5KDP

E491A mutant of choline TMA-lyase

Summary for 5KDP

• Entry DOI: 10.2210/pdb5kdp/pdb
• Descriptor: Choline trimethylamine-lyase, SODIUM ION, MALONATE ION, ... (4 entities in total)
• Functional Keywords: mutant, radical, lyase
• Biological source: Desulfovibrio alaskensis
• Total number of polymer chains: 2
• Total formula weight: 183714.43

Authors

Funk, M.A.,Drennan, C.L. (deposition date: 2016-06-08, release date: 2016-09-28, Last modification date: 2023-09-27)

Primary citation

Bodea, S.,Funk, M.A.,Balskus, E.P.,Drennan, C.L.
Molecular Basis of C-N Bond Cleavage by the Glycyl Radical Enzyme Choline Trimethylamine-Lyase.
Cell Chem Biol, 23:1206-1216, 2016

PubMed Abstract: Deamination of choline catalyzed by the glycyl radical enzyme choline trimethylamine-lyase (CutC) has emerged as an important route for the production of trimethylamine, a microbial metabolite associated with both human disease and biological methane production. Here, we have determined five high-resolution X-ray structures of wild-type CutC and mechanistically informative mutants in the presence of choline. Within an unexpectedly polar active site, CutC orients choline through hydrogen bonding with a putative general base, and through close interactions between phenolic and carboxylate oxygen atoms of the protein scaffold and the polarized methyl groups of the trimethylammonium moiety. These structural data, along with biochemical analysis of active site mutants, support a mechanism that involves direct elimination of trimethylamine. This work broadens our understanding of radical-based enzyme catalysis and will aid in the rational design of inhibitors of bacterial trimethylamine production.

PubMed: 27642068
DOI: 10.1016/j.chembiol.2016.07.020

Experimental method

X-RAY DIFFRACTION (1.9 Å)