Steric and Electronic Effects in the Enzymatic Catalysis of Choline-TMA Lyase

An important microbial enzymatic pathway in the gut is choline/phosphatidylcholine degradation in which intestinal microbes utilize dietary choline to produce TMA via the choline utilization cluster polypeptide C (CutC) enzyme, a member of the glycyl radical enzyme family. Our goal in this theoretical work was to study the reaction mechanism and elucidate how the enzyme environment (steric and electronic) modulates the reaction path. Dissecting the effect of the enzyme environment on the reaction mechanism and shedding light on how steric and electronic effects affect the reaction path is an insightful and significant contribution of this work. Our theoretical results suggest that the final product of enzyme catalysis might be carbinolamine and not TMA and acetaldehyde. In addition, we found out that Glu491 plays the role of a base in this reaction (a disputed fact) by temporarily abstracting a proton from the hydroxylic group of choline sometime during the reaction—with the proton transfer being critical for the reaction to proceed to completion. We also found that the choice of computational protocol not only alters the reaction energetics but can change the reaction path by creating new intermediates and transition states or eliminating existing ones.