› 3pby

X-ray diffraction
1.3Å resolution

Crystal structure of the mutant L123S of orotidine 5'-monophosphate decarboxylase from Methanobacterium thermoautotrophicum complexed with 6-azauridine 5'-monophosphate

Released:
DOI: 10.2210/pdb3pby/pdb
PDB entry 3pby coloured by chain, front view.
PDB entry 3pby coloured by chain, side view.
PDB entry 3pby coloured by chain, top view.
Source organism: Methanothermobacter thermautotrophicus str. Delta H
Primary publication:
Mechanism of the orotidine 5'-monophosphate decarboxylase-catalyzed reaction: importance of residues in the orotate binding site.
Iiams V, Desai BJ, Fedorov AA, Fedorov EV, Almo SC, Gerlt JA
Biochemistry 50 8497-507 (2011)
PMID: 21870810

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: 24.86 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 UP6 2 x UP6
Ligand GOL 1 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X4A
Spacegroup: P21
Unit cell:
a: 59.768Å b: 64.046Å c: 61.611Å
α: 90° β: 115.5° γ: 90°
R-values:
R R work R free
0.161 0.16 0.169
Expression system: Escherichia coli

Quick links

Citations

2 review citations

DNA demethylation pathways: Additional players and regulators.
Bochtler et al. (2017)
1 more

1 mention without citation

Mechanism of the orotidine 5'-monophosphate decarboxylase-catalyzed reaction: importance of residues in the orotate binding site.
Iiams et al. (2011)