{"gene":"UBE2L3","run_date":"2026-06-10T10:51:56","timeline":{"discoveries":[{"year":1999,"finding":"Crystal structure of the E6AP HECT domain bound to UbcH7 revealed the determinants of E2-E3 specificity and showed how ubiquitin is transferred from the E2 to the E3 via a thioester intermediate; conserved residues in the HECT catalytic cleft are required for ubiquitin-thioester bond formation.","method":"X-ray crystallography; active-site mutagenesis","journal":"Science","confidence":"High","confidence_rationale":"Tier 1 / Strong — crystal structure plus mutagenesis in a single rigorous study, foundational mechanistic paper","pmids":["10558980"],"is_preprint":false},{"year":2000,"finding":"Crystal structure of c-Cbl bound to UbcH7 (and a kinase peptide) showed that the RING domain recruits UbcH7 via a conserved E2 surface motif also used by HECT E3s, and revealed a rigid coupling between substrate-binding and E2-binding domains with a conserved channel leading to the E2 active site, suggesting RING E3s act as scaffolds positioning substrate and E2 for ubiquitin transfer.","method":"X-ray crystallography","journal":"Cell","confidence":"High","confidence_rationale":"Tier 1 / Strong — crystal structure with functional validation, widely replicated and cited","pmids":["10966114"],"is_preprint":false},{"year":1999,"finding":"The c-Cbl RING finger domain directly interacts with UbcH7; this interaction is disrupted by the oncogenic 70Z-Cbl deletion. c-Cbl and UbcH7 synergistically promote ligand-induced ubiquitination of the EGFR in vitro and in vivo, while 70Z-Cbl suppresses this ubiquitination.","method":"Yeast two-hybrid; in vitro binding assay; in vivo ubiquitination assay","journal":"Journal of Biological Chemistry","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal binding assays plus functional in vivo ubiquitination, replicated by structural study (PMID:10966114)","pmids":["10531381"],"is_preprint":false},{"year":1996,"finding":"UbcH7 (UBE2L3) was cloned and shown to interact with the HECT E3 ligase E6-AP and to efficiently substitute for UbcH5 in E6-AP-dependent ubiquitination in vitro, establishing UbcH7 as a functional E2 for HECT-type E3s.","method":"Biochemical interaction assay; in vitro ubiquitination reconstitution","journal":"Journal of Biological Chemistry","confidence":"High","confidence_rationale":"Tier 1 / Strong — in vitro reconstitution of E2-E3 activity, independently confirmed in multiple subsequent studies","pmids":["8576257"],"is_preprint":false},{"year":1998,"finding":"Multiple human HECT-domain proteins form thioester complexes with ubiquitin using UbcH7 or UbcH5 as their preferred E2, dividing the HECT family into at least two classes based on E2 specificity; the HECT domain alone is necessary and sufficient for ubiquitin thioester adduct formation.","method":"In vitro ubiquitin thioester formation assay; E2 specificity binding assays","journal":"Journal of Biological Chemistry","confidence":"High","confidence_rationale":"Tier 1 / Moderate — in vitro biochemical reconstitution with domain dissection, multiple HECT proteins tested","pmids":["9575161"],"is_preprint":false},{"year":2011,"finding":"UbcH7 lacks intrinsic E3-independent reactivity with lysine (unlike many other E2s), explaining its preference for HECT-type E3s. UbcH7 is active with RBR family E3s (parkin, HHARI), which function as RING/HECT hybrids: they bind UbcH7 via a RING domain but transfer ubiquitin through an obligate thioester-linked intermediate requiring a conserved cysteine in RING2.","method":"In vitro lysine reactivity assay; in vitro ubiquitination assay; mutagenesis of RBR catalytic cysteine","journal":"Nature","confidence":"High","confidence_rationale":"Tier 1 / Strong — multiple orthogonal in vitro assays plus mutagenesis defining mechanism; foundational paper for RBR E3 mechanism","pmids":["21532592"],"is_preprint":false},{"year":1999,"finding":"UbcH7 interacts with HHARI and H7-AP1 via their RING finger and IBR domains in vitro. This interaction is specific: both proteins bind UbcH8 but not UbcH5 or UbcH1, linking a subset of RING/IBR proteins to the ubiquitin pathway via UbcH7.","method":"Yeast two-hybrid; in vitro binding assay","journal":"Journal of Biological Chemistry","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — yeast two-hybrid plus in vitro binding, no functional ubiquitination reconstitution","pmids":["10521492"],"is_preprint":false},{"year":2001,"finding":"HHARI interacts and co-localizes with UbcH7 in the perinuclear region of mammalian cells. A minimal interaction region (residues 186-254 of HHARI) was defined; specific residues in the RING1 domain and the distance between RING1 and IBR are critical. Mutation of RING1 from RING-HC to RING-H2 type abolishes binding to UbcH7.","method":"Co-immunoprecipitation; co-localization (immunofluorescence); deletion/point mutagenesis","journal":"Journal of Biological Chemistry","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — co-IP plus localization plus mutagenesis, single lab","pmids":["11278816"],"is_preprint":false},{"year":2004,"finding":"UbcH7 is specifically involved in ubiquitination of HPV E7; E7 interacts with the SCF complex containing Cul1 and Skp2 and can be ubiquitinated by the Cul1-containing ubiquitin ligase in vitro. E7 half-life is significantly longer in Skp2-/- MEFs than wild-type.","method":"In vitro ubiquitination assay; co-immunoprecipitation; Skp2-/- MEF genetic analysis","journal":"Journal of Virology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — in vitro reconstitution plus genetic (Skp2 KO) validation, single lab","pmids":["15113913"],"is_preprint":false},{"year":2004,"finding":"UBCH7 acts as a transcriptional coactivator for steroid hormone receptors (PR, GR, AR, RAR) in a hormone-dependent manner; its ubiquitin conjugation activity is required for this coactivation function. UBCH7 is recruited to estrogen receptor- and PR-responsive promoters in a hormone-dependent manner and interacts with SRC-1.","method":"Transient transfection reporter assay; siRNA depletion; chromatin immunoprecipitation (ChIP); co-immunoprecipitation","journal":"Molecular and Cellular Biology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — ChIP plus functional reporter assays plus co-IP, single lab","pmids":["15367689"],"is_preprint":false},{"year":2006,"finding":"UbcH7 physically interacts with the glucocorticoid receptor (GR) and reduces GR-dependent gene expression when overexpressed; a dominant-negative UbcH7 (C89S, catalytically inactive) fails to repress GR transactivation and abolishes ligand-dependent GR protein downregulation, establishing that UbcH7 regulates GR turnover via its ubiquitin-conjugating activity.","method":"Co-immunoprecipitation; transient transfection reporter assay; dominant-negative mutagenesis; proteasome inhibitor rescue","journal":"Journal of Endocrinology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — multiple orthogonal approaches (co-IP, reporter, mutagenesis), single lab","pmids":["17003263"],"is_preprint":false},{"year":2014,"finding":"UbcH7 regulates both steady-state and replicative stress-induced ubiquitination and proteasomal degradation of 53BP1. Depletion of UbcH7 stabilizes 53BP1, inhibits DSB end resection, shifts repair from homologous recombination to NHEJ, and sensitizes cells to DNA damage.","method":"shRNA library screen; siRNA knockdown; ubiquitination assay; DSB repair assay (HR/NHEJ reporters)","journal":"PNAS","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — functional screen followed by mechanistic validation with multiple readouts, single lab","pmids":["25422456"],"is_preprint":false},{"year":2014,"finding":"UBE2L3, UBE2N, and UBE2D2/3 synergistically contribute to Parkin-mediated mitophagy; UBE2L3 knockdown reduces autophagic clearance of depolarized mitochondria and reduces ubiquitination of mitochondrial substrates (mitofusins, TOM20, TOM70, VDAC1) without interfering with PINK1 stabilization or Parkin translocation.","method":"siRNA knockdown; mitophagy assay; ubiquitination assay; flow cytometry","journal":"Journal of Cell Science","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — multiple knockdowns with defined phenotypic and molecular readouts, single lab","pmids":["24906799"],"is_preprint":false},{"year":2015,"finding":"UBE2L3 is the preferred E2 conjugating enzyme for the LUBAC complex (HOIL-1/HOIP) in vivo and is essential for LUBAC-mediated NF-κB activation. Dominant-negative UBE2L3 (C86S) or UBE2L3 silencing abolishes LUBAC-induced NF-κB upregulation.","method":"HEK293-NF-κB reporter assay; dominant-negative mutagenesis; siRNA knockdown; imaging flow cytometry for NF-κB translocation in primary cells","journal":"American Journal of Human Genetics / Lancet","confidence":"High","confidence_rationale":"Tier 2 / Strong — multiple orthogonal methods (reporter, mutagenesis, primary cell imaging), replicated in two publications from same group","pmids":["25640675","26312912"],"is_preprint":false},{"year":2005,"finding":"HIV Nef mediates exclusion of UbcH7 from lipid rafts via formation of a p85Cool-1/betaPix–c-Cbl–Cdc42 ternary complex that displaces UbcH7 from rafts, preventing ubiquitination of activated Vav and thereby increasing T cell signaling.","method":"Lipid raft fractionation; co-immunoprecipitation; siRNA knockdown of p85Cool-1/betaPix","journal":"Immunity","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — biochemical fractionation plus co-IP plus knockdown rescue, single lab","pmids":["16356860"],"is_preprint":false},{"year":2009,"finding":"The RBR E3 ligase Triad1 interacts with UbcH7 through its first RING domain and with Ubc13 through its second RING domain; both interactions and full-length Triad1 are required for inhibition of myeloid colony formation, demonstrating that UbcH7-dependent ubiquitination through Triad1 is biologically essential for myelopoiesis.","method":"In vitro binding assay; domain mutagenesis; myeloid clonogenic assay","journal":"Leukemia","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — domain mutagenesis plus functional clonogenic assay, single lab","pmids":["19340006"],"is_preprint":false},{"year":2009,"finding":"UbcH7 overexpression delays S phase entry while its depletion lengthens S phase and decreases cell proliferation; UbcH7 depletion increases Chk1 levels and decreases phosphorylated PTEN, indicating UbcH7 regulates S phase length through a PTEN/Akt/Chk1 pathway.","method":"Overexpression; siRNA knockdown; cell cycle analysis (flow cytometry); Western blot","journal":"Cell Division","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single lab, single method per readout, pathway placement inferred without direct epistasis testing","pmids":["19664228"],"is_preprint":false},{"year":2015,"finding":"Ndfip1 acts as an adaptor that recruits UbcH7 to the HECT E3 Itch: Ndfip1 N-terminus binds UbcH7 while its PY motif binds Itch, enhancing Itch ligase activity and Itch-mediated K63 ubiquitination of Tak1, limiting airway inflammation.","method":"Co-immunoprecipitation; in vitro ubiquitination assay; Ndfip1-/- mouse model; Itch-/- mouse model; siRNA/mutagenesis rescue","journal":"Journal of Immunology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — co-IP, in vitro ubiquitination, and KO mouse phenotype with mutant rescue, single lab","pmids":["25632008"],"is_preprint":false},{"year":2017,"finding":"HHARI RING1 contains a Zn2+-loop II extension not present in canonical RING E3s that acts as a steric wedge to prevent closed E2~Ub conformation, structurally explaining how RBR RING1 domains promote open E2~Ub conformation to favor Ub transfer to the E3 active site rather than direct transfer to substrate.","method":"X-ray crystallography; structural comparison","journal":"Structure","confidence":"High","confidence_rationale":"Tier 1 / Moderate — crystal structure with structural mechanistic interpretation, single lab but rigorous","pmids":["28552575"],"is_preprint":false},{"year":2018,"finding":"UbcH7~Ub conjugate binds to the RING1/IBR interface of parkin in the open (not closed) E2~Ub state; NMR and mass spectrometry show that parkin phosphorylation and UbcH7~Ub recruitment act synergistically to rearrange the RING0/RING2 interface and alter reactivity of the RING2 catalytic cysteine (Rcat), driving parkin ubiquitination activity.","method":"NMR chemical shift perturbation; hydrogen-deuterium exchange mass spectrometry; in vitro ubiquitination assay","journal":"EMBO Journal","confidence":"High","confidence_rationale":"Tier 1 / Moderate — NMR plus MS plus functional assay, multiple orthogonal methods in one study","pmids":["30446597"],"is_preprint":false},{"year":2018,"finding":"UBCH7/UBE2L3 overexpression stabilizes p27Kip1 and delays the G1-to-S cell cycle transition; depletion of UBE2L3 increases p27Kip1 turnover. The stabilization mechanism involves UBE2L3-catalyzed conjugation of heterotypic ubiquitin chains on p27Kip1 that are proteolytically incompetent.","method":"Overexpression; siRNA knockdown; cell cycle analysis; in vitro ubiquitination assay with heterotypic chain characterization","journal":"FASEB Journal","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — in vitro ubiquitination plus cellular KD/OE with chain-type characterization, single lab","pmids":["30113882"],"is_preprint":false},{"year":2014,"finding":"MAP1B light chain 1 (LC1) interacts with UBE2L3 (via yeast two-hybrid and co-IP), and the LC1/UBE2L3 complex co-immunoprecipitates with CaV2.2 N-type Ca2+ channels, promoting their ubiquitination and proteasomal degradation, thereby reducing channel surface expression and current amplitude.","method":"Yeast two-hybrid; co-immunoprecipitation; patch-clamp electrophysiology; proteasome inhibitor rescue","journal":"Pflügers Archiv","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — yeast two-hybrid, co-IP, and functional electrophysiology with pharmacological rescue, single lab","pmids":["24566975"],"is_preprint":false},{"year":2023,"finding":"UBE2L3 promotes pro-IL-1β ubiquitylation and proteasomal disposal; deletion of Ube2l3 in mice reduces pro-IL-1β turnover in macrophages, leading to excessive mature IL-1β production and neutrophilic inflammation. An RNAi screen identified HECT E3 ligases TRIP12 and AREL1 as the E3 partners adding destabilizing K27-, K29-, and K33-linked poly-ubiquitin chains on pro-IL-1β.","method":"Ube2l3 conditional knockout mouse; RNAi screen; ubiquitination assays; inflammasome activation assays","journal":"Nature Communications","confidence":"High","confidence_rationale":"Tier 2 / Strong — KO mouse with defined in vivo phenotype plus mechanistic RNAi screen identifying E3 partners and chain topology, multiple orthogonal methods","pmids":["37474493"],"is_preprint":false},{"year":2023,"finding":"UBE2L3 is critical for NF-κB activation downstream of TLR7 stimulation via interaction with LUBAC. Dimethyl fumarate (DMF), which directly inhibits UBE2L3, blocks TLR7-induced NF-κB activation, differentiation of memory B cells and plasmablasts, and autoantibody secretion in SLE B cells.","method":"siRNA knockdown; NF-κB reporter assay; flow cytometry for B cell differentiation; ELISA for autoantibodies","journal":"Journal of Autoimmunity","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — genetic and pharmacological inhibition with multiple cellular readouts, single lab","pmids":["37001433"],"is_preprint":false},{"year":2024,"finding":"MARCHF8 E3 ubiquitin ligase binds to and ubiquitinates both CUL1 and UBE2L3, leading to their degradation and thereby preventing ubiquitination and degradation of HPV16 E7; overexpression of CUL1 or UBE2L3 restores E7 degradation and suppresses tumor growth in vivo.","method":"Co-immunoprecipitation; ubiquitination assay; siRNA knockdown; in vivo tumor xenograft","journal":"Journal of Virology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — co-IP plus ubiquitination assay plus in vivo rescue, single lab","pmids":["38226814"],"is_preprint":false},{"year":2024,"finding":"SMURF1 (but not SMURF2) works with UbcH7 to ubiquitinate p27 with K29-linked chains in vitro, stabilizing p27. SMURF1, UbcH7, and p27 co-localize at the leading edge of migrating cells, and knockdown of SMURF1 or UbcH7 reduces cell migration.","method":"In vitro ubiquitination screen; in vitro ubiquitination with K29R/K29O mutant ubiquitin; siRNA knockdown; co-localization by fluorescence microscopy; cell migration assay","journal":"Journal of Biological Chemistry","confidence":"Medium","confidence_rationale":"Tier 1 / Moderate — in vitro reconstitution with chain-type mutants plus cellular co-localization and functional migration assay, single lab","pmids":["38301893"],"is_preprint":false},{"year":2025,"finding":"UBE2L3 specifically binds MLKL via co-immunoprecipitation and promotes its ubiquitination; overexpression of UBE2L3 reduces MLKL expression, while UBE2L3 knockdown increases MLKL phosphorylation and promotes necroptosis in osteosarcoma cells and in vivo.","method":"Co-immunoprecipitation; ubiquitination assay; siRNA knockdown; in vivo tumor xenograft; immunohistochemistry","journal":"World Journal of Surgical Oncology","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single lab, co-IP plus knockdown, limited mechanistic depth","pmids":["39988669"],"is_preprint":false},{"year":2026,"finding":"In vivo CRISPR screen identified UBE2L3 as a regulator of autophagy in TNBC; mechanistically, UBE2L3 interacts with E3 ligase SMURF2 to ubiquitinate and degrade TSC2, thereby activating mTOR and suppressing autophagy.","method":"In vivo CRISPR/Cas9 library screen; co-immunoprecipitation; ubiquitination assay; autophagy assays","journal":"International Journal of Biological Sciences","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single lab, co-IP plus ubiquitination assay, mechanistic pathway placement partially inferred","pmids":["41943836"],"is_preprint":false}],"current_model":"UBE2L3 (UbcH7) is an E2 ubiquitin-conjugating enzyme that lacks intrinsic lysine reactivity, making it inactive with canonical RING E3s but active with HECT-type E3s (e.g., E6-AP, Itch, TRIP12, AREL1) and RBR E3s (e.g., parkin, HHARI, Triad1) that function as RING/HECT hybrids requiring an E3 thioester intermediate; through these partnerships it ubiquitinates diverse substrates including EGFR (via c-Cbl), pro-IL-1β (destabilizing K27/K29/K33 chains via TRIP12/AREL1), p27Kip1 (stabilizing heterotypic chains via SMURF1), 53BP1, TSC2, and MLKL, and acts as the preferred E2 for the LUBAC complex to drive linear ubiquitin chain-dependent NF-κB activation in immune cells, thereby linking UBE2L3 expression levels to autoimmune disease susceptibility."},"narrative":{"mechanistic_narrative":"UBE2L3 (UbcH7) is an E2 ubiquitin-conjugating enzyme whose catalytic specificity is defined by an inability to react with free lysine independently of an E3, restricting it to E3 ligases that employ an obligate thioester-linked ubiquitin intermediate [PMID:21532592]. Consistent with this, it functions efficiently with HECT-domain E3 ligases, originally established through its interaction with E6-AP and its ability to drive E6-AP-dependent ubiquitination in vitro [PMID:8576257], and it partitions the HECT family by E2 preference, supporting thioester adduct formation on the HECT domain [PMID:9575161]. Structural work on the E6AP HECT domain bound to UbcH7 defined the E2-E3 interface and showed how ubiquitin transits from E2 to E3 via a thioester relay [PMID:10558980], while the c-Cbl RING–UbcH7 structure revealed that RING domains recruit UbcH7 through a conserved E2 surface used by HECT E3s as well, positioning substrate and E2 for transfer [PMID:10966114, PMID:10531381]. UBE2L3 is also the cognate E2 for RING-between-RING (RBR) E3 ligases—parkin, HHARI, and Triad1—which behave as RING/HECT hybrids: UbcH7 is engaged via a RING domain but ubiquitin passes through a conserved RING2 catalytic cysteine [PMID:21532592, PMID:19340006], with the RBR RING1 acting as a steric wedge that holds the E2~Ub conjugate in an open conformation to favor transfer to the E3 active site [PMID:28552575, PMID:30446597]. Through these partnerships UBE2L3 ubiquitinates a broad substrate range, including EGFR via c-Cbl [PMID:10531381], 53BP1 to control DNA double-strand break repair pathway choice [PMID:25422456], mitochondrial proteins during Parkin-mediated mitophagy [PMID:24906799], and pro-IL-1β, which it targets with destabilizing K27/K29/K33 chains through the HECT E3s TRIP12 and AREL1 to limit mature IL-1β output and inflammation [PMID:37474493]. It can also catalyze proteolytically incompetent heterotypic chains that stabilize substrates such as p27Kip1 [PMID:30113882, PMID:38301893]. UBE2L3 is the preferred E2 for the LUBAC complex (HOIP/HOIL-1), driving linear-ubiquitin-dependent NF-κB activation in immune cells, including downstream of TLR7 in autoreactive B cells [PMID:25640675, PMID:26312912, PMID:37001433].","teleology":[{"year":1996,"claim":"Establishing that UbcH7 is a functional E2 for HECT-type E3 ligases answered the basic question of which ligase class it serves.","evidence":"biochemical interaction and in vitro ubiquitination reconstitution with E6-AP","pmids":["8576257"],"confidence":"High","gaps":["Did not define structural basis of E2-E3 recognition","Substrate range beyond the reconstituted system unknown"]},{"year":1998,"claim":"Showing that multiple HECT proteins form ubiquitin thioesters preferentially with UbcH7 or UbcH5 defined an E2-specificity logic within the HECT family.","evidence":"in vitro thioester formation and E2 specificity assays with domain dissection","pmids":["9575161"],"confidence":"High","gaps":["Determinants of UbcH7 vs UbcH5 selection not resolved at residue level","In vivo relevance per HECT E3 untested"]},{"year":1999,"claim":"Crystallography of the E6AP HECT domain with UbcH7 and the c-Cbl RING with UbcH7 revealed that both ligase classes engage a shared E2 surface and defined the thioester transfer geometry, unifying RING and HECT mechanisms around UbcH7.","evidence":"X-ray crystallography with active-site mutagenesis; yeast two-hybrid and in vivo EGFR ubiquitination","pmids":["10558980","10966114","10531381"],"confidence":"High","gaps":["Did not address why UbcH7 fails with most RING E3s in cells","Substrate channeling dynamics not captured"]},{"year":1999,"claim":"Identifying UbcH7 binding to RING/IBR proteins HHARI and H7-AP1, and later their perinuclear co-localization, extended its partnerships beyond classic HECT and RING ligases.","evidence":"yeast two-hybrid, in vitro binding, co-IP, co-localization, and interface mutagenesis","pmids":["10521492","11278816"],"confidence":"Medium","gaps":["No functional ubiquitination reconstitution in early work","Physiological substrates of HHARI/UbcH7 unidentified"]},{"year":2004,"claim":"Functional links to HPV E7 turnover and to steroid-receptor coactivation broadened UbcH7's cellular roles beyond a generic conjugating enzyme.","evidence":"in vitro ubiquitination, Skp2-/- MEFs, reporter assays, ChIP, and co-IP","pmids":["15113913","15367689"],"confidence":"Medium","gaps":["Direct E3 for E7 in vivo not fully resolved","Mechanism coupling conjugation activity to transcriptional coactivation unclear"]},{"year":2006,"claim":"Demonstrating that catalytically inactive UbcH7 (C89S) cannot drive ligand-dependent GR downregulation tied receptor turnover directly to UbcH7's conjugating activity.","evidence":"co-IP, reporter assay, dominant-negative mutagenesis, proteasome inhibitor rescue","pmids":["17003263"],"confidence":"Medium","gaps":["Cognate E3 for GR not defined","Single-lab observation"]},{"year":2011,"claim":"Discovering that UbcH7 lacks intrinsic lysine reactivity but functions with RBR E3s via an obligate thioester intermediate explained its E3-class restriction and defined RBR ligases as RING/HECT hybrids.","evidence":"in vitro lysine reactivity and ubiquitination assays with RBR catalytic cysteine mutagenesis","pmids":["21532592"],"confidence":"High","gaps":["Conformational basis of open vs closed E2~Ub not yet structurally resolved","Range of RBR substrates not enumerated"]},{"year":2014,"claim":"Cellular studies placed UbcH7 in DNA repair pathway choice, mitophagy, and ion channel regulation, showing the same E2 acts across distinct cellular processes through different E3/adaptor partners.","evidence":"shRNA/siRNA knockdown with DSB repair reporters; mitophagy and ubiquitination assays; yeast two-hybrid, co-IP, and patch-clamp","pmids":["25422456","24906799","24566975"],"confidence":"Medium","gaps":["E3 ligase identity not pinned down in each context","Substrate ubiquitin chain topology mostly uncharacterized"]},{"year":2015,"claim":"Identifying UBE2L3 as the preferred E2 for LUBAC and the Ndfip1-Itch axis established its role in NF-κB-driven and inflammatory signaling.","evidence":"NF-κB reporter, dominant-negative C86S, siRNA, primary-cell imaging; co-IP, in vitro ubiquitination, Ndfip1-/- and Itch-/- mice","pmids":["25640675","26312912","25632008"],"confidence":"High","gaps":["Mechanism linking UBE2L3 expression level to autoimmune susceptibility not fully resolved","Quantitative contribution relative to other LUBAC E2s unclear"]},{"year":2018,"claim":"Structural and biophysical analyses of HHARI and parkin showed how RBR RING1 enforces an open E2~Ub conformation and how parkin phosphorylation plus UbcH7~Ub recruitment synergistically activate the catalytic cysteine, defining the activation mechanism.","evidence":"X-ray crystallography, NMR, HDX-MS, and in vitro ubiquitination","pmids":["28552575","30446597"],"confidence":"High","gaps":["Full catalytic cycle dynamics not captured in one structure","Generalizability across all RBR family members untested"]},{"year":2018,"claim":"Showing UBE2L3 builds proteolytically incompetent heterotypic chains on p27Kip1 demonstrated that it can stabilize rather than destabilize substrates depending on chain topology.","evidence":"overexpression/knockdown, cell cycle analysis, in vitro ubiquitination with chain characterization","pmids":["30113882"],"confidence":"Medium","gaps":["E3 ligase responsible not identified in this study","Physiological prevalence of these chains unknown"]},{"year":2023,"claim":"Conditional Ube2l3 knockout in mice defined an in vivo anti-inflammatory function via TRIP12/AREL1-dependent K27/K29/K33 ubiquitylation of pro-IL-1β and connected UBE2L3-LUBAC to TLR7-driven B-cell autoimmunity.","evidence":"Ube2l3 conditional KO mouse, RNAi screen, ubiquitination and inflammasome assays; siRNA, NF-κB reporter, B-cell differentiation, DMF inhibition","pmids":["37474493","37001433"],"confidence":"High","gaps":["How chain topology dictates pro-IL-1β proteasomal disposal mechanistically unclear","DMF target selectivity for UBE2L3 in vivo not fully delineated"]},{"year":2024,"claim":"Partner-specific studies identified SMURF1 cooperation in K29-linked p27 stabilization at the migrating cell edge and MARCHF8-mediated degradation of UBE2L3 controlling HPV E7 levels, refining its substrate and regulatory networks.","evidence":"in vitro ubiquitination with chain mutants, co-localization, migration assays; co-IP, ubiquitination, and xenograft rescue","pmids":["38301893","38226814"],"confidence":"Medium","gaps":["Reciprocal validation across systems limited","In vivo significance of the SMURF1/p27 axis untested"]},{"year":2026,"claim":"Reports linking UBE2L3 to MLKL-dependent necroptosis and to SMURF2-mediated TSC2/mTOR/autophagy control in cancer extend its proposed roles but rest on limited mechanistic depth.","evidence":"co-IP, ubiquitination, knockdown, xenografts; in vivo CRISPR screen and autophagy assays","pmids":["39988669","41943836"],"confidence":"Low","gaps":["Single-lab co-IP/knockdown without reciprocal validation","Direct ubiquitination of stated substrates and chain topology not firmly established","Pathway placement partially inferred"]},{"year":null,"claim":"It remains unresolved how UBE2L3 expression level and chain-type output are selected across its many E3 partners to produce opposite (stabilizing vs degradative) outcomes on different substrates in vivo.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No unifying model linking E3 partner choice to chain topology","Quantitative control of substrate fate by UBE2L3 abundance not established"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0140096","term_label":"catalytic activity, acting on a protein","supporting_discovery_ids":[3,4,5,22]},{"term_id":"GO:0016740","term_label":"transferase activity","supporting_discovery_ids":[0,3,5]}],"localization":[{"term_id":"GO:0005829","term_label":"cytosol","supporting_discovery_ids":[7]},{"term_id":"GO:0005886","term_label":"plasma membrane","supporting_discovery_ids":[14,25]}],"pathway":[{"term_id":"R-HSA-392499","term_label":"Metabolism of proteins","supporting_discovery_ids":[0,3,4,5]},{"term_id":"R-HSA-168256","term_label":"Immune System","supporting_discovery_ids":[13,22,23]},{"term_id":"R-HSA-73894","term_label":"DNA Repair","supporting_discovery_ids":[11]},{"term_id":"R-HSA-9612973","term_label":"Autophagy","supporting_discovery_ids":[12,27]},{"term_id":"R-HSA-162582","term_label":"Signal Transduction","supporting_discovery_ids":[13,17,23]}],"complexes":["LUBAC"],"partners":["E6-AP","CBL","HHARI","PARK2","TRIP12","AREL1","SMURF1","ITCH"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"P68036","full_name":"Ubiquitin-conjugating enzyme E2 L3","aliases":["E2 ubiquitin-conjugating enzyme L3","L-UBC","UbcH7","Ubiquitin carrier protein L3","Ubiquitin-conjugating enzyme E2-F1","Ubiquitin-protein ligase L3"],"length_aa":154,"mass_kda":17.9,"function":"Ubiquitin-conjugating enzyme E2 that specifically acts with HECT-type and RBR family E3 ubiquitin-protein ligases. Does not function with most RING-containing E3 ubiquitin-protein ligases because it lacks intrinsic E3-independent reactivity with lysine; in contrast, it has activity with the RBR family E3 enzymes, such as PRKN, RNF31 and ARIH1, that function like RING-HECT hybrids. Accepts ubiquitin from the E1 complex and catalyzes its covalent attachment to other proteins. Mediates ubiquitination by the CUL9-RBX1 complex (PubMed:38605244). In vitro catalyzes 'Lys-11'-linked polyubiquitination. Involved in the selective degradation of short-lived and abnormal proteins. Down-regulated during the S-phase it is involved in progression through the cell cycle. Regulates nuclear hormone receptors transcriptional activity. May play a role in myelopoiesis","subcellular_location":"Nucleus; Cytoplasm","url":"https://www.uniprot.org/uniprotkb/P68036/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":true,"resolved_as":"","url":"https://depmap.org/portal/gene/UBE2L3","classification":"Common Essential","n_dependent_lines":1165,"n_total_lines":1208,"dependency_fraction":0.9644039735099338},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[{"gene":"UBA1","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/search/UBE2L3","total_profiled":1310},"omim":[{"mim_id":"619675","title":"U-BOX DOMAIN-CONTAINING PROTEIN 5; UBOX5","url":"https://www.omim.org/entry/619675"},{"mim_id":"619454","title":"RING FINGER PROTEIN 144A; RNF144A","url":"https://www.omim.org/entry/619454"},{"mim_id":"618869","title":"RING FINGER PROTEIN 144B; RNF144B","url":"https://www.omim.org/entry/618869"},{"mim_id":"615211","title":"UBIQUITIN-LIKE PROTEIN CONTAINING PHD AND RING FINGER DOMAINS 2, E3 UBIQUITIN PROTEIN LIGASE; UHRF2","url":"https://www.omim.org/entry/615211"},{"mim_id":"614454","title":"UBIQUITIN PROTEIN LIGASE E3C; UBE3C","url":"https://www.omim.org/entry/614454"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Approved","locations":[{"location":"Nucleoplasm","reliability":"Approved"},{"location":"Cytosol","reliability":"Approved"},{"location":"Primary cilium transition zone","reliability":"Additional"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/UBE2L3"},"hgnc":{"alias_symbol":["UBCH7"],"prev_symbol":[]},"alphafold":{"accession":"P68036","domains":[{"cath_id":"3.10.110.10","chopping":"1-149","consensus_level":"medium","plddt":94.5561,"start":1,"end":149}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/P68036","model_url":"https://alphafold.ebi.ac.uk/files/AF-P68036-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-P68036-F1-predicted_aligned_error_v6.png","plddt_mean":95.56},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=UBE2L3","jax_strain_url":"https://www.jax.org/strain/search?query=UBE2L3"},"sequence":{"accession":"P68036","fasta_url":"https://rest.uniprot.org/uniprotkb/P68036.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/P68036/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/P68036"}},"corpus_meta":[{"pmid":"10966114","id":"PMC_10966114","title":"Structure of a c-Cbl-UbcH7 complex: RING domain function in ubiquitin-protein ligases.","date":"2000","source":"Cell","url":"https://pubmed.ncbi.nlm.nih.gov/10966114","citation_count":722,"is_preprint":false},{"pmid":"10558980","id":"PMC_10558980","title":"Structure of an E6AP-UbcH7 complex: insights into ubiquitination by the E2-E3 enzyme cascade.","date":"1999","source":"Science (New York, N.Y.)","url":"https://pubmed.ncbi.nlm.nih.gov/10558980","citation_count":473,"is_preprint":false},{"pmid":"21532592","id":"PMC_21532592","title":"UBCH7 reactivity profile reveals parkin and HHARI to be RING/HECT hybrids.","date":"2011","source":"Nature","url":"https://pubmed.ncbi.nlm.nih.gov/21532592","citation_count":461,"is_preprint":false},{"pmid":"10531381","id":"PMC_10531381","title":"Ligand-induced ubiquitination of the epidermal growth factor receptor involves the interaction of the c-Cbl RING finger and UbcH7.","date":"1999","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/10531381","citation_count":278,"is_preprint":false},{"pmid":"9575161","id":"PMC_9575161","title":"Characterization of human hect domain family members and their interaction with UbcH5 and UbcH7.","date":"1998","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/9575161","citation_count":143,"is_preprint":false},{"pmid":"8576257","id":"PMC_8576257","title":"Cloning of human ubiquitin-conjugating enzymes UbcH6 and UbcH7 (E2-F1) and characterization of their interaction with E6-AP and RSP5.","date":"1996","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/8576257","citation_count":137,"is_preprint":false},{"pmid":"10521492","id":"PMC_10521492","title":"The ubiquitin-conjugating enzymes UbcH7 and UbcH8 interact with RING finger/IBR motif-containing domains of HHARI and H7-AP1.","date":"1999","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/10521492","citation_count":101,"is_preprint":false},{"pmid":"24906799","id":"PMC_24906799","title":"The ubiquitin-conjugating enzymes UBE2N, UBE2L3 and UBE2D2/3 are essential for Parkin-dependent mitophagy.","date":"2014","source":"Journal of cell science","url":"https://pubmed.ncbi.nlm.nih.gov/24906799","citation_count":96,"is_preprint":false},{"pmid":"25640675","id":"PMC_25640675","title":"UBE2L3 polymorphism amplifies NF-κB activation and promotes plasma cell development, linking linear ubiquitination to multiple autoimmune diseases.","date":"2015","source":"American journal of human genetics","url":"https://pubmed.ncbi.nlm.nih.gov/25640675","citation_count":84,"is_preprint":false},{"pmid":"15113913","id":"PMC_15113913","title":"The papillomavirus E7 oncoprotein is ubiquitinated by UbcH7 and Cullin 1- and Skp2-containing E3 ligase.","date":"2004","source":"Journal of virology","url":"https://pubmed.ncbi.nlm.nih.gov/15113913","citation_count":80,"is_preprint":false},{"pmid":"15367689","id":"PMC_15367689","title":"The ubiquitin-conjugating enzyme UBCH7 acts as a coactivator for steroid hormone receptors.","date":"2004","source":"Molecular and cellular biology","url":"https://pubmed.ncbi.nlm.nih.gov/15367689","citation_count":74,"is_preprint":false},{"pmid":"11278816","id":"PMC_11278816","title":"Features of the parkin/ariadne-like ubiquitin ligase, HHARI, that regulate its interaction with the ubiquitin-conjugating enzyme, Ubch7.","date":"2001","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/11278816","citation_count":69,"is_preprint":false},{"pmid":"27729585","id":"PMC_27729585","title":"Mechanism and disease association of E2-conjugating enzymes: lessons from UBE2T and UBE2L3.","date":"2016","source":"The Biochemical journal","url":"https://pubmed.ncbi.nlm.nih.gov/27729585","citation_count":62,"is_preprint":false},{"pmid":"22476155","id":"PMC_22476155","title":"A functional haplotype of UBE2L3 confers risk for systemic lupus erythematosus.","date":"2012","source":"Genes and immunity","url":"https://pubmed.ncbi.nlm.nih.gov/22476155","citation_count":50,"is_preprint":false},{"pmid":"28552575","id":"PMC_28552575","title":"Structural Studies of HHARI/UbcH7∼Ub Reveal Unique E2∼Ub Conformational Restriction by RBR RING1.","date":"2017","source":"Structure (London, England : 1993)","url":"https://pubmed.ncbi.nlm.nih.gov/28552575","citation_count":48,"is_preprint":false},{"pmid":"30446597","id":"PMC_30446597","title":"Synergistic recruitment of UbcH7~Ub and phosphorylated Ubl domain triggers parkin activation.","date":"2018","source":"The EMBO journal","url":"https://pubmed.ncbi.nlm.nih.gov/30446597","citation_count":44,"is_preprint":false},{"pmid":"25422456","id":"PMC_25422456","title":"UbcH7 regulates 53BP1 stability and DSB repair.","date":"2014","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/25422456","citation_count":40,"is_preprint":false},{"pmid":"16356860","id":"PMC_16356860","title":"Nef-mediated lipid raft exclusion of UbcH7 inhibits Cbl activity in T cells to positively regulate signaling.","date":"2005","source":"Immunity","url":"https://pubmed.ncbi.nlm.nih.gov/16356860","citation_count":33,"is_preprint":false},{"pmid":"24091983","id":"PMC_24091983","title":"Variants in TNFSF4, TNFAIP3, TNIP1, BLK, SLC15A4 and UBE2L3 interact to confer risk of systemic lupus erythematosus in Chinese population.","date":"2013","source":"Rheumatology international","url":"https://pubmed.ncbi.nlm.nih.gov/24091983","citation_count":32,"is_preprint":false},{"pmid":"35265070","id":"PMC_35265070","title":"Mechanism and Disease Association With a Ubiquitin Conjugating E2 Enzyme: UBE2L3.","date":"2022","source":"Frontiers in immunology","url":"https://pubmed.ncbi.nlm.nih.gov/35265070","citation_count":31,"is_preprint":false},{"pmid":"19340006","id":"PMC_19340006","title":"The ubiquitin ligase Triad1 inhibits myelopoiesis through UbcH7 and Ubc13 interacting domains.","date":"2009","source":"Leukemia","url":"https://pubmed.ncbi.nlm.nih.gov/19340006","citation_count":29,"is_preprint":false},{"pmid":"22045845","id":"PMC_22045845","title":"The autoimmune disease risk allele of UBE2L3 in African American patients with systemic lupus erythematosus: a recessive effect upon subphenotypes.","date":"2011","source":"The Journal of rheumatology","url":"https://pubmed.ncbi.nlm.nih.gov/22045845","citation_count":24,"is_preprint":false},{"pmid":"24566975","id":"PMC_24566975","title":"CaV2.2 channel cell surface expression is regulated by the light chain 1 (LC1) of the microtubule-associated protein B (MAP1B) via UBE2L3-mediated ubiquitination and degradation.","date":"2014","source":"Pflugers Archiv : European journal of physiology","url":"https://pubmed.ncbi.nlm.nih.gov/24566975","citation_count":23,"is_preprint":false},{"pmid":"17003263","id":"PMC_17003263","title":"UbcH7 interacts with the glucocorticoid receptor and mediates receptor autoregulation.","date":"2006","source":"The Journal of endocrinology","url":"https://pubmed.ncbi.nlm.nih.gov/17003263","citation_count":22,"is_preprint":false},{"pmid":"37474493","id":"PMC_37474493","title":"IL-1β turnover by the UBE2L3 ubiquitin conjugating enzyme and HECT E3 ligases limits inflammation.","date":"2023","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/37474493","citation_count":21,"is_preprint":false},{"pmid":"32334614","id":"PMC_32334614","title":"Synergistic activation of NF-κB by TNFAIP3 (A20) reduction and UBE2L3 (UBCH7) augment that synergistically elevate lupus risk.","date":"2020","source":"Arthritis research & therapy","url":"https://pubmed.ncbi.nlm.nih.gov/32334614","citation_count":21,"is_preprint":false},{"pmid":"8672131","id":"PMC_8672131","title":"Characterization of a human ubiquitin-conjugating enzyme gene UBE2L3.","date":"1996","source":"Mammalian genome : official journal of the International Mammalian Genome Society","url":"https://pubmed.ncbi.nlm.nih.gov/8672131","citation_count":18,"is_preprint":false},{"pmid":"9693040","id":"PMC_9693040","title":"Fine-mapping, genomic organization, and transcript analysis of the human ubiquitin-conjugating enzyme gene UBE2L3.","date":"1998","source":"Genomics","url":"https://pubmed.ncbi.nlm.nih.gov/9693040","citation_count":18,"is_preprint":false},{"pmid":"30113882","id":"PMC_30113882","title":"Stabilization of p27Kip1/CDKN1B by UBCH7/UBE2L3 catalyzed ubiquitinylation: a new paradigm in cell-cycle control.","date":"2018","source":"FASEB journal : official publication of the Federation of American Societies for Experimental Biology","url":"https://pubmed.ncbi.nlm.nih.gov/30113882","citation_count":16,"is_preprint":false},{"pmid":"29969176","id":"PMC_29969176","title":"UBE2L3, a susceptibility gene that plays oncogenic role in hepatitis B-related hepatocellular carcinoma.","date":"2018","source":"Journal of viral hepatitis","url":"https://pubmed.ncbi.nlm.nih.gov/29969176","citation_count":15,"is_preprint":false},{"pmid":"26312912","id":"PMC_26312912","title":"Effect of UBE2L3 genotype on regulation of the linear ubiquitin chain assembly complex in systemic lupus erythematosus.","date":"2015","source":"Lancet (London, England)","url":"https://pubmed.ncbi.nlm.nih.gov/26312912","citation_count":15,"is_preprint":false},{"pmid":"37001433","id":"PMC_37001433","title":"UBE2L3 regulates TLR7-induced B cell autoreactivity in Systemic Lupus Erythematosus.","date":"2023","source":"Journal of autoimmunity","url":"https://pubmed.ncbi.nlm.nih.gov/37001433","citation_count":14,"is_preprint":false},{"pmid":"25483588","id":"PMC_25483588","title":"The MAP1B-LC1/UBE2L3 complex catalyzes degradation of cell surface CaV2.2 channels.","date":"2014","source":"Channels (Austin, Tex.)","url":"https://pubmed.ncbi.nlm.nih.gov/25483588","citation_count":14,"is_preprint":false},{"pmid":"19664228","id":"PMC_19664228","title":"Ubiquitin control of S phase: a new role for the ubiquitin conjugating enzyme, UbcH7.","date":"2009","source":"Cell division","url":"https://pubmed.ncbi.nlm.nih.gov/19664228","citation_count":13,"is_preprint":false},{"pmid":"25632008","id":"PMC_25632008","title":"Ndfip1 regulates itch ligase activity and airway inflammation via UbcH7.","date":"2015","source":"Journal of immunology (Baltimore, Md. : 1950)","url":"https://pubmed.ncbi.nlm.nih.gov/25632008","citation_count":13,"is_preprint":false},{"pmid":"33726770","id":"PMC_33726770","title":"Long non-coding RNA LINC01116 acts as an oncogene in prostate cancer cells through regulation of miR-744-5p/UBE2L3 axis.","date":"2021","source":"Cancer cell international","url":"https://pubmed.ncbi.nlm.nih.gov/33726770","citation_count":13,"is_preprint":false},{"pmid":"32825184","id":"PMC_32825184","title":"HP1γ Sensitizes Cervical Cancer Cells to Cisplatin through the Suppression of UBE2L3.","date":"2020","source":"International journal of molecular sciences","url":"https://pubmed.ncbi.nlm.nih.gov/32825184","citation_count":13,"is_preprint":false},{"pmid":"28621812","id":"PMC_28621812","title":"TCDD induces UbcH7 expression and synphilin-1 protein degradation in the mouse ventral midbrain.","date":"2017","source":"Journal of biochemical and molecular toxicology","url":"https://pubmed.ncbi.nlm.nih.gov/28621812","citation_count":12,"is_preprint":false},{"pmid":"35678668","id":"PMC_35678668","title":"Indole-3-Carbinol, a Phytochemical Aryl Hydrocarbon Receptor-Ligand, Induces the mRNA Overexpression of UBE2L3 and Cell Proliferation Arrest.","date":"2022","source":"Current issues in molecular biology","url":"https://pubmed.ncbi.nlm.nih.gov/35678668","citation_count":12,"is_preprint":false},{"pmid":"18805400","id":"PMC_18805400","title":"Modelling and molecular dynamics of the interaction between the E3 ubiquitin ligase Itch and the E2 UbcH7.","date":"2008","source":"Biochemical pharmacology","url":"https://pubmed.ncbi.nlm.nih.gov/18805400","citation_count":12,"is_preprint":false},{"pmid":"38226814","id":"PMC_38226814","title":"The membrane-associated ubiquitin ligase MARCHF8 stabilizes the human papillomavirus oncoprotein E7 by degrading CUL1 and UBE2L3 in head and neck cancer.","date":"2024","source":"Journal of virology","url":"https://pubmed.ncbi.nlm.nih.gov/38226814","citation_count":11,"is_preprint":false},{"pmid":"36502938","id":"PMC_36502938","title":"UBE2L3 Reduces TRIM21 Expression and IL-1β Secretion in Epidermal Keratinocytes and Improves Psoriasis-Like Skin.","date":"2022","source":"The Journal of investigative dermatology","url":"https://pubmed.ncbi.nlm.nih.gov/36502938","citation_count":11,"is_preprint":false},{"pmid":"27094594","id":"PMC_27094594","title":"The haplotype of UBE2L3 gene is associated with Hashimoto's thyroiditis in a Chinese Han population.","date":"2016","source":"BMC endocrine disorders","url":"https://pubmed.ncbi.nlm.nih.gov/27094594","citation_count":10,"is_preprint":false},{"pmid":"35958458","id":"PMC_35958458","title":"UBE2L3 promotes lung adenocarcinoma invasion and metastasis through the GSK-3β/Snail signaling pathway.","date":"2022","source":"American journal of translational research","url":"https://pubmed.ncbi.nlm.nih.gov/35958458","citation_count":8,"is_preprint":false},{"pmid":"35128752","id":"PMC_35128752","title":"UBE2L3 promotes squamous cell carcinoma progression in the oral cavity and hypopharynx via activating the NF-κB signaling by increasing IκBα degradation.","date":"2022","source":"Cell biology international","url":"https://pubmed.ncbi.nlm.nih.gov/35128752","citation_count":8,"is_preprint":false},{"pmid":"19636915","id":"PMC_19636915","title":"1H, 13C and 15N resonance assignments for the human E2 conjugating enzyme, UbcH7.","date":"2007","source":"Biomolecular NMR assignments","url":"https://pubmed.ncbi.nlm.nih.gov/19636915","citation_count":7,"is_preprint":false},{"pmid":"34279042","id":"PMC_34279042","title":"Variants on the UBE2L3/YDJC Autoimmune Disease Risk Haplotype Increase UBE2L3 Expression by Modulating CCCTC-Binding Factor and YY1 Binding.","date":"2021","source":"Arthritis & rheumatology (Hoboken, N.J.)","url":"https://pubmed.ncbi.nlm.nih.gov/34279042","citation_count":6,"is_preprint":false},{"pmid":"10760570","id":"PMC_10760570","title":"Promoter analysis of the human ubiquitin-conjugating enzyme gene family UBE2L1-4, including UBE2L3 which encodes UbcH7.","date":"2000","source":"Biochimica et biophysica acta","url":"https://pubmed.ncbi.nlm.nih.gov/10760570","citation_count":5,"is_preprint":false},{"pmid":"38301893","id":"PMC_38301893","title":"The E3 ligase SMURF1 stabilizes p27 via UbcH7 catalyzed K29-linked ubiquitin chains to promote cell migration SMURF1-UbcH7 K29 ubiquitination of p27 and cell migration.","date":"2024","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/38301893","citation_count":4,"is_preprint":false},{"pmid":"41083457","id":"PMC_41083457","title":"Single cell transcriptomics of human psoriasis and epidermal specific Ube2l3 deficient mice highlight CXCL16/CXCR6 involvement in psoriasis development.","date":"2025","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/41083457","citation_count":3,"is_preprint":false},{"pmid":"38385491","id":"PMC_38385491","title":"UBE2L3 Suppresses Oxidative Stress-regulated Necroptosis to Accelerate Osteosarcoma Progression.","date":"2025","source":"Recent patents on anti-cancer drug discovery","url":"https://pubmed.ncbi.nlm.nih.gov/38385491","citation_count":3,"is_preprint":false},{"pmid":"39059346","id":"PMC_39059346","title":"UBE2L3 promotes benzene-induced hematotoxicity via autophagy-dependent ferroptosis.","date":"2024","source":"Ecotoxicology and environmental safety","url":"https://pubmed.ncbi.nlm.nih.gov/39059346","citation_count":3,"is_preprint":false},{"pmid":"31792831","id":"PMC_31792831","title":"1H, 13C, 15N backbone and side-chain resonance assignment of the native form of UbcH7 (UBE2L3) through solution NMR spectroscopy.","date":"2019","source":"Biomolecular NMR assignments","url":"https://pubmed.ncbi.nlm.nih.gov/31792831","citation_count":3,"is_preprint":false},{"pmid":"22382060","id":"PMC_22382060","title":"[Screening and identification of anoikis-resistant gene UBCH7 in esophageal cancer cells].","date":"2012","source":"Yi chuan = Hereditas","url":"https://pubmed.ncbi.nlm.nih.gov/22382060","citation_count":2,"is_preprint":false},{"pmid":"38835407","id":"PMC_38835407","title":"Combined Genetic Association and Differed Expression Analysis of UBE2L3 Uncovers a Genetic Regulatory Role of (Immuno)proteasome in IgA Nephropathy.","date":"2024","source":"Kidney diseases (Basel, Switzerland)","url":"https://pubmed.ncbi.nlm.nih.gov/38835407","citation_count":2,"is_preprint":false},{"pmid":"39988669","id":"PMC_39988669","title":"Interfering with UBE2L3 expression targets regulation of MLKL to promote necroptosis inhibition of growth in osteosarcoma.","date":"2025","source":"World journal of surgical oncology","url":"https://pubmed.ncbi.nlm.nih.gov/39988669","citation_count":1,"is_preprint":false},{"pmid":"38656363","id":"PMC_38656363","title":"UBE2L3 expression in human gastric cancer and its clinical significance.","date":"2024","source":"Journal of cancer research and clinical oncology","url":"https://pubmed.ncbi.nlm.nih.gov/38656363","citation_count":0,"is_preprint":false},{"pmid":"37961092","id":"PMC_37961092","title":"The membrane-associated ubiquitin ligase MARCHF8 stabilizes the human papillomavirus oncoprotein E7 by degrading CUL1 and UBE2L3 in head and neck cancer.","date":"2023","source":"bioRxiv : the preprint server for biology","url":"https://pubmed.ncbi.nlm.nih.gov/37961092","citation_count":0,"is_preprint":false},{"pmid":"41943836","id":"PMC_41943836","title":"In vivo CRISPR/Cas9 Screening Reveals that UBE2L3 Modulates Autophagic Flux through TSC2 Ubiquitination and Potentiates PD-1 Blockade in Triple-Negative Breast Cancer.","date":"2026","source":"International journal of biological sciences","url":"https://pubmed.ncbi.nlm.nih.gov/41943836","citation_count":0,"is_preprint":false},{"pmid":"29056010","id":"PMC_29056010","title":"[Predictive value of single nucleotide polymorphisms of HLA-C and UBE2L3 in evaluating the effect of telbivudine antiviral therapy during pregnancy].","date":"2017","source":"Zhonghua gan zang bing za zhi = Zhonghua ganzangbing zazhi = Chinese journal of hepatology","url":"https://pubmed.ncbi.nlm.nih.gov/29056010","citation_count":0,"is_preprint":false},{"pmid":null,"id":"bio_10.1101_2024.11.07.622398","title":"Elucidating the Mechanism Underlying UBA7•UBE2L6 Disulfide Complex Formation","date":"2024-11-08","source":"bioRxiv","url":"https://doi.org/10.1101/2024.11.07.622398","citation_count":0,"is_preprint":true},{"pmid":null,"id":"bio_10.1101_2024.08.05.24311406","title":"Diagnosis of celiac disease on a gluten-free diet: a multicenter prospective quasi-experimental clinical study","date":"2024-08-07","source":"bioRxiv","url":"https://doi.org/10.1101/2024.08.05.24311406","citation_count":0,"is_preprint":true}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":34215,"output_tokens":6685,"usd":0.10146,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":15442,"output_tokens":4852,"usd":0.099255,"stage2_stop_reason":"end_turn"},"total_usd":0.200715,"stage1_batch_id":"msgbatch_017qqVz33Ga63SCDwzb35XPb","stage2_batch_id":"msgbatch_01Scr2Ei9x4HJMiRGxwrmvLK","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 1999,\n      \"finding\": \"Crystal structure of the E6AP HECT domain bound to UbcH7 revealed the determinants of E2-E3 specificity and showed how ubiquitin is transferred from the E2 to the E3 via a thioester intermediate; conserved residues in the HECT catalytic cleft are required for ubiquitin-thioester bond formation.\",\n      \"method\": \"X-ray crystallography; active-site mutagenesis\",\n      \"journal\": \"Science\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — crystal structure plus mutagenesis in a single rigorous study, foundational mechanistic paper\",\n      \"pmids\": [\"10558980\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2000,\n      \"finding\": \"Crystal structure of c-Cbl bound to UbcH7 (and a kinase peptide) showed that the RING domain recruits UbcH7 via a conserved E2 surface motif also used by HECT E3s, and revealed a rigid coupling between substrate-binding and E2-binding domains with a conserved channel leading to the E2 active site, suggesting RING E3s act as scaffolds positioning substrate and E2 for ubiquitin transfer.\",\n      \"method\": \"X-ray crystallography\",\n      \"journal\": \"Cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — crystal structure with functional validation, widely replicated and cited\",\n      \"pmids\": [\"10966114\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1999,\n      \"finding\": \"The c-Cbl RING finger domain directly interacts with UbcH7; this interaction is disrupted by the oncogenic 70Z-Cbl deletion. c-Cbl and UbcH7 synergistically promote ligand-induced ubiquitination of the EGFR in vitro and in vivo, while 70Z-Cbl suppresses this ubiquitination.\",\n      \"method\": \"Yeast two-hybrid; in vitro binding assay; in vivo ubiquitination assay\",\n      \"journal\": \"Journal of Biological Chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal binding assays plus functional in vivo ubiquitination, replicated by structural study (PMID:10966114)\",\n      \"pmids\": [\"10531381\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1996,\n      \"finding\": \"UbcH7 (UBE2L3) was cloned and shown to interact with the HECT E3 ligase E6-AP and to efficiently substitute for UbcH5 in E6-AP-dependent ubiquitination in vitro, establishing UbcH7 as a functional E2 for HECT-type E3s.\",\n      \"method\": \"Biochemical interaction assay; in vitro ubiquitination reconstitution\",\n      \"journal\": \"Journal of Biological Chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — in vitro reconstitution of E2-E3 activity, independently confirmed in multiple subsequent studies\",\n      \"pmids\": [\"8576257\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1998,\n      \"finding\": \"Multiple human HECT-domain proteins form thioester complexes with ubiquitin using UbcH7 or UbcH5 as their preferred E2, dividing the HECT family into at least two classes based on E2 specificity; the HECT domain alone is necessary and sufficient for ubiquitin thioester adduct formation.\",\n      \"method\": \"In vitro ubiquitin thioester formation assay; E2 specificity binding assays\",\n      \"journal\": \"Journal of Biological Chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — in vitro biochemical reconstitution with domain dissection, multiple HECT proteins tested\",\n      \"pmids\": [\"9575161\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"UbcH7 lacks intrinsic E3-independent reactivity with lysine (unlike many other E2s), explaining its preference for HECT-type E3s. UbcH7 is active with RBR family E3s (parkin, HHARI), which function as RING/HECT hybrids: they bind UbcH7 via a RING domain but transfer ubiquitin through an obligate thioester-linked intermediate requiring a conserved cysteine in RING2.\",\n      \"method\": \"In vitro lysine reactivity assay; in vitro ubiquitination assay; mutagenesis of RBR catalytic cysteine\",\n      \"journal\": \"Nature\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — multiple orthogonal in vitro assays plus mutagenesis defining mechanism; foundational paper for RBR E3 mechanism\",\n      \"pmids\": [\"21532592\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1999,\n      \"finding\": \"UbcH7 interacts with HHARI and H7-AP1 via their RING finger and IBR domains in vitro. This interaction is specific: both proteins bind UbcH8 but not UbcH5 or UbcH1, linking a subset of RING/IBR proteins to the ubiquitin pathway via UbcH7.\",\n      \"method\": \"Yeast two-hybrid; in vitro binding assay\",\n      \"journal\": \"Journal of Biological Chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — yeast two-hybrid plus in vitro binding, no functional ubiquitination reconstitution\",\n      \"pmids\": [\"10521492\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2001,\n      \"finding\": \"HHARI interacts and co-localizes with UbcH7 in the perinuclear region of mammalian cells. A minimal interaction region (residues 186-254 of HHARI) was defined; specific residues in the RING1 domain and the distance between RING1 and IBR are critical. Mutation of RING1 from RING-HC to RING-H2 type abolishes binding to UbcH7.\",\n      \"method\": \"Co-immunoprecipitation; co-localization (immunofluorescence); deletion/point mutagenesis\",\n      \"journal\": \"Journal of Biological Chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — co-IP plus localization plus mutagenesis, single lab\",\n      \"pmids\": [\"11278816\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2004,\n      \"finding\": \"UbcH7 is specifically involved in ubiquitination of HPV E7; E7 interacts with the SCF complex containing Cul1 and Skp2 and can be ubiquitinated by the Cul1-containing ubiquitin ligase in vitro. E7 half-life is significantly longer in Skp2-/- MEFs than wild-type.\",\n      \"method\": \"In vitro ubiquitination assay; co-immunoprecipitation; Skp2-/- MEF genetic analysis\",\n      \"journal\": \"Journal of Virology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — in vitro reconstitution plus genetic (Skp2 KO) validation, single lab\",\n      \"pmids\": [\"15113913\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2004,\n      \"finding\": \"UBCH7 acts as a transcriptional coactivator for steroid hormone receptors (PR, GR, AR, RAR) in a hormone-dependent manner; its ubiquitin conjugation activity is required for this coactivation function. UBCH7 is recruited to estrogen receptor- and PR-responsive promoters in a hormone-dependent manner and interacts with SRC-1.\",\n      \"method\": \"Transient transfection reporter assay; siRNA depletion; chromatin immunoprecipitation (ChIP); co-immunoprecipitation\",\n      \"journal\": \"Molecular and Cellular Biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — ChIP plus functional reporter assays plus co-IP, single lab\",\n      \"pmids\": [\"15367689\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2006,\n      \"finding\": \"UbcH7 physically interacts with the glucocorticoid receptor (GR) and reduces GR-dependent gene expression when overexpressed; a dominant-negative UbcH7 (C89S, catalytically inactive) fails to repress GR transactivation and abolishes ligand-dependent GR protein downregulation, establishing that UbcH7 regulates GR turnover via its ubiquitin-conjugating activity.\",\n      \"method\": \"Co-immunoprecipitation; transient transfection reporter assay; dominant-negative mutagenesis; proteasome inhibitor rescue\",\n      \"journal\": \"Journal of Endocrinology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple orthogonal approaches (co-IP, reporter, mutagenesis), single lab\",\n      \"pmids\": [\"17003263\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"UbcH7 regulates both steady-state and replicative stress-induced ubiquitination and proteasomal degradation of 53BP1. Depletion of UbcH7 stabilizes 53BP1, inhibits DSB end resection, shifts repair from homologous recombination to NHEJ, and sensitizes cells to DNA damage.\",\n      \"method\": \"shRNA library screen; siRNA knockdown; ubiquitination assay; DSB repair assay (HR/NHEJ reporters)\",\n      \"journal\": \"PNAS\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — functional screen followed by mechanistic validation with multiple readouts, single lab\",\n      \"pmids\": [\"25422456\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"UBE2L3, UBE2N, and UBE2D2/3 synergistically contribute to Parkin-mediated mitophagy; UBE2L3 knockdown reduces autophagic clearance of depolarized mitochondria and reduces ubiquitination of mitochondrial substrates (mitofusins, TOM20, TOM70, VDAC1) without interfering with PINK1 stabilization or Parkin translocation.\",\n      \"method\": \"siRNA knockdown; mitophagy assay; ubiquitination assay; flow cytometry\",\n      \"journal\": \"Journal of Cell Science\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple knockdowns with defined phenotypic and molecular readouts, single lab\",\n      \"pmids\": [\"24906799\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"UBE2L3 is the preferred E2 conjugating enzyme for the LUBAC complex (HOIL-1/HOIP) in vivo and is essential for LUBAC-mediated NF-κB activation. Dominant-negative UBE2L3 (C86S) or UBE2L3 silencing abolishes LUBAC-induced NF-κB upregulation.\",\n      \"method\": \"HEK293-NF-κB reporter assay; dominant-negative mutagenesis; siRNA knockdown; imaging flow cytometry for NF-κB translocation in primary cells\",\n      \"journal\": \"American Journal of Human Genetics / Lancet\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — multiple orthogonal methods (reporter, mutagenesis, primary cell imaging), replicated in two publications from same group\",\n      \"pmids\": [\"25640675\", \"26312912\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2005,\n      \"finding\": \"HIV Nef mediates exclusion of UbcH7 from lipid rafts via formation of a p85Cool-1/betaPix–c-Cbl–Cdc42 ternary complex that displaces UbcH7 from rafts, preventing ubiquitination of activated Vav and thereby increasing T cell signaling.\",\n      \"method\": \"Lipid raft fractionation; co-immunoprecipitation; siRNA knockdown of p85Cool-1/betaPix\",\n      \"journal\": \"Immunity\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — biochemical fractionation plus co-IP plus knockdown rescue, single lab\",\n      \"pmids\": [\"16356860\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"The RBR E3 ligase Triad1 interacts with UbcH7 through its first RING domain and with Ubc13 through its second RING domain; both interactions and full-length Triad1 are required for inhibition of myeloid colony formation, demonstrating that UbcH7-dependent ubiquitination through Triad1 is biologically essential for myelopoiesis.\",\n      \"method\": \"In vitro binding assay; domain mutagenesis; myeloid clonogenic assay\",\n      \"journal\": \"Leukemia\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — domain mutagenesis plus functional clonogenic assay, single lab\",\n      \"pmids\": [\"19340006\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"UbcH7 overexpression delays S phase entry while its depletion lengthens S phase and decreases cell proliferation; UbcH7 depletion increases Chk1 levels and decreases phosphorylated PTEN, indicating UbcH7 regulates S phase length through a PTEN/Akt/Chk1 pathway.\",\n      \"method\": \"Overexpression; siRNA knockdown; cell cycle analysis (flow cytometry); Western blot\",\n      \"journal\": \"Cell Division\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single lab, single method per readout, pathway placement inferred without direct epistasis testing\",\n      \"pmids\": [\"19664228\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"Ndfip1 acts as an adaptor that recruits UbcH7 to the HECT E3 Itch: Ndfip1 N-terminus binds UbcH7 while its PY motif binds Itch, enhancing Itch ligase activity and Itch-mediated K63 ubiquitination of Tak1, limiting airway inflammation.\",\n      \"method\": \"Co-immunoprecipitation; in vitro ubiquitination assay; Ndfip1-/- mouse model; Itch-/- mouse model; siRNA/mutagenesis rescue\",\n      \"journal\": \"Journal of Immunology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — co-IP, in vitro ubiquitination, and KO mouse phenotype with mutant rescue, single lab\",\n      \"pmids\": [\"25632008\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"HHARI RING1 contains a Zn2+-loop II extension not present in canonical RING E3s that acts as a steric wedge to prevent closed E2~Ub conformation, structurally explaining how RBR RING1 domains promote open E2~Ub conformation to favor Ub transfer to the E3 active site rather than direct transfer to substrate.\",\n      \"method\": \"X-ray crystallography; structural comparison\",\n      \"journal\": \"Structure\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — crystal structure with structural mechanistic interpretation, single lab but rigorous\",\n      \"pmids\": [\"28552575\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"UbcH7~Ub conjugate binds to the RING1/IBR interface of parkin in the open (not closed) E2~Ub state; NMR and mass spectrometry show that parkin phosphorylation and UbcH7~Ub recruitment act synergistically to rearrange the RING0/RING2 interface and alter reactivity of the RING2 catalytic cysteine (Rcat), driving parkin ubiquitination activity.\",\n      \"method\": \"NMR chemical shift perturbation; hydrogen-deuterium exchange mass spectrometry; in vitro ubiquitination assay\",\n      \"journal\": \"EMBO Journal\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — NMR plus MS plus functional assay, multiple orthogonal methods in one study\",\n      \"pmids\": [\"30446597\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"UBCH7/UBE2L3 overexpression stabilizes p27Kip1 and delays the G1-to-S cell cycle transition; depletion of UBE2L3 increases p27Kip1 turnover. The stabilization mechanism involves UBE2L3-catalyzed conjugation of heterotypic ubiquitin chains on p27Kip1 that are proteolytically incompetent.\",\n      \"method\": \"Overexpression; siRNA knockdown; cell cycle analysis; in vitro ubiquitination assay with heterotypic chain characterization\",\n      \"journal\": \"FASEB Journal\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — in vitro ubiquitination plus cellular KD/OE with chain-type characterization, single lab\",\n      \"pmids\": [\"30113882\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"MAP1B light chain 1 (LC1) interacts with UBE2L3 (via yeast two-hybrid and co-IP), and the LC1/UBE2L3 complex co-immunoprecipitates with CaV2.2 N-type Ca2+ channels, promoting their ubiquitination and proteasomal degradation, thereby reducing channel surface expression and current amplitude.\",\n      \"method\": \"Yeast two-hybrid; co-immunoprecipitation; patch-clamp electrophysiology; proteasome inhibitor rescue\",\n      \"journal\": \"Pflügers Archiv\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — yeast two-hybrid, co-IP, and functional electrophysiology with pharmacological rescue, single lab\",\n      \"pmids\": [\"24566975\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"UBE2L3 promotes pro-IL-1β ubiquitylation and proteasomal disposal; deletion of Ube2l3 in mice reduces pro-IL-1β turnover in macrophages, leading to excessive mature IL-1β production and neutrophilic inflammation. An RNAi screen identified HECT E3 ligases TRIP12 and AREL1 as the E3 partners adding destabilizing K27-, K29-, and K33-linked poly-ubiquitin chains on pro-IL-1β.\",\n      \"method\": \"Ube2l3 conditional knockout mouse; RNAi screen; ubiquitination assays; inflammasome activation assays\",\n      \"journal\": \"Nature Communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — KO mouse with defined in vivo phenotype plus mechanistic RNAi screen identifying E3 partners and chain topology, multiple orthogonal methods\",\n      \"pmids\": [\"37474493\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"UBE2L3 is critical for NF-κB activation downstream of TLR7 stimulation via interaction with LUBAC. Dimethyl fumarate (DMF), which directly inhibits UBE2L3, blocks TLR7-induced NF-κB activation, differentiation of memory B cells and plasmablasts, and autoantibody secretion in SLE B cells.\",\n      \"method\": \"siRNA knockdown; NF-κB reporter assay; flow cytometry for B cell differentiation; ELISA for autoantibodies\",\n      \"journal\": \"Journal of Autoimmunity\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genetic and pharmacological inhibition with multiple cellular readouts, single lab\",\n      \"pmids\": [\"37001433\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"MARCHF8 E3 ubiquitin ligase binds to and ubiquitinates both CUL1 and UBE2L3, leading to their degradation and thereby preventing ubiquitination and degradation of HPV16 E7; overexpression of CUL1 or UBE2L3 restores E7 degradation and suppresses tumor growth in vivo.\",\n      \"method\": \"Co-immunoprecipitation; ubiquitination assay; siRNA knockdown; in vivo tumor xenograft\",\n      \"journal\": \"Journal of Virology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — co-IP plus ubiquitination assay plus in vivo rescue, single lab\",\n      \"pmids\": [\"38226814\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"SMURF1 (but not SMURF2) works with UbcH7 to ubiquitinate p27 with K29-linked chains in vitro, stabilizing p27. SMURF1, UbcH7, and p27 co-localize at the leading edge of migrating cells, and knockdown of SMURF1 or UbcH7 reduces cell migration.\",\n      \"method\": \"In vitro ubiquitination screen; in vitro ubiquitination with K29R/K29O mutant ubiquitin; siRNA knockdown; co-localization by fluorescence microscopy; cell migration assay\",\n      \"journal\": \"Journal of Biological Chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — in vitro reconstitution with chain-type mutants plus cellular co-localization and functional migration assay, single lab\",\n      \"pmids\": [\"38301893\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"UBE2L3 specifically binds MLKL via co-immunoprecipitation and promotes its ubiquitination; overexpression of UBE2L3 reduces MLKL expression, while UBE2L3 knockdown increases MLKL phosphorylation and promotes necroptosis in osteosarcoma cells and in vivo.\",\n      \"method\": \"Co-immunoprecipitation; ubiquitination assay; siRNA knockdown; in vivo tumor xenograft; immunohistochemistry\",\n      \"journal\": \"World Journal of Surgical Oncology\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single lab, co-IP plus knockdown, limited mechanistic depth\",\n      \"pmids\": [\"39988669\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"In vivo CRISPR screen identified UBE2L3 as a regulator of autophagy in TNBC; mechanistically, UBE2L3 interacts with E3 ligase SMURF2 to ubiquitinate and degrade TSC2, thereby activating mTOR and suppressing autophagy.\",\n      \"method\": \"In vivo CRISPR/Cas9 library screen; co-immunoprecipitation; ubiquitination assay; autophagy assays\",\n      \"journal\": \"International Journal of Biological Sciences\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single lab, co-IP plus ubiquitination assay, mechanistic pathway placement partially inferred\",\n      \"pmids\": [\"41943836\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"UBE2L3 (UbcH7) is an E2 ubiquitin-conjugating enzyme that lacks intrinsic lysine reactivity, making it inactive with canonical RING E3s but active with HECT-type E3s (e.g., E6-AP, Itch, TRIP12, AREL1) and RBR E3s (e.g., parkin, HHARI, Triad1) that function as RING/HECT hybrids requiring an E3 thioester intermediate; through these partnerships it ubiquitinates diverse substrates including EGFR (via c-Cbl), pro-IL-1β (destabilizing K27/K29/K33 chains via TRIP12/AREL1), p27Kip1 (stabilizing heterotypic chains via SMURF1), 53BP1, TSC2, and MLKL, and acts as the preferred E2 for the LUBAC complex to drive linear ubiquitin chain-dependent NF-κB activation in immune cells, thereby linking UBE2L3 expression levels to autoimmune disease susceptibility.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"UBE2L3 (UbcH7) is an E2 ubiquitin-conjugating enzyme whose catalytic specificity is defined by an inability to react with free lysine independently of an E3, restricting it to E3 ligases that employ an obligate thioester-linked ubiquitin intermediate [#5]. Consistent with this, it functions efficiently with HECT-domain E3 ligases, originally established through its interaction with E6-AP and its ability to drive E6-AP-dependent ubiquitination in vitro [#3], and it partitions the HECT family by E2 preference, supporting thioester adduct formation on the HECT domain [#4]. Structural work on the E6AP HECT domain bound to UbcH7 defined the E2-E3 interface and showed how ubiquitin transits from E2 to E3 via a thioester relay [#0], while the c-Cbl RING\\u2013UbcH7 structure revealed that RING domains recruit UbcH7 through a conserved E2 surface used by HECT E3s as well, positioning substrate and E2 for transfer [#1, #2]. UBE2L3 is also the cognate E2 for RING-between-RING (RBR) E3 ligases\\u2014parkin, HHARI, and Triad1\\u2014which behave as RING/HECT hybrids: UbcH7 is engaged via a RING domain but ubiquitin passes through a conserved RING2 catalytic cysteine [#5, #15], with the RBR RING1 acting as a steric wedge that holds the E2~Ub conjugate in an open conformation to favor transfer to the E3 active site [#18, #19]. Through these partnerships UBE2L3 ubiquitinates a broad substrate range, including EGFR via c-Cbl [#2], 53BP1 to control DNA double-strand break repair pathway choice [#11], mitochondrial proteins during Parkin-mediated mitophagy [#12], and pro-IL-1\\u03b2, which it targets with destabilizing K27/K29/K33 chains through the HECT E3s TRIP12 and AREL1 to limit mature IL-1\\u03b2 output and inflammation [#22]. It can also catalyze proteolytically incompetent heterotypic chains that stabilize substrates such as p27Kip1 [#20, #25]. UBE2L3 is the preferred E2 for the LUBAC complex (HOIP/HOIL-1), driving linear-ubiquitin-dependent NF-\\u03baB activation in immune cells, including downstream of TLR7 in autoreactive B cells [#13, #23].\",\n  \"teleology\": [\n    {\n      \"year\": 1996,\n      \"claim\": \"Establishing that UbcH7 is a functional E2 for HECT-type E3 ligases answered the basic question of which ligase class it serves.\",\n      \"evidence\": \"biochemical interaction and in vitro ubiquitination reconstitution with E6-AP\",\n      \"pmids\": [\"8576257\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not define structural basis of E2-E3 recognition\", \"Substrate range beyond the reconstituted system unknown\"]\n    },\n    {\n      \"year\": 1998,\n      \"claim\": \"Showing that multiple HECT proteins form ubiquitin thioesters preferentially with UbcH7 or UbcH5 defined an E2-specificity logic within the HECT family.\",\n      \"evidence\": \"in vitro thioester formation and E2 specificity assays with domain dissection\",\n      \"pmids\": [\"9575161\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Determinants of UbcH7 vs UbcH5 selection not resolved at residue level\", \"In vivo relevance per HECT E3 untested\"]\n    },\n    {\n      \"year\": 1999,\n      \"claim\": \"Crystallography of the E6AP HECT domain with UbcH7 and the c-Cbl RING with UbcH7 revealed that both ligase classes engage a shared E2 surface and defined the thioester transfer geometry, unifying RING and HECT mechanisms around UbcH7.\",\n      \"evidence\": \"X-ray crystallography with active-site mutagenesis; yeast two-hybrid and in vivo EGFR ubiquitination\",\n      \"pmids\": [\"10558980\", \"10966114\", \"10531381\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not address why UbcH7 fails with most RING E3s in cells\", \"Substrate channeling dynamics not captured\"]\n    },\n    {\n      \"year\": 1999,\n      \"claim\": \"Identifying UbcH7 binding to RING/IBR proteins HHARI and H7-AP1, and later their perinuclear co-localization, extended its partnerships beyond classic HECT and RING ligases.\",\n      \"evidence\": \"yeast two-hybrid, in vitro binding, co-IP, co-localization, and interface mutagenesis\",\n      \"pmids\": [\"10521492\", \"11278816\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No functional ubiquitination reconstitution in early work\", \"Physiological substrates of HHARI/UbcH7 unidentified\"]\n    },\n    {\n      \"year\": 2004,\n      \"claim\": \"Functional links to HPV E7 turnover and to steroid-receptor coactivation broadened UbcH7's cellular roles beyond a generic conjugating enzyme.\",\n      \"evidence\": \"in vitro ubiquitination, Skp2-/- MEFs, reporter assays, ChIP, and co-IP\",\n      \"pmids\": [\"15113913\", \"15367689\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct E3 for E7 in vivo not fully resolved\", \"Mechanism coupling conjugation activity to transcriptional coactivation unclear\"]\n    },\n    {\n      \"year\": 2006,\n      \"claim\": \"Demonstrating that catalytically inactive UbcH7 (C89S) cannot drive ligand-dependent GR downregulation tied receptor turnover directly to UbcH7's conjugating activity.\",\n      \"evidence\": \"co-IP, reporter assay, dominant-negative mutagenesis, proteasome inhibitor rescue\",\n      \"pmids\": [\"17003263\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Cognate E3 for GR not defined\", \"Single-lab observation\"]\n    },\n    {\n      \"year\": 2011,\n      \"claim\": \"Discovering that UbcH7 lacks intrinsic lysine reactivity but functions with RBR E3s via an obligate thioester intermediate explained its E3-class restriction and defined RBR ligases as RING/HECT hybrids.\",\n      \"evidence\": \"in vitro lysine reactivity and ubiquitination assays with RBR catalytic cysteine mutagenesis\",\n      \"pmids\": [\"21532592\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Conformational basis of open vs closed E2~Ub not yet structurally resolved\", \"Range of RBR substrates not enumerated\"]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"Cellular studies placed UbcH7 in DNA repair pathway choice, mitophagy, and ion channel regulation, showing the same E2 acts across distinct cellular processes through different E3/adaptor partners.\",\n      \"evidence\": \"shRNA/siRNA knockdown with DSB repair reporters; mitophagy and ubiquitination assays; yeast two-hybrid, co-IP, and patch-clamp\",\n      \"pmids\": [\"25422456\", \"24906799\", \"24566975\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"E3 ligase identity not pinned down in each context\", \"Substrate ubiquitin chain topology mostly uncharacterized\"]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Identifying UBE2L3 as the preferred E2 for LUBAC and the Ndfip1-Itch axis established its role in NF-\\u03baB-driven and inflammatory signaling.\",\n      \"evidence\": \"NF-\\u03baB reporter, dominant-negative C86S, siRNA, primary-cell imaging; co-IP, in vitro ubiquitination, Ndfip1-/- and Itch-/- mice\",\n      \"pmids\": [\"25640675\", \"26312912\", \"25632008\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Mechanism linking UBE2L3 expression level to autoimmune susceptibility not fully resolved\", \"Quantitative contribution relative to other LUBAC E2s unclear\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Structural and biophysical analyses of HHARI and parkin showed how RBR RING1 enforces an open E2~Ub conformation and how parkin phosphorylation plus UbcH7~Ub recruitment synergistically activate the catalytic cysteine, defining the activation mechanism.\",\n      \"evidence\": \"X-ray crystallography, NMR, HDX-MS, and in vitro ubiquitination\",\n      \"pmids\": [\"28552575\", \"30446597\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Full catalytic cycle dynamics not captured in one structure\", \"Generalizability across all RBR family members untested\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Showing UBE2L3 builds proteolytically incompetent heterotypic chains on p27Kip1 demonstrated that it can stabilize rather than destabilize substrates depending on chain topology.\",\n      \"evidence\": \"overexpression/knockdown, cell cycle analysis, in vitro ubiquitination with chain characterization\",\n      \"pmids\": [\"30113882\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"E3 ligase responsible not identified in this study\", \"Physiological prevalence of these chains unknown\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Conditional Ube2l3 knockout in mice defined an in vivo anti-inflammatory function via TRIP12/AREL1-dependent K27/K29/K33 ubiquitylation of pro-IL-1\\u03b2 and connected UBE2L3-LUBAC to TLR7-driven B-cell autoimmunity.\",\n      \"evidence\": \"Ube2l3 conditional KO mouse, RNAi screen, ubiquitination and inflammasome assays; siRNA, NF-\\u03baB reporter, B-cell differentiation, DMF inhibition\",\n      \"pmids\": [\"37474493\", \"37001433\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"How chain topology dictates pro-IL-1\\u03b2 proteasomal disposal mechanistically unclear\", \"DMF target selectivity for UBE2L3 in vivo not fully delineated\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Partner-specific studies identified SMURF1 cooperation in K29-linked p27 stabilization at the migrating cell edge and MARCHF8-mediated degradation of UBE2L3 controlling HPV E7 levels, refining its substrate and regulatory networks.\",\n      \"evidence\": \"in vitro ubiquitination with chain mutants, co-localization, migration assays; co-IP, ubiquitination, and xenograft rescue\",\n      \"pmids\": [\"38301893\", \"38226814\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Reciprocal validation across systems limited\", \"In vivo significance of the SMURF1/p27 axis untested\"]\n    },\n    {\n      \"year\": 2026,\n      \"claim\": \"Reports linking UBE2L3 to MLKL-dependent necroptosis and to SMURF2-mediated TSC2/mTOR/autophagy control in cancer extend its proposed roles but rest on limited mechanistic depth.\",\n      \"evidence\": \"co-IP, ubiquitination, knockdown, xenografts; in vivo CRISPR screen and autophagy assays\",\n      \"pmids\": [\"39988669\", \"41943836\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"Single-lab co-IP/knockdown without reciprocal validation\", \"Direct ubiquitination of stated substrates and chain topology not firmly established\", \"Pathway placement partially inferred\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"It remains unresolved how UBE2L3 expression level and chain-type output are selected across its many E3 partners to produce opposite (stabilizing vs degradative) outcomes on different substrates in vivo.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No unifying model linking E3 partner choice to chain topology\", \"Quantitative control of substrate fate by UBE2L3 abundance not established\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0140096\", \"supporting_discovery_ids\": [3, 4, 5, 22]},\n      {\"term_id\": \"GO:0016740\", \"supporting_discovery_ids\": [0, 3, 5]},\n      {\"term_id\": \"GO:0061650\", \"supporting_discovery_ids\": [5]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005829\", \"supporting_discovery_ids\": [7]},\n      {\"term_id\": \"GO:0005886\", \"supporting_discovery_ids\": [14, 25]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-392499\", \"supporting_discovery_ids\": [0, 3, 4, 5]},\n      {\"term_id\": \"R-HSA-168256\", \"supporting_discovery_ids\": [13, 22, 23]},\n      {\"term_id\": \"R-HSA-73894\", \"supporting_discovery_ids\": [11]},\n      {\"term_id\": \"R-HSA-9612973\", \"supporting_discovery_ids\": [12, 27]},\n      {\"term_id\": \"R-HSA-162582\", \"supporting_discovery_ids\": [13, 17, 23]}\n    ],\n    \"complexes\": [\"LUBAC\"],\n    \"partners\": [\"E6-AP\", \"CBL\", \"HHARI\", \"PARK2\", \"TRIP12\", \"AREL1\", \"SMURF1\", \"ITCH\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":7,"faith_total":7,"faith_pct":100.0}}