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Structure paper

TitleStructural insights into Ubr1-mediated N-degron polyubiquitination.
Journal, issue, pagesNature, Vol. 600, Issue 7888, Page 334-338, Year 2021
Publish dateNov 17, 2021
AuthorsMan Pan / Qingyun Zheng / Tian Wang / Lujun Liang / Junxiong Mao / Chong Zuo / Ruichao Ding / Huasong Ai / Yuan Xie / Dong Si / Yuanyuan Yu / Lei Liu / Minglei Zhao /
PubMed AbstractThe 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- ...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.
External linksNature / PubMed:34789879 / PubMed Central
MethodsEM (single particle)
Resolution3.35 - 7.69 Å
Structure data

23806

7mex

EMDB-23806, PDB-7mex:
Structure of yeast Ubr1 in complex with Ubc2 and N-degron
Method: EM (single particle) / Resolution: 3.35 Å

23807

7mey

EMDB-23807, PDB-7mey:
Structure of yeast Ubr1 in complex with Ubc2 and monoubiquitinated N-degron
Method: EM (single particle) / Resolution: 3.67 Å

EMDB-24935:
CryoEM map of yeast Ubr1 in complex with monoubiquitinated N-degron
Method: EM (single particle) / Resolution: 6.04 Å

EMDB-24936:
CryoEM map of yeast Ubr1
Method: EM (single particle) / Resolution: 7.69 Å

Chemicals

ChemComp-ZN:
Unknown entry

ChemComp-Z3V:
2-(ethylamino)ethane-1-thiol

Source
  • saccharomyces cerevisiae (strain atcc 204508 / s288c) (yeast)
  • homo sapiens (human)
  • saccharomyces cerevisiae s288c (yeast)
  • Saccharomyces cerevisiae (brewer's yeast)
KeywordsTRANSFERASE / Ubiquitin E3 ligase / ubiquitination / Ubr1 / Ubc2 / Degron / N-end rule

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