Molecular basis of ubiquitin-independent recognition and degradation of ODC/Antizyme by the 26S proteasome

The ubiquitin-proteasome system represents the main pathway for targeted protein degradation in eukaryotic cells. The majority of substrates is recruited for degradation through ubiquitin modifications, and the underlying principles are well established. However, the requirements for ubiquitin-independent substrates are still poorly understood. Here, we reveal the mechanisms for the antizyme-mediated degradation of the yeast ornithine decarboxylase (yODC), the first reported ubiquitin-independent substrate of the 26S proteasome. Using biochemical studies and cryo-EM structure determination, we show how antizyme binding makes the yODC monomer prone for degradation by exposing an interface that is normally buried in the catalytically active ODC dimer. Together with a surface on antizyme, yODC forms a two-part interface that binds the N-terminal coiled coil of two ATPase subunits, Rpt4 and Rpt5, for delivery to the 26S proteasome motor. This positions the N-terminal unstructured region of yODC for insertion into the ATPase channel to initiate degradation, which we found does not depend on a specific sequence. Interestingly, binding of the globular yODC/antizyme complex to the Rpt4/Rpt5 coiled coil allosterically stabilizes a proteasome conformation that facilitates substrate engagement by the ATPase motor and may represent a primed pre-initiation state with a general role in ubiquitin-dependent and -independent degradation.