› 6vue

X-ray diffraction
2.28Å resolution

wild-type choline TMA lyase in complex with 1-methyl-1,2,3,6-tetrahydropyridin-3-ol

Released:
DOI: 10.2210/pdb6vue/pdb
PDB entry 6vue coloured by chain, front view.
PDB entry 6vue coloured by chain, side view.
PDB entry 6vue coloured by chain, top view.
Source organism: Oleidesulfovibrio alaskensis G20
Primary publication:
Discovery of a Cyclic Choline Analog That Inhibits Anaerobic Choline Metabolism by Human Gut Bacteria.
Bollenbach M, Ortega M, Orman M, Drennan CL, Balskus EP
ACS Med Chem Lett 11 1980-1985 (2020)
PMID: 33062182

Function and Biology Details

Reaction catalysed: 
Choline = trimethylamine + acetaldehyde
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-174246 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Choline trimethylamine-lyase Chains: A, B
Molecule details ›
Chains: A, B
Length: 815 amino acids
Theoretical weight: 91.59 KDa
Source organism: Oleidesulfovibrio alaskensis G20
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q30W70 (Residues: 53-846; Coverage: 94%)
Gene names: Dde_3282, cutC
Sequence domains:

Ligands and Environments

2 bound ligands:
Ligand NA 2 x NA
Ligand RP7 2 x RP7
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-E
Spacegroup: P42212
Unit cell:
a: 228.525Å b: 228.525Å c: 78.792Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.165 0.164 0.197
Expression system: Escherichia coli BL21(DE3)

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Citations

2 review citations

A structural metagenomics pipeline for examining the gut microbiome.
Walker et al. (2022)
1 more