Design Principles Involving Protein Disorder Facilitate Specific Substrate Selection and Degradation by the Ubiquitin-Proteasome System

Abstract

The ubiquitin-proteasome system (UPS) regulates diverse cellular pathways by the timely removal (or processing) of proteins. Here we review the role of structural disorder and conformational flexibility in the different aspects of degradation. First, we discuss post-translational modifications within disordered regions that regulate E3 ligase localization, conformation, and enzymatic activity, and also the role of flexible linkers in mediating ubiquitin transfer and reaction processivity. Next we review well studied substrates and discuss that substrate elements (degrons) recognized by E3 ligases are highly disordered: short linear motifs recognized by many E3s constitute an important class of degrons, and these are almost always present in disordered regions. Substrate lysines targeted for ubiquitination are also often located in neighboring regions of the E3 docking motifs and are therefore part of the disordered segment. Finally, biochemical experiments and predictions show that initiation of degradation at the 26S proteasome requires a partially unfolded region to facilitate substrate entry into the proteasomal core.

Keywords: E3 ligase; E3 ubiquitin ligase; intrinsically disordered protein; proteasome; protein degradation; protein phosphorylation; protein structural disorder; regulated degradation; ubiquitylation (ubiquitination).

FIGURE 1.

Main subclasses of E3 ubiquitin ligases, architectures, and structural disorder. Top, classification table for E3 ligases based on structural and functional domain composition. The specific functional characteristics for each subclass are indicated, such as interaction with E2 and/or with the substrate (S), functioning as a scaffold or adaptor/substrate recognition subunit in msE3s. Middle, representative models (schematic diagrams) of different E3 ligase-E2-substrate complexes (numbering corresponds to top panel). The small superscript numbers in the table above are linked to the diagrams in this panel. Color scheme: Ub and poly-Ub chains (orange), ubiquitin-conjugation (E2) enzymes (light pink), E3 ligase (pale green), scaffold protein cullin (light violet), adaptor protein (light blue), substrate recognition subunits (pink), and substrates (S) (blue). Subunits of APC/C are shown according to their functional class. Bottom, ribbon diagram of the crystal structure (PDB code: 4A4C) of human CBL (chain A) (left), WWP1 HECT domain E3 Ligase (PDB code: 1ND7) (middle), and the multi-subunit SCF complex (PDB code: 1LDK) (right). The structures are shown colored by IUPred (97) residue-wise disorder scores (color scale is shown). IUPred disorder scores range from 0 to 1; the higher the score, the greater the predicted disorder. 0.5 and greater indicate disordered residues.

FIGURE 2.

Primary degrons and their major properties. Top left, pie chart showing the overlap of substrate primary degron instances (171 experimentally validated instances from 157 substrates) relative to Pfam domains (98). Top middle, pie chart showing the predicted secondary structure distribution of primary degron residues (using PSIPRED (99)). Top right, pie chart showing the major Gene Ontology (GO) categories associated with substrates carrying known primary degrons. Bottom, schematic diagrams of substrate proteins (blue) with the primary degron (yellow) indicated. The diagrams show three possible locations of primary degrons relative to domains: degron at chain termini; degron in interdomain linker regions; and degron within domains. Specific examples of proteins corresponding to each category are shown using domain diagrams. Primary degron sequences are shown in red. Domains (cylinder) and inter-domain or non-domain (thick straight line) regions are in gray. RNA pol II, RNA polymerase II.