Transition Path Sampling Study of the Feruloyl Esterase Mechanism

Silveira, Rodrigo L.; Knott, Brandon C.; Pereira, Caroline S.; Crowley, Michael F.; Skaf, Munir S.; Beckham, Gregg T.

doi:10.1021/acs.jpcb.0c09725

Title: Transition Path Sampling Study of the Feruloyl Esterase Mechanism

Journal Article · Mon Feb 22 00:00:00 EST 2021 · Journal of Physical Chemistry. B, Condensed Matter, Materials, Surfaces, Interfaces and Biophysical Chemistry

DOI:https://doi.org/10.1021/acs.jpcb.0c09725· OSTI ID:1770879

Silveira, Rodrigo L. ^[1]; Knott, Brandon C. ^[2]; Pereira, Caroline S. ^[3];

^[2];

^[4];

^[2]

National Renewable Energy Lab. (NREL), Golden, CO (United States); Univ of Campinas, Sao Paulo (Brazil); Federal Univ. of Rio de Janeiro (Brazil)
National Renewable Energy Lab. (NREL), Golden, CO (United States)
National Renewable Energy Lab. (NREL), Golden, CO (United States); Univ of Campinas, Sao Paulo (Brazil)
Univ of Campinas, Sao Paulo (Brazil)

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. Altogether, these results reveal the pivotal role of active-site dynamics in the catalytic mechanism of AnFaeA, which is likely similar in other serine hydrolases.

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Research Organization:: National Renewable Energy Lab. (NREL), Golden, CO (United States)

Sponsoring Organization:: USDOE Office of Energy Efficiency and Renewable Energy (EERE), Transportation Office. Bioenergy Technologies Office; National Science Foundation (NSF); Sao Paulo Research Foundation

Grant/Contract Number:: AC36-08GO28308; ACI-1548562; 2013/08293-7; 2014/10448-1; 2015/25031-1; 2016/22956-7; 2017/01151-3

OSTI ID:: 1770879

Report Number(s):: NREL/JA-2800-78136; MainId:32045; UUID:242d5c49-f325-404b-a082-1ed081f4de2c; MainAdminID:18817

Journal Information:: Journal of Physical Chemistry. B, Condensed Matter, Materials, Surfaces, Interfaces and Biophysical Chemistry, Vol. 125, Issue 8; ISSN 1520-6106

Publisher:: American Chemical SocietyCopyright Statement

Country of Publication:: United States

Language:: English

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enzymes
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proteases
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