protein (79). Translocation through the channel may constitute the first committed step in proteolysis by these ATP-dependent proteases.
In the case of both the bacterial and eukaryotic chaperone components, the rings apposed coaxially to the proteolytic cylinder are composed of six ATPase-containing subunits (6, 33, 34). Considering that the cognate proteolytic cylinders are 7-membered double or quadruple rings (see, e.g., refs. 31, 32, 36), with the exception of six-fold symmetric HslV (35), there is an obvious symmetry mismatch. With such a 6-on-7 interface, the chaperone subunits cannot form a 1-to-1 match with proteolytic subunits in the same way that, for example, GroEL subunits match up exactly with subunits of the GroES cochaperonin partner (3). It is unclear how this unusual and evolutionarily preserved behavior may translate into a functional role. Is it designed to inherently weaken the association between the two components? This seems unlikely, because most chaperone/protease complexes appear to be stable as long as ATP is present. The symmetry mismatch may dispose to rotational sliding or ratcheting of the faces of the respective rings across each other (6). Perhaps it is a manifestation of a mechanism of translocation of substrate protein down the axial channel, such that a polypeptide chain is “spooled” through a narrow opening into the proteolytic chamber by a rotational or ratcheting motion (see, e.g., ref. 36). This model cannot apply toallATP-dependent proteases, however. As mentioned above, the ATPase and proteolytic domains are contained within a single polypeptide in the Lon and membrane-bound metalloproteases, where linking of these domains would prevent relative rotation. Interestingly, in EM images of the eukaryotic proteasome, the two asymmetric 19S complexes are observed in a 2-fold rotational orientation with respect to each other, potentially requiring coupled rotation to satisfy a ratchet model (e.g., ref. 10; see Fig. 2)
In the case of the proteasomal cap structure, not only is there an eight-subunit “base” containing six ATPase subunits, but also an ˜400-kDa “lid” structure, comprising eight subunits in yeast, connected to the base by what looks like a “hinge” in EM images (ref. 37; Fig. 2). When the lid is removed from the yeast proteasome by a mutation eliminating a protein supporting the connection to the base (Rpn10), ubiquitinated proteins can no longer be degraded. Thus, the lid appears to be specifically required for recognition of ubiquitin conjugates. By contrast, with only the base structure remaining attached to the 20S proteasome rings, a nonubiquitinated protein, casein, can still be efficiently degraded (37). These observations would seem to support a model of recognition wherein the lid structure binds the ubiquitin moiety of a ubiquitinated protein while the