C
Spacegroup: C2221
Unit cell:
a: 58.184Å b: 103.161Å c: 73.687Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.155 0.155 0.183
Expression system: Escherichia coli

Quick links

Citations

5 review citations

Mechanisms and free energies of enzymatic reactions.
Gao et al. (2006)
4 more

1 mention without citation

Structural characterization of the molecular events during a slow substrate-product transition in orotidine 5'-monophosphate decarboxylase.
Fujihashi et al. (2009)