Dataset for: Mechanistic Insights into Lysine Cyclodeaminase Catalysis

This dataset contains the raw data and processed experimental data supporting the above publication. This study investigates the molecular basis of substrate selectivity in lysine cyclodeaminase (LCD), an enzyme that catalyzes the conversion of L-lysine into L-pipecolic acid, an important building block for food additives and pharmaceutical intermediates. A combination of molecular docking, substrate tunnel engineering, classical molecular dynamics, well-tempered metadynamics simulations, and experimental validation was used to elucidate the catalytic mechanism and identify the factors limiting the conversion of L-lysine ethyl ester. Computational analyses showed that both substrates can access and bind the active site, and tunnel-engineered LCD variants with improved substrate access were successfully designed. However, experimental assays confirmed that these variants remained inactive toward L-lysine ethyl ester. Mechanistic simulations revealed that, unlike L-lysine, the esterified substrate preferentially adopts higher-energy, non-productive conformations that prevent efficient cyclization despite successful binding. These findings demonstrate that substrate selectivity is primarily governed by steric and dynamic constraints during catalysis rather than substrate accessibility, providing a mechanistic framework for the rational engineering of LCD variants with an expanded substrate scope.