{"gene":"UBE3B","run_date":"2026-06-10T10:51:56","timeline":{"discoveries":[{"year":2016,"finding":"UBE3B is a mitochondrion-associated HECT-domain E3 ubiquitin ligase; mutating the catalytic cysteine (C1036A) or deleting the HECT domain (aa 758–1068) abolishes ubiquitylation activity. UBE3B knockdown induces changes in mitochondrial morphology and physiology and a decrease in mitochondrial volume. UBE3B interacts with calmodulin via its N-terminal IQ motif (aa 29–58); deletion of the IQ motif increases in vitro ubiquitylation activity, and changes in calcium levels disrupt the calmodulin–UBE3B interaction.","method":"In vitro ubiquitylation assay, active-site mutagenesis (C1036A), domain deletion, Co-IP/pulldown for calmodulin binding, subcellular fractionation/imaging, siRNA knockdown with mitochondrial morphology readout","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1 / Strong — in vitro ubiquitylation assay with active-site mutagenesis and domain deletions, calmodulin interaction confirmed by pulldown, localization by fractionation, KD phenotype; multiple orthogonal methods in one study","pmids":["28003368"],"is_preprint":false},{"year":2019,"finding":"UBE3B ubiquitinates branched-chain α-ketoacid dehydrogenase kinase (BCKDK) in vivo; BCKDK was identified as a UBE3B substrate through interactome profiling of 22 UBE3B interactors. Loss of Ube3b in mice perturbs nucleotide metabolism and the TCA cycle, and reduces substrate-induced mitochondrial respiration in skeletal muscle.","method":"Co-immunoprecipitation/mass spectrometry interactome screen, in vivo ubiquitylation assay, Ube3b knockout mouse metabolomics (plasma and cortex), mitochondrial respiration assay","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"High","confidence_rationale":"Tier 2 / Moderate — substrate identification by MS-based interactome plus in vivo ubiquitylation, corroborated by metabolomic profiling in KO mice and patient plasma","pmids":["30808755"],"is_preprint":false},{"year":2020,"finding":"Ube3b ubiquitinates Ppp3cc (the catalytic γ-subunit of calcineurin); overexpression of Ppp3cc phenocopies Ube3b loss with respect to increased dendritic spine density. Ube3b KO neurons exhibit increased dendritic spine density, aberrant spine morphology, altered synaptic physiology, and changes in hippocampal circuit activity. Ube3b regulates dendritic branching in a cell-autonomous manner.","method":"In vitro/in vivo ubiquitylation assay, Ube3b knockout mouse model, overexpression of Ppp3cc as epistasis test, dendritic spine imaging, electrophysiology","journal":"Molecular psychiatry","confidence":"High","confidence_rationale":"Tier 2 / Strong — substrate ubiquitylation assay combined with epistasis (Ppp3cc overexpression phenocopying KO), KO mouse with multiple orthogonal cellular phenotypes","pmids":["32249816"],"is_preprint":false},{"year":2020,"finding":"TRIB3 interacts with MYC to suppress UBE3B-mediated MYC ubiquitination and proteasomal degradation, thereby stabilizing MYC and enhancing its transcriptional activity in lymphoma cells. UBE3B directly ubiquitinates MYC, and TRIB3 acts as a negative regulator of this UBE3B–MYC axis.","method":"Co-immunoprecipitation, in vitro/cellular ubiquitylation assay, TRIB3 deletion mouse model (MycEμ lymphoma), patient-derived xenograft, peptide disruption of TRIB3–MYC interaction","journal":"Nature communications","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal Co-IP, ubiquitylation assay, genetic deletion model, and xenograft rescue; multiple orthogonal methods across in vitro and in vivo settings","pmids":["33298911"],"is_preprint":false},{"year":2021,"finding":"UBE3B undergoes self-ubiquitylation at K665, which induces oligomerization and inactivation in mammalian cells (analogous to NEDD4 self-inactivation). This autoubiquitylation-dependent mechanism was demonstrated using a split-CAT bacterial reporter system and validated in yeast and mammalian cell models.","method":"Split-CAT genetic selection assay in E. coli, site-directed mutagenesis (K665), yeast and mammalian cell validation of oligomerization and inactivation","journal":"Journal of molecular biology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — novel split-reporter assay with mutagenesis, validated in multiple model systems but single lab, abstract-level detail","pmids":["34599943"],"is_preprint":false},{"year":2023,"finding":"UBE3B physically interacts with HIF-2α and promotes its K63-linked polyubiquitination at residues K394, K497, and K503, thereby inhibiting VHL E3 ligase complex-mediated HIF-2α degradation and stabilizing HIF-2α. K394/497/503R mutation of HIF-2α abolishes UBE3B-mediated cancer growth and metastasis.","method":"Co-immunoprecipitation, in vitro/cellular K63-linkage-specific ubiquitylation assay, site-directed mutagenesis of HIF-2α ubiquitination sites, UBE3B knockdown in vitro and xenograft in vivo","journal":"Oncogene","confidence":"High","confidence_rationale":"Tier 1-2 / Moderate — in vitro ubiquitylation assay with mutagenesis of specific lysine residues, Co-IP, and in vivo xenograft rescue; multiple orthogonal methods in one study","pmids":["37783786"],"is_preprint":false},{"year":2024,"finding":"VHL is an E3 ubiquitin ligase for UBE3B: VHL directly binds UBE3B and promotes its K48-linked polyubiquitination at K286 and K427 in a PHD-independent manner, leading to proteasomal degradation of UBE3B. K286/427R mutation of UBE3B abolishes the inhibitory effect of VHL on breast tumor growth and metastasis.","method":"Co-immunoprecipitation, in vitro/cellular ubiquitylation assay (K48-linkage specific), site-directed mutagenesis (K286R/K427R), in vivo xenograft models","journal":"Cell death & disease","confidence":"High","confidence_rationale":"Tier 1-2 / Moderate — in vitro ubiquitylation with specific-lysine mutagenesis, Co-IP, and in vivo rescue experiments; multiple orthogonal methods","pmids":["38914543"],"is_preprint":false},{"year":2025,"finding":"UBE3B ubiquitinates NCOA4 (nuclear receptor coactivator 4), suppressing NCOA4-mediated ferritinophagy and thereby reducing ferrous iron release and ferroptosis in alveolar epithelial cells. Nrf2 transcriptionally activates UBE3B expression, placing UBE3B in a Nrf2/UBE3B/NCOA4 regulatory axis.","method":"Western blot, overexpression/knockdown of UBE3B, Nrf2 knockdown rescue experiments, measurement of ferrous ion content and ferroptosis markers in alveolar epithelial cells","journal":"Biology direct","confidence":"Medium","confidence_rationale":"Tier 3 / Weak — single lab, western blot-based mechanistic inference; ubiquitylation of NCOA4 by UBE3B stated but supporting assay detail is limited in the abstract","pmids":["40671136"],"is_preprint":false},{"year":2026,"finding":"UBE3B regulates the synaptic proteome: quantitative proteomics of neural stem cells identified 116 proteins with increased levels and reduced ubiquitination upon UBE3B loss. UBE3B interacts with synaptic proteins including ATP1A1, DOCK7, NLGN2, and STX12 (confirmed by Co-IP). Ube3b CNS-specific KO mice show reduced excitatory synapse density, diminished spontaneous cortical circuit activity, decreased AMPA receptor surface expression, and hyperexcitability of excitatory cortical neurons.","method":"Quantitative proteomics and ubiquitome profiling, Co-immunoprecipitation of synaptic interactors, Ube3b conditional CNS KO mouse, electrophysiology, AMPA receptor surface expression assay, dendritic morphology imaging","journal":"Autism research : official journal of the International Society for Autism Research","confidence":"High","confidence_rationale":"Tier 2 / Moderate — proteome-wide ubiquitome profiling plus reciprocal Co-IP of specific interactors, validated in conditional KO mouse with multiple orthogonal cellular phenotypes","pmids":["41844341"],"is_preprint":false},{"year":2003,"finding":"UBE3B encodes a HECT-domain E3 ubiquitin ligase. Alternative splicing of exon 20 generates a transcript containing an in-frame stop codon that would truncate the protein before the HECT domain, predicting a non-functional variant lacking catalytic activity. This represents a potential mechanism for regulating intracellular levels of functional UBE3B.","method":"cDNA cloning, RT-PCR, bioinformatic analysis of alternative splicing","journal":"Genomics","confidence":"Low","confidence_rationale":"Tier 4 / Weak — cDNA/transcript characterization with no functional assay confirming the regulatory mechanism; prediction based on sequence analysis","pmids":["12837265"],"is_preprint":false},{"year":2012,"finding":"Disruption of mouse Ube3b reduces viability, weight, and brain size, and causes downregulation of cholesterol synthesis. The C. elegans ortholog oxi-1 functions in the ubiquitin/proteasome system in vivo and is especially required under oxidative stress conditions, establishing UBE3B as a functional HECT E3 ligase with roles in neuronal development.","method":"Mouse Ube3b knockout model (viability, weight, brain size phenotyping), cholesterol synthesis assay, C. elegans oxi-1 genetic analysis under oxidative stress","journal":"American journal of human genetics","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — KO mouse with specific metabolic and developmental phenotypes plus ortholog functional genetics in C. elegans; two organisms but single publication","pmids":["23200864"],"is_preprint":false}],"current_model":"UBE3B is a HECT-domain E3 ubiquitin ligase that localizes to mitochondria and is regulated by calmodulin binding via its N-terminal IQ motif (with calcium-dependent dissociation increasing activity) and by self-ubiquitylation at K665 (inducing oligomerization and inactivation); its substrates include BCKDK, Ppp3cc (calcineurin γ-subunit), MYC, HIF-2α (K63-linked stabilizing ubiquitination), and NCOA4, while VHL reciprocally targets UBE3B itself for K48-linked proteasomal degradation; in neurons, UBE3B fine-tunes the synaptic proteome (interacting with ATP1A1, DOCK7, NLGN2, STX12) to control dendritic spine density, excitatory synapse maintenance, AMPA receptor surface expression, and cortical circuit activity, with its loss causing metabolic dysregulation, mitochondrial dysfunction, and the intellectual disability/growth retardation phenotypes of Kaufman oculocerebrofacial syndrome."},"narrative":{"mechanistic_narrative":"UBE3B is a mitochondrion-associated HECT-domain E3 ubiquitin ligase whose catalytic activity depends on its C-terminal HECT cysteine and is gated by an N-terminal IQ motif that binds calmodulin, with calcium-dependent dissociation relieving autoinhibition [PMID:28003368]. Its activity is further controlled by self-ubiquitylation at K665, which drives oligomerization and inactivation [PMID:34599943]. Through its ligase activity UBE3B shapes both metabolism and the neuronal synaptic proteome: it ubiquitylates the branched-chain ketoacid dehydrogenase kinase BCKDK and is required for normal nucleotide/TCA-cycle metabolism and mitochondrial respiration in muscle [PMID:30808755], and it ubiquitylates the calcineurin catalytic subunit Ppp3cc to restrain dendritic spine density, excitatory synapse number, and cortical circuit activity [PMID:32249816, PMID:41844341]. UBE3B governs a broad synaptic ubiquitome and interacts with synaptic proteins including ATP1A1, DOCK7, NLGN2, and STX12 [PMID:41844341]. In a cancer-relevant axis, UBE3B directly ubiquitylates MYC to promote its proteasomal turnover, an event antagonized by TRIB3 [PMID:33298911], yet it also stabilizes HIF-2α via K63-linked polyubiquitylation that blocks VHL-mediated degradation [PMID:37783786]; reciprocally, VHL ubiquitylates UBE3B itself with K48 linkages at K286/K427 to target it for degradation [PMID:38914543]. Loss of Ube3b in mice reduces viability, brain size, and cholesterol synthesis, consistent with UBE3B's developmental and metabolic roles [PMID:23200864]. Biallelic UBE3B loss underlies Kaufman oculocerebrofacial syndrome, with the metabolic perturbations recapitulated in patient plasma [PMID:30808755].","teleology":[{"year":2003,"claim":"Established UBE3B as a HECT-domain E3 ligase gene and raised the question of how functional protein levels are tuned, identifying an alternative splice form predicted to truncate before the HECT domain.","evidence":"cDNA cloning, RT-PCR, and bioinformatic splicing analysis","pmids":["12837265"],"confidence":"Low","gaps":["No functional assay confirming the truncated isoform is produced or regulatory","Catalytic activity not demonstrated","No substrate or pathway context"]},{"year":2012,"claim":"Connected UBE3B loss to a developmental and metabolic phenotype, showing the ligase is required for normal growth, brain size, and cholesterol synthesis in vivo.","evidence":"Ube3b knockout mouse phenotyping and C. elegans oxi-1 genetics under oxidative stress","pmids":["23200864"],"confidence":"Medium","gaps":["No direct substrate identified","Mechanism linking ligase activity to cholesterol synthesis unresolved","Subcellular site of action not defined"]},{"year":2016,"claim":"Defined the biochemical core of UBE3B function: a catalytically active mitochondrion-associated HECT ligase whose activity is regulated by calcium/calmodulin binding through an N-terminal IQ motif.","evidence":"In vitro ubiquitylation with C1036A and HECT-deletion mutants, calmodulin Co-IP/pulldown, fractionation, and siRNA knockdown with mitochondrial readouts","pmids":["28003368"],"confidence":"High","gaps":["Physiological substrates not yet identified","Structural basis of IQ-motif autoinhibition undefined","Link between calmodulin regulation and specific cellular outcomes unclear"]},{"year":2019,"claim":"Identified the first physiological substrate, BCKDK, placing UBE3B in control of branched-chain metabolism and mitochondrial respiration.","evidence":"Interactome MS screen, in vivo ubiquitylation assay, and KO mouse metabolomics with respiration assays","pmids":["30808755"],"confidence":"High","gaps":["Ubiquitin linkage type and fate of ubiquitylated BCKDK not specified","How BCKDK turnover quantitatively explains metabolic phenotype unclear"]},{"year":2020,"claim":"Linked UBE3B to synaptic function by showing it ubiquitylates the calcineurin subunit Ppp3cc to restrain dendritic spine density, with overexpression epistasis confirming the axis.","evidence":"Ubiquitylation assay, Ube3b KO neurons, Ppp3cc overexpression epistasis, spine imaging, and electrophysiology","pmids":["32249816"],"confidence":"High","gaps":["Ubiquitin linkage and whether Ppp3cc is degraded vs regulated not defined","Circuit-level consequences only partially mapped"]},{"year":2020,"claim":"Revealed an oncogenic relevance: UBE3B directly ubiquitylates MYC for degradation, and TRIB3 antagonizes this to stabilize MYC in lymphoma.","evidence":"Reciprocal Co-IP, ubiquitylation assays, TRIB3 deletion lymphoma model, and patient-derived xenograft","pmids":["33298911"],"confidence":"High","gaps":["Conditions favoring MYC degradation vs stabilization across tissues unclear","Whether UBE3B-MYC axis operates in non-lymphoma contexts untested"]},{"year":2021,"claim":"Uncovered an intrinsic autoregulatory switch: self-ubiquitylation at K665 drives oligomerization and inactivation of UBE3B.","evidence":"Split-CAT bacterial selection assay, K665 mutagenesis, validation in yeast and mammalian cells","pmids":["34599943"],"confidence":"Medium","gaps":["Structural basis of oligomerization not resolved","Physiological trigger for autoinactivation in vivo unknown","Single-lab assay system"]},{"year":2023,"claim":"Showed UBE3B can also stabilize a substrate: K63-linked polyubiquitylation of HIF-2α blocks VHL-mediated degradation and drives cancer growth and metastasis.","evidence":"Co-IP, K63-linkage-specific ubiquitylation assays, HIF-2α lysine mutagenesis, knockdown and xenograft","pmids":["37783786"],"confidence":"High","gaps":["How linkage specificity (K63 vs K48) is determined per substrate unknown","Interplay with the UBE3B-MYC degradative axis unresolved"]},{"year":2024,"claim":"Placed UBE3B within a reciprocal regulatory loop with VHL, which ubiquitylates UBE3B (K48 at K286/K427) for proteasomal degradation, suppressing breast tumor growth.","evidence":"Co-IP, K48-linkage ubiquitylation assays, K286R/K427R mutagenesis, and xenograft models","pmids":["38914543"],"confidence":"High","gaps":["PHD-independent recognition mechanism by VHL not structurally defined","Whether UBE3B-HIF-2α and VHL-UBE3B loops form a feedback circuit untested"]},{"year":2025,"claim":"Extended UBE3B's substrate repertoire to NCOA4, defining a Nrf2/UBE3B/NCOA4 axis that suppresses ferritinophagy and ferroptosis.","evidence":"Western blot, UBE3B overexpression/knockdown, Nrf2 knockdown rescue, and ferroptosis marker measurement in alveolar epithelial cells","pmids":["40671136"],"confidence":"Medium","gaps":["Direct ubiquitylation assay detail limited","Ubiquitin linkage and NCOA4 fate not characterized","Single-lab, western-blot-based inference"]},{"year":2026,"claim":"Mapped UBE3B's neuronal role at proteome scale, identifying a synaptic ubiquitome and direct synaptic interactors controlling excitatory synapse density and circuit excitability.","evidence":"Quantitative proteomics/ubiquitome profiling, reciprocal Co-IP of ATP1A1/DOCK7/NLGN2/STX12, conditional CNS KO mouse, electrophysiology, and AMPA receptor surface assays","pmids":["41844341"],"confidence":"High","gaps":["Which interactors are direct substrates vs adaptors not fully resolved","Causal substrate driving AMPA receptor and excitability phenotypes not pinpointed"]},{"year":null,"claim":"How UBE3B selects between degradative (K48) and stabilizing (K63) ubiquitin linkages on different substrates, and how its calmodulin and self-ubiquitylation switches integrate to govern context-specific activity, remains unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No structural model coupling regulatory inputs to linkage specificity","Substrate-recognition determinants undefined","Tissue-specific substrate prioritization unknown"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0016740","term_label":"transferase activity","supporting_discovery_ids":[0,1,2,3,5,6]},{"term_id":"GO:0140096","term_label":"catalytic activity, acting on a protein","supporting_discovery_ids":[0,1,2,3,5,7]},{"term_id":"GO:0016874","term_label":"ligase activity","supporting_discovery_ids":[0,9]},{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[0]}],"localization":[{"term_id":"GO:0005739","term_label":"mitochondrion","supporting_discovery_ids":[0,1]}],"pathway":[{"term_id":"R-HSA-392499","term_label":"Metabolism of proteins","supporting_discovery_ids":[0,1,2,3,5,6]},{"term_id":"R-HSA-112316","term_label":"Neuronal System","supporting_discovery_ids":[2,8]},{"term_id":"R-HSA-1430728","term_label":"Metabolism","supporting_discovery_ids":[1,10]},{"term_id":"R-HSA-1643685","term_label":"Disease","supporting_discovery_ids":[3,5,6]}],"complexes":[],"partners":["CALM1","BCKDK","PPP3CC","MYC","HIF2A","VHL","NCOA4","NLGN2"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q7Z3V4","full_name":"Ubiquitin-protein ligase E3B","aliases":["HECT-type ubiquitin transferase E3B"],"length_aa":1068,"mass_kda":123.1,"function":"E3 ubiquitin-protein ligase which accepts ubiquitin from an E2 ubiquitin-conjugating enzyme in the form of a thioester and then directly transfers the ubiquitin to targeted substrates. Ubiquitinates BCKDK and targets it for degradation, thereby regulating various metabolic processes (By similarity). Involved in the positive regulation of neurite branching in hippocampal neurons and the control of neuronal spine number and morphology, through the ubiquitination of PPP3CC (By similarity)","subcellular_location":"Postsynaptic density","url":"https://www.uniprot.org/uniprotkb/Q7Z3V4/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/UBE3B","classification":"Not Classified","n_dependent_lines":1,"n_total_lines":1208,"dependency_fraction":0.0008278145695364238},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[{"gene":"NAPG","stoichiometry":10.0},{"gene":"BET1L","stoichiometry":0.2},{"gene":"CALM1","stoichiometry":0.2},{"gene":"CALM2","stoichiometry":0.2},{"gene":"CAPZB","stoichiometry":0.2},{"gene":"EDC4","stoichiometry":0.2},{"gene":"ELOVL1","stoichiometry":0.2},{"gene":"GPAT3","stoichiometry":0.2},{"gene":"LIG1","stoichiometry":0.2},{"gene":"MAN1A2","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/search/UBE3B","total_profiled":1310},"omim":[{"mim_id":"608047","title":"UBIQUITIN-PROTEIN LIGASE E3B; UBE3B","url":"https://www.omim.org/entry/608047"},{"mim_id":"244450","title":"KAUFMAN OCULOCEREBROFACIAL SYNDROME; KOS","url":"https://www.omim.org/entry/244450"},{"mim_id":"217980","title":"CORPUS CALLOSUM, AGENESIS OF, WITH FACIAL ANOMALIES AND ROBIN SEQUENCE","url":"https://www.omim.org/entry/217980"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Approved","locations":[{"location":"Nuclear speckles","reliability":"Approved"},{"location":"Mitochondria","reliability":"Additional"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/UBE3B"},"hgnc":{"alias_symbol":[],"prev_symbol":[]},"alphafold":{"accession":"Q7Z3V4","domains":[{"cath_id":"-","chopping":"454-648","consensus_level":"medium","plddt":91.1068,"start":454,"end":648},{"cath_id":"3.30.2160.10","chopping":"744-926","consensus_level":"medium","plddt":87.9649,"start":744,"end":926},{"cath_id":"3.30.2410.10","chopping":"932-1002_1026-1060","consensus_level":"high","plddt":83.6963,"start":932,"end":1060},{"cath_id":"1.20.5","chopping":"18-58","consensus_level":"medium","plddt":91.2588,"start":18,"end":58}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q7Z3V4","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q7Z3V4-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q7Z3V4-F1-predicted_aligned_error_v6.png","plddt_mean":84.69},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=UBE3B","jax_strain_url":"https://www.jax.org/strain/search?query=UBE3B"},"sequence":{"accession":"Q7Z3V4","fasta_url":"https://rest.uniprot.org/uniprotkb/Q7Z3V4.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q7Z3V4/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q7Z3V4"}},"corpus_meta":[{"pmid":"23200864","id":"PMC_23200864","title":"Deficiency for the ubiquitin ligase UBE3B in a blepharophimosis-ptosis-intellectual-disability syndrome.","date":"2012","source":"American journal of human genetics","url":"https://pubmed.ncbi.nlm.nih.gov/23200864","citation_count":83,"is_preprint":false},{"pmid":"33298911","id":"PMC_33298911","title":"TRIB3 promotes MYC-associated lymphoma development through suppression of UBE3B-mediated MYC degradation.","date":"2020","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/33298911","citation_count":47,"is_preprint":false},{"pmid":"23687348","id":"PMC_23687348","title":"Loss of function of the E3 ubiquitin-protein ligase UBE3B causes Kaufman oculocerebrofacial syndrome.","date":"2013","source":"Journal of medical genetics","url":"https://pubmed.ncbi.nlm.nih.gov/23687348","citation_count":39,"is_preprint":false},{"pmid":"28003368","id":"PMC_28003368","title":"UBE3B Is a Calmodulin-regulated, Mitochondrion-associated E3 Ubiquitin Ligase.","date":"2016","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/28003368","citation_count":36,"is_preprint":false},{"pmid":"30808755","id":"PMC_30808755","title":"The ubiquitin ligase UBE3B, disrupted in intellectual disability and absent speech, regulates metabolic pathways by targeting BCKDK.","date":"2019","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/30808755","citation_count":29,"is_preprint":false},{"pmid":"25306138","id":"PMC_25306138","title":"In frame exon skipping in UBE3B is associated with developmental disorders and increased mortality in cattle.","date":"2014","source":"BMC genomics","url":"https://pubmed.ncbi.nlm.nih.gov/25306138","citation_count":29,"is_preprint":false},{"pmid":"12837265","id":"PMC_12837265","title":"Characterization of the human UBE3B gene: structure, expression, evolution, and alternative splicing.","date":"2003","source":"Genomics","url":"https://pubmed.ncbi.nlm.nih.gov/12837265","citation_count":24,"is_preprint":false},{"pmid":"32249816","id":"PMC_32249816","title":"The murine ortholog of Kaufman oculocerebrofacial syndrome protein Ube3b regulates synapse number by ubiquitinating Ppp3cc.","date":"2020","source":"Molecular psychiatry","url":"https://pubmed.ncbi.nlm.nih.gov/32249816","citation_count":19,"is_preprint":false},{"pmid":"37783786","id":"PMC_37783786","title":"UBE3B promotes breast cancer progression by antagonizing HIF-2α degradation.","date":"2023","source":"Oncogene","url":"https://pubmed.ncbi.nlm.nih.gov/37783786","citation_count":13,"is_preprint":false},{"pmid":"25691420","id":"PMC_25691420","title":"Kaufman oculocerebrofacial syndrome in sisters with novel compound heterozygous mutation in UBE3B.","date":"2015","source":"American journal of medical genetics. Part A","url":"https://pubmed.ncbi.nlm.nih.gov/25691420","citation_count":13,"is_preprint":false},{"pmid":"23743024","id":"PMC_23743024","title":"UBE3B and ZRANB1 polymorphisms and transcript abundance are associated with water holding capacity of porcine M. longissimus dorsi.","date":"2013","source":"Meat science","url":"https://pubmed.ncbi.nlm.nih.gov/23743024","citation_count":12,"is_preprint":false},{"pmid":"38914543","id":"PMC_38914543","title":"VHL suppresses UBE3B-mediated breast tumor growth and metastasis.","date":"2024","source":"Cell death & disease","url":"https://pubmed.ncbi.nlm.nih.gov/38914543","citation_count":11,"is_preprint":false},{"pmid":"40671136","id":"PMC_40671136","title":"Nrf2/UBE3B protects against acute lung injury by inhibiting ferritinophagy through the ubiquitination of NCOA4.","date":"2025","source":"Biology direct","url":"https://pubmed.ncbi.nlm.nih.gov/40671136","citation_count":5,"is_preprint":false},{"pmid":"34599943","id":"PMC_34599943","title":"Split Chloramphenicol Acetyl-Transferase Assay Reveals Self-Ubiquitylation-Dependent Regulation of UBE3B.","date":"2021","source":"Journal of molecular biology","url":"https://pubmed.ncbi.nlm.nih.gov/34599943","citation_count":5,"is_preprint":false},{"pmid":"36623761","id":"PMC_36623761","title":"The murine ortholog of Kaufman oculocerebrofacial syndrome gene Ube3b is crucial for the maintenance of the excitatory synapses in the young adult stage.","date":"2023","source":"Neuroscience letters","url":"https://pubmed.ncbi.nlm.nih.gov/36623761","citation_count":1,"is_preprint":false},{"pmid":"38410982","id":"PMC_38410982","title":"Novel UBE3B mutations: report of eight patients with Kaufman oculocerebrofacial syndrome with additional clinical findings from a highly consanguineous population.","date":"2024","source":"Clinical dysmorphology","url":"https://pubmed.ncbi.nlm.nih.gov/38410982","citation_count":1,"is_preprint":false},{"pmid":"40305433","id":"PMC_40305433","title":"Multiple association studies identify 3 novel candidate genes for teat number trait in Danish Landrace and Large White pigs: BRINP3, LIN52, and UBE3B.","date":"2025","source":"Journal of animal science","url":"https://pubmed.ncbi.nlm.nih.gov/40305433","citation_count":1,"is_preprint":false},{"pmid":"41844341","id":"PMC_41844341","title":"The E3 Ubiquitin Ligase UBE3B Regulates Synaptic Development and Cortical Network Activity.","date":"2026","source":"Autism research : official journal of the International Society for Autism Research","url":"https://pubmed.ncbi.nlm.nih.gov/41844341","citation_count":0,"is_preprint":false},{"pmid":"41318572","id":"PMC_41318572","title":"Kaufman oculocerebrofacial syndrome: case report of a UBE3B splice site variant and clinical overview of reported patients.","date":"2025","source":"Molecular cytogenetics","url":"https://pubmed.ncbi.nlm.nih.gov/41318572","citation_count":0,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":11206,"output_tokens":3381,"usd":0.042167,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":10924,"output_tokens":3990,"usd":0.077185,"stage2_stop_reason":"end_turn"},"total_usd":0.119352,"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\": 2016,\n      \"finding\": \"UBE3B is a mitochondrion-associated HECT-domain E3 ubiquitin ligase; mutating the catalytic cysteine (C1036A) or deleting the HECT domain (aa 758–1068) abolishes ubiquitylation activity. UBE3B knockdown induces changes in mitochondrial morphology and physiology and a decrease in mitochondrial volume. UBE3B interacts with calmodulin via its N-terminal IQ motif (aa 29–58); deletion of the IQ motif increases in vitro ubiquitylation activity, and changes in calcium levels disrupt the calmodulin–UBE3B interaction.\",\n      \"method\": \"In vitro ubiquitylation assay, active-site mutagenesis (C1036A), domain deletion, Co-IP/pulldown for calmodulin binding, subcellular fractionation/imaging, siRNA knockdown with mitochondrial morphology readout\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — in vitro ubiquitylation assay with active-site mutagenesis and domain deletions, calmodulin interaction confirmed by pulldown, localization by fractionation, KD phenotype; multiple orthogonal methods in one study\",\n      \"pmids\": [\"28003368\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"UBE3B ubiquitinates branched-chain α-ketoacid dehydrogenase kinase (BCKDK) in vivo; BCKDK was identified as a UBE3B substrate through interactome profiling of 22 UBE3B interactors. Loss of Ube3b in mice perturbs nucleotide metabolism and the TCA cycle, and reduces substrate-induced mitochondrial respiration in skeletal muscle.\",\n      \"method\": \"Co-immunoprecipitation/mass spectrometry interactome screen, in vivo ubiquitylation assay, Ube3b knockout mouse metabolomics (plasma and cortex), mitochondrial respiration assay\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — substrate identification by MS-based interactome plus in vivo ubiquitylation, corroborated by metabolomic profiling in KO mice and patient plasma\",\n      \"pmids\": [\"30808755\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"Ube3b ubiquitinates Ppp3cc (the catalytic γ-subunit of calcineurin); overexpression of Ppp3cc phenocopies Ube3b loss with respect to increased dendritic spine density. Ube3b KO neurons exhibit increased dendritic spine density, aberrant spine morphology, altered synaptic physiology, and changes in hippocampal circuit activity. Ube3b regulates dendritic branching in a cell-autonomous manner.\",\n      \"method\": \"In vitro/in vivo ubiquitylation assay, Ube3b knockout mouse model, overexpression of Ppp3cc as epistasis test, dendritic spine imaging, electrophysiology\",\n      \"journal\": \"Molecular psychiatry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — substrate ubiquitylation assay combined with epistasis (Ppp3cc overexpression phenocopying KO), KO mouse with multiple orthogonal cellular phenotypes\",\n      \"pmids\": [\"32249816\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"TRIB3 interacts with MYC to suppress UBE3B-mediated MYC ubiquitination and proteasomal degradation, thereby stabilizing MYC and enhancing its transcriptional activity in lymphoma cells. UBE3B directly ubiquitinates MYC, and TRIB3 acts as a negative regulator of this UBE3B–MYC axis.\",\n      \"method\": \"Co-immunoprecipitation, in vitro/cellular ubiquitylation assay, TRIB3 deletion mouse model (MycEμ lymphoma), patient-derived xenograft, peptide disruption of TRIB3–MYC interaction\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal Co-IP, ubiquitylation assay, genetic deletion model, and xenograft rescue; multiple orthogonal methods across in vitro and in vivo settings\",\n      \"pmids\": [\"33298911\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"UBE3B undergoes self-ubiquitylation at K665, which induces oligomerization and inactivation in mammalian cells (analogous to NEDD4 self-inactivation). This autoubiquitylation-dependent mechanism was demonstrated using a split-CAT bacterial reporter system and validated in yeast and mammalian cell models.\",\n      \"method\": \"Split-CAT genetic selection assay in E. coli, site-directed mutagenesis (K665), yeast and mammalian cell validation of oligomerization and inactivation\",\n      \"journal\": \"Journal of molecular biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — novel split-reporter assay with mutagenesis, validated in multiple model systems but single lab, abstract-level detail\",\n      \"pmids\": [\"34599943\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"UBE3B physically interacts with HIF-2α and promotes its K63-linked polyubiquitination at residues K394, K497, and K503, thereby inhibiting VHL E3 ligase complex-mediated HIF-2α degradation and stabilizing HIF-2α. K394/497/503R mutation of HIF-2α abolishes UBE3B-mediated cancer growth and metastasis.\",\n      \"method\": \"Co-immunoprecipitation, in vitro/cellular K63-linkage-specific ubiquitylation assay, site-directed mutagenesis of HIF-2α ubiquitination sites, UBE3B knockdown in vitro and xenograft in vivo\",\n      \"journal\": \"Oncogene\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 / Moderate — in vitro ubiquitylation assay with mutagenesis of specific lysine residues, Co-IP, and in vivo xenograft rescue; multiple orthogonal methods in one study\",\n      \"pmids\": [\"37783786\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"VHL is an E3 ubiquitin ligase for UBE3B: VHL directly binds UBE3B and promotes its K48-linked polyubiquitination at K286 and K427 in a PHD-independent manner, leading to proteasomal degradation of UBE3B. K286/427R mutation of UBE3B abolishes the inhibitory effect of VHL on breast tumor growth and metastasis.\",\n      \"method\": \"Co-immunoprecipitation, in vitro/cellular ubiquitylation assay (K48-linkage specific), site-directed mutagenesis (K286R/K427R), in vivo xenograft models\",\n      \"journal\": \"Cell death & disease\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 / Moderate — in vitro ubiquitylation with specific-lysine mutagenesis, Co-IP, and in vivo rescue experiments; multiple orthogonal methods\",\n      \"pmids\": [\"38914543\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"UBE3B ubiquitinates NCOA4 (nuclear receptor coactivator 4), suppressing NCOA4-mediated ferritinophagy and thereby reducing ferrous iron release and ferroptosis in alveolar epithelial cells. Nrf2 transcriptionally activates UBE3B expression, placing UBE3B in a Nrf2/UBE3B/NCOA4 regulatory axis.\",\n      \"method\": \"Western blot, overexpression/knockdown of UBE3B, Nrf2 knockdown rescue experiments, measurement of ferrous ion content and ferroptosis markers in alveolar epithelial cells\",\n      \"journal\": \"Biology direct\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single lab, western blot-based mechanistic inference; ubiquitylation of NCOA4 by UBE3B stated but supporting assay detail is limited in the abstract\",\n      \"pmids\": [\"40671136\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"UBE3B regulates the synaptic proteome: quantitative proteomics of neural stem cells identified 116 proteins with increased levels and reduced ubiquitination upon UBE3B loss. UBE3B interacts with synaptic proteins including ATP1A1, DOCK7, NLGN2, and STX12 (confirmed by Co-IP). Ube3b CNS-specific KO mice show reduced excitatory synapse density, diminished spontaneous cortical circuit activity, decreased AMPA receptor surface expression, and hyperexcitability of excitatory cortical neurons.\",\n      \"method\": \"Quantitative proteomics and ubiquitome profiling, Co-immunoprecipitation of synaptic interactors, Ube3b conditional CNS KO mouse, electrophysiology, AMPA receptor surface expression assay, dendritic morphology imaging\",\n      \"journal\": \"Autism research : official journal of the International Society for Autism Research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — proteome-wide ubiquitome profiling plus reciprocal Co-IP of specific interactors, validated in conditional KO mouse with multiple orthogonal cellular phenotypes\",\n      \"pmids\": [\"41844341\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2003,\n      \"finding\": \"UBE3B encodes a HECT-domain E3 ubiquitin ligase. Alternative splicing of exon 20 generates a transcript containing an in-frame stop codon that would truncate the protein before the HECT domain, predicting a non-functional variant lacking catalytic activity. This represents a potential mechanism for regulating intracellular levels of functional UBE3B.\",\n      \"method\": \"cDNA cloning, RT-PCR, bioinformatic analysis of alternative splicing\",\n      \"journal\": \"Genomics\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 4 / Weak — cDNA/transcript characterization with no functional assay confirming the regulatory mechanism; prediction based on sequence analysis\",\n      \"pmids\": [\"12837265\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"Disruption of mouse Ube3b reduces viability, weight, and brain size, and causes downregulation of cholesterol synthesis. The C. elegans ortholog oxi-1 functions in the ubiquitin/proteasome system in vivo and is especially required under oxidative stress conditions, establishing UBE3B as a functional HECT E3 ligase with roles in neuronal development.\",\n      \"method\": \"Mouse Ube3b knockout model (viability, weight, brain size phenotyping), cholesterol synthesis assay, C. elegans oxi-1 genetic analysis under oxidative stress\",\n      \"journal\": \"American journal of human genetics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — KO mouse with specific metabolic and developmental phenotypes plus ortholog functional genetics in C. elegans; two organisms but single publication\",\n      \"pmids\": [\"23200864\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"UBE3B is a HECT-domain E3 ubiquitin ligase that localizes to mitochondria and is regulated by calmodulin binding via its N-terminal IQ motif (with calcium-dependent dissociation increasing activity) and by self-ubiquitylation at K665 (inducing oligomerization and inactivation); its substrates include BCKDK, Ppp3cc (calcineurin γ-subunit), MYC, HIF-2α (K63-linked stabilizing ubiquitination), and NCOA4, while VHL reciprocally targets UBE3B itself for K48-linked proteasomal degradation; in neurons, UBE3B fine-tunes the synaptic proteome (interacting with ATP1A1, DOCK7, NLGN2, STX12) to control dendritic spine density, excitatory synapse maintenance, AMPA receptor surface expression, and cortical circuit activity, with its loss causing metabolic dysregulation, mitochondrial dysfunction, and the intellectual disability/growth retardation phenotypes of Kaufman oculocerebrofacial syndrome.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"UBE3B is a mitochondrion-associated HECT-domain E3 ubiquitin ligase whose catalytic activity depends on its C-terminal HECT cysteine and is gated by an N-terminal IQ motif that binds calmodulin, with calcium-dependent dissociation relieving autoinhibition [#0]. Its activity is further controlled by self-ubiquitylation at K665, which drives oligomerization and inactivation [#4]. Through its ligase activity UBE3B shapes both metabolism and the neuronal synaptic proteome: it ubiquitylates the branched-chain ketoacid dehydrogenase kinase BCKDK and is required for normal nucleotide/TCA-cycle metabolism and mitochondrial respiration in muscle [#1], and it ubiquitylates the calcineurin catalytic subunit Ppp3cc to restrain dendritic spine density, excitatory synapse number, and cortical circuit activity [#2, #8]. UBE3B governs a broad synaptic ubiquitome and interacts with synaptic proteins including ATP1A1, DOCK7, NLGN2, and STX12 [#8]. In a cancer-relevant axis, UBE3B directly ubiquitylates MYC to promote its proteasomal turnover, an event antagonized by TRIB3 [#3], yet it also stabilizes HIF-2\\u03b1 via K63-linked polyubiquitylation that blocks VHL-mediated degradation [#5]; reciprocally, VHL ubiquitylates UBE3B itself with K48 linkages at K286/K427 to target it for degradation [#6]. Loss of Ube3b in mice reduces viability, brain size, and cholesterol synthesis, consistent with UBE3B's developmental and metabolic roles [#10]. Biallelic UBE3B loss underlies Kaufman oculocerebrofacial syndrome, with the metabolic perturbations recapitulated in patient plasma [#1].\",\n  \"teleology\": [\n    {\n      \"year\": 2003,\n      \"claim\": \"Established UBE3B as a HECT-domain E3 ligase gene and raised the question of how functional protein levels are tuned, identifying an alternative splice form predicted to truncate before the HECT domain.\",\n      \"evidence\": \"cDNA cloning, RT-PCR, and bioinformatic splicing analysis\",\n      \"pmids\": [\"12837265\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"No functional assay confirming the truncated isoform is produced or regulatory\", \"Catalytic activity not demonstrated\", \"No substrate or pathway context\"]\n    },\n    {\n      \"year\": 2012,\n      \"claim\": \"Connected UBE3B loss to a developmental and metabolic phenotype, showing the ligase is required for normal growth, brain size, and cholesterol synthesis in vivo.\",\n      \"evidence\": \"Ube3b knockout mouse phenotyping and C. elegans oxi-1 genetics under oxidative stress\",\n      \"pmids\": [\"23200864\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No direct substrate identified\", \"Mechanism linking ligase activity to cholesterol synthesis unresolved\", \"Subcellular site of action not defined\"]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"Defined the biochemical core of UBE3B function: a catalytically active mitochondrion-associated HECT ligase whose activity is regulated by calcium/calmodulin binding through an N-terminal IQ motif.\",\n      \"evidence\": \"In vitro ubiquitylation with C1036A and HECT-deletion mutants, calmodulin Co-IP/pulldown, fractionation, and siRNA knockdown with mitochondrial readouts\",\n      \"pmids\": [\"28003368\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Physiological substrates not yet identified\", \"Structural basis of IQ-motif autoinhibition undefined\", \"Link between calmodulin regulation and specific cellular outcomes unclear\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Identified the first physiological substrate, BCKDK, placing UBE3B in control of branched-chain metabolism and mitochondrial respiration.\",\n      \"evidence\": \"Interactome MS screen, in vivo ubiquitylation assay, and KO mouse metabolomics with respiration assays\",\n      \"pmids\": [\"30808755\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Ubiquitin linkage type and fate of ubiquitylated BCKDK not specified\", \"How BCKDK turnover quantitatively explains metabolic phenotype unclear\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Linked UBE3B to synaptic function by showing it ubiquitylates the calcineurin subunit Ppp3cc to restrain dendritic spine density, with overexpression epistasis confirming the axis.\",\n      \"evidence\": \"Ubiquitylation assay, Ube3b KO neurons, Ppp3cc overexpression epistasis, spine imaging, and electrophysiology\",\n      \"pmids\": [\"32249816\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Ubiquitin linkage and whether Ppp3cc is degraded vs regulated not defined\", \"Circuit-level consequences only partially mapped\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Revealed an oncogenic relevance: UBE3B directly ubiquitylates MYC for degradation, and TRIB3 antagonizes this to stabilize MYC in lymphoma.\",\n      \"evidence\": \"Reciprocal Co-IP, ubiquitylation assays, TRIB3 deletion lymphoma model, and patient-derived xenograft\",\n      \"pmids\": [\"33298911\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Conditions favoring MYC degradation vs stabilization across tissues unclear\", \"Whether UBE3B-MYC axis operates in non-lymphoma contexts untested\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Uncovered an intrinsic autoregulatory switch: self-ubiquitylation at K665 drives oligomerization and inactivation of UBE3B.\",\n      \"evidence\": \"Split-CAT bacterial selection assay, K665 mutagenesis, validation in yeast and mammalian cells\",\n      \"pmids\": [\"34599943\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Structural basis of oligomerization not resolved\", \"Physiological trigger for autoinactivation in vivo unknown\", \"Single-lab assay system\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Showed UBE3B can also stabilize a substrate: K63-linked polyubiquitylation of HIF-2\\u03b1 blocks VHL-mediated degradation and drives cancer growth and metastasis.\",\n      \"evidence\": \"Co-IP, K63-linkage-specific ubiquitylation assays, HIF-2\\u03b1 lysine mutagenesis, knockdown and xenograft\",\n      \"pmids\": [\"37783786\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"How linkage specificity (K63 vs K48) is determined per substrate unknown\", \"Interplay with the UBE3B-MYC degradative axis unresolved\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Placed UBE3B within a reciprocal regulatory loop with VHL, which ubiquitylates UBE3B (K48 at K286/K427) for proteasomal degradation, suppressing breast tumor growth.\",\n      \"evidence\": \"Co-IP, K48-linkage ubiquitylation assays, K286R/K427R mutagenesis, and xenograft models\",\n      \"pmids\": [\"38914543\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"PHD-independent recognition mechanism by VHL not structurally defined\", \"Whether UBE3B-HIF-2\\u03b1 and VHL-UBE3B loops form a feedback circuit untested\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Extended UBE3B's substrate repertoire to NCOA4, defining a Nrf2/UBE3B/NCOA4 axis that suppresses ferritinophagy and ferroptosis.\",\n      \"evidence\": \"Western blot, UBE3B overexpression/knockdown, Nrf2 knockdown rescue, and ferroptosis marker measurement in alveolar epithelial cells\",\n      \"pmids\": [\"40671136\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct ubiquitylation assay detail limited\", \"Ubiquitin linkage and NCOA4 fate not characterized\", \"Single-lab, western-blot-based inference\"]\n    },\n    {\n      \"year\": 2026,\n      \"claim\": \"Mapped UBE3B's neuronal role at proteome scale, identifying a synaptic ubiquitome and direct synaptic interactors controlling excitatory synapse density and circuit excitability.\",\n      \"evidence\": \"Quantitative proteomics/ubiquitome profiling, reciprocal Co-IP of ATP1A1/DOCK7/NLGN2/STX12, conditional CNS KO mouse, electrophysiology, and AMPA receptor surface assays\",\n      \"pmids\": [\"41844341\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Which interactors are direct substrates vs adaptors not fully resolved\", \"Causal substrate driving AMPA receptor and excitability phenotypes not pinpointed\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How UBE3B selects between degradative (K48) and stabilizing (K63) ubiquitin linkages on different substrates, and how its calmodulin and self-ubiquitylation switches integrate to govern context-specific activity, remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No structural model coupling regulatory inputs to linkage specificity\", \"Substrate-recognition determinants undefined\", \"Tissue-specific substrate prioritization unknown\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0016740\", \"supporting_discovery_ids\": [0, 1, 2, 3, 5, 6]},\n      {\"term_id\": \"GO:0140096\", \"supporting_discovery_ids\": [0, 1, 2, 3, 5, 7]},\n      {\"term_id\": \"GO:0016874\", \"supporting_discovery_ids\": [0, 9]},\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [0]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005739\", \"supporting_discovery_ids\": [0, 1]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-392499\", \"supporting_discovery_ids\": [0, 1, 2, 3, 5, 6]},\n      {\"term_id\": \"R-HSA-112316\", \"supporting_discovery_ids\": [2, 8]},\n      {\"term_id\": \"R-HSA-1430728\", \"supporting_discovery_ids\": [1, 10]},\n      {\"term_id\": \"R-HSA-1643685\", \"supporting_discovery_ids\": [3, 5, 6]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\"CALM1\", \"BCKDK\", \"PPP3CC\", \"MYC\", \"HIF2A\", \"VHL\", \"NCOA4\", \"NLGN2\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":7,"faith_total":7,"faith_pct":100.0}}