Transition Path Sampling Study of the Feruloyl Esterase Mechanism

• Published in: The journal of physical chemistry. B Vol. 125; no. 8; pp. 2018 - 2030
• Main Authors: Silveira, Rodrigo L, Knott, Brandon C, Pereira, Caroline S, Crowley, Michael F, Skaf, Munir S, Beckham, Gregg T
• Format: Journal Article
• Language: English
• Published: United States American Chemical Society 04.03.2021
• Subjects: active sites; amidases; aspartic acid; Aspergillus niger; B: Biophysical and Biochemical Systems and Processes; biotechnology; carbon; Carboxylic Ester Hydrolases - genetics; Catalysis; dissociation; drugs; enzymes; esterases; feruloyl esterase; histidine; Hydrolases; INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY; Lewis bases; lipases; peptidases; peptides; proteases; quantum mechanics; reaction mechanisms; Sampling Studies; serine; serine hydrolases
• ISSN: 1520-6106; 1520-5207; 1520-5207
• DOI: 10.1021/acs.jpcb.0c09725

Serine hydrolases cleave peptide and ester bonds and are ubiquitous in nature, with applications in biotechnology, in materials, and as drug targets. The serine hydrolase two-step mechanism employs a serine–histidine–aspartate/glutamate catalytic triad, where the histidine residue acts as a base to activate poor nucleophiles (a serine residue or a water molecule) and as an acid to allow the dissociation of poor leaving groups. This mechanism has been the subject of debate regarding how histidine shuttles the proton from the nucleophile to the leaving group. To elucidate the reaction mechanism of serine hydrolases, we employ quantum mechanics/molecular mechanics-based transition path sampling to obtain the reaction coordinate using the Aspergillus niger feruloyl esterase A (AnFaeA) as a model enzyme. The optimal reaction coordinates include terms involving nucleophilic attack on the carbonyl carbon and proton transfer to, and dissociation of, the leaving group. During the reaction, the histidine residue undergoes a reorientation on the time scale of hundreds of femtoseconds that supports the “moving histidine” mechanism, thus calling into question the “ring flip” mechanism. We find a concerted mechanism, where the transition state coincides with the tetrahedral intermediate with the histidine residue pointed between the nucleophile and the leaving group. Moreover, motions of the catalytic aspartate toward the histidine occur concertedly with proton abstraction by the catalytic histidine and help stabilize the transition state, thus partially explaining how serine hydrolases enable poor nucleophiles to attack the substrate carbonyl carbon. Rate calculations indicate that the second step (deacylation) is rate-determining, with a calculated rate constant of 66 s–1. Overall, these results reveal the pivotal role of active-site dynamics in the catalytic mechanism of AnFaeA, which is likely similar in other serine hydrolases.