Functions of the 19S complex in proteasomal degradation

Abstract

The 26S proteasome degrades ubiquitylated proteins. It consists of the 20S proteasome and the PA700/19S complex. PA700 plays essential roles in processing ubiquitylated substrates; it can bind, deubiquitylate, and unfold ubiquitylated proteins, which then translocate into the proteolytic chamber of the 20S proteasome for degradation. Here, we summarize the current knowledge of PA700-mediated substrate binding and deubiquitylation, and provide models to explain how substrate binding and deubiquitylation could regulate proteasomal degradation. We also discuss the features and potential therapeutic uses of the two recently identified small molecule inhibitors of the proteasome-residing deubiquitylating enzymes.

Figure 1. Subunit organization of the yeast 26S proteasome

(a) Subnanometer cryoelectron microscopy reconstruction of the yeast 26S proteasome. The subunits of the 19S complex are colored with the 20S proteasome in grey. (b) Side and top views of the 19S complex. Figures were adopted from reference with permission. The ubiquitin receptors S5a/Rpn10 and Adrm1/Rpn13 and the deubiquitylating enzymes Rpn11, Uch37 and Usp14/Ubp6 are particularly relevant to this review. Uch37 and Usp14/Ubp6 are not present in the shown 26S proteasome structure.

Figure 2. Simplified models for recognition of ubiquitylated proteins by the two integral ubiquitin receptors of the mammalian 26S proteasome

For substrates conjugated with a polyUb chain (a and b), the polyUb chain could bind S5a (a-i), Adrm1 (a-ii) or both (b). For substrates conjugated with multiple short Ub chains (c), the substrate could be recognized through one Ub chain binding to one of the receptors; as an example, binding of one Ub chain to Adrm1 is shown in (c-i), or S5a and Adrm1 could each bind one Ub chain (c-ii). In addition to binding of a polyUb chain or polyUb chains, an unstructured region (broken white line) in a substrate might interact with the ATPase(s), thereby bringing the substrate close to the entrance of the substrate translocation channel.

Figure 3. Models for Ub chain amputation and trimming in regulating proteasomal degradation

In these models, Adrm1 and Uch37 are used as examples for polyUb chain binding and trimming, respectively. In productive degradation (a), a polyUb chain provides initial binding affinity for the proteasome while the substrate engages with the substrate translocation channel, meanwhile partial Ub chain trimming could occur (left). In one circumstance (i), the Ub chain could be trimmed and then released from the Ub receptor before encountering Rpn11. Accompanying substrate degradation, the remaining conjugated Ub or Ub chain would move along with the substrate towards the substrate translocation channel and finally be released from the substrate by Rpn11-mediated chain amputation. Alternatively (ii), the Ub chain could be amputated by Rpn11 before dissociating from the Ub receptor. Subsequent Ub chain trimming cleaves the free Ub chain, which vacates the Ub receptor for new substrate binding. In both a (i) and (ii), Rpn11-catalyzed chain amputation would prevent unfolding and degradation of Ub, which can facilitate substrate unfolding and translocation. In nonproductive degradation (b), if a conjugated polyUb chain is trimmed before the substrate engages with the substrate translocation channel, the substrate could be released from the proteasome without degradation (i). Conversely, trimming the chain too slowly could restrict the substrate from being further unfolded and/or translocated even when a substrate has already engaged with the substrate translocation channel (ii). In this circumstance, prolonged tethering of a polyUb chain on the Ub receptor could clog the 26S proteasome.