Figure 6–84 Processive protein digestion by the proteasome. (A) The proteasome cap recognizes proteins marked by a polyubiquitin chain (see Figure 3–70), and subsequently translocates them into the proteasome core, where they are digested. At an early stage, the ubiquitin is cleaved from the substrate protein and is recycled. Translocation into the core of the proteasome is mediated by a ring of ATPases that unfold the substrate protein as it is threaded through the ring and into the proteasome core. This unfoldase ring is depicted in Figure 6–85). (B) Detailed structure of the proteasome cap. The cap includes a ubiquitin receptor, which holds a ubiquitylated protein in place while it begins to be pulled into the proteasome core, and a ubiquitin hydrolase, which cleaves ubiquitin from the doomed protein. (A, from S. Prakash and A. Matouschek, Trends Biochem. Sci. 29:593–600, 2004. With permission from Elsevier. B, adapted from G.C. Lander et al., Nature 482:186–191, 2012.)
A crucial property of the proteasome, and one reason for the complexity of its design, is the processivity of its mechanism: in contrast to a “simple” protease that cleaves a substrate’s polypeptide chain just once before dissociating, the proteasome keeps the entire substrate bound until all of it is converted into short peptides.
One would expect that a machine as efficient as the proteasome would be tightly regulated; in particular, it must be able to distinguish abnormal proteins from those that are properly folded. The 19S cap of the proteasome acts as a gate at the entrance to the inner proteolytic core, and only those proteins marked for destruction are threaded through the cap. The destruction “mark” is the covalent attachment of the small protein ubiquitin. As we saw in Chapter 3, ubiquitin modification of proteins is used for many purposes in the cell. The particular type of ubiquitin linkage that concerns us here is a chain of ubiquitin molecules linked together at lysine 48 (see Figure 3–69); this is the distinguishing feature of the ubiquitin tag that marks a protein for destruction in the proteasome.
A special set of E3 molecules (see Figure 3–70B) is responsible for the ubiquitylation of denatured or otherwise misfolded proteins, as well as proteins containing oxidized or other abnormal amino acids. Abnormal proteins tend to display on their surface hydrophobic amino acid sequences or conformational motifs that are recognized as degradation signals by these E3 molecules; these sequences are buried and therefore inaccessible in the normal, properly folded version. However, a proteolytic pathway that recognizes and destroys abnormal proteins must be able to distinguish completed proteins that have “wrong” conformations from the many growing polypeptides on ribosomes (as well as polypeptides just released from ribosomes) that have not yet achieved their normal folded conformation. This is not a trivial problem; in the course of carrying out its main job, the ubiquitin–proteasome system probably destroys many nascent and newly formed protein molecules, not because these proteins are abnormal as such, but because they have transiently exposed degradation signals that are buried in their mature (folded) state.