Trends in Cell Biology
ReviewThe lore of the RINGs: substrate recognition and catalysis by ubiquitin ligases
Section snippets
Substrate recognition by simple and multicomponent E2–E3 complexes
After activation by an E1 enzyme, the E2 ubiquitin-conjugating enzyme and E3 ubiquitin ligase cooperate to assemble the multiubiquitin chain on a protein substrate. In studies so far, the E3 ubiquitin ligase uses protein–protein interaction domains outside the catalytic domain to bind to substrate. We discuss the architecture and substrate binding activities of the HECT domain E3 enzymes and four classes of RING finger E3 ubiquitin ligases: the SCF, VBC and anaphase-promoting (APC) complexes,
HECT domain proteins
HECT domain proteins are found in eukaryotes from yeast to humans and are defined by a 350 amino acid HECT domain (homologous to E6-AP C terminus), originally identified in E6-AP (Ref. 3). E6-AP is the cellular ubiquitin ligase recruited by the human papilloma virus E6 oncoprotein to induce degradation of the p53 tumour suppressor4. Within the HECT domain of E6, a conserved cysteine forms a thioester with ubiquitin. This intermediate is essential for ubiquitylation. HECT domain proteins are
SCF (Skp1, cullin, F-box) complexes
The SCF class of ubiquitin ligases contains at least four proteins: Skp1, Cul1, Roc1/Rbx1/Hrt1 and an F-box protein (see Fig. 1). SCF substrates are bound directly by adaptors called F-box proteins, which contain an ∼45-residue motif called an F-box and bind to substrates9 through protein–protein interaction domains (reviewed in Ref. 1). The F-box is required for binding to Skp1, a protein that is important in SCF complexes but potentially plays other roles (see below). Skp1 in turn associates
The von Hippel-Lindau (VHL)–Elongin B–Elongin C (VBC) ubiquitin ligase
The von Hippel-Lindau (VHL–Elongin B–Elongin C (or VBC) ubiquitin ligase contains the VHL tumour suppressor, which is inactivated in von Hippel-Lindau disease and in over 80% of sporadic renal cell carcinomas1, 36. The VBC ubiquitin ligase is structurally similar to the SCF E3 complex (Fig. 1). It contains Roc1/Rbx1, the cullin Cul2, a protein homologous to Skp1 called elongin C, a probable adaptor protein called VHL and another factor called elongin B (Fig. 1). VHL binds to elongin C through a
The anaphase-promoting complex (APC) ubiquitin ligase
The APC was the first multicomponent ubiquitin ligase described and is required for the degradation of substrates controlling the metaphase-to-anaphase transition and the destruction of cyclin B to allow the exit from mitosis42, 43, 44. Similar to the SCF and VBC complexes, the APC contains a cullin homologue, Apc2, and a RING-H2 finger protein similar to Roc1/Rbx1, called Apc11. Also, like the SCF, the APC associates with proteins that activate the APC towards specific substrates42. Two
Single protein RING finger (SPRF) E3 ubiquitin ligases
The identification of RING finger proteins in SCF complexes and other E3 proteins suggests the broad use of these domains for ubiquitylation56. As stated earlier, RING fingers are zinc-binding domains with a defined octet of cysteine and histidine residues. The subtype RING-H2 domain contains histidines at positions 4 and 5 (see Fig. 2) and is the form found in Roc1/Rbx1, Roc2, Apc11 and other ubiquitin ligases. Another subtype RING-HC (or C3HC4) contains only one histidine (at position 4) and
Catalysis
Little is known about the catalytic mechanisms employed by the various E3 ubiquitin ligases. Apart from the HECT domain ubiquitin ligases, which accept ubiquitin from E2 enzymes to create a thioester bond and directly catalyse ubiquitin transfer to the target protein62, 63, no other ubiquitin ligases are currently thought to form thioester bonds with ubiquitin. Because the common feature of non-HECT domain ubiquitin ligases is the RING finger, this domain appears central to catalysis. The
Regulation of activity of E3 complexes by ubiquitin-like molecules
Some examples of how modifications or other factors regulate ubiquitin ligase complexes are known. SCF ubiquitin ligases have been found to be regulated by phosphorylation at least at the level of substrate recognition or subunit recruitment (as discussed above), through posttranslational modification by other ubiquitin-like molecules (UBLs) and by accessory factors, including targeting to subcellular localizations and assembly into multiprotein complexes (for reviews, see 69, 70). Because of
Summary: different mechanisms for ubiquitin ligase activity?
The recent discoveries defining the functional domains of known ubiquitin ligases suggest a simple model where the RING or HECT catalytic domains are tethered to specific substrates by protein–protein recognition domains. This tether appears to facilitate formation of the multiubiquitin chain, although the mechanisms remain unclear.
Why some ubiquitin ligases use HECT domains, which form a thioester-linked ubiquityl intermediate, and others RING fingers, which apparently do not, also remains
Uncited reference
75
Acknowledgements
We apologize to many authors who we could not cite because of space constraints. This work was supported in part by grants from the NIH [GM54811 and GM60439], Medical Scientist Training Program (to J.D.R.R.) and Cancer Biology Training grants (to L.F. and B.K.K.) and from the Howard Hughes Medical Institute (to P.K.J., A.G.E., and J.Y.H.).
References (76)
SCF and Cullin/Ring H2-based ubiquitin ligases
Annu. Rev. Cell Dev. Biol.
(1999)Ubiquitin, E6-AP, and their role in p53 inactivation
Pharmacol. Ther.
(1998)The HPV-16 E6 and E6-AP complex functions as a ubiquitin-protein ligase in the ubiquitination of p53
Cell
(1993)Functional domains of the Rsp5 ubiquitin-protein ligase
Mol. Cell. Biol.
(1999)Cullin-3 targets cyclin E for ubiquitination and controls S phase in mammalian cells
Genes Dev.
(1999)Cdc53/cullin and the essential Hrt1 RING-H2 subunit of SCF define a ubiquitin ligase module that activates the E2 enzyme Cdc34
Genes Dev.
(1999)F-box proteins are receptors that recruit phosphorylated substrates to the SCF ubiquitin-ligase complex
Cell
(1997)Identification of a family of human F-box proteins
Curr. Biol.
(1999)A family of mammalian F-box proteins
Curr. Biol.
(1999)Characterization of the human suppressor of fused, a negative regulator of the zinc-finger transcription factor Gli
J. Cell Sci.
(1999)
Two F-box/WD-repeat proteins Pop1 and Pop2 form hetero- and homo-complexes together with cullin-1 in the fission yeast SCF (Skp1-Cullin-1-F-box) ubiquitin ligase
Genes To Cells
The unstable F-box protein p58-Ctf13 forms the structural core of the CBF3 kinetochore complex
J. Cell Biol.
The VHL tumour-suppressor gene paradigm
Trends Genet.
The conserved SOCS box motif in suppressors of cytokine signaling binds to elongins B and C and may couple bound proteins to proteasomal degradation
Proc. Natl. Acad. Sci. U. S. A.
Cell cycle: oiling the gears of anaphase
Curr. Biol.
Mass spectrometric analysis of the anaphase-promoting complex from yeast: identification of a subunit related to cullins
Science
Cyclin is degraded by the ubiquitin pathway
Nature
Inhibitory phosphorylation of the APC regulator Hct1 is controlled by the kinase Cdc28 and the phosphatase Cdc14
Curr. Biol.
Control of cyclin ubiquitination by CDK-regulated binding of Hct1 to the anaphase promoting complex
Science
The tyrosine kinase negative regulator c-Cbl as a RING-type, E2-dependent ubiquitin-protein ligase
Science
Mdm2 is a RING finger-dependent ubiquitin protein ligase for itself and p53
J. Biol. Chem.
Activity of MDM2, a ubiquitin ligase, toward p53 or itself is dependent on the RING finger domain of the ligase
Oncogene
A family of proteins structurally and functionally related to the E6-AP ubiquitin-protein ligase
Proc. Natl. Acad. Sci. U. S. A.
RING fingers mediate ubiquitin-conjugating enzyme (E2)-dependent ubiquitination
Proc. Natl. Acad. Sci. U. S. A.
Functional and physical characterization of the cell cycle ubiquitin-conjugating enzyme CDC34 (UBC3). Identification of a functional determinant within the tail that facilitates CDC34 self-association
J. Biol. Chem.
Proteolysis and the cell cycle: with this RING I do thee destroy
Curr. Opin. Genet. Dev.
The F-box: a new motif for ubiquitin dependent proteolysis in cell cycle regulation and signal transduction
Prog. Biophys. Mol. Biol.
Ubiquitin-like proteins: new wines in new bottles
Gene
SUMO-1 modification of IκBα inhibits NF-κB activation
Mol. Cell
SUMO-1 modification of Mdm2 prevents its self-ubiquitination and increases Mdm2 ability to ubiquitinate p53
Cell
A complex of Cdc4p, Skp1p and Cdc53p/cullin catalyzes ubiquitination of the phophorylated CDK inhibitor Sic1p
Cell
Ubiquitination of the G1 cyclin Cln2p by a Cdc34p-dependent pathway
EMBO J.
Proteolysis and the cell cycle: with this RING I do thee destroy
Curr. Opin. Genet. Dev.
From Src Homology domains to other signaling modules: proposal of the ‘protein recognition code’
Oncogene
WW (WWP) domains: from structure to function
Curr. Top. Microbiol. Immunol.
A SMAD ubiquitin ligase targets the BMP pathway and affects embryonic pattern formation
Nature
SKP1 connects cell cycle regulators to the ubiquitin proteolysis machinery through a novel motif, the F-box
Cell
Rbx1, a component of the VHL tumor suppressor complex and SCF ubiquitin ligase
Science
Cited by (563)
Proteostasis in aging-associated ocular disease
2022, Molecular Aspects of MedicineCharacterization of TRIM16, a member of the fish-specific finTRIM family, in olive flounder Paralichthys olivaceus
2022, Fish and Shellfish ImmunologyCitation Excerpt :PoTRIM16 mRNA levels fluctuated markedly during early development. In addition, fish embryos and hatchlings are exposed to pathogens long before they are able to develop a mature immune response and while no immunoglobulins are present [24–26]. Therefore, our results provide insight into the development of the innate immune response in fish eggs.
The effect of TRIM5 variants on the susceptibility to HIV-1 infection and disease progression in the Polish population
2024, Annals of Human GeneticsThe Auto-Regulation of ATL2 E3 Ubiquitin Ligase Plays an Important Role in the Immune Response against Alternaria brassicicola in Arabidopsis thaliana
2024, International Journal of Molecular Sciences