7MEY

Structure of yeast Ubr1 in complex with Ubc2 and monoubiquitinated N-degron

Summary for 7MEY

• Entry DOI: 10.2210/pdb7mey/pdb
• EMDB information: 23806 23807
• Descriptor: E3 ubiquitin-protein ligase UBR1, Ubiquitin, Ubiquitin-conjugating enzyme E2 2, ... (7 entities in total)
• Functional Keywords: ubiquitin e3 ligase, ubiquitination, ubr1, ubc2, degron, n-end rule, transferase
• Biological source: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast); More
• Total number of polymer chains: 5
• Total formula weight: 266976.22

Authors

Pan, M.,Zheng, Q.,Wang, T.,Liang, L.,Yu, Y.,Liu, L.,Zhao, M. (deposition date: 2021-04-08, release date: 2021-11-24, Last modification date: 2021-12-22)

Primary citation

Pan, M.,Zheng, Q.,Wang, T.,Liang, L.,Mao, J.,Zuo, C.,Ding, R.,Ai, H.,Xie, Y.,Si, D.,Yu, Y.,Liu, L.,Zhao, M.
Structural insights into Ubr1-mediated N-degron polyubiquitination.
Nature, 600:334-338, 2021

PubMed Abstract: The N-degron pathway targets proteins that bear a destabilizing residue at the N terminus for proteasome-dependent degradation. In yeast, Ubr1-a single-subunit E3 ligase-is responsible for the Arg/N-degron pathway. How Ubr1 mediates the initiation of ubiquitination and the elongation of the ubiquitin chain in a linkage-specific manner through a single E2 ubiquitin-conjugating enzyme (Ubc2) remains unknown. Here we developed chemical strategies to mimic the reaction intermediates of the first and second ubiquitin transfer steps, and determined the cryo-electron microscopy structures of Ubr1 in complex with Ubc2, ubiquitin and two N-degron peptides, representing the initiation and elongation steps of ubiquitination. Key structural elements, including a Ubc2-binding region and an acceptor ubiquitin-binding loop on Ubr1, were identified and characterized. These structures provide mechanistic insights into the initiation and elongation of ubiquitination catalysed by Ubr1.

PubMed: 34789879
DOI: 10.1038/s41586-021-04097-8

Experimental method

ELECTRON MICROSCOPY (3.67 Å)