Structural bases for understanding the stereoselectivity in ketone reductions with ADH from Thermus thermophilus: A quantitative model

Automated structural analysis of alcohol dehydrogenase from Thermus thermophilus (ADHTt), a new carbonyl reductase recently described belonging to the SDR superfamily, allows to identify the aminoacidic residues responsible for the reductive catalytic activity, namely Ser-135, Tyr-148 and Lys-152. A series of acetophenone like compounds reduced with such enzyme was docked showing a distinct preference for binding to the active center. Favorable docking conformations calculated with two different protocols fall into two low-energy ensembles. These conformational ensembles are distinguished by the relative position of a given structure, presenting either the si- or re-face of the ketone to the nicotinamide mononucleotide (NMN) moiety reductant. For the ketones presented here, there is a correspondence between the major enantiomer obtained from the experimental data and the conformer found to have the most stable interaction energy with the receptor site in all cases. Furthermore, based on these two energy data sets we were able to build a reliable quantitative model (R2 = 0.98; crossvalidation q2 = 0.78) to predict the percentage of conversion from docking energy and the nature of the substrate with the following equation: conversion (%) = 30.80 Ed − 72.84σ + 224.34, where Ed is docking energy and σ is the Mulliken charge of the adjacent group of the ketone. The receptor site modeling, docking simulations, and enzyme–substrate geometry optimizations lead to a model for understanding the enantioselectivity of this NADH dependent carbonyl reductase.

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► Ketone bio-reduction.
► Alcohol dehydrogenase from Thermus thermophilus.
► Description of cofactor and substrate binding site.
► Rational explanation of enzymatic enantioselectivity.
► Quantitative semiempirical model.