How do cells select target proteins for ubiquitin addition? As an initial step, the carboxyl end of ubiquitin needs to be activated. This activation is accomplished when a protein called a ubiquitin-activating enzyme (E1) uses ATP hydrolysis energy to attach ubiquitin to itself through a high-energy covalent bond (a thioester). E1 then passes this activated ubiquitin to one of a set of ubiquitin-conjugating (E2) enzymes, each of which acts in conjunction with a set of accessory (E3) proteins called ubiquitin ligases. There are roughly 30 structurally similar but distinct E2 enzymes in mammals, and hundreds of different E3 proteins that form complexes with specific E2 enzymes.
Figure 3–70 illustrates the process used to mark proteins for proteasomal degradation. [Similar mechanisms are used to attach ubiquitin (and SUMO) to other types of target proteins.] Here, the ubiquitin ligase binds to specific degradation signals, called degrons, in protein substrates, thereby helping E2 to form a polyubiquitin chain linked to a lysine of the substrate protein. This polyubiquitin chain on a target protein will then be recognized by a specific receptor in the proteasome, causing the target protein to be destroyed. Distinct ubiquitin ligases recognize different degradation signals, thereby targeting distinct subsets of intracellular proteins for destruction, often in response to specific signals (see Figure 6–86).
Figure 3–67 The structure of the Ras protein in its GTP-bound form. This monomeric GTPase illustrates the structure of a GTP-binding domain, which is present in a large family of GTP-binding proteins. The red regions change their conformation when the GTP molecule is hydrolyzed to GDP and inorganic phosphate by the protein; the GDP remains bound to the protein, while the inorganic phosphate is released. The special role of the “switch helix” in proteins related to Ras is  explained in the text (see Figure 3–72  and Movie 15.7).
Figure 3–68 a comparison of two major intracellular signaling mechanisms in eukaryotic cells. In both cases, a signaling protein is activated by the addition of a phosphate group and inactivated by the removal of this phosphate. Note that the addition of a phosphate to a protein can also be inhibitory. (Adapted from E.R. Kantrowitz and W.N. Lipscomb, Trends Biochem. Sci. 15:53–59, 1990.)
Protein Complexes with Interchangeable Parts Make Efficient Use of Genetic Information
The SCF ubiquitin ligase is a protein complex that binds different “target proteins” at different times in the cell cycle, covalently adding polyubiquitin polypeptide chains to these targets. Its C-shaped structure is formed from five protein subunits, the largest of which serves as a scaffold on which the rest of the complex is built. The structure underlies a remarkable mechanism (Figure 3–71). At one end of the C is an E2 ubiquitin-conjugating enzyme. At the other end is a substrate-binding arm, a subunit known as an F-box protein. These two subunits are separated by a gap of about 5 nm. When this protein complex is activated, the F-box protein binds to a specific site on a target protein, positioning the protein in the gap so that some of its lysine side chains contact the ubiquitin-conjugating enzyme. The enzyme can then catalyze repeated additions of ubiquitin polypeptide to these lysines (see Figure 3–71C), producing polyubiquitin chains that mark the target proteins for rapid destruction in a proteasome.