› 3p5y

X-ray diffraction
1.6Å resolution

Crystal structure of the mutant T159A of orotidine 5'-monophosphate decarboxylase from Methanobacterium thermoautotrophicum complexed with inhibitor BMP

Released:
DOI: 10.2210/pdb3p5y/pdb
PDB entry 3p5y coloured by chain, front view.
PDB entry 3p5y coloured by chain, side view.
PDB entry 3p5y coloured by chain, top view.
Source organism: Methanothermobacter thermautotrophicus str. Delta H
Primary publication:
Conformational changes in orotidine 5'-monophosphate decarboxylase: a structure-based explanation for how the 5'-phosphate group activates the enzyme.
Desai BJ, Wood BM, Fedorov AA, Fedorov EV, Goryanova B, Amyes TL, Richard JP, Almo SC, Gerlt JA
Biochemistry 51 8665-78 (2012)
PMID: 23030629

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-127822 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Orotidine 5'-phosphate decarboxylase Chains: A, B
Molecule details ›
Chains: A, B
Length: 228 amino acids
Theoretical weight: 24.85 KDa
Source organism: Methanothermobacter thermautotrophicus str. Delta H
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

2 bound ligands:
Ligand BMP 2 x BMP
Ligand GOL 1 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X4A
Spacegroup: P212121
Unit cell:
a: 52.608Å b: 74.038Å c: 117.503Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.206 0.204 0.23
Expression system: Escherichia coli

Quick links

Citations

1 review citation

A reevaluation of the origin of the rate acceleration for enzyme-catalyzed hydride transfer.
Reyes et al. (2017)
7 other articles

1 mention without citation

Conformational changes in orotidine 5'-monophosphate decarboxylase: a structure-based explanation for how the 5'-phosphate group activates the enzyme.
Desai et al. (2012)