Ubiquitin and Ubiquitin-like Modifiers

1. E1 Ubiquitin/Ubl Activating Enzymes The ubiquitin super family is characterized by small protein modifiers that are covalently attached to proteins substrates through a series of biochemically similar steps (Figure 1). E1, E2, and E3 are the activating enzyme, conjugating enzyme, and ligase, respectively for the various Ubl pathways; the number of distinct enzymes at each step varies for the particular modifier system. M represents ubiquitin or any other Ubl. S is the substrate and D is the demodifying enzyme that removes the modifier and returns the substrate to the unmodified form. The first step in the conjugation process is activation of the modifier through an ATP-dependent reaction that forms a linkage between the modifier and the activation enzyme (E1). Subsequently the modifier is transferred to the conjugation enzyme (E2), through a thioester linkage. Finally, the modifier is transferred to the substrate using an E3 ligase that provides substrate specificity. This final conjugation of the modifier to the substrate occurs through an isopeptide bond linking the C-terminus of the modifier with the epsilon amino group of a lysine residue in the target protein. Depending on the substrate, more than one lysine may be modified and more than one type of modifier may be utilized; in some cases the different modifications occur on separate lysine residues while in other cases different modifiers compete for the same lysine, often with opposing functional effects. Additionally, depending on the modifier used both mono- and poly-chains of the modifier can be formed resulting in different outcomes for the substrate.