GO:0031624 ubiquitin conjugating enzyme binding: Mechanism, Genes and Research Methods
Research-grade guide for scientists and biopharma professionals
Key Takeaways
• GO:0031624 (ubiquitin conjugating enzyme binding) is a molecular function describing the selective binding of a protein to any ubiquitin conjugating enzyme (E2).
• E2 binding is the central step of the ubiquitin transfer cascade, positioning the E2~ubiquitin thioester for E3-mediated substrate ubiquitylation.
• E2 enzymes such as UBE2C, UBE2S, UBE2T, UBE2Q2, UBE2O, Ube2d2 and Ube2k are directly implicated in cancer, fibrosis, autoimmune hepatitis and APC/C regulation.
• Structural and biophysical studies show that E2 binding interfaces are druggable and can be blocked by ubiquitin variants or small molecules.
• Dimerization and allosteric regulation of E2s such as UBE2S modulate E3 ligase activity and processivity.
• CRISPR knockout, point-mutation, knock-in and overexpression models are essential to test whether an E2-binding interface is causally required for a phenotype.
Description
GO:0031624, ubiquitin conjugating enzyme binding, is a molecular function term that captures the physical interaction between a protein and a ubiquitin conjugating enzyme (E2). In the ubiquitin system, E1 activates ubiquitin, E2 carries the activated ubiquitin as a thioester, and E3 ligases recruit both the E2~ubiquitin conjugate and the substrate to catalyze isopeptide bond formation. Proteins annotated with GO:0031624 therefore act as E2-binding partners that help assemble, orient, or regulate this catalytic machinery. Because E2 enzymes are the obligatory hub of all ubiquitylation reactions, E2-binding proteins influence nearly every ubiquitin-dependent process, including proteasomal degradation, DNA repair, cell-cycle progression and immune signaling. Researchers study GO:0031624 to understand how E3 ligases achieve substrate specificity and how E2 enzymes are recruited to distinct cellular compartments. Structural work on E3 ligases has revealed that E2-binding domains such as RING, HECT and RBR folds use distinct surfaces to engage E2 enzymes, and that the geometry of the E2~ubiquitin conjugate determines whether ubiquitin is transferred processively or distributively. This makes E2 binding a focal point for drug discovery, since blocking an E2-E3 interface can selectively disable a disease-relevant ubiquitylation pathway. The term is also clinically important because individual E2 enzymes are emerging as biomarkers and therapeutic targets. UBE2C is a potential cancer biomarker, UBE2Q2 participates in HUWE1-mediated protection against renal tubulointerstitial fibrosis, UBE2O primes hepatocytes to restore immune tolerance in autoimmune hepatitis, and UBE2S dimerization regulates the APC/C. Together, these findings show that GO:0031624 is not a generic binding annotation but a mechanistically defined function with direct disease relevance.
ubiquitin conjugating enzyme binding At A Glance
| GO ID | GO:0031624 |
|---|---|
| GO term | ubiquitin conjugating enzyme binding |
| Ontology | molecular_function |
| Synonym | none |
| Definition | Binding to a ubiquitin conjugating enzyme, any of the E2 proteins. |
| Major function | Recruitment and regulation of E2 enzymes within the ubiquitin transfer cascade |
| Example E2 partners | UBE2C, UBE2S, UBE2T, UBE2Q2, UBE2O, Ube2d2, Ube2k |
| Related machinery | E1 activating enzymes, E3 ligases, ubiquitin, proteasome |
| Druggability | E2-binding interfaces can be targeted by ubiquitin variants and small molecules |
What Is GO:0031624?
In our own words, GO:0031624 describes the ability of a protein to bind to a ubiquitin conjugating enzyme, meaning any of the E2 proteins that accept activated ubiquitin from an E1 enzyme and transfer it to a substrate. This binding event is non-covalent and is typically mediated by defined structural surfaces on the E2 and its partner, such as the RING domain of an E3 ligase or a dedicated E2-binding motif. The term is a molecular function, not a biological process or cellular component, so it should be used to annotate the binding activity itself rather than the downstream ubiquitylation outcome.
Why Is ubiquitin conjugating enzyme binding Important in Cell Biology?
GO:0031624 is important because E2 binding is the point at which the ubiquitin cascade becomes committed to a specific E3 ligase and substrate. Without E2 recruitment, no ubiquitin can be transferred, so proteins that bind E2 enzymes act as gatekeepers of degradation, signaling and DNA repair. This centrality explains why E2-binding interfaces are being explored as drug targets and why E2 enzymes themselves are candidate biomarkers in cancer and other diseases.
• E2 binding is required for all E3-mediated ubiquitylation reactions.
• UBE2C is a potential cancer biomarker and is associated with cell-cycle regulation.
• UBE2Q2 participates in HUWE1-mediated protection against renal tubulointerstitial fibrosis.
• UBE2O primes hepatocytes to restore immune tolerance in autoimmune hepatitis.
• UBE2S dimerization regulates the human APC/C-associated ubiquitin-conjugating enzyme.
• UBE2T has small-molecule binding sites that can be exploited for inhibitor design.
• Ubiquitin variants can inhibit Ube2d2 and Ube2k, providing tool compounds for E2 biology.
• E2-binding surfaces are structurally diverse across RING, HECT and RBR E3 ligases.
• Dysregulated E2 binding can contribute to fibrosis, autoimmunity and cancer.
• CRISPR models enable causal testing of E2-binding interfaces in disease-relevant cells.
Molecular Mechanism of ubiquitin conjugating enzyme binding
E2 recognition by E3 ligases
In simple terms: E3 ligases grab the E2 enzyme so that ubiquitin can be handed over.
The first step in ubiquitin conjugating enzyme binding is recognition of the E2 by an E3 ligase or another E2-binding protein. Structural studies show that RING, HECT and RBR E3 ligases use distinct folds to engage the E2, and that the E2-binding surface is often a shallow groove that accommodates the E2 catalytic domain. This recognition event positions the E2~ubiquitin thioester near the substrate lysine, enabling efficient transfer.
Conformational activation of the E2~ubiquitin conjugate
In simple terms: Binding changes the shape of the E2 so that ubiquitin is ready to be released.
E2 binding is not merely a tethering event; it also induces conformational changes in the E2~ubiquitin conjugate. Structural and biophysical work on E3 ligases has shown that the closed conformation of the E2~ubiquitin conjugate is required for efficient catalysis, and that E3 binding can stabilize this state. Ubiquitin variants that inhibit Ube2d2 and Ube2k act by trapping or distorting these conformations, demonstrating that the E2-binding interface is functionally coupled to catalysis.
Dimerization and allosteric regulation of E2 enzymes
In simple terms: Some E2 enzymes pair up, and this pairing controls how they work.
Dimerization regulates the human APC/C-associated ubiquitin-conjugating enzyme UBE2S, showing that E2-E2 contacts can modulate processivity and substrate selection. This means that GO:0031624 annotations can include E2-binding proteins that promote or disrupt E2 dimerization, adding an additional layer of regulation beyond simple E3 recruitment.
Inhibition by ubiquitin variants and small molecules
In simple terms: Engineered proteins and drugs can stick to E2 enzymes and block their function.
Fragment-based screening has identified small-molecule binding sites on UBE2T, and ubiquitin variants have been developed that inhibit Ube2d2 and Ube2k. These inhibitors validate E2 binding as a druggable interface and provide chemical tools to dissect GO:0031624-dependent pathways in cells.
Disease-linked E2 binding in fibrosis and autoimmunity
In simple terms: When E2 binding goes wrong, it can drive fibrosis or autoimmune disease.
UBE2Q2 participates in HUWE1-mediated protection against renal tubulointerstitial fibrosis, and UBE2O primes hepatocytes to restore immune tolerance in autoimmune hepatitis. These examples show that E2-binding events are not only housekeeping but can determine disease outcomes in kidney and liver tissue.
Key Genes Involved in GO:0031624 ubiquitin conjugating enzyme binding
The following genes and proteins are directly linked to ubiquitin conjugating enzyme binding (GO:0031624) through published biochemical, structural or disease studies.
| Gene | Major Role | Research Relevance |
|---|---|---|
| UBE2C | E2 enzyme involved in cell-cycle progression | Potential cancer biomarker |
| UBE2S | APC/C-associated E2 enzyme | Dimerization regulates APC/C activity |
| UBE2T | E2 enzyme with small-molecule binding sites | Fragment-based inhibitor discovery |
| UBE2Q2 | E2 enzyme in HUWE1-mediated protection | Renal tubulointerstitial fibrosis |
| UBE2O | E2 enzyme that primes hepatocytes | Autoimmune hepatitis immune tolerance |
| Ube2d2 | E2 enzyme inhibited by ubiquitin variants | Structural and biophysical characterization |
| Ube2k | E2 enzyme inhibited by ubiquitin variants | Tool compound development |
| HUWE1 | E3 ligase that partners with UBE2Q2 | Fibrosis protection |
| APC/C | E3 ligase complex that binds UBE2S | Cell-cycle regulation |
| YBX1 | Y-box binding protein 1 targeted by UBE2O axis | Autoimmune hepatitis |
| IL-6 | Interleukin-6 cytokine in UBE2O pathway | Immune tolerance |
| RING E3 ligases | E3 family that binds E2 enzymes | Structural diversity of E2 binding |
| HECT E3 ligases | E3 family with distinct E2-binding mode | E2 recognition mechanisms |
| RBR E3 ligases | E3 family with hybrid E2-binding architecture | E2 recruitment and activation |
| Ubiquitin | Modifier transferred from E2 to substrate | Cascade chemistry |
| E1 activating enzymes | Activate ubiquitin for E2 loading | Upstream cascade component |
| Proteasome | Degrades ubiquitylated substrates | Downstream outcome of E2 binding |
How Is ubiquitin conjugating enzyme binding Regulated?
GO:0031624 is regulated at multiple levels. E3 ligases control which E2 is recruited and when, through their E2-binding domains and conformational states. E2 dimerization can further regulate activity, as shown for UBE2S at the APC/C. Inhibitory proteins and engineered ubiquitin variants can block E2 binding, demonstrating that the interface is accessible to regulation by protein-protein interactions and small molecules. In disease contexts, E2-binding pathways are modulated by E3 ligases such as HUWE1 and by signaling axes involving YBX1 and IL-6.
ubiquitin conjugating enzyme binding and Human Disease
| Gene | Disease / Biology | Potential Experimental Model |
|---|---|---|
| UBE2C | Cancer biomarker and cell-cycle dysregulation | Knockout and overexpression in cancer cell lines |
| UBE2Q2 | Renal tubulointerstitial fibrosis | Knockout in kidney tubular cells |
| UBE2O | Autoimmune hepatitis | Knockout and knock-in in hepatocytes |
| UBE2S | APC/C regulation and cell-cycle progression | Point-mutation of dimerization interface |
| UBE2T | Small-molecule inhibition and cancer | Fragment-based screening and point mutation |
Cancer and cell-cycle dysregulation
UBE2C is a potential cancer biomarker, and its E2 activity is linked to cell-cycle progression. Because E2 binding is required for E3-mediated ubiquitylation, alterations in E2 recruitment can contribute to uncontrolled proliferation and genomic instability.
Renal tubulointerstitial fibrosis
UBE2Q2 participates in HUWE1-mediated protection against renal tubulointerstitial fibrosis, indicating that E2-binding events in kidney cells can restrain fibrotic remodeling.
Autoimmune hepatitis
UBE2O primes hepatocytes to restore immune tolerance in autoimmune hepatitis via inhibition of the Y-box binding protein 1/interleukin-6 axis, linking E2 function to liver immune homeostasis.
Targeted inhibition of E2 enzymes
Small-molecule binding sites on UBE2T and inhibitory ubiquitin variants against Ube2d2 and Ube2k show that E2-binding interfaces can be pharmacologically modulated, opening avenues for therapeutic intervention.
From ubiquitin conjugating enzyme binding-Related Genes to Experimental Models
| Research Question | Suitable Model |
|---|---|
| Is the E2-binding interface required for substrate ubiquitylation? | CRISPR knockout of the E2 or its binding partner |
| Does a specific E2 residue mediate E3 recruitment? | Point mutation of the E2-binding surface |
| Can a disease-associated E2 variant alter binding? | Knock-in of the variant allele |
| Where does the E2 bind in cells? | Tagged knock-in with fluorescent or affinity tag |
| Does E2 overexpression drive a phenotype? | Overexpression of wild-type or mutant E2 |
| Can a small molecule block E2 binding? | Point-mutation and overexpression models plus inhibitor treatment |
How to Study the ubiquitin conjugating enzyme binding Process
| Method | What It Measures | Typical Application |
|---|---|---|
| X-ray crystallography | Three-dimensional structure of E2-E3 complexes | Mapping E2-binding interfaces |
| NMR spectroscopy | Conformational changes upon E2 binding | Detecting closed E2~ubiquitin states |
| Fragment-based screening | Small-molecule binding to E2 enzymes | Identifying UBE2T inhibitors |
| Ubiquitin variant binding assays | Inhibition of E2 enzymes | Characterizing Ube2d2 and Ube2k inhibitors |
| Ubiquitylation assays | Substrate modification by E2-E3 pairs | Testing E2-binding requirement |
| Dimerization assays | E2-E2 interactions | Studying UBE2S at the APC/C |
| Disease-model phenotyping | Fibrosis or immune tolerance readouts | Testing UBE2Q2 and UBE2O function |
| CRISPR knockout screens | Causal role of E2-binding genes | Identifying dependencies in cancer cells |
Structural and biophysical characterization
X-ray crystallography, NMR and biophysical assays are used to define E2-binding interfaces and measure affinity. Structural work on E3 ligases has revealed the diversity of E2-binding folds, and ubiquitin variant studies have mapped inhibitory surfaces on Ube2d2 and Ube2k.
Fragment-based and small-molecule screening
Fragment-based screening can identify small-molecule binding sites on E2 enzymes such as UBE2T, providing starting points for chemical probes that block GO:0031624-dependent interactions.
Cell-based ubiquitylation assays
Ubiquitylation assays in cells, combined with knockout or point-mutation models, measure whether E2 binding is required for substrate modification and downstream degradation.
Disease-model phenotyping
Kidney fibrosis and autoimmune hepatitis models can be used to test whether E2-binding proteins such as UBE2Q2 and UBE2O modify disease phenotypes.
How CRISPR Can Be Used to Study GO:0031624 ubiquitin conjugating enzyme binding
Knockout
CRISPR knockout of an E2 enzyme or its binding partner removes the interaction entirely, allowing researchers to test whether GO:0031624-dependent ubiquitylation is required for a phenotype such as fibrosis protection or immune tolerance.
Point Mutation
Point mutation of the E2-binding surface can disrupt a single interface without deleting the whole protein, which is useful for testing whether a specific residue mediates E3 recruitment or dimerization.
Knock-in
Knock-in of disease-associated E2 variants or tagged alleles allows researchers to study binding in a physiological context and to track E2 localization in cells.
Overexpression
Overexpression of wild-type or mutant E2 enzymes can drive gain-of-function phenotypes and is used to test whether increased E2 binding promotes cancer or immune dysregulation.
How EDITGENE Supports ubiquitin conjugating enzyme binding Research
Researchers studying ubiquitin conjugating enzyme binding-related genes often need to determine whether a candidate gene is causally involved in a disease phenotype or is merely correlated with it. EDITGENE provides the CRISPR models and screening services needed to move from correlation to causation.
Contact EDITGENE today to design your custom CRISPR model for ubiquitin conjugating enzyme binding research.
Frequently Asked Questions About ubiquitin conjugating enzyme binding
What is GO:0031624?
GO:0031624 is the Gene Ontology molecular function term for ubiquitin conjugating enzyme binding, defined as binding to a ubiquitin conjugating enzyme, any of the E2 proteins.
What genes are involved in ubiquitin conjugating enzyme binding?
Genes include UBE2C, UBE2S, UBE2T, UBE2Q2, UBE2O, Ube2d2 and Ube2k, as well as E3 ligases such as HUWE1 and the APC/C.
Why is ubiquitin conjugating enzyme binding important?
It is required for E3-mediated ubiquitylation, which controls protein degradation, cell-cycle progression, DNA repair and immune signaling.
Which diseases are linked to E2 binding?
E2 binding has been linked to cancer, renal tubulointerstitial fibrosis and autoimmune hepatitis.
Can E2 binding be inhibited by drugs?
Yes, small-molecule binding sites on UBE2T and inhibitory ubiquitin variants against Ube2d2 and Ube2k have been reported.
What is the role of UBE2C in cancer?
UBE2C is a potential cancer biomarker and is associated with cell-cycle regulation.
How does UBE2S regulate the APC/C?
UBE2S dimerization regulates the human APC/C-associated ubiquitin-conjugating enzyme, affecting its activity.
What experimental models are used to study E2 binding?
CRISPR knockout, point-mutation, knock-in and overexpression models are commonly used, along with structural and biophysical assays.
What is the relationship between UBE2O and autoimmune hepatitis?
UBE2O primes hepatocytes to restore immune tolerance in autoimmune hepatitis via inhibiting the Y-box binding protein 1/interleukin-6 axis.
How can I study GO:0031624 in my lab?
You can use CRISPR knockout, point-mutation, knock-in or overexpression models combined with ubiquitylation assays and structural methods.
Conclusion
GO:0031624 (ubiquitin conjugating enzyme binding) is a mechanistically defined molecular function that sits at the heart of the ubiquitin cascade. It determines which E2 enzymes are recruited, how they are activated, and whether substrates are modified in a processive or distributive manner. The term is directly linked to cancer, fibrosis and autoimmune hepatitis through E2 enzymes such as UBE2C, UBE2Q2 and UBE2O. Because E2-binding interfaces are structurally diverse and druggable, they represent attractive targets for chemical probes and therapeutics. CRISPR-based knockout, point-mutation, knock-in and overexpression models provide the causal evidence needed to translate these interactions into disease-relevant biology.
References
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- 2. Wang Z et al.. 2022. [Ubiquitin-conjugating enzyme UBE2Q2 participates in HUWE1-mediated protection on renal tubulointerstitial fibrosis].. Sheng Li Xue Bao 74(1):117-124 PMID: 35199132
- 3. Xie C et al.. 2014. Ubiquitin-conjugating enzyme E2C: a potential cancer biomarker.. Int J Biochem Cell Biol 47:113-7 PMID: 24361302
- 4. Loh YY et al.. 2024. Identification of small-molecule binding sites of a ubiquitin-conjugating enzyme-UBE2T through fragment-based screening.. Protein Sci 33(3):e4904 PMID: 38358126
- 5. Lei Y et al.. 2026. Ubiquitin-Conjugating Enzyme E2O Primes Hepatocytes to Restore Immune Tolerance in Autoimmune Hepatitis via Inhibiting Y-Box Binding Protein 1/Interleukin-6 Axis.. Cell Mol Gastroenterol Hepatol 20(7):101765 PMID: 41780884
- 6. Liess AKL et al.. 2020. Dimerization regulates the human APC/C-associated ubiquitin-conjugating enzyme UBE2S.. Sci Signal 13(654) PMID: 33082289
- 7. McAlpine JMRB et al.. 2024. Structural and biophysical characterisation of ubiquitin variants that inhibit the ubiquitin conjugating enzyme Ube2d2.. FEBS J 291(23):5305-5321 PMID: 39473070
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