Mechanism of Cellulose Hydrolysis by Inverting GH8 Endoglucanases: A QM/MM Metadynamics Study

dc.contributor.author Petersen, Luis
dc.contributor.author Ardèvol, Albert
dc.contributor.author Reilly, Peter
dc.contributor.author Rovira, Carme
dc.contributor.author Reilly, Peter
dc.contributor.department Chemical and Biological Engineering
dc.date 2018-02-13T03:07:09.000
dc.date.accessioned 2020-06-30T01:07:56Z
dc.date.available 2020-06-30T01:07:56Z
dc.date.copyright Thu Jan 01 00:00:00 UTC 2009
dc.date.embargo 2012-11-10
dc.date.issued 2009-04-29
dc.description.abstract <p>A detailed understanding of the catalytic strategy of cellulases is key to finding alternative ways to hydrolyze cellulose to mono-, di-, and oligosaccharides. Endoglucanases from glycoside hydrolase family 8 (GH8) catalyze the hydrolysis of β-1,4-glycosidic bonds in cellulose by an inverting mechanism believed to involve a oxacarbenium ion-like transition state (TS) with a boat-type conformation of the glucosyl unit in subsite −1. In this work, hydrolysis by <em>Clostridium thermocellum</em> endo-1,4-glucanase A was computationally simulated with quantum mechanics/molecular mechanics metadynamics based on density functional theory. Our calculations show that the glucosyl residue in subsite −1 in the Michaelis complex is in a distorted <sup>2</sup><em>S</em><sub>O</sub>/<sup>2,5</sup><em>B</em> ring conformation, agreeing well with its crystal structure. In addition, our simulations capture the cationic oxacarbenium ion-like character of the TS with a partially formed double bond between the ring oxygen and C5′ carbon atoms. They also provide previously unknown structural information of important states along the reaction pathway. The simulations clearly show for the first time in GH8 members that the TS features a boat-type conformation of the glucosyl unit in subsite −1. The overall catalytic mechanism follows a D<sub>N</sub>*A<sub>N</sub>-like mechanism and a β-<sup>2</sup><em>S</em><sub>O</sub> → <sup>2,5</sup><em>B</em> [TS] → α-<sup>5</sup><em>S</em><sub>1</sub> conformational itinerary along the reaction coordinate, consistent with the anti-periplanar lone pair hypothesis. Because of the structural similarities and sequence homology among all GH8 members, our results can be extended to all GH8 cellulases, xylanases, and other endoglucanases. In addition, we provide evidence supporting the role of Asp278 as the catalytic proton acceptor (general base) for GH8a subfamily members.</p>
dc.description.comments <p>Posted with permission from <em>The Journal of Physical Chemistry B</em>, 113, no. 20 (2009): 7331–7339, doi:<a href="http://dx.doi.org/10.1021/jp811470d" target="_blank">10.1021/jp811470d</a>. Copyright 2009 American Chemical Society.</p>
dc.format.mimetype application/pdf
dc.identifier archive/lib.dr.iastate.edu/cbe_pubs/14/
dc.identifier.articleid 1010
dc.identifier.contextkey 3459854
dc.identifier.s3bucket isulib-bepress-aws-west
dc.identifier.submissionpath cbe_pubs/14
dc.identifier.uri https://dr.lib.iastate.edu/handle/20.500.12876/13229
dc.language.iso en
dc.source.bitstream archive/lib.dr.iastate.edu/cbe_pubs/14/jp811470d.pdf|||Fri Jan 14 20:05:42 UTC 2022
dc.source.uri 10.1021/jp811470d
dc.subject.disciplines Biochemical and Biomolecular Engineering
dc.subject.disciplines Biological Engineering
dc.subject.disciplines Chemical Engineering
dc.title Mechanism of Cellulose Hydrolysis by Inverting GH8 Endoglucanases: A QM/MM Metadynamics Study
dc.type article
dc.type.genre article
dspace.entity.type Publication
relation.isAuthorOfPublication 0727532a-2892-42e2-84ab-5af5088f76c6
relation.isOrgUnitOfPublication 86545861-382c-4c15-8c52-eb8e9afe6b75
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