The structural basis for coordinated ATP dependent substrate processing within the proteasome and other AAA ATPases

Because ubiquitinated proteins are anchored to the proteasome by virtue of their ubiquitin chains, premature deubiquitination may interfere with substrate degradation by dissociating it from the proteasome. Conversely, failure to remove or trim the polyubiquitin chain would prevent further processing and may even clog the proteasome. Thus, although the catalytic centers of 19S regulatory complex and of the 20S proteolytic core are far apart, they must act in a synchronized manner. However, a molecular mechanism that support the tight coordination between the proteasome and its regulatory complex is not defined yet.

Here we demonstrate the importance of two phenylalanine residues in linking the ATPase activity of the proteasome regulatory ATPase to the presence of the 20S core particle. While the ATPase activity of PAN F232A was found to be independent of the 20S, PAN F268A activity was strictly coordinated with the 20S proteasome.This mutant forms a more stable complex with the 20S proteasome that dissociated only once the cycle of substrate processing by the proteasome is completed. We propose a molecular mechanism whereby the association between the ATPase ring and the 20S core particle induces structural transition (mediated by these phenylalanine residues), which affects the conformation of the Walker A and Walker B modules within the P loop regulating ATP hydrolysis and the associated functions of the proteasome regulatory complex. A mechanism that is presumably general to other ATPases from the AAA family.