Who with whom: functional coordination of E2 enzymes by RING E3 ligases during poly-ubiquitylation

Protein modification with poly‐ubiquitin chains is a crucial process involved in a myriad of cellular pathways. Chain synthesis requires two steps: substrate modification with ubiquitin (priming) followed by repetitive ubiquitin‐to‐ubiquitin attachment (elongation). RING‐type E3 ligases catalyze both reactions in collaboration with specific priming and elongating E2 enzymes. We provide kinetic insight into poly‐ubiquitylation during protein quality control by showing that priming is the rate‐determining step in protein degradation as directed by the yeast ERAD RING E3 ligases, Hrd1 and Doa10. Doa10 cooperates with the dedicated priming E2, Ubc6, while both E3s use Ubc7 for elongation. Here, we provide direct evidence that Hrd1 uses Ubc7 also for priming. We found that Ubc6 has an unusually high basal activity that does not require strong stimulation from an E3. Doa10 exploits this property to pair with Ubc6 over Ubc7 during priming. Our work not only illuminates the mechanisms of specific E2/E3 interplay in ERAD, but also offers a basis to understand how RING E3s may have properties that are tailored to pair with their preferred E2s.
Kinetic analyses of ERAD E3 (Hrd1, Doa10) and E2 (Ubc6, Ubc7) enzymes reveal the rate‐limiting nature of the ubiquitin chain priming step, and the molecular basis for respective E2 preferences of these E3s during priming.