› 5m1e

X-ray diffraction
2.62Å resolution

Crystal structure of N-terminally tagged UbiD from E. coli reconstituted with prFMN cofactor

Released:
DOI: 10.2210/pdb5m1e/pdb
PDB entry 5m1e coloured by chain, front view.
PDB entry 5m1e coloured by chain, side view.
PDB entry 5m1e coloured by chain, top view.
Source organism: Escherichia coli CFT073
Primary publication:
Oxidative Maturation and Structural Characterization of Prenylated FMN Binding by UbiD, a Decarboxylase Involved in Bacterial Ubiquinone Biosynthesis.
Marshall SA, Fisher K, Ní Cheallaigh A, White MD, Payne KA, Parker DA, Rigby SE, Leys D
J Biol Chem 292 4623-4637 (2017)
PMID: 28057757

Function and Biology Details

Reaction catalysed: 
A 4-hydroxy-3-polyprenylbenzoate = a 2-polyprenylphenol + CO(2)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo hexamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-141981 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
3-octaprenyl-4-hydroxybenzoate carboxy-lyase Chains: A, B, C
Molecule details ›
Chains: A, B, C
Length: 517 amino acids
Theoretical weight: 57.84 KDa
Source organism: Escherichia coli CFT073
Expression system: Escherichia coli
UniProt:
  • Canonical: P0AAB5 (Residues: 1-497; Coverage: 100%)
Gene names: c4790, ubiD
Sequence domains:
Structure domains: UbiD C-terminal domain-like

Ligands and Environments

3 bound ligands:
Ligand MN 3 x MN
Ligand 7D9 3 x 7D9
Ligand NA 3 x NA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I03
Spacegroup: P43212
Unit cell:
a: 194.52Å b: 194.52Å c: 107.41Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.177 0.175 0.212
Expression system: Escherichia coli

Quick links

Citations

4 review citations

Non-Oxidative Enzymatic (De)Carboxylation of (Hetero)Aromatics and Acrylic Acid Derivatives.
Payer et al. (2019)
3 more

1 mention without citation

Oxidative Maturation and Structural Characterization of Prenylated FMN Binding by UbiD, a Decarboxylase Involved in Bacterial Ubiquinone Biosynthesis.
Marshall et al. (2017)