Affinage

UBE2E3

Ubiquitin-conjugating enzyme E2 E3 · UniProt Q969T4

Length
207 aa
Mass
22.9 kDa
Annotated
2026-04-28
43 papers in source corpus 18 papers cited in narrative 18 extracted findings

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

UBE2E3 is a class III ubiquitin-conjugating enzyme (E2) that functions as a monoubiquitylation-restricted catalyst whose product specificity is governed by backside residues of its UBC domain and Lys48 of ubiquitin (PMID:24901938). It forms a Cys-145-dependent thioester with ubiquitin and partners with both HECT-type E3 ligases (Nedd4-2, Nedd4) to regulate epithelial Na+ channel surface expression and RING-type E3 ligases (ARA54, RNF8, PJA1, Mulan) to ubiquitinate substrates including TDP-43 (PMID:10343118, PMID:14993279, PMID:11322894, PMID:24825905, PMID:32686212). Through its importin-11-mediated nuclear localization, UBE2E3 promotes NRF2 nuclear accumulation and antioxidant gene transcription, and its depletion triggers a p53/p21/p16-dependent cellular senescence program characterized by increased mitochondrial and lysosomal mass and elevated autophagic flux (PMID:25378586, PMID:29879550, PMID:18614808). Loss of UBE2E3 consistently impairs proliferation and induces senescence across multiple cell types including retinal pigment epithelial cells, bone marrow mesenchymal stem cells, granulosa cells, and Sertoli cells (PMID:18614808, PMID:34820159, PMID:37628741, PMID:38391926).

Mechanistic history

Synthesis pass · year-by-year structured walk · 11 steps
  1. 1999 High

    Establishing UBE2E3 as a bona fide E2 enzyme resolved whether this gene product possessed ubiquitin-conjugating activity and identified Cys-145 as the catalytic residue.

    Evidence In vitro thioester formation assay with recombinant GST-UBE2E3 and C145S mutagenesis

    PMID:10343118

    Open questions at the time
    • No E3 partner or substrate identified at this stage
    • No chain-linkage specificity determined
  2. 2001 High

    Demonstrating that UBE2E3 physically and functionally pairs with RING-finger E3 ligases ARA54 and RNF8 established it as a RING E3-compatible E2 and mapped the interaction to its UBC domain.

    Evidence Yeast two-hybrid, deletion mutagenesis, in vitro ubiquitination, and co-IP in COS-7 cells

    PMID:11322894

    Open questions at the time
    • No physiological substrate identified
    • Autoubiquitination shown but substrate ubiquitination not tested
  3. 2004 High

    Identifying UBE2E3 as the E2 for Nedd4-2 in ENaC regulation provided the first physiological context, linking it to HECT-type E3s and ion channel trafficking.

    Evidence Co-IP, Xenopus oocyte electrophysiology, dominant-negative C→S mutant, transepithelial transport in mpkCCD cells

    PMID:14993279

    Open questions at the time
    • Direct ubiquitination of ENaC subunits by UBE2E3 not reconstituted
    • Relative contribution versus other E2s in vivo unclear
  4. 2008 High

    Showing that UBE2E3 localizes to the nucleus and is essential for RPE cell proliferation connected its enzymatic activity to a specific cell-biological role and revealed a proliferation-to-quiescence switch upon its loss.

    Evidence siRNA knockdown in RPE cells, Ki-67/p27 immunolabeling, rescue experiments, beta-galactosidase reporter mouse for developmental downregulation

    PMID:18614808

    Open questions at the time
    • Nuclear substrates responsible for proliferation phenotype unknown
    • Whether quiescence versus senescence was not distinguished at this point
  5. 2011 High

    Revealing that UBE2E3's unique N-terminal extension prevents it from partnering with TRIM21/Ro52, unlike its paralogs UBE2E1/E2, established paralog-specific E3 selectivity within the UBE2E family.

    Evidence In vitro ubiquitination panel and NMR mapping of E2–E3 interface with multiple UBE2E variants

    PMID:21862588

    Open questions at the time
    • Structural basis of why UBE2E3's N-terminus is uniquely incompatible not resolved at atomic detail
  6. 2014 High

    Four contemporaneous studies defined UBE2E3's substrate (TDP-43), its intrinsic monoubiquitylation restriction mechanism, its role in NRF2 nuclear import via importin-11, and its partnership with mitochondrial E3 Mulan, collectively establishing UBE2E3 as a versatile but product-constrained E2 operating in nuclear, cytoplasmic, and mitochondrial compartments.

    Evidence Y2H/Co-IP/ubiquitination assays for TDP-43 (PMID:24825905); reconstituted ubiquitylation with systematic backside mutagenesis (PMID:24901938); siRNA/fractionation/qPCR for NRF2 pathway (PMID:25378586); modified Y2H/Co-IP for Mulan–GABARAP interaction (PMID:25224329)

    PMID:24825905 PMID:24901938 PMID:25224329 PMID:25378586

    Open questions at the time
    • Structural basis for backside-residue constraint not solved
    • Whether monoubiquitylation restriction holds in all E3 contexts in vivo untested
    • Direct ubiquitination site on TDP-43 not mapped
    • Functional consequence of Mulan–UBE2E3–GABARAP complex on mitophagy not demonstrated
  7. 2018 High

    Demonstrating that UBE2E3 loss triggers senescence via a p53/p21/p16-dependent program—with accompanying organelle remodeling—unified earlier proliferation and NRF2 findings into a coherent anti-senescence mechanism.

    Evidence siRNA knockdown, SA-β-Gal, SASP markers, organelle mass staining, autophagic flux, co-depletion epistasis with p53/p21/p16

    PMID:29879550

    Open questions at the time
    • Direct ubiquitination target(s) linking UBE2E3 to p53/p21/p16 pathway unknown
    • Whether NRF2 loss fully explains the senescence phenotype not resolved
  8. 2020 High

    Identifying PJA1 as an E3 ligase partnering with UBE2E3 to suppress TDP-43 aggregation in neurons, and showing that OTUB1 noncatalytically inhibits UBE2E3 polyubiquitination but uniquely cannot suppress its autoubiquitination, refined the regulatory landscape of UBE2E3 activity.

    Evidence Co-IP and in vivo motor neuron model for PJA1–TDP-43 (PMID:32686212); quantitative kinetic in vitro assays for OTUB1 regulation (PMID:32049508)

    PMID:32049508 PMID:32686212

    Open questions at the time
    • Whether PJA1 is the predominant E3 for TDP-43 ubiquitination in disease-relevant neurons unclear
    • Structural basis of OTUB1's failure to suppress UBE2E3 autoubiquitination not determined
  9. 2021 Medium

    Extending the anti-senescence role of UBE2E3 to bone marrow mesenchymal stem cells and linking it to NRF2-dependent osteogenic differentiation broadened the tissue relevance of the UBE2E3–NRF2 axis.

    Evidence Gain- and loss-of-function experiments in BMSCs with senescence and osteogenic differentiation assays, Nrf2 pathway analysis

    PMID:34820159

    Open questions at the time
    • Whether UBE2E3 directly ubiquitinates an NRF2 pathway component in BMSCs not shown
    • Mechanism linking UBE2E3 to NRF2 not reconstituted biochemically in this system
  10. 2023 Medium

    Identification of miR-143-3p as a direct UBE2E3-targeting microRNA in granulosa cells, and of RCBTB1 as a co-immunoprecipitating partner within a potential CUL3-containing complex in RPE cells, expanded the regulatory and interaction network around UBE2E3.

    Evidence 3′UTR luciferase reporter for miR-143-3p (PMID:37628741); Co-IP from iPSC-derived RPE cells for RCBTB1/CUL3 (PMID:37408192)

    PMID:37408192 PMID:37628741

    Open questions at the time
    • RCBTB1–CUL3–UBE2E3 complex not functionally reconstituted
    • Single Co-IP for RCBTB1 without reciprocal validation
    • Whether miR-143-3p regulation of UBE2E3 operates in vivo not established
  11. 2024 Medium

    Additional miRNA-mediated regulation of UBE2E3 was confirmed in Sertoli cells (miR-143-3p) and breast cells (miR-379-5p), with UBE2E3 depletion consistently linked to senescence and proliferative defects across diverse tissues.

    Evidence miRNA mimic/inhibitor transfection, 3′UTR reporters, siRNA knockdown, BTB permeability assay (PMID:38391926); resazurin/BrdU/caspase assays (PMID:39621672)

    PMID:38391926 PMID:39621672

    Open questions at the time
    • Paradoxical increase in both proliferation and apoptosis upon UBE2E3 knockdown in breast cells unexplained mechanistically
    • Whether blood-testis barrier dysfunction is a direct UBE2E3 substrate effect or secondary to senescence unknown

Open questions

Synthesis pass · forward-looking unresolved questions
  • Critical open questions include the identity of UBE2E3's direct ubiquitination substrate(s) that trigger the p53/p21/p16 senescence cascade, the structural basis of its monoubiquitylation restriction at atomic resolution, and whether its NRF2-regulatory function is catalytic (ubiquitin-dependent) or noncatalytic.
  • No substrate linking UBE2E3 catalysis to p53/p21/p16 activation identified
  • No high-resolution structure of UBE2E3 in complex with any E3 partner
  • Catalytic vs. noncatalytic role in NRF2 nuclear import not distinguished

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0016740 transferase activity 5 GO:0140096 catalytic activity, acting on a protein 3 GO:0031386 protein tag activity 2
Localization
GO:0005634 nucleus 2 GO:0005739 mitochondrion 1
Pathway
R-HSA-392499 Metabolism of proteins 5 R-HSA-8953897 Cellular responses to stimuli 3 R-HSA-9612973 Autophagy 2 R-HSA-382551 Transport of small molecules 1
Partners
ARA54IPO11MUL1NEDD4NEDD4LOTUB1PJA1RNF8

Evidence

Reading pass · 18 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
1999 UBE2E3 (cloned from human cDNA) forms a thioester bond with ubiquitin in an E1-dependent manner; a C145S active-site mutant fails to form this thioester, establishing Cys-145 as the catalytic residue essential for E2 function. In vitro thioester formation assay with recombinant GST-UBE2E3 and active-site mutagenesis (C145S) Cytogenetics and cell genetics High 10343118
2001 UBE2E3 interacts with the RING-finger E3 ligases ARA54 and RNF8 through its UBC domain (and their RING domains), and supports their E2-dependent autoubiquitination activity in vitro and in cells. Yeast two-hybrid screen, deletion mutagenesis, in vitro ubiquitination assay with insect-cell-expressed proteins, co-IP in COS-7 cells European journal of biochemistry High 11322894
2004 UBE2E3 acts as the E2 enzyme partnered with the E3 ligase Nedd4-2 to regulate the epithelial Na+ channel (ENaC); UBE2E3 and Nedd4-2 co-immunoprecipitate, and catalytically inactive UBE2E3-CS increases ENaC surface expression, dependent on ENaC PY motifs and ubiquitination sites. Co-immunoprecipitation, Xenopus oocyte electrophysiology, dominant-negative (C→S) mutant expression, transepithelial Na+ transport assay in mpkCCD cells Molecular and cellular biology High 14993279
2005 UBE2E3 can serve as the E2 enzyme for Nedd4 as well as Nedd4-2, though less efficiently than UbcH5b, in in vitro ubiquitination assays. In vitro ubiquitination assay The international journal of biochemistry & cell biology Medium 16337426
2008 UBE2E3 localizes to the nucleus of retinal pigment epithelial (RPE) cells and is essential for their proliferation; siRNA depletion causes cell-cycle exit, loss of Ki-67, accumulation of p27Kip1, and increased cell area. The mouse ortholog UbcM2 is transcriptionally downregulated during RPE maturation in vivo. siRNA knockdown, immunofluorescence localization, Ki-67/p27Kip1 immunolabeling, cell counting, rescue experiments, beta-galactosidase reporter mouse Investigative ophthalmology & visual science High 18614808
2011 The N-terminal extension unique to UBE2E3 (among class III E2 enzymes) prevents it from functionally interacting with the Ro52 (TRIM21) RING-domain E3 ligase, whereas the N-terminal extensions of UBE2E1 and UBE2E2 permit this interaction. In vitro ubiquitination assay panel, NMR mapping of E2/E3 interface, Ro52 RING mutants The Journal of biological chemistry High 21862588
2014 UBE2E3 ubiquitinates TDP-43; catalytically inactive UBE2E3(C145S) is much less efficient, all three UBE2E members enhance TDP-43 ubiquitination, and siRNA silencing of UBE2E3 reduces TDP-43 ubiquitination and affects its solubility. Yeast two-hybrid screen (human brain library), co-immunoprecipitation, ubiquitination assays in HEK293E cells with proteasome inhibition, siRNA knockdown, active-site mutant (C145S) The Journal of biological chemistry High 24825905
2014 UBE2E3 (UbcM2) is intrinsically restricted to monoubiquitylation; this restriction is governed by multiple backside residues of the enzyme (remote from the active site) and by Lys48 of ubiquitin. Backside mutants gain the ability to synthesize K63-linked (and to a lesser extent K6- and K48-linked) polyubiquitin chains. Fully recombinant in vitro ubiquitylation assay, systematic backside-residue mutagenesis, ubiquitin chain-linkage analysis Biochemistry High 24901938
2014 UBE2E3 and its nuclear import receptor importin-11 regulate the subcellular distribution and transcriptional activity of the antioxidant transcription factor NRF2; knockdown of UBE2E3 reduces nuclear NRF2, decreases NRF2 target gene expression, and relocalizes NRF2 to a perinuclear cluster of mitochondria. siRNA knockdown, subcellular fractionation/immunofluorescence localization, target gene expression analysis (qPCR), complementary knockdown of importin-11 Molecular biology of the cell High 25378586
2014 UBE2E3 interacts with the mitochondrial outer membrane E3 ligase Mulan, and the Mulan–UBE2E3 complex recruits GABARAP (an autophagy/mitophagy regulator) via an LC3-interacting region (LIR) in Mulan's RING finger; this interaction requires the presence of UBE2E3. Modified yeast two-hybrid screen using Mulan RING fused to E2 enzymes, co-immunoprecipitation Cellular signalling Medium 25224329
2018 Loss of UBE2E3 induces cellular senescence independently of overt DNA damage; this senescence is partially suppressed by co-depletion of p53, p21CIP1/WAF1, or p16INK4a, and is accompanied by increased mitochondrial and lysosomal mass and elevated autophagic flux. siRNA knockdown, senescence assays (SA-β-Gal, SASP markers), organelle mass staining, autophagic flux measurement, co-depletion epistasis experiments Redox biology High 29879550
2020 The E3 ligase Praja1 (PJA1) binds to TDP-43 C-terminal fragments and to UBE2E3, and suppresses TDP-43 phosphorylation and cytoplasmic aggregate formation; PJA1 is one of the principal E3 ubiquitin ligases acting with UBE2E3 on TDP-43. Co-immunoprecipitation, adenoviral overexpression in neural stem cell-derived neurons, in vivo mouse facial motor neuron model, DNA microarray/candidate screen Neuropathology Medium 32686212
2020 OTUB1, a K48-specific deubiquitinase, noncatalytically inhibits the polyubiquitination activity of UBE2E3 (as well as UBE2E1 and UBE2E2), but uniquely cannot suppress UBE2E3's autoubiquitination activity, revealing a functional distinction between UBE2E3 and its paralogs in OTUB1-mediated regulation. Quantitative kinetic/thermodynamic in vitro ubiquitination assays, DUB activity assays with purified components Biochemistry High 32049508
2021 UBE2E3 knockdown in bone marrow mesenchymal stem cells (BMSCs) accelerates cellular senescence and inhibits osteogenic differentiation, while overexpression of UBE2E3 in old BMSCs attenuates senescence and enhances osteogenic differentiation; this is mechanistically linked to regulation of Nrf2. siRNA knockdown, lentiviral overexpression, senescence assays, osteogenic differentiation assays, Nrf2 pathway analysis in BMSCs PeerJ Medium 34820159
2023 RCBTB1 co-immunoprecipitates with UBE2E3 and CUL3 from RPE cell lysates, placing RCBTB1 as a component of a UBE2E3/CUL3-containing complex involved in the antioxidant (NRF2) response in retinal pigment epithelial cells. Co-immunoprecipitation from iPSC-derived RPE cells Cells Low 37408192
2023 miR-143-3p directly targets UBE2E3 in ovarian granulosa cells; overexpression of miR-143-3p reduces UBE2E3 protein, inhibits granulosa cell proliferation, induces senescence-associated secretory phenotype, and impedes steroid hormone synthesis. miR-143-3p mimic transfection, luciferase 3'UTR reporter assay, proliferation/senescence/SASP assays in granulosa cells International journal of molecular sciences Medium 37628741
2024 miR-143-3p targets UBE2E3 in Sertoli cells; knockdown of UBE2E3 limits Sertoli cell proliferation, promotes senescence, and causes blood-testis barrier dysfunction. miR-143-3p mimic/inhibitor transfection, luciferase reporter, siRNA knockdown of UBE2E3, BTB permeability assay, proliferation/senescence assays Cells Medium 38391926
2024 miR-379-5p directly targets UBE2E3 mRNA via its 3'UTR; miR-379-5p mimic reduces UBE2E3 protein levels and decreases breast cell viability and proliferation, while siRNA silencing of UBE2E3 paradoxically increases both proliferation and apoptosis. miR-379-5p mimic transfection, luciferase 3'UTR reporter assay (WT vs. scrambled binding site), siRNA knockdown, resazurin viability assay, BrdU proliferation assay, caspase 3/7 apoptosis assay PloS one Medium 39621672

Source papers

Stage 0 corpus · 43 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
1998 SUMO-1 modification of IkappaBalpha inhibits NF-kappaB activation. Molecular cell 925 9734360
1997 Ubch9 conjugates SUMO but not ubiquitin. FEBS letters 314 9409737
1999 Identification of the enzyme required for activation of the small ubiquitin-like protein SUMO-1. The Journal of biological chemistry 304 10187858
2012 The circadian protein period 1 contributes to blood pressure control and coordinately regulates renal sodium transport genes. Hypertension (Dallas, Tex. : 1979) 120 22526258
2012 Selective histone deacetylase (HDAC) inhibition imparts beneficial effects in Huntington's disease mice: implications for the ubiquitin-proteasomal and autophagy systems. Human molecular genetics 99 22965876
1999 Control of NF-kappa B transcriptional activation by signal induced proteolysis of I kappa B alpha. Philosophical transactions of the Royal Society of London. Series B, Biological sciences 86 10582246
2001 N-Terminally extended human ubiquitin-conjugating enzymes (E2s) mediate the ubiquitination of RING-finger proteins, ARA54 and RNF8. European journal of biochemistry 85 11322894
2011 Anti-Ro52 autoantibodies from patients with Sjögren's syndrome inhibit the Ro52 E3 ligase activity by blocking the E3/E2 interface. The Journal of biological chemistry 72 21862588
2014 UBE2E ubiquitin-conjugating enzymes and ubiquitin isopeptidase Y regulate TDP-43 protein ubiquitination. The Journal of biological chemistry 71 24825905
2014 Mulan E3 ubiquitin ligase interacts with multiple E2 conjugating enzymes and participates in mitophagy by recruiting GABARAP. Cellular signalling 71 25224329
2004 p14 Arf promotes small ubiquitin-like modifier conjugation of Werners helicase. The Journal of biological chemistry 53 15355988
2021 Sex-stratified gene-by-environment genome-wide interaction study of trauma, posttraumatic-stress, and suicidality. Neurobiology of stress 39 33665242
2021 Genome-wide association studies detects candidate genes for wool traits by re-sequencing in Chinese fine-wool sheep. BMC genomics 35 33602144
2020 Praja1 RING-finger E3 ubiquitin ligase suppresses neuronal cytoplasmic TDP-43 aggregate formation. Neuropathology : official journal of the Japanese Society of Neuropathology 30 32686212
2004 Participation of the ubiquitin-conjugating enzyme UBE2E3 in Nedd4-2-dependent regulation of the epithelial Na+ channel. Molecular and cellular biology 30 14993279
2012 Identification of cellular proteins required for replication of human immunodeficiency virus type 1. AIDS research and human retroviruses 29 22404213
2010 Identification of target genes and pathways associated with chicken microRNA miR-143. Animal genetics 29 20064147
2014 The ubiquitin-conjugating enzyme UBE2E3 and its import receptor importin-11 regulate the localization and activity of the antioxidant transcription factor NRF2. Molecular biology of the cell 27 25378586
2005 The ubiquitin-protein ligases Nedd4 and Nedd4-2 show similar ubiquitin-conjugating enzyme specificities. The international journal of biochemistry & cell biology 25 16337426
2014 The ubiquitin-conjugating enzyme, UbcM2, is restricted to monoubiquitylation by a two-fold mechanism that involves backside residues of E2 and Lys48 of ubiquitin. Biochemistry 22 24901938
2015 Quantitative candidate gene association studies of metabolic traits in Han Chinese type 2 diabetes patients. Genetics and molecular research : GMR 21 26634513
2008 The human ubiquitin conjugating enzyme, UBE2E3, is required for proliferation of retinal pigment epithelial cells. Investigative ophthalmology & visual science 19 18614808
2023 miR-143-3p Promotes Ovarian Granulosa Cell Senescence and Inhibits Estradiol Synthesis by Targeting UBE2E3 and LHCGR. International journal of molecular sciences 17 37628741
2018 Loss of the ubiquitin conjugating enzyme UBE2E3 induces cellular senescence. Redox biology 17 29879550
2021 UBE2E3 regulates cellular senescence and osteogenic differentiation of BMSCs during aging. PeerJ 16 34820159
2020 UBA2 activates Wnt/β-catenin signaling pathway during protection of R28 retinal precursor cells from hypoxia by extracellular vesicles derived from placental mesenchymal stem cells. Stem cell research & therapy 16 33008487
2015 Transcription regulation of nuclear receptor PXR: Role of SUMO-1 modification and NDSM in receptor function. Molecular and cellular endocrinology 15 26549688
2024 Inhibition of miR-143-3p Restores Blood-Testis Barrier Function and Ameliorates Sertoli Cell Senescence. Cells 13 38391926
2023 Disruption in networking of KCMF1 linked ubiquitin ligase impairs autophagy in CD8+ memory T cells of patients with renal cell carcinoma. Cancer letters 13 37084875
2014 The stability of herpes simplex virus 1 ICP0 early after infection is defined by the RING finger and the UL13 protein kinase. Journal of virology 12 24574411
2021 Epigenomic Profiles of African-American Transthyretin Val122Ile Carriers Reveals Putatively Dysregulated Amyloid Mechanisms. Circulation. Genomic and precision medicine 10 33428857
1999 cDNA cloning, characterization, and chromosome mapping of UBE2E3 (alias UbcH9), encoding an N-terminally extended human ubiquitin-conjugating enzyme. Cytogenetics and cell genetics 10 10343118
2020 Comprehensive Analysis of Differently Expressed and Methylated Genes in Preeclampsia. Computational and mathematical methods in medicine 9 33204297
2020 Comparison of Cross-Regulation by Different OTUB1:E2 Complexes. Biochemistry 8 32049508
2019 Identification of Important Invasion-Related Genes in Non-functional Pituitary Adenomas. Journal of molecular neuroscience : MN 7 30982163
2018 iTRAQ-Based Proteomic Analysis reveals possible target-related proteins and signal networks in human osteoblasts overexpressing FGFR2. Proteome science 6 29950929
2020 Genes regulating membrane-associated E-cadherin and proliferation in adenomatous polyposis coli mutant colon cancer cells: High content siRNA screen. PloS one 5 33057364
2023 Mitochondrial Dysfunction and Impaired Antioxidant Responses in Retinal Pigment Epithelial Cells Derived from a Patient with RCBTB1-Associated Retinopathy. Cells 4 37408192
2024 miR-379-5p affects breast cancer cell behavior by targeting UBE2E3 ubiquitin conjugating enzyme. PloS one 3 39621672
2023 Identification and Characterization of Physiological Pairing of E2 Ubiquitin-Conjugating Enzymes and E3 Ubiquitin Ligases. Methods in molecular biology (Clifton, N.J.) 2 36413307
2026 Genome-Wide Association Study for Glucocorticoid-Induced Ocular Hypertension. medRxiv : the preprint server for health sciences 0 41503457
2026 Genomic and transcriptomic analyses revealed potential candidate genes for egg production traits in domesticated ducks. Poultry science 0 41764961
2025 Preliminary exploration of potential biomarkers for heart failure and bipolar disorder: an exploratory study based on bioinformatics. Frontiers in psychiatry 0 41000338