A ubiquitin ligase (also called an E3 ubiquitin ligase) is a protein which covalently attaches ubiquitin to a lysine residue on a target protein. The ubiquitin ligase is typically involved in polyubiquitination: a second ubiquitin is attached to the first, a third is attached to the second, and so forth. Polyubiquitination marks proteins for degradation by the proteasome.
However, there are some ubiquitination events which are limited to mono-ubiquitination, in which only a single ubiquitin is added by the ubiquitiin ligase to a substrate molecule. Mono-ubiquitinated proteins are not targeted to the proteasome for degradation, but may instead be altered in their cellular location or function, for example via binding other proteins that have domains capable of binding ubiquitin.
The ubiquitin ligase is referred to as an E3 and operates in conjunction with an E1 ubiquitin-activating enzyme and an E2 ubiquitin-conjugating enzyme. There is one major E1 enzyme, shared by all ubiquitin ligases, which uses ATP to activate ubiquitin for conjugation and transfers it to an E2 enzyme. The E2 enzyme interacts with a specific E3 partner and transfers the ubiquitin to the target protein. The E3, which may be a multi-protein complex, is generally responsible for targeting ubiquitination to specific substrate proteins. In some cases it receives the ubiquitin from the E2 enzyme and transfers it to the target protein; in other cases it acts by interacting with both the E2 enzyme and the substrate but never itself receives the ubiquitin.
Ubiquitin ligase families
The Anaphase-promoting complex (APC) and the SCF complex (Skp1-Cullin-F-box protein complex) are two examples of ubiquitin ligase protein scaffold involved in recognition and ubiquitination of specific target proteins for degradation by the proteasome.
Each contains particular protein domains capable of binding the E2 conjugase, as well as a substrate-specific domain for binding the target. Many E2- and substrate-binding domains exist. This wide variety has been discovered to fall into specific groups called ubiquitin-ligase families.
- A RING (really interesting new gene) domain binds the E2 conjugase and might mediate enzymatic activity in the E2-E3 complex.
- An F-box domain (as in the SCF complex) binds the ubiquitinated substrate. (e.g. - Cdc 4, which binds the target protein Sic1; Grr1, which binds Cln).
- A HECT domain - involved in the tranfer of ubiquitin from the E2 to the substrate.