E3 ubiquitin ligase Cbl (blue) in complex with E2 (cyan) and substrate peptide (green). PDB entry 
|PDB structures||RCSB PDB PDBe PDBsum|
|Gene Ontology||AmiGO / EGO|
A ubiquitin ligase (also called an E3 ubiquitin ligase) is a ligase enzyme that combines with a ubiquitin-containing E2 ubiquitin-conjugating enzyme, recognizes the target protein that is to be ubiquinated, and causes the attachment of ubiquitin to a lysine on the target protein via an isopeptide bond. An E3 ubiquitin ligase targets specific protein substrates for degradation by the proteasome. In general, the ubiquitin ligase is involved in poly-ubiquitination: a second ubiquitin is attached to the first, a third is attached to the second, and so forth. Poly-ubiquitination marks proteins for degradation by the proteasome.
However, there are some ubiquitination events that are limited to mono-ubiquitination, in which only a single ubiquitin is added by the ubiquitin 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.
Further complicating matters, different lysines on ubiquitin can be targeted by an E3 to make chains. The most common lysine is Lys48 on the ubiquitin chain. This is the lysine used to make polyubiquitin, which is recognized by the proteasome. However, Lys63 can also be used, and chains using this lysine are important for DNA repair, among other functions.
- ATP + ubiquitin + protein lysine AMP + diphosphate + protein N-ubiquityllysine
This enzyme belongs to the family of ligases, to be specific those forming carbon-nitrogen bonds as acid-D-amino-acid ligases (peptide synthases). The systematic name of this enzyme class is ubiquitin:protein-lysine N-ligase (AMP-forming). This enzyme is also called ubiquitin-activating enzyme. This enzyme participates in 3 metabolic pathways: ubiquitin-mediated proteolysis, Parkinson's disease, and Huntington's disease.
As of late 2007, 75 structures have been solved for this class of enzymes, with PDB accession codes 1A3S, 1AYZ, 1C4Z, 1FBV, 1FXT, 1FZY, 1I7K, 1IYF, 1J7D, 1JAS, 1JAT, 1JBB, 1KPS, 1PZV, 1Q34, 1QCQ, 1TTE, 1U9A, 1U9B, 1UMH, 1UMI, 1UR6, 1W4U, 1WD2, 1WZV, 1WZW, 1X23, 1XR9, 1Y6L, 1Y8X, 1YH6, 1YLA, 1YRV, 1Z2U, 1Z3D, 1Z5S, 1Z6U, 1ZDN, 1ZUO, 2A4D, 2A7L, 2AAK, 2AWF, 2AYV, 2BEP, 2BF8, 2C4O, 2C4P, 2CLW, 2CYX, 2E2C, 2EKE, 2ESK, 2ESO, 2ESP, 2ESQ, 2F4W, 2FO3, 2FUH, 2GJD, 2GMI, 2GRN, 2GRO, 2GRP, 2GRQ, 2GRR, 2H2Y, 2O25, 2OB4, 2OGB, 2ONU, 2UCZ, 2UYZ, 2Z6O, and 2Z6P.
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, that 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, in general, 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 be found to 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, which is involved in the transfer of ubiquitin from the E2 to the substrate.
Individual E3 ubiquitin ligases
- Dou, H.; Buetow, L.; Hock, A.; Sibbet, G. J.; Vousden, K. H.; Huang, D. T. (2012). "Structural basis for autoinhibition and phosphorylation-dependent activation of c-Cbl". Nature Structural & Molecular Biology 19 (2): 184–192. doi:10.1038/nsmb.2231. PMID 22266821.
- Ardley HC, Robinson PA (2005). "E3 ubiquitin ligases". ESSAYS IN BIOCHEMISTRY 41: 15–30. doi:10.1042/EB0410015. PMID 16250895.
- Bai, Chang; Partha Sen; Kay Hofmann; Lei Ma; Mark Goebl; J. Wade Harper; Stephen J. Elledge (July 1996). "SKP1 Connects Cell Cycle Regulators to the Ubiquitin Proteolysis Machinery through a Novel Motif, the F-Box" (PDF). Cell 86 (2): 263–274. doi:10.1016/S0092-8674(00)80098-7. PMID 8706131. Retrieved 2009-02-09.
- Quips article describing E3 Ligase function at PDBe
- Ubiquitin-Protein Ligases at the US National Library of Medicine Medical Subject Headings (MeSH)
- EC 184.108.40.206