Structure of E3 ligase E6AP with a proteasome-binding site provided by substrate receptor hRpn10

Nat Commun. 2020 Mar 10;11(1):1291. doi: 10.1038/s41467-020-15073-7.

Abstract

Regulated proteolysis by proteasomes involves ~800 enzymes for substrate modification with ubiquitin, including ~600 E3 ligases. We report here that E6AP/UBE3A is distinguished from other E3 ligases by having a 12 nM binding site at the proteasome contributed by substrate receptor hRpn10/PSMD4/S5a. Intrinsically disordered by itself, and previously uncharacterized, the E6AP-binding domain in hRpn10 locks into a well-defined helical structure to form an intermolecular 4-helix bundle with the E6AP AZUL, which is unique to this E3. We thus name the hRpn10 AZUL-binding domain RAZUL. We further find in human cells that loss of RAZUL by CRISPR-based gene editing leads to loss of E6AP at proteasomes. Moreover, proteasome-associated ubiquitin is reduced following E6AP knockdown or displacement from proteasomes, suggesting that E6AP ubiquitinates substrates at or for the proteasome. Altogether, our findings indicate E6AP to be a privileged E3 for the proteasome, with a dedicated, high affinity binding site contributed by hRpn10.

Publication types

  • Research Support, N.I.H., Intramural

MeSH terms

  • Binding Sites
  • HCT116 Cells
  • Humans
  • Models, Biological
  • Models, Molecular
  • Proteasome Endopeptidase Complex / metabolism*
  • Protein Binding
  • Protein Domains
  • Protein Structure, Secondary
  • RNA-Binding Proteins / chemistry
  • RNA-Binding Proteins / metabolism*
  • Substrate Specificity
  • Ubiquitin-Protein Ligases / chemistry
  • Ubiquitin-Protein Ligases / metabolism*

Substances

  • PSMD4 protein, human
  • RNA-Binding Proteins
  • UBE3A protein, human
  • Ubiquitin-Protein Ligases
  • Proteasome Endopeptidase Complex