Structural insights into Ubr1-mediated N-degron polyubiquitination

Nature. 2021 Dec;600(7888):334-338. doi: 10.1038/s41586-021-04097-8. Epub 2021 Nov 17.


The N-degron pathway targets proteins that bear a destabilizing residue at the N terminus for proteasome-dependent degradation1. In yeast, Ubr1-a single-subunit E3 ligase-is responsible for the Arg/N-degron pathway2. 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.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Binding Sites
  • Biocatalysis
  • Cryoelectron Microscopy
  • Lysine / metabolism
  • Models, Molecular
  • Proteasome Endopeptidase Complex / metabolism*
  • Proteolysis
  • Reproducibility of Results
  • Saccharomyces cerevisiae / enzymology
  • Saccharomyces cerevisiae / metabolism*
  • Saccharomyces cerevisiae Proteins / chemistry*
  • Saccharomyces cerevisiae Proteins / metabolism*
  • Saccharomyces cerevisiae Proteins / ultrastructure
  • Ubiquitin / metabolism*
  • Ubiquitin-Conjugating Enzymes / metabolism
  • Ubiquitin-Protein Ligases / chemistry*
  • Ubiquitin-Protein Ligases / metabolism*
  • Ubiquitin-Protein Ligases / ultrastructure
  • Ubiquitination*


  • Saccharomyces cerevisiae Proteins
  • Ubiquitin
  • RAD6 protein, S cerevisiae
  • Ubiquitin-Conjugating Enzymes
  • UBR1 protein, S cerevisiae
  • Ubiquitin-Protein Ligases
  • Proteasome Endopeptidase Complex
  • Lysine