› 3g1y

X-ray diffraction
1.4Å resolution

Crystal structure of the mutant D70N of orotidine 5'-monophosphate decarboxylase from Methanobacterium thermoautotrophicum complexed with sulfate

Released:
DOI: 10.2210/pdb3g1y/pdb
PDB entry 3g1y coloured by chain, front view.
PDB entry 3g1y coloured by chain, side view.
PDB entry 3g1y coloured by chain, top view.
Source organism: Methanothermobacter thermautotrophicus str. Delta H
Primary publication:
Mechanism of the orotidine 5'-monophosphate decarboxylase-catalyzed reaction: evidence for substrate destabilization.
Chan KK, Wood BM, Fedorov AA, Fedorov EV, Imker HJ, Amyes TL, Richard JP, Almo SC, Gerlt JA
Biochemistry 48 5518-31 (2009)
PMID: 19435314

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: 24.88 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

1 bound ligand:
Ligand SO4 2 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X4A
Spacegroup: P41
Unit cell:
a: 56.569Å b: 56.569Å c: 127.353Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.231 0.229 0.246
Expression system: Escherichia coli

Quick links

Citations

5 review citations

Enzyme activation through the utilization of intrinsic dianion binding energy.
Amyes et al. (2017)
4 more

1 mention without citation

Mechanism of the orotidine 5'-monophosphate decarboxylase-catalyzed reaction: evidence for substrate destabilization.
Chan et al. (2009)