Figure 1.

The chemical reactions and enzymes used in the canonical ubiquitination cascade. The structure of ubiquitin (Protein Data Bank accession number 1UBQ) with labeled landmark structural elements (including M1, the seven lysine residues, Arg₄₂, Ilu₄₄, and Gly₇₆) important for its functionality is shown (top). Note that the ribbon diagram has been oriented in two different angles to better view the relevant residues. The E1 enzyme uses ATP to activate ubiquitin by acyl-adenylation of its carboxyl terminus. Ubiquitin from the ubiquitin-AMP intermediate is transferred to the active site cysteine in E1 via the formation of a thioester bond between the carboxy-terminal carboxyl group of ubiquitin and the E1 cysteine sulfhydryl group; AMP is concomitantly released (light purple background). The E2 ubiquitin-conjugating enzyme catalyzes the transfer of ubiquitin from E1-thio-Ub to the active site cysteine of the E2 via a trans(thio)esterification reaction (light green background). Depending on the E3 ubiquitin ligase used, ubiquitin on the E2-thio-Ub conjugate can be transferred to the protein substrate by at least two mechanisms. For members of the HECT and RBR family, ubiquitin is delivered to the active site cysteine of the E3 ligase before being transferred to the substrate. For E3 ligases in the RING family, ubiquitin is directly transferred from E2 to the substrate in a process facilitated by the E3 (yellow background). The major roles of the several distinct polyubiquitin chains formed at the primary methionine or one of the seven lysine residues are indicated (orange background). PPi, inorganic pyrophosphate.