Substrate-interacting pore loops of two ATPase subunits determine the degradation efficiency of the 26S proteasome

The 26S proteasome is the major eukaryotic protease responsible for protein quality control, proteostasis, and the modulation of numerous vital processes through the degradation of regulatory proteins. Commitment to degradation occurs when conserved pore loops in the proteasomal heterohexameric ATPase motor engage the flexible initiation region of a polyubiquitinated protein substrate for subsequent mechanical unfolding and translocation into a proteolytic chamber. Here, we used in vitro biochemical and single-molecule FRET-based assays with mutant reconstituted 26S proteasomes from yeast to characterize how the pore-1 loops of individual ATPase subunits in the AAA+ motor contribute to the different steps of substrate degradation and affect the proteasome conformational dynamics. We found that the pore-1 loop of the Rpt6 ATPase subunit plays particularly important roles in substrate capture, engagement, and unfolding, while the pore-1 loop of the Rpt4 ATPase is critical for providing sufficient grip for substrate unraveling and maintaining a processing-competent state of the proteasome. Interestingly, these pore-1-loop contributions correlate with their positions in the spiral-staircase arrangements of ATPase subunits in the substrate-free and substrate-degrading proteasome, providing new insights into the mechanisms of substrate processing by the 26S proteasome and related hexameric ATPase motors.