Perilous journey: a tour of the ubiquitin-proteasome system

Abstract

Eukaryotic cells are equipped to degrade proteins via the ubiquitin-proteasome system (UPS). Proteins become degraded upon their conjugation to chains of ubiquitin where they are then directed to the 26S proteasome, a macromolecular protease. The transfer of ubiquitin to proteins and their subsequent degradation are highly complex processes, and new research is beginning to uncover the molecular details of how ubiquitination and degradation take place in the cell. We review some of the new data providing insights into how these processes occur. Although distinct mechanisms are often observed, some common themes are emerging for how the UPS guides protein substrates through their final journey.

Keywords: E1-activating; E2-conjugating; E3-ligase; proteolysis; ubiquitin proteasome system.

Figure 1

(A) Schematic representation of the different modifications occurring at the carboxyl end of ubiquitin during ubiquitination. (i) RING (really interesting new gene) and RING-like E3s mediate the direct transfer of ubiquitin from the E2 onto the substrate; (ii) an additional trans-thioesterification step is mediated by HECT (homologous to E6-AP carboxyl terminus) and RBR (ring between ring) E3s before substrate ubiquitination. (B) Model for substrate ubiquitination mediated by RING and RING-like E3s. The conformation of ubiquitin on the E2 can be labile due to its flexible tail. Binding of the E2~ubiquitin (linked via a thioester bond) to the E3 serves to fasten the ubiquitin and its carboxyl tail against the E2, thereby accelerating the rate of ubiquitin transfer to substrate.

Figure 2

Proposed model for substrate recognition and processing by the proteasome. The schematic represents a cutaway view through the center of the 26S proteasome. When the proteasome is not bound to a ubiquitinated substrate (left), the 19S conformation places the Rpn11 (proteasome regulatory particle base subunit 11) active site (represented by the star outline) in a position that is inaccessible to the substrate translocation pore. Furthermore, the channel formed by a ring of six ATPases that promote substrate translocation (blue) is not properly aligned with the 20S aperture. When the proteasome binds to a ubiquitinated substrate, the conformation of the 19S is rearranged such that the unfolded protein can enter the 20S chamber and the Rpn11 active site (yellow star) can cleave the poly-ubiquitin chain. In this model, only substrates conjugated to poly-ubiquitin chains containing four or more protomers can be efficiently processed because only these chains have the minimal length that is necessary to span the distance between one of the two ubiquitin receptors (Rpn10 or Rpn13) and Rpn11. Upon removal of the ubiquitin chain, the substrate is translocated by the ATP-dependent action of the ATPases into the 20S subunit where it is hydrolyzed into short peptides.

Figure I

Catalysis of ubiquitin transfer.