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Determinants of chemoselectivity in ubiquitination by the J2 family of ubiquitin-conjugating enzymes

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Názov: Determinants of chemoselectivity in ubiquitination by the J2 family of ubiquitin-conjugating enzymes
Autori: Anuruti Swarnkar, Florian Leidner, Ashok K Rout, Sofia Ainatzi, Claudia C Schmidt, Stefan Becker, Henning Urlaub, Christian Griesinger, Helmut Grubmüller, Alexander Stein
Prispievatelia: Swarnkar, Anuruti, Leidner, Florian, Rout, Ashok K, Ainatzi, Sofia, Schmidt, Claudia C, Becker, Stefan, Urlaub, Henning, Griesinger, Christian, Grubmüller, Helmut, Stein, Alexander
Zdroj: EMBO J
The EMBO Journal
Informácie o vydavateľovi: Springer Science and Business Media LLC, 2024.
Rok vydania: 2024
Predmety: 0301 basic medicine, 0303 health sciences, Saccharomyces cerevisiae Proteins, Ubiquitin, Protein Conformation, Ubiquitin-Protein Ligases, Ubiquitination, Saccharomyces cerevisiae, Molecular Dynamics Simulation, Crystallography, X-Ray, Article, Substrate Specificity, 03 medical and health sciences, Catalytic Domain, Ubiquitin-Conjugating Enzymes, Serine, Humans
Popis: Ubiquitin-conjugating enzymes (E2) play a crucial role in the attachment of ubiquitin to proteins. Together with ubiquitin ligases (E3), they catalyze the transfer of ubiquitin (Ub) onto lysines with high chemoselectivity. A subfamily of E2s, including yeast Ubc6 and human Ube2J2, also mediates noncanonical modification of serines, but the structural determinants for this chemical versatility remain unknown. Using a combination of X-ray crystallography, molecular dynamics (MD) simulations, and reconstitution approaches, we have uncovered a two-layered mechanism that underlies this unique reactivity. A rearrangement of the Ubc6/Ube2J2 active site enhances the reactivity of the E2-Ub thioester, facilitating attack by weaker nucleophiles. Moreover, a conserved histidine in Ubc6/Ube2J2 activates a substrate serine by general base catalysis. Binding of RING-type E3 ligases further increases the serine selectivity inherent to Ubc6/Ube2J2, via an allosteric mechanism that requires specific positioning of the ubiquitin tail at the E2 active site. Our results elucidate how subtle structural modifications to the highly conserved E2 fold yield distinct enzymatic activity.
Druh dokumentu: Article
Other literature type
Jazyk: English
ISSN: 1460-2075
DOI: 10.1038/s44318-024-00301-3
Prístupová URL adresa: https://pubmed.ncbi.nlm.nih.gov/39533056
https://resolver.sub.uni-goettingen.de/purl?gro-2/146921
Rights: CC BY
URL: http://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (http://creativecommons.org/licenses/by/4.0/) . Creative Commons Public Domain Dedication waiver http://creativecommons.org/publicdomain/zero/1.0/ (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data associated with this article, unless otherwise stated in a credit line to the data, but does not extend to the graphical or creative elements of illustrations, charts, or figures. This waiver removes legal barriers to the re-use and mining of research data. According to standard scholarly practice, it is recommended to provide appropriate citation and attribution whenever technically possible.
Prístupové číslo: edsair.doi.dedup.....41c327359e238066021f942d69aa09b6
Databáza: OpenAIRE
Popis
Abstrakt:Ubiquitin-conjugating enzymes (E2) play a crucial role in the attachment of ubiquitin to proteins. Together with ubiquitin ligases (E3), they catalyze the transfer of ubiquitin (Ub) onto lysines with high chemoselectivity. A subfamily of E2s, including yeast Ubc6 and human Ube2J2, also mediates noncanonical modification of serines, but the structural determinants for this chemical versatility remain unknown. Using a combination of X-ray crystallography, molecular dynamics (MD) simulations, and reconstitution approaches, we have uncovered a two-layered mechanism that underlies this unique reactivity. A rearrangement of the Ubc6/Ube2J2 active site enhances the reactivity of the E2-Ub thioester, facilitating attack by weaker nucleophiles. Moreover, a conserved histidine in Ubc6/Ube2J2 activates a substrate serine by general base catalysis. Binding of RING-type E3 ligases further increases the serine selectivity inherent to Ubc6/Ube2J2, via an allosteric mechanism that requires specific positioning of the ubiquitin tail at the E2 active site. Our results elucidate how subtle structural modifications to the highly conserved E2 fold yield distinct enzymatic activity.
ISSN:14602075
DOI:10.1038/s44318-024-00301-3