› 3wjx

X-ray diffraction
1.23Å resolution

Wild-type orotidine 5'-monophosphate decarboxylase from M. thermoautotrophicus complexed with 6-amino-UMP

Released:
DOI: 10.2210/pdb3wjx/pdb
PDB entry 3wjx coloured by chain, front view.
PDB entry 3wjx coloured by chain, side view.
PDB entry 3wjx coloured by chain, top view.
Source organism: Methanothermobacter thermautotrophicus str. Delta H
Primary publication:
Substrate distortion contributes to the catalysis of orotidine 5'-monophosphate decarboxylase.
Fujihashi M, Ishida T, Kuroda S, Kotra LP, Pai EF, Miki K
J Am Chem Soc 135 17432-43 (2013)
PMID: 24151964

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 Chain: A
Molecule details ›
Chain: A
Length: 252 amino acids
Theoretical weight: 27.38 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 NUP 1 x NUP
Ligand GOL 2 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL41XU
Spacegroup: C2221
Unit cell:
a: 57.885Å b: 103.351Å c: 73.579Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.156 0.156 0.164
Expression system: Escherichia coli

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Citations

4 review citations

Transition metal catalysis in confined spaces.
Leenders et al. (2015)
3 more