Both ubiquitin and ubiquitin-like proteins (of which there are more than a dozen in humans) can be covalently linked to a target protein in a regulated fashion, in a manner analogous to phosphorylation. Deubiquitinases can reverse ubiquitinylation in a manner analogous to the action of phosphatases. These ubiquitin modifications are structurally far more complex than phosphorylation, however, and so can mediate many distinct interactions between the ubiquitinylated protein and other cellular proteins. Ubiquitinylation can involve attachment of a single ubiquitin to a protein (monoubiquitinylation), addition of multiple, single ubiquitin molecules to different sites on one target protein (multiubiquitinylation), or addition of a polymeric chain of ubiquitins to a protein (polyubiquitinylation). An additional source of variation is that different amino groups in the ubiquitin molecule can be used to form an isopeptide bond with the C-terminal Gly-76 in another ubiquitin to form a polyubiquitin chain. All seven lysine residues in ubiquitin (Lys-6, Lys-11, Lys-27, Lys-29, Lys-33, Lys-48, and Lys-63) and its N-terminal amino group can participate in inter-ubiquitin linkages. Different ubiquitin ligases are specific both for targets (substrates) to be ubiquitinylated and for the lysine side chains on the ubiquitins that participate in the inter-ubiquitin isopeptide linkages (Lys-63 or Lys-48, etc.) (Figure 3-36). These multiple forms of ubiquitinylation result in the generation of a wide variety of recognition surfaces that can participate in many protein-protein interactions with the hundreds of proteins (>200 in humans) that contain more than a dozen distinct ubiquitin-binding domains (UBD). In addition, any given polyubiquitin chain has the potential to bind simultaneously to more than one UBD-containing protein, leading to the formation of ubiquitinylation-dependent multiprotein complexes. Some deubiquitinases can remove an intact polyubiquitin chain from a modified protein (“anchored” chain) and thus generate a polyubiquitin chain not covalently linked to another protein (“unanchored” chain). Even these unanchored chains may serve a regulatory role. With this great structural diversity, it is not surprising that cells use ubiquitinylation and deubiquitinylation to control many different cellular functions.

We have already seen how polyubiquitinylation via Lys-48 residues is used to tag proteins for proteasomal degradation. There is evidence that polyubiquitinylation via other Lys residues (for example, Lys-11 and Lys-33, but not Lys-63) can also target proteins for proteasomal degradation. Strikingly, ubiquitinylation unrelated to protein degradation can also control diverse cell functions, including cellular internalization of molecules via endocytosis (see Chapter 14), repair of damaged DNA, metabolism, messenger RNA synthesis (transcription), defense against pathogens, cell division/cell cycle progression, cell signaling pathways, trafficking of proteins within a cell, and apoptosis. The lysine used to form the inter-ubiquitin isopeptide bonds can vary depending on the cellular system that is regulated (see Figure 3-36). For example, polyubiquitinylation with Lys-63 linkages is used in many cellular identification and signaling systems, such as recognition of the presence of intracellular viruses and bacteria and the consequent induction of a protective immune response, as well as direction of these pathogens to lysosomes for degradation. Lys-11-linked polyubiquitin chains regulate cell division. Lys-33-linked chains help suppress the activity of receptors on specialized white blood cells, called T lymphocytes (see Chapter 23), and so control the activity and function of those lymphocytes.

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