{"gene":"UBE2A","run_date":"2026-06-10T10:51:56","timeline":{"discoveries":[{"year":2002,"finding":"hHR6A (UBE2A) is phosphorylated by CDK1 and CDK2 on Ser120, resulting in a 4-fold increase in ubiquitin-conjugating activity in vitro; in vivo, phosphorylation peaks during G2/M phase with a concomitant increase in histone H2B ubiquitylation; mutation of Ser120 to alanine abolished activity while aspartate substitution (phosphomimetic) increased activity ~3-fold; genetic complementation in S. cerevisiae confirmed Ser120 is critical for cellular proliferation.","method":"Solid-phase phosphorylation screen, in vitro kinase assay, site-directed mutagenesis, cell cycle synchronization/immunoblot, yeast complementation","journal":"The EMBO journal","confidence":"High","confidence_rationale":"Tier 1 / Strong — multiple orthogonal methods including in vitro kinase assay, mutagenesis, in vivo cell cycle analysis, and genetic complementation in a single rigorous study","pmids":["11953320"],"is_preprint":false},{"year":2000,"finding":"Human RAD18 protein physically interacts with HHR6A (UBE2A) and HHR6B; co-expressed in yeast cells, stable RAD18–HHR6A and RAD18–HHR6B complexes were purified to near homogeneity, indicating UBE2A participates in a conserved RAD6–RAD18 lesion bypass complex.","method":"Co-expression in yeast, protein complex purification, co-immunoprecipitation","journal":"Nucleic acids research","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal complex purification to near homogeneity plus co-IP; replicated with both paralogs","pmids":["10908344"],"is_preprint":false},{"year":2011,"finding":"RAD6A (UBE2A) forms an asymmetric ternary complex with a RAD18 dimer (RAD6A–(RAD18)₂); only one of the two RAD18 subunits needs its RAD6-binding domain (R6BD) for complex formation and ligase activity; loss of both R6BDs abolishes activity even at high RAD6A concentrations, indicating that precise juxtaposition via R6BD is required; mutations in both RING or SAP domains strongly reduce activity, but inactivation of only one subunit is without effect.","method":"Differential tagging of RAD18 subunits, co-immunoprecipitation, in vitro ubiquitin ligase assay, site-directed mutagenesis","journal":"Nucleic acids research","confidence":"High","confidence_rationale":"Tier 1–2 / Moderate — in vitro ligase assay combined with mutagenesis and reciprocal co-IP in a single study with multiple orthogonal methods","pmids":["21967848"],"is_preprint":false},{"year":2013,"finding":"RAD6A (UBE2A) acts as an E2 ubiquitin-conjugating enzyme that, together with the E3 ligase Parkin, ubiquitinates mitochondrial proteins to facilitate clearance of dysfunctional mitochondria (mitophagy); Drosophila dRad6-deficient neurons show mitochondrial failure and synaptic dysfunction; mouse Ube2a KO and patient-derived mutant cells show defective mitochondria; in vitro and in vivo ubiquitination assays confirmed UBE2A–Parkin functional cooperation.","method":"Drosophila dRad6 knockout, mouse Ube2a knockout, patient-derived cell lines, in vitro ubiquitination assay, in vivo ubiquitination assay, mitochondrial function assays","journal":"Molecular cell","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — in vitro reconstitution of ubiquitination combined with multiple organism KO models and patient cells; replicated across species","pmids":["23685073"],"is_preprint":false},{"year":2003,"finding":"ZNF198 protein interacts with HHR6A (UBE2A) and HHR6B as identified by yeast two-hybrid and confirmed by co-immunoprecipitation; human RAD18 is also present in the ZNF198/HHR6 protein complex; cells expressing the ZNF198/FGFR1 fusion kinase show increased UVB sensitivity, suggesting the fusion acts dominant-negatively on the DNA repair complex.","method":"Yeast two-hybrid, co-immunoprecipitation, UV sensitivity assay","journal":"Oncogene","confidence":"Medium","confidence_rationale":"Tier 2–3 / Moderate — yeast two-hybrid confirmed by co-IP, with functional UV sensitivity readout; single lab","pmids":["12776193"],"is_preprint":false},{"year":1996,"finding":"HHR6A (UBE2A) protein localizes to the nucleus, with preferential localization to euchromatin (transcriptionally active regions) as shown by immunogold electron microscopy; elevated expression in testis coincides with the replacement of histones by transition proteins, supporting a role in ubiquitin-mediated histone modification during spermatogenesis.","method":"Immunohistochemistry, immunogold electron microscopy, 2D immunoblot, Northern blot","journal":"Developmental biology","confidence":"Medium","confidence_rationale":"Tier 2–3 / Moderate — direct localization by immunogold EM with functional contextual link to chromatin; single lab but multiple methods","pmids":["8575614"],"is_preprint":false},{"year":2004,"finding":"mHR6A (Ube2a) is an essential maternal factor; mHR6A knockout females fail to produce offspring because oocyte-derived mHR6A is required for embryonic development beyond the two-cell stage; loss does not alter histone H3 methylation at this stage, but reveals a dose-dependent and redundant requirement for HR6A and HR6B in both somatic and germline cells.","method":"Mouse knockout, histological analysis, embryonic development assay, histone H3 methylation immunostaining","journal":"Molecular and cellular biology","confidence":"High","confidence_rationale":"Tier 2 / Strong — clean knockout mouse with defined embryonic phenotype and negative H3-methylation control; rigorous genetic analysis","pmids":["15169909"],"is_preprint":false},{"year":2018,"finding":"The pathogenic Q93E mutation in UBE2A impairs aminolysis (ubiquitin transfer to lysine) without preventing ubiquitin conjugation to the catalytic cysteine; the low reactivity is not rescued by the E3 ligase RAD18 in the context of PCNA ubiquitination; reactivity is restored at high pH or with a low-pKa amine nucleophile, indicating Q93 is essential for deprotonating the incoming lysine to enable ubiquitin transfer.","method":"In vitro ubiquitination assay, pH-dependent reactivity assay, chemical rescue with low-pKa amine, active-site mutagenesis, NMR (structural context noted)","journal":"Nature chemical biology","confidence":"High","confidence_rationale":"Tier 1 / Moderate — in vitro reconstitution with mutagenesis, chemical rescue, and mechanistic pH analysis in a single rigorous study","pmids":["30531907"],"is_preprint":false},{"year":2015,"finding":"Ube2a knockout mice show a major deficit in spatial learning but normal motor coordination and epilepsy thresholds; hippocampal electrophysiology reveals no deficit in basal synaptic transmission or LTP but a significant deficit in mGluR-dependent long-term depression (LTD), placing UBE2A in the mGluR-LTD signaling pathway relevant to neurodevelopmental disorders.","method":"Mouse Ube2a knockout, Morris water maze, hippocampal electrophysiology (LTP, mGluR-LTD recording)","journal":"Human molecular genetics","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — clean KO with defined electrophysiological phenotype and pathway placement; single lab","pmids":["26476408"],"is_preprint":false},{"year":2024,"finding":"UBE2A is specifically recruited by a hemiRING zinc finger module within the E3 ligase UBR4; cryo-EM structure of the UBE2A–UBR4 E2–E3 complex reveals atomic-level specificity determinants of the hemiRING for UBE2A/UBE2B; the UZI subdomain allosterically and modestly activates Ub-loaded UBE2A; the intrinsically high lysine reactivity of UBE2A cooperates with this activation to determine substrate specificity in the N-degron pathway.","method":"Cryo-EM structure determination, in vitro ubiquitination assay, mutagenesis, biochemical interaction assays","journal":"Nature structural & molecular biology","confidence":"High","confidence_rationale":"Tier 1 / Strong — cryo-EM structure with functional mutagenesis and in vitro reconstitution in a single rigorous study","pmids":["38182926"],"is_preprint":false},{"year":2026,"finding":"Cryo-EM structure of a chemically trapped RNF20/RNF40–RAD6A(UBE2A)–Ub–H2BS112GlcNAc nucleosome complex shows that the H2BS112GlcNAc moiety directly contacts the E2 enzyme RAD6A (not the E3); mutagenesis and kinetics demonstrate that this interaction allosterically enhances the nucleophilicity of H2B K120, stimulating ubiquitin transfer; structure–activity analysis identified essential roles for the C2 N-acetyl group and β-configuration of C1 of the GlcNAc moiety.","method":"Chemical synthesis of GlcNAc-modified nucleosomes, cryo-EM, in vitro ubiquitination kinetics, mutagenesis, structure–activity relationship analysis","journal":"Nature chemical biology","confidence":"High","confidence_rationale":"Tier 1 / Strong — cryo-EM structure combined with in vitro kinetics, mutagenesis, and chemical SAR in a single rigorous study","pmids":["41495224"],"is_preprint":false},{"year":2023,"finding":"UBE2A/B undergoes force- and contact-inhibition-dependent nucleocytoplasmic shuttling, identified as a mechanosensing transcriptional trans-acting factor; DHS-proteomics and next-generation sequencing showed that UBE2A/B regulates downstream gene expression (including YAP target genes) through histone ubiquitination, defining a YAP-independent mechanotransduction/contact-inhibition pathway.","method":"DHS-proteomics, nucleocytoplasmic fractionation, live-cell imaging, siRNA knockdown, next-generation sequencing, histone ubiquitination assay","journal":"The Biochemical journal","confidence":"Medium","confidence_rationale":"Tier 2–3 / Weak — single lab, multiple methods but pathway placement relies partly on correlative genomics; mechanistic follow-up limited","pmids":["37818922"],"is_preprint":false},{"year":2019,"finding":"De novo UBE2A mutations acquired during chronic myeloid leukemia progression to blast crisis decrease UBE2A ubiquitin-conjugating activity in vitro, leading to impaired myeloid differentiation in CML cells.","method":"In vitro ubiquitin-conjugating activity assay, CML cell differentiation assay, parallel sequencing of patient samples","journal":"Haematologica","confidence":"Medium","confidence_rationale":"Tier 2–3 / Moderate — in vitro activity assay combined with cell-based differentiation phenotype; single lab","pmids":["30819912"],"is_preprint":false}],"current_model":"UBE2A (RAD6A/HHR6A) is an E2 ubiquitin-conjugating enzyme that: (1) forms a stable ternary complex with the E3 ligase RAD18 dimer to mediate post-replication DNA damage bypass and PCNA monoubiquitination; (2) cooperates with Parkin E3 to ubiquitinate mitochondrial proteins and drive mitophagy, maintaining neuronal function; (3) is allosterically activated by CDK1/2-mediated phosphorylation of Ser120 during G2/M, stimulating histone H2B ubiquitylation; (4) ubiquitinates H2B K120 in complex with RNF20/RNF40, a reaction allosterically stimulated when RAD6A contacts H2B S112 GlcNAc; (5) is specifically recruited by the hemiRING module of the N-degron E3 ligase UBR4; (6) relies on residue Q93 to deprotonate the incoming lysine nucleophile during ubiquitin transfer; (7) shuttles between nucleus and cytoplasm in response to mechanical force and contact inhibition to regulate gene expression via histone ubiquitination; and (8) is an essential maternal factor required for embryonic development beyond the two-cell stage."},"narrative":{"mechanistic_narrative":"UBE2A (RAD6A/HHR6A) is an E2 ubiquitin-conjugating enzyme that channels ubiquitin to distinct E3 ligases to control chromatin modification, DNA damage tolerance, and mitochondrial quality control [PMID:10908344, PMID:23685073, PMID:41495224]. Catalysis depends on an active-site glutamine, Q93, which deprotonates the incoming lysine nucleophile to enable ubiquitin transfer from the catalytic cysteine; the pathogenic Q93E substitution selectively blocks this aminolysis step [PMID:30531907]. In DNA damage bypass, UBE2A forms an asymmetric ternary complex with a RAD18 dimer in which precise R6BD-mediated juxtaposition of a single RAD18 subunit is required for ligase activity [PMID:10908344, PMID:21967848]. With RNF20/RNF40 it monoubiquitinates histone H2B at K120, a reaction allosterically stimulated when RAD6A directly contacts an H2B S112 GlcNAc moiety that raises the nucleophilicity of K120 [PMID:41495224]; this histone-ubiquitination activity is further gated by CDK1/2 phosphorylation of Ser120, which boosts conjugating activity and peaks at G2/M [PMID:11953320]. UBE2A is also recruited by the hemiRING module of the N-degron E3 ligase UBR4, whose UZI subdomain modestly activates Ub-loaded enzyme [PMID:38182926], and cooperates with the E3 Parkin to ubiquitinate mitochondrial proteins and drive mitophagy required for neuronal function [PMID:23685073]. Genetically, UBE2A is an essential maternal factor needed for embryonic development beyond the two-cell stage [PMID:15169909] and is required for hippocampal mGluR-dependent long-term depression and spatial learning [PMID:26476408].","teleology":[{"year":1996,"claim":"Established where UBE2A acts in the cell, linking it physically to transcriptionally active chromatin rather than a diffuse cytoplasmic role.","evidence":"Immunogold electron microscopy and expression profiling in testis","pmids":["8575614"],"confidence":"Medium","gaps":["Does not identify the histone substrate or the E3 partner mediating chromatin association","Functional link to histone modification is contextual, not biochemical"]},{"year":2000,"claim":"Defined UBE2A's role in DNA damage tolerance by showing it forms a stable, conserved complex with the E3 ligase RAD18.","evidence":"Co-expression and complex purification in yeast, co-immunoprecipitation, with both paralogs","pmids":["10908344"],"confidence":"High","gaps":["Does not resolve complex stoichiometry or the substrate ubiquitinated","No structural detail of the interaction interface"]},{"year":2002,"claim":"Revealed cell-cycle regulation of UBE2A activity, connecting CDK phosphorylation of Ser120 to a G2/M peak in histone H2B ubiquitylation.","evidence":"In vitro kinase assay, phosphomimetic/phospho-dead mutagenesis, cell-cycle immunoblot, yeast complementation","pmids":["11953320"],"confidence":"High","gaps":["Structural basis of how Ser120 phosphorylation activates the enzyme not defined","Which E3 directs the cell-cycle H2B ubiquitylation not established here"]},{"year":2003,"claim":"Extended the UBE2A interactome by placing ZNF198 in a UBE2A/RAD18 repair complex with functional consequences for UV response.","evidence":"Yeast two-hybrid, co-immunoprecipitation, UV sensitivity assay","pmids":["12776193"],"confidence":"Medium","gaps":["Direct vs. indirect ZNF198 association within the complex not dissected","Mechanism by which the fusion kinase acts dominant-negatively unresolved"]},{"year":2004,"claim":"Demonstrated a developmental requirement, showing maternal UBE2A is essential for embryos to progress past the two-cell stage.","evidence":"Mouse knockout, embryonic development assay, H3 methylation immunostaining control","pmids":["15169909"],"confidence":"High","gaps":["The relevant ubiquitination substrate driving the arrest not identified","Redundancy with HR6B complicates assigning a unique molecular target"]},{"year":2011,"claim":"Resolved the architecture of the RAD6A–RAD18 ligase, showing an asymmetric RAD6A–(RAD18)2 complex where one R6BD-bearing subunit suffices for activity.","evidence":"Differential subunit tagging, co-IP, in vitro ubiquitin ligase assay, mutagenesis","pmids":["21967848"],"confidence":"High","gaps":["No atomic structure of the ternary complex","Functional reason for the asymmetric dimer arrangement unexplained"]},{"year":2013,"claim":"Expanded UBE2A function beyond chromatin/DNA repair by showing it partners with Parkin to ubiquitinate mitochondrial proteins and drive mitophagy in neurons.","evidence":"Drosophila and mouse knockouts, patient cells, in vitro and in vivo ubiquitination assays, mitochondrial function assays","pmids":["23685073"],"confidence":"High","gaps":["Specific mitochondrial substrates ubiquitinated by UBE2A–Parkin not enumerated","How UBE2A is recruited to depolarized mitochondria unclear"]},{"year":2015,"claim":"Linked UBE2A loss to a defined synaptic phenotype, placing it in the mGluR-dependent LTD pathway underlying spatial learning.","evidence":"Mouse knockout, Morris water maze, hippocampal LTP/LTD electrophysiology","pmids":["26476408"],"confidence":"Medium","gaps":["Molecular substrate connecting UBE2A to mGluR-LTD signaling not identified","Single lab; mechanism downstream of the conjugating activity unresolved"]},{"year":2018,"claim":"Defined the chemical mechanism of ubiquitin transfer, showing Q93 deprotonates the acceptor lysine and that the pathogenic Q93E mutation selectively impairs aminolysis.","evidence":"In vitro ubiquitination, pH-dependent reactivity, chemical rescue with low-pKa amine, active-site mutagenesis, NMR context","pmids":["30531907"],"confidence":"High","gaps":["Whether all E3-directed reactions share this Q93 dependence not tested across partners","Structural snapshot of the deprotonation transition state not provided"]},{"year":2023,"claim":"Identified UBE2A as a mechanosensitive transcriptional regulator that shuttles between nucleus and cytoplasm to control gene expression via histone ubiquitination.","evidence":"DHS-proteomics, nucleocytoplasmic fractionation, live-cell imaging, siRNA, NGS, histone ubiquitination assay","pmids":["37818922"],"confidence":"Medium","gaps":["Pathway placement relies partly on correlative genomics","Mechanism coupling mechanical force to shuttling not defined"]},{"year":2024,"claim":"Provided the structural basis of E2–E3 selectivity, showing UBE2A is captured by the hemiRING module of UBR4 in the N-degron pathway.","evidence":"Cryo-EM of UBE2A–UBR4 complex, mutagenesis, in vitro ubiquitination","pmids":["38182926"],"confidence":"High","gaps":["Physiological N-degron substrates handled through this complex in cells not catalogued","Extent of UZI-mediated activation relative to other E3s unclear"]},{"year":2026,"claim":"Explained allosteric control of H2B ubiquitylation, showing an H2B S112 GlcNAc directly contacts RAD6A to enhance K120 nucleophilicity.","evidence":"Cryo-EM of trapped RNF20/RNF40–RAD6A–Ub–H2BS112GlcNAc nucleosome, kinetics, mutagenesis, GlcNAc SAR","pmids":["41495224"],"confidence":"High","gaps":["Cellular conditions controlling H2B S112 GlcNAcylation not defined","Crosstalk with Ser120 phosphorylation in the same reaction not integrated"]},{"year":null,"claim":"How UBE2A's multiple regulatory inputs — Ser120 phosphorylation, H2B GlcNAc allostery, and E3 partner identity — are coordinated to select among its chromatin, repair, and mitophagy roles in vivo remains unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No unifying model integrating cell-cycle, mechanosensing, and substrate-specific cues","Substrate-level distinction between UBE2A and paralog UBE2B in each pathway not fully resolved"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0140096","term_label":"catalytic activity, acting on a protein","supporting_discovery_ids":[1,2,3,7,9,10]},{"term_id":"GO:0016740","term_label":"transferase activity","supporting_discovery_ids":[0,7,10]},{"term_id":"GO:0031386","term_label":"protein tag activity","supporting_discovery_ids":[1,3]}],"localization":[{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[5,11]},{"term_id":"GO:0000228","term_label":"nuclear chromosome","supporting_discovery_ids":[5]},{"term_id":"GO:0005829","term_label":"cytosol","supporting_discovery_ids":[11]}],"pathway":[{"term_id":"R-HSA-73894","term_label":"DNA Repair","supporting_discovery_ids":[1,2]},{"term_id":"R-HSA-4839726","term_label":"Chromatin organization","supporting_discovery_ids":[0,10,11]},{"term_id":"R-HSA-9612973","term_label":"Autophagy","supporting_discovery_ids":[3]},{"term_id":"R-HSA-392499","term_label":"Metabolism of proteins","supporting_discovery_ids":[7,9]},{"term_id":"R-HSA-1640170","term_label":"Cell Cycle","supporting_discovery_ids":[0]}],"complexes":["RAD6A–RAD18 (RAD6A–(RAD18)2) lesion-bypass complex","RNF20/RNF40–RAD6A H2B ubiquitylation complex","UBE2A–UBR4 E2–E3 N-degron complex"],"partners":["RAD18","RNF20","RNF40","PARKIN","UBR4","ZNF198"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"P49459","full_name":"Ubiquitin-conjugating enzyme E2 A","aliases":["E2 ubiquitin-conjugating enzyme A","RAD6 homolog A","HR6A","hHR6A","Ubiquitin carrier protein A","Ubiquitin-protein ligase A"],"length_aa":152,"mass_kda":17.3,"function":"E2 ubiquitin-conjugating enzyme that accepts ubiquitin from the ubiquitin-activating enzyme E1 and transfers it to a E3 ubiquitin-protein ligase (PubMed:16337599, PubMed:20061386, PubMed:23685073, PubMed:25582440, PubMed:38297121). In vitro catalyzes 'Lys-11', as well as 'Lys-48'-linked polyubiquitination (PubMed:20061386). Together with the E3 enzyme BRE1 (RNF20 and/or RNF40), plays a role in transcription regulation by catalyzing the monoubiquitination of histone H2B at 'Lys-120' to form H2BK120ub1 (PubMed:16337599). H2BK120ub1 gives a specific tag for epigenetic transcriptional activation, elongation by RNA polymerase II, telomeric silencing, and is also a prerequisite for H3K4me and H3K79me formation (PubMed:16337599). Involved in mitophagy by acting as a E2 ubiquitin-conjugating enzyme for PRKN (PubMed:23685073). In association with the E3 enzyme UBR4, is involved in N-end rule-dependent protein degradation (PubMed:38182926). In association with the E3 ubiquitin-protein ligase complex SIFI, inhibits the mitochondrial stress response by acting as a E2 ubiquitin-conjugating enzyme for UBR4 and KCMF1 (PubMed:38297121)","subcellular_location":"Late endosome; Lysosome","url":"https://www.uniprot.org/uniprotkb/P49459/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/UBE2A","classification":"Not Classified","n_dependent_lines":134,"n_total_lines":1208,"dependency_fraction":0.11092715231788079},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[{"gene":"DDX6","stoichiometry":0.2},{"gene":"RNF40","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/search/UBE2A","total_profiled":1310},"omim":[{"mim_id":"617858","title":"PROTEASOME INHIBITOR SUBUNIT 1; PSMF1","url":"https://www.omim.org/entry/617858"},{"mim_id":"617676","title":"PROTEASOME 26S SUBUNIT, NON-ATPase, 3; PSMD3","url":"https://www.omim.org/entry/617676"},{"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":"614277","title":"UBIQUITIN-CONJUGATING ENZYME E2 W; UBE2W","url":"https://www.omim.org/entry/614277"},{"mim_id":"613831","title":"UBIQUITIN PROTEIN LIGASE E3 COMPONENT N-RECOGNIN 3; UBR3","url":"https://www.omim.org/entry/613831"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Approved","locations":[{"location":"Nucleoplasm","reliability":"Approved"},{"location":"Plasma membrane","reliability":"Approved"},{"location":"Cytosol","reliability":"Approved"},{"location":"Vesicles","reliability":"Additional"},{"location":"Flagellar centriole","reliability":"Additional"},{"location":"Mid piece","reliability":"Additional"},{"location":"Principal piece","reliability":"Additional"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/UBE2A"},"hgnc":{"alias_symbol":["UBC2","HHR6A","RAD6A","HR6A"],"prev_symbol":[]},"alphafold":{"accession":"P49459","domains":[{"cath_id":"3.10.110.10","chopping":"3-148","consensus_level":"high","plddt":95.4066,"start":3,"end":148}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/P49459","model_url":"https://alphafold.ebi.ac.uk/files/AF-P49459-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-P49459-F1-predicted_aligned_error_v6.png","plddt_mean":94.12},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=UBE2A","jax_strain_url":"https://www.jax.org/strain/search?query=UBE2A"},"sequence":{"accession":"P49459","fasta_url":"https://rest.uniprot.org/uniprotkb/P49459.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/P49459/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/P49459"}},"corpus_meta":[{"pmid":"27929395","id":"PMC_27929395","title":"Deficiency in the Ubiquitin Conjugating Enzyme UBE2A in Alzheimer's Disease (AD) is Linked to Deficits in a Natural Circular miRNA-7 Sponge (circRNA; 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Part A","url":"https://pubmed.ncbi.nlm.nih.gov/25287747","citation_count":20,"is_preprint":false},{"pmid":"29283210","id":"PMC_29283210","title":"UBE2A deficiency in two siblings: A novel splicing variant inherited from a maternal germline mosaicism.","date":"2017","source":"American journal of medical genetics. 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type Nascimento.","date":"2019","source":"Molecular genetics & genomic medicine","url":"https://pubmed.ncbi.nlm.nih.gov/31566921","citation_count":9,"is_preprint":false},{"pmid":"31683936","id":"PMC_31683936","title":"Alternative Splicing of RAD6B and Not RAD6A is Selectively Increased in Melanoma: Identification and Functional Characterization.","date":"2019","source":"Cells","url":"https://pubmed.ncbi.nlm.nih.gov/31683936","citation_count":7,"is_preprint":false},{"pmid":"32415735","id":"PMC_32415735","title":"Refinement of the clinical and mutational spectrum of UBE2A deficiency syndrome.","date":"2020","source":"Clinical genetics","url":"https://pubmed.ncbi.nlm.nih.gov/32415735","citation_count":6,"is_preprint":false},{"pmid":"37818922","id":"PMC_37818922","title":"UBE2A/B is the trans-acting factor mediating mechanotransduction and contact inhibition.","date":"2023","source":"The Biochemical 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Tex.)","url":"https://pubmed.ncbi.nlm.nih.gov/22722497","citation_count":4,"is_preprint":false},{"pmid":"35846913","id":"PMC_35846913","title":"A novel UBE2A splice site variant causing intellectual disability type Nascimento.","date":"2022","source":"Clinical case reports","url":"https://pubmed.ncbi.nlm.nih.gov/35846913","citation_count":3,"is_preprint":false},{"pmid":"33368912","id":"PMC_33368912","title":"A novel missense mutation in the UBE2A gene causes intellectual disability in the large X-linked family.","date":"2021","source":"The journal of gene medicine","url":"https://pubmed.ncbi.nlm.nih.gov/33368912","citation_count":2,"is_preprint":false},{"pmid":"41495224","id":"PMC_41495224","title":"Allosteric activation of RNF20/RNF40-RAD6A-mediated H2BK120 monoubiquitylation by H2BS112 GlcNAcylation.","date":"2026","source":"Nature chemical biology","url":"https://pubmed.ncbi.nlm.nih.gov/41495224","citation_count":1,"is_preprint":false},{"pmid":"26463350","id":"PMC_26463350","title":"Identification and characterization of a ubiquitinconjugating enzyme UBE2A gene from lamprey.","date":"2016","source":"Fish physiology and biochemistry","url":"https://pubmed.ncbi.nlm.nih.gov/26463350","citation_count":0,"is_preprint":false},{"pmid":"40695520","id":"PMC_40695520","title":"[A large family of Nascimento form of syndromic X-linked intellectual developmental disorder caused by large segment deletion of the UBE2A gene: a case report and literature review].","date":"2025","source":"Zhongguo dang dai er ke za zhi = Chinese journal of contemporary pediatrics","url":"https://pubmed.ncbi.nlm.nih.gov/40695520","citation_count":0,"is_preprint":false},{"pmid":"40156274","id":"PMC_40156274","title":"Sudden infant death in a neonate with X-linked intellectual disability type Nascimento because of UBE2A 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substitution (phosphomimetic) increased activity ~3-fold; genetic complementation in S. cerevisiae confirmed Ser120 is critical for cellular proliferation.\",\n      \"method\": \"Solid-phase phosphorylation screen, in vitro kinase assay, site-directed mutagenesis, cell cycle synchronization/immunoblot, yeast complementation\",\n      \"journal\": \"The EMBO journal\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — multiple orthogonal methods including in vitro kinase assay, mutagenesis, in vivo cell cycle analysis, and genetic complementation in a single rigorous study\",\n      \"pmids\": [\"11953320\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2000,\n      \"finding\": \"Human RAD18 protein physically interacts with HHR6A (UBE2A) and HHR6B; co-expressed in yeast cells, stable RAD18–HHR6A and RAD18–HHR6B complexes were purified to near homogeneity, indicating UBE2A participates in a conserved RAD6–RAD18 lesion bypass complex.\",\n      \"method\": \"Co-expression in yeast, protein complex purification, co-immunoprecipitation\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal complex purification to near homogeneity plus co-IP; replicated with both paralogs\",\n      \"pmids\": [\"10908344\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"RAD6A (UBE2A) forms an asymmetric ternary complex with a RAD18 dimer (RAD6A–(RAD18)₂); only one of the two RAD18 subunits needs its RAD6-binding domain (R6BD) for complex formation and ligase activity; loss of both R6BDs abolishes activity even at high RAD6A concentrations, indicating that precise juxtaposition via R6BD is required; mutations in both RING or SAP domains strongly reduce activity, but inactivation of only one subunit is without effect.\",\n      \"method\": \"Differential tagging of RAD18 subunits, co-immunoprecipitation, in vitro ubiquitin ligase assay, site-directed mutagenesis\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Moderate — in vitro ligase assay combined with mutagenesis and reciprocal co-IP in a single study with multiple orthogonal methods\",\n      \"pmids\": [\"21967848\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"RAD6A (UBE2A) acts as an E2 ubiquitin-conjugating enzyme that, together with the E3 ligase Parkin, ubiquitinates mitochondrial proteins to facilitate clearance of dysfunctional mitochondria (mitophagy); Drosophila dRad6-deficient neurons show mitochondrial failure and synaptic dysfunction; mouse Ube2a KO and patient-derived mutant cells show defective mitochondria; in vitro and in vivo ubiquitination assays confirmed UBE2A–Parkin functional cooperation.\",\n      \"method\": \"Drosophila dRad6 knockout, mouse Ube2a knockout, patient-derived cell lines, in vitro ubiquitination assay, in vivo ubiquitination assay, mitochondrial function assays\",\n      \"journal\": \"Molecular cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — in vitro reconstitution of ubiquitination combined with multiple organism KO models and patient cells; replicated across species\",\n      \"pmids\": [\"23685073\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2003,\n      \"finding\": \"ZNF198 protein interacts with HHR6A (UBE2A) and HHR6B as identified by yeast two-hybrid and confirmed by co-immunoprecipitation; human RAD18 is also present in the ZNF198/HHR6 protein complex; cells expressing the ZNF198/FGFR1 fusion kinase show increased UVB sensitivity, suggesting the fusion acts dominant-negatively on the DNA repair complex.\",\n      \"method\": \"Yeast two-hybrid, co-immunoprecipitation, UV sensitivity assay\",\n      \"journal\": \"Oncogene\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2–3 / Moderate — yeast two-hybrid confirmed by co-IP, with functional UV sensitivity readout; single lab\",\n      \"pmids\": [\"12776193\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1996,\n      \"finding\": \"HHR6A (UBE2A) protein localizes to the nucleus, with preferential localization to euchromatin (transcriptionally active regions) as shown by immunogold electron microscopy; elevated expression in testis coincides with the replacement of histones by transition proteins, supporting a role in ubiquitin-mediated histone modification during spermatogenesis.\",\n      \"method\": \"Immunohistochemistry, immunogold electron microscopy, 2D immunoblot, Northern blot\",\n      \"journal\": \"Developmental biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2–3 / Moderate — direct localization by immunogold EM with functional contextual link to chromatin; single lab but multiple methods\",\n      \"pmids\": [\"8575614\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2004,\n      \"finding\": \"mHR6A (Ube2a) is an essential maternal factor; mHR6A knockout females fail to produce offspring because oocyte-derived mHR6A is required for embryonic development beyond the two-cell stage; loss does not alter histone H3 methylation at this stage, but reveals a dose-dependent and redundant requirement for HR6A and HR6B in both somatic and germline cells.\",\n      \"method\": \"Mouse knockout, histological analysis, embryonic development assay, histone H3 methylation immunostaining\",\n      \"journal\": \"Molecular and cellular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — clean knockout mouse with defined embryonic phenotype and negative H3-methylation control; rigorous genetic analysis\",\n      \"pmids\": [\"15169909\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"The pathogenic Q93E mutation in UBE2A impairs aminolysis (ubiquitin transfer to lysine) without preventing ubiquitin conjugation to the catalytic cysteine; the low reactivity is not rescued by the E3 ligase RAD18 in the context of PCNA ubiquitination; reactivity is restored at high pH or with a low-pKa amine nucleophile, indicating Q93 is essential for deprotonating the incoming lysine to enable ubiquitin transfer.\",\n      \"method\": \"In vitro ubiquitination assay, pH-dependent reactivity assay, chemical rescue with low-pKa amine, active-site mutagenesis, NMR (structural context noted)\",\n      \"journal\": \"Nature chemical biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — in vitro reconstitution with mutagenesis, chemical rescue, and mechanistic pH analysis in a single rigorous study\",\n      \"pmids\": [\"30531907\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"Ube2a knockout mice show a major deficit in spatial learning but normal motor coordination and epilepsy thresholds; hippocampal electrophysiology reveals no deficit in basal synaptic transmission or LTP but a significant deficit in mGluR-dependent long-term depression (LTD), placing UBE2A in the mGluR-LTD signaling pathway relevant to neurodevelopmental disorders.\",\n      \"method\": \"Mouse Ube2a knockout, Morris water maze, hippocampal electrophysiology (LTP, mGluR-LTD recording)\",\n      \"journal\": \"Human molecular genetics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — clean KO with defined electrophysiological phenotype and pathway placement; single lab\",\n      \"pmids\": [\"26476408\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"UBE2A is specifically recruited by a hemiRING zinc finger module within the E3 ligase UBR4; cryo-EM structure of the UBE2A–UBR4 E2–E3 complex reveals atomic-level specificity determinants of the hemiRING for UBE2A/UBE2B; the UZI subdomain allosterically and modestly activates Ub-loaded UBE2A; the intrinsically high lysine reactivity of UBE2A cooperates with this activation to determine substrate specificity in the N-degron pathway.\",\n      \"method\": \"Cryo-EM structure determination, in vitro ubiquitination assay, mutagenesis, biochemical interaction assays\",\n      \"journal\": \"Nature structural & molecular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — cryo-EM structure with functional mutagenesis and in vitro reconstitution in a single rigorous study\",\n      \"pmids\": [\"38182926\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"Cryo-EM structure of a chemically trapped RNF20/RNF40–RAD6A(UBE2A)–Ub–H2BS112GlcNAc nucleosome complex shows that the H2BS112GlcNAc moiety directly contacts the E2 enzyme RAD6A (not the E3); mutagenesis and kinetics demonstrate that this interaction allosterically enhances the nucleophilicity of H2B K120, stimulating ubiquitin transfer; structure–activity analysis identified essential roles for the C2 N-acetyl group and β-configuration of C1 of the GlcNAc moiety.\",\n      \"method\": \"Chemical synthesis of GlcNAc-modified nucleosomes, cryo-EM, in vitro ubiquitination kinetics, mutagenesis, structure–activity relationship analysis\",\n      \"journal\": \"Nature chemical biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — cryo-EM structure combined with in vitro kinetics, mutagenesis, and chemical SAR in a single rigorous study\",\n      \"pmids\": [\"41495224\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"UBE2A/B undergoes force- and contact-inhibition-dependent nucleocytoplasmic shuttling, identified as a mechanosensing transcriptional trans-acting factor; DHS-proteomics and next-generation sequencing showed that UBE2A/B regulates downstream gene expression (including YAP target genes) through histone ubiquitination, defining a YAP-independent mechanotransduction/contact-inhibition pathway.\",\n      \"method\": \"DHS-proteomics, nucleocytoplasmic fractionation, live-cell imaging, siRNA knockdown, next-generation sequencing, histone ubiquitination assay\",\n      \"journal\": \"The Biochemical journal\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2–3 / Weak — single lab, multiple methods but pathway placement relies partly on correlative genomics; mechanistic follow-up limited\",\n      \"pmids\": [\"37818922\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"De novo UBE2A mutations acquired during chronic myeloid leukemia progression to blast crisis decrease UBE2A ubiquitin-conjugating activity in vitro, leading to impaired myeloid differentiation in CML cells.\",\n      \"method\": \"In vitro ubiquitin-conjugating activity assay, CML cell differentiation assay, parallel sequencing of patient samples\",\n      \"journal\": \"Haematologica\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2–3 / Moderate — in vitro activity assay combined with cell-based differentiation phenotype; single lab\",\n      \"pmids\": [\"30819912\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"UBE2A (RAD6A/HHR6A) is an E2 ubiquitin-conjugating enzyme that: (1) forms a stable ternary complex with the E3 ligase RAD18 dimer to mediate post-replication DNA damage bypass and PCNA monoubiquitination; (2) cooperates with Parkin E3 to ubiquitinate mitochondrial proteins and drive mitophagy, maintaining neuronal function; (3) is allosterically activated by CDK1/2-mediated phosphorylation of Ser120 during G2/M, stimulating histone H2B ubiquitylation; (4) ubiquitinates H2B K120 in complex with RNF20/RNF40, a reaction allosterically stimulated when RAD6A contacts H2B S112 GlcNAc; (5) is specifically recruited by the hemiRING module of the N-degron E3 ligase UBR4; (6) relies on residue Q93 to deprotonate the incoming lysine nucleophile during ubiquitin transfer; (7) shuttles between nucleus and cytoplasm in response to mechanical force and contact inhibition to regulate gene expression via histone ubiquitination; and (8) is an essential maternal factor required for embryonic development beyond the two-cell stage.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"UBE2A (RAD6A/HHR6A) is an E2 ubiquitin-conjugating enzyme that channels ubiquitin to distinct E3 ligases to control chromatin modification, DNA damage tolerance, and mitochondrial quality control [#1, #3, #10]. Catalysis depends on an active-site glutamine, Q93, which deprotonates the incoming lysine nucleophile to enable ubiquitin transfer from the catalytic cysteine; the pathogenic Q93E substitution selectively blocks this aminolysis step [#7]. In DNA damage bypass, UBE2A forms an asymmetric ternary complex with a RAD18 dimer in which precise R6BD-mediated juxtaposition of a single RAD18 subunit is required for ligase activity [#1, #2]. With RNF20/RNF40 it monoubiquitinates histone H2B at K120, a reaction allosterically stimulated when RAD6A directly contacts an H2B S112 GlcNAc moiety that raises the nucleophilicity of K120 [#10]; this histone-ubiquitination activity is further gated by CDK1/2 phosphorylation of Ser120, which boosts conjugating activity and peaks at G2/M [#0]. UBE2A is also recruited by the hemiRING module of the N-degron E3 ligase UBR4, whose UZI subdomain modestly activates Ub-loaded enzyme [#9], and cooperates with the E3 Parkin to ubiquitinate mitochondrial proteins and drive mitophagy required for neuronal function [#3]. Genetically, UBE2A is an essential maternal factor needed for embryonic development beyond the two-cell stage [#6] and is required for hippocampal mGluR-dependent long-term depression and spatial learning [#8].\",\n  \"teleology\": [\n    {\n      \"year\": 1996,\n      \"claim\": \"Established where UBE2A acts in the cell, linking it physically to transcriptionally active chromatin rather than a diffuse cytoplasmic role.\",\n      \"evidence\": \"Immunogold electron microscopy and expression profiling in testis\",\n      \"pmids\": [\"8575614\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Does not identify the histone substrate or the E3 partner mediating chromatin association\", \"Functional link to histone modification is contextual, not biochemical\"]\n    },\n    {\n      \"year\": 2000,\n      \"claim\": \"Defined UBE2A's role in DNA damage tolerance by showing it forms a stable, conserved complex with the E3 ligase RAD18.\",\n      \"evidence\": \"Co-expression and complex purification in yeast, co-immunoprecipitation, with both paralogs\",\n      \"pmids\": [\"10908344\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Does not resolve complex stoichiometry or the substrate ubiquitinated\", \"No structural detail of the interaction interface\"]\n    },\n    {\n      \"year\": 2002,\n      \"claim\": \"Revealed cell-cycle regulation of UBE2A activity, connecting CDK phosphorylation of Ser120 to a G2/M peak in histone H2B ubiquitylation.\",\n      \"evidence\": \"In vitro kinase assay, phosphomimetic/phospho-dead mutagenesis, cell-cycle immunoblot, yeast complementation\",\n      \"pmids\": [\"11953320\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Structural basis of how Ser120 phosphorylation activates the enzyme not defined\", \"Which E3 directs the cell-cycle H2B ubiquitylation not established here\"]\n    },\n    {\n      \"year\": 2003,\n      \"claim\": \"Extended the UBE2A interactome by placing ZNF198 in a UBE2A/RAD18 repair complex with functional consequences for UV response.\",\n      \"evidence\": \"Yeast two-hybrid, co-immunoprecipitation, UV sensitivity assay\",\n      \"pmids\": [\"12776193\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct vs. indirect ZNF198 association within the complex not dissected\", \"Mechanism by which the fusion kinase acts dominant-negatively unresolved\"]\n    },\n    {\n      \"year\": 2004,\n      \"claim\": \"Demonstrated a developmental requirement, showing maternal UBE2A is essential for embryos to progress past the two-cell stage.\",\n      \"evidence\": \"Mouse knockout, embryonic development assay, H3 methylation immunostaining control\",\n      \"pmids\": [\"15169909\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"The relevant ubiquitination substrate driving the arrest not identified\", \"Redundancy with HR6B complicates assigning a unique molecular target\"]\n    },\n    {\n      \"year\": 2011,\n      \"claim\": \"Resolved the architecture of the RAD6A–RAD18 ligase, showing an asymmetric RAD6A–(RAD18)2 complex where one R6BD-bearing subunit suffices for activity.\",\n      \"evidence\": \"Differential subunit tagging, co-IP, in vitro ubiquitin ligase assay, mutagenesis\",\n      \"pmids\": [\"21967848\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"No atomic structure of the ternary complex\", \"Functional reason for the asymmetric dimer arrangement unexplained\"]\n    },\n    {\n      \"year\": 2013,\n      \"claim\": \"Expanded UBE2A function beyond chromatin/DNA repair by showing it partners with Parkin to ubiquitinate mitochondrial proteins and drive mitophagy in neurons.\",\n      \"evidence\": \"Drosophila and mouse knockouts, patient cells, in vitro and in vivo ubiquitination assays, mitochondrial function assays\",\n      \"pmids\": [\"23685073\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Specific mitochondrial substrates ubiquitinated by UBE2A–Parkin not enumerated\", \"How UBE2A is recruited to depolarized mitochondria unclear\"]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Linked UBE2A loss to a defined synaptic phenotype, placing it in the mGluR-dependent LTD pathway underlying spatial learning.\",\n      \"evidence\": \"Mouse knockout, Morris water maze, hippocampal LTP/LTD electrophysiology\",\n      \"pmids\": [\"26476408\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Molecular substrate connecting UBE2A to mGluR-LTD signaling not identified\", \"Single lab; mechanism downstream of the conjugating activity unresolved\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Defined the chemical mechanism of ubiquitin transfer, showing Q93 deprotonates the acceptor lysine and that the pathogenic Q93E mutation selectively impairs aminolysis.\",\n      \"evidence\": \"In vitro ubiquitination, pH-dependent reactivity, chemical rescue with low-pKa amine, active-site mutagenesis, NMR context\",\n      \"pmids\": [\"30531907\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether all E3-directed reactions share this Q93 dependence not tested across partners\", \"Structural snapshot of the deprotonation transition state not provided\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Identified UBE2A as a mechanosensitive transcriptional regulator that shuttles between nucleus and cytoplasm to control gene expression via histone ubiquitination.\",\n      \"evidence\": \"DHS-proteomics, nucleocytoplasmic fractionation, live-cell imaging, siRNA, NGS, histone ubiquitination assay\",\n      \"pmids\": [\"37818922\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Pathway placement relies partly on correlative genomics\", \"Mechanism coupling mechanical force to shuttling not defined\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Provided the structural basis of E2–E3 selectivity, showing UBE2A is captured by the hemiRING module of UBR4 in the N-degron pathway.\",\n      \"evidence\": \"Cryo-EM of UBE2A–UBR4 complex, mutagenesis, in vitro ubiquitination\",\n      \"pmids\": [\"38182926\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Physiological N-degron substrates handled through this complex in cells not catalogued\", \"Extent of UZI-mediated activation relative to other E3s unclear\"]\n    },\n    {\n      \"year\": 2026,\n      \"claim\": \"Explained allosteric control of H2B ubiquitylation, showing an H2B S112 GlcNAc directly contacts RAD6A to enhance K120 nucleophilicity.\",\n      \"evidence\": \"Cryo-EM of trapped RNF20/RNF40–RAD6A–Ub–H2BS112GlcNAc nucleosome, kinetics, mutagenesis, GlcNAc SAR\",\n      \"pmids\": [\"41495224\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Cellular conditions controlling H2B S112 GlcNAcylation not defined\", \"Crosstalk with Ser120 phosphorylation in the same reaction not integrated\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How UBE2A's multiple regulatory inputs — Ser120 phosphorylation, H2B GlcNAc allostery, and E3 partner identity — are coordinated to select among its chromatin, repair, and mitophagy roles in vivo remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No unifying model integrating cell-cycle, mechanosensing, and substrate-specific cues\", \"Substrate-level distinction between UBE2A and paralog UBE2B in each pathway not fully resolved\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0140096\", \"supporting_discovery_ids\": [1, 2, 3, 7, 9, 10]},\n      {\"term_id\": \"GO:0016740\", \"supporting_discovery_ids\": [0, 7, 10]},\n      {\"term_id\": \"GO:0031386\", \"supporting_discovery_ids\": [1, 3]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [5, 11]},\n      {\"term_id\": \"GO:0000228\", \"supporting_discovery_ids\": [5]},\n      {\"term_id\": \"GO:0005829\", \"supporting_discovery_ids\": [11]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-73894\", \"supporting_discovery_ids\": [1, 2]},\n      {\"term_id\": \"R-HSA-4839726\", \"supporting_discovery_ids\": [0, 10, 11]},\n      {\"term_id\": \"R-HSA-9612973\", \"supporting_discovery_ids\": [3]},\n      {\"term_id\": \"R-HSA-392499\", \"supporting_discovery_ids\": [7, 9]},\n      {\"term_id\": \"R-HSA-1640170\", \"supporting_discovery_ids\": [0]}\n    ],\n    \"complexes\": [\n      \"RAD6A–RAD18 (RAD6A–(RAD18)2) lesion-bypass complex\",\n      \"RNF20/RNF40–RAD6A H2B ubiquitylation complex\",\n      \"UBE2A–UBR4 E2–E3 N-degron complex\"\n    ],\n    \"partners\": [\n      \"RAD18\",\n      \"RNF20\",\n      \"RNF40\",\n      \"Parkin\",\n      \"UBR4\",\n      \"ZNF198\"\n    ],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":6,"faith_total":6,"faith_pct":100.0}}