Theoretical study of primary reaction of Pseudozyma antarctica lipase B as the starting point to understand its promiscuity

Abstract

Pseudozyma antarctica lipase B (PALB) is a serine hydrolase that catalyzes the hydrolysis of carboxylic acid esters in aqueous medium but it has also shown catalytic activity for a plethora of reactions. This promiscuous activity has found widespread applications. In the present paper, the primary reaction of PALB, its native hydrolytic activity, has been studied using hybrid quantum mechanical/molecular mechanical (QM/MM) potentials. Free energy surfaces, obtained from QM/MM Molecular Dynamics (MD) simulations, show that the reaction takes place by means of a multi-step mechanism where the first step, the activation of the carbonyl group of the substrate and the nucleophilic attack of Ser105 to the carbonyl carbon atom, presents the highest energy transition state. Our results, which are in good agreement with kinetic experimental data, suggest that the origin of the catalytic activity of the enzyme is due to favorable interactions established between the residues of the active site that create an oxyanion hole, Gln106 and Thr40, as well as the Asp187 that is capable of modulating the pKa of His224 to act as a base or an acid depending on the step of the catalytic process. Our results can be used to rationalize the design of an optimum biocatalyst to accelerate fundamental reactions in organic synthesis based on the protein scaffold of PALB.