A conserved asparagine in a ubiquitin-conjugating enzyme positions the substrate for nucleophilic attack

© 2019 Wiley Periodicals, Inc.

Détails bibliographiques
Publié dans:Journal of computational chemistry. - 1984. - 40(2019), 22 vom: 15. Aug., Seite 1969-1977
Auteur principal: Jones, Walker M (Auteur)
Autres auteurs: Davis, Aaron G, Wilson, R Hunter, Elliott, Katherine L, Sumner, Isaiah
Format: Article en ligne
Langue:English
Publié: 2019
Accès à la collection:Journal of computational chemistry
Sujets:Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S. BOMD E2 QM/MM Ubc13 molecular dynamics ubiquitin ubiquitination plus... Asparagine 7006-34-0 Ubiquitin-Conjugating Enzymes EC 2.3.2.23
Description
Résumé:© 2019 Wiley Periodicals, Inc.
The mechanism used by the ubiquitin-conjugating enzyme, Ubc13, to catalyze ubiquitination is probed with three computational techniques: Born-Oppenheimer molecular dynamics, single point quantum mechanics/molecular mechanics energies, and classical molecular dynamics. These simulations support a long-held hypothesis and show that Ubc13-catalyzed ubiquitination uses a stepwise, nucleophilic attack mechanism. Furthermore, they show that the first step-the formation of a tetrahedral, zwitterionic intermediate-is rate limiting. However, these simulations contradict another popular hypothesis that supposes that the negative charge on the intermediate is stabilized by a highly conserved asparagine (Asn79 in Ubc13). Instead, calculated reaction profiles of the N79A mutant illustrate how charge stabilization actually increases the barrier to product formation. Finally, an alternate role for Asn79 is suggested by simulations of wild-type, N79A, N79D, and H77A Ubc13: it stabilizes the motion of the electrophile prior to the reaction, positioning it for nucleophilic attack. © 2019 Wiley Periodicals, Inc
Description:Date Completed 11.08.2020
Date Revised 11.08.2020
published: Print-Electronic
Citation Status MEDLINE
ISSN:1096-987X
DOI:10.1002/jcc.25852