{"gene":"UBE2D1","run_date":"2026-06-10T10:51:56","timeline":{"discoveries":[{"year":2024,"finding":"UBE2D1 (UbcH5) is a promiscuous E2 ubiquitin-conjugating enzyme that functions as the midpoint of the E1-E2-E3 ubiquitin conjugation cascade; a multivalent engineered protein inhibitor targeting simultaneously the RING- and backside-binding sites of UBE2D was developed and shown in HeLa cells to phenocopy UBE2D knockdown by reducing cisplatin IC50 and increasing abundance of ~20% of identified proteins, consistent with reduced ubiquitin-mediated degradation and proteotoxic stress.","method":"Engineered protein inhibitor design targeting RING- and backside-binding sites; HeLa cell KD/inhibitor treatment with whole-cell proteomics and cisplatin sensitivity assay","journal":"bioRxiv","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — clean cellular inhibitor with defined binding sites and two orthogonal readouts (proteomics + drug sensitivity), single lab, preprint only","pmids":["bio_10.1101_2024.09.02.610852"],"is_preprint":true},{"year":2024,"finding":"TCF25 imposes K48 polyubiquitin-linkage specificity on Listerin-mediated ubiquitination of nascent chains by physically interacting with the RING domain of Listerin and the acceptor ubiquitin (UbA), orienting UbA so that its K48 is directly positioned to attack the thioester bond of the UBE2D1~Ub conjugate; TCF25 itself is also K48-specifically ubiquitinated by Listerin via UBE2D1.","method":"Functional biochemical reconstitution assay; AlphaFold3 structural modeling; identification of TCF25–Listerin RING and TCF25–acceptor Ub interactions by binding studies","journal":"bioRxiv","confidence":"Medium","confidence_rationale":"Tier 1 / Weak — in vitro biochemical reconstitution with structural modeling, single lab, preprint only","pmids":["bio_10.1101_2024.10.17.618946"],"is_preprint":true},{"year":2002,"finding":"The previously reported iron-transport stimulator SFT corresponds to intron 6/exon 7 of UBE2D1 (UbcH5A), an E2 ubiquitin-conjugating enzyme involved in iron-dependent ubiquitination of HIF-1α by the VHL E3 ligase complex; in vitro studies on HepG2 cells failed to demonstrate UbcH5A regulation in response to iron loading or chelation, indicating prior SFT expression data reflect UbcH5A mRNA.","method":"Sequence analysis of SFT cDNA vs. UbcH5A genomic locus; RT-PCR expression assay; in vitro iron loading/chelation in HepG2 cells","journal":"Blood","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — sequence/molecular identity established by multiple methods (sequencing, RT-PCR, cell assay), single lab; negative functional result for iron regulation is clearly stated","pmids":["12480712"],"is_preprint":false}],"current_model":"UBE2D1 (UbcH5A) is a promiscuous E2 ubiquitin-conjugating enzyme that occupies the central position of the E1–E2–E3 ubiquitin cascade, transferring ubiquitin to substrates via its RING-binding and backside surfaces; when paired with the RING E3 Listerin in ribosome-associated quality control, the adaptor TCF25 binds simultaneously to Listerin's RING domain and the acceptor ubiquitin to orient K48 for chain-linkage specificity on the UBE2D1~Ub thioester, and selective inhibition of UBE2D1 in cells broadly impairs ubiquitin-mediated protein degradation."},"narrative":{"mechanistic_narrative":"UBE2D1 (UbcH5A) is a promiscuous E2 ubiquitin-conjugating enzyme that occupies the midpoint of the E1–E2–E3 conjugation cascade and broadly supports ubiquitin-mediated protein degradation [PMID:bio_10.1101_2024.09.02.610852]. It engages E3 ligases and substrates through both its RING-binding and backside surfaces, and an engineered inhibitor blocking both sites simultaneously phenocopies UBE2D knockdown in HeLa cells, increasing the abundance of ~20% of detected proteins and sensitizing cells to cisplatin—consistent with impaired degradation and proteotoxic stress [PMID:bio_10.1101_2024.09.02.610852]. In ribosome-associated quality control, UBE2D1 charged with ubiquitin acts with the RING E3 Listerin, where the adaptor TCF25 binds Listerin's RING domain and the acceptor ubiquitin to orient its K48 for nucleophilic attack on the UBE2D1~Ub thioester, thereby imposing K48-linkage specificity on nascent-chain ubiquitination [PMID:bio_10.1101_2024.10.17.618946]. The gene was also shown to correspond to the previously reported iron-transport stimulator SFT, clarifying that those data reflect UbcH5A mRNA, although iron loading or chelation did not regulate UbcH5A in HepG2 cells [PMID:12480712].","teleology":[{"year":2002,"claim":"Resolved the molecular identity of the putative iron-transport factor SFT, establishing that the relevant sequence is UBE2D1 (UbcH5A) rather than a distinct iron transporter.","evidence":"Sequence analysis of SFT cDNA against the UbcH5A locus, RT-PCR, and iron loading/chelation in HepG2 cells","pmids":["12480712"],"confidence":"Medium","gaps":["No demonstration that UbcH5A is regulated by iron status","Does not define UBE2D1's catalytic role in HIF-1α ubiquitination directly","Single-lab molecular identity assignment"]},{"year":2024,"claim":"Defined how E3-adaptor context confers chain-linkage specificity on a promiscuous E2, showing TCF25 orients the acceptor ubiquitin's K48 toward the UBE2D1~Ub thioester during Listerin-mediated quality-control ubiquitination.","evidence":"In vitro biochemical reconstitution with AlphaFold3 modeling and binding studies of TCF25–Listerin RING and TCF25–acceptor Ub interactions (preprint)","pmids":["bio_10.1101_2024.10.17.618946"],"confidence":"Medium","gaps":["Preprint, single lab; awaits peer review and experimental structure","Specificity mechanism shown for the Listerin/RQC context only","Cellular relevance of the modeled orientation not tested in vivo"]},{"year":2024,"claim":"Established that simultaneous blockade of UBE2D1's RING- and backside-binding surfaces is sufficient to impair bulk ubiquitin-dependent degradation, validating the dual-surface engagement model of E2 function.","evidence":"Engineered multivalent protein inhibitor with defined binding sites; HeLa knockdown/inhibitor treatment with whole-cell proteomics and cisplatin sensitivity (preprint)","pmids":["bio_10.1101_2024.09.02.610852"],"confidence":"Medium","gaps":["Preprint, single lab; not independently replicated","Cross-reactivity across the UBE2D family not fully resolved","Specific substrates driving the ~20% proteome increase not enumerated"]},{"year":null,"claim":"The full spectrum of E3 partners, substrates, and linkage outcomes that UBE2D1 mediates beyond the Listerin/RQC pathway remains undefined.","evidence":"","pmids":[],"confidence":"Low","gaps":["No comprehensive E3 partner map in the corpus","Chain-type preferences outside K48/Listerin context uncharacterized","No experimental structure of UBE2D1 in the corpus"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0140096","term_label":"catalytic activity, acting on a protein","supporting_discovery_ids":[0,1]},{"term_id":"GO:0016740","term_label":"transferase activity","supporting_discovery_ids":[0,1]}],"localization":[],"pathway":[{"term_id":"R-HSA-392499","term_label":"Metabolism of proteins","supporting_discovery_ids":[0,1]}],"complexes":[],"partners":["TCF25","LTN1"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"P51668","full_name":"Ubiquitin-conjugating enzyme E2 D1","aliases":["(E3-independent) E2 ubiquitin-conjugating enzyme D1","E2 ubiquitin-conjugating enzyme D1","Stimulator of Fe transport","SFT","UBC4/5 homolog","UbcH5","Ubiquitin carrier protein D1","Ubiquitin-conjugating enzyme E2(17)KB 1","Ubiquitin-conjugating enzyme E2-17 kDa 1","Ubiquitin-protein ligase D1"],"length_aa":147,"mass_kda":16.6,"function":"Accepts ubiquitin from the E1 complex and catalyzes its covalent attachment to other proteins (PubMed:22496338). In vitro catalyzes 'Lys-48'-linked polyubiquitination (PubMed:20061386). Mediates the selective degradation of short-lived and abnormal proteins. Functions in the E6/E6-AP-induced ubiquitination of p53/TP53. Mediates ubiquitination of PEX5 and auto-ubiquitination of STUB1, TRAF6 and TRIM63/MURF1 (PubMed:18042044, PubMed:18359941). Ubiquitinates STUB1-associated HSP90AB1 in vitro (PubMed:18042044). Lacks inherent specificity for any particular lysine residue of ubiquitin (PubMed:18042044). Essential for viral activation of IRF3 (PubMed:19854139). Mediates polyubiquitination of CYP3A4 (PubMed:19103148)","subcellular_location":"Cytoplasm","url":"https://www.uniprot.org/uniprotkb/P51668/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/UBE2D1","classification":"Not Classified","n_dependent_lines":2,"n_total_lines":1208,"dependency_fraction":0.0016556291390728477},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/UBE2D1","total_profiled":1310},"omim":[{"mim_id":"621515","title":"UBIQUITIN-CONJUGATING ENZYME E2 D4; UBE2D4","url":"https://www.omim.org/entry/621515"},{"mim_id":"620051","title":"RING FINGER PROTEIN 41, E3 UBIQUITIN PROTEIN LIGASE; RNF41","url":"https://www.omim.org/entry/620051"},{"mim_id":"616386","title":"POTASSIUM CHANNEL TETRAMERIZATION DOMAIN-CONTAINING PROTEIN 17; KCTD17","url":"https://www.omim.org/entry/616386"},{"mim_id":"616136","title":"RING FINGER PROTEIN 220; RNF220","url":"https://www.omim.org/entry/616136"},{"mim_id":"616017","title":"TRIPARTITE MOTIF-CONTAINING PROTEIN 69; TRIM69","url":"https://www.omim.org/entry/616017"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Approved","locations":[{"location":"Plasma membrane","reliability":"Approved"},{"location":"Cytosol","reliability":"Approved"}],"tissue_specificity":"Tissue enhanced","tissue_distribution":"Detected in all","driving_tissues":[{"tissue":"skeletal muscle","ntpm":129.9},{"tissue":"tongue","ntpm":61.1}],"url":"https://www.proteinatlas.org/search/UBE2D1"},"hgnc":{"alias_symbol":["UbcH5A","UBCH5","UBC4/5","E2(17)KB1"],"prev_symbol":["SFT"]},"alphafold":{"accession":"P51668","domains":[{"cath_id":"3.10.110.10","chopping":"1-147","consensus_level":"medium","plddt":96.3964,"start":1,"end":147}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/P51668","model_url":"https://alphafold.ebi.ac.uk/files/AF-P51668-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-P51668-F1-predicted_aligned_error_v6.png","plddt_mean":96.38},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=UBE2D1","jax_strain_url":"https://www.jax.org/strain/search?query=UBE2D1"},"sequence":{"accession":"P51668","fasta_url":"https://rest.uniprot.org/uniprotkb/P51668.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/P51668/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/P51668"}},"corpus_meta":[{"pmid":"19718788","id":"PMC_19718788","title":"Expanding 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grasses.","date":"2000","source":"Genome","url":"https://pubmed.ncbi.nlm.nih.gov/11195345","citation_count":9,"is_preprint":false},{"pmid":"26072162","id":"PMC_26072162","title":"A sucrose:fructan-6-fructosyltransferase (6-SFT) gene from Psathyrostachys huashanica confers abiotic stress tolerance in tobacco.","date":"2015","source":"Gene","url":"https://pubmed.ncbi.nlm.nih.gov/26072162","citation_count":8,"is_preprint":false},{"pmid":"22698728","id":"PMC_22698728","title":"Carbohydrate profiling in seeds and seedlings of transgenic triticale modified in the expression of sucrose:sucrose-1-fructosyltransferase (1-SST) and sucrose:fructan-6-fructosyltransferase (6-SFT).","date":"2012","source":"Journal of bioscience and bioengineering","url":"https://pubmed.ncbi.nlm.nih.gov/22698728","citation_count":6,"is_preprint":false},{"pmid":"32247097","id":"PMC_32247097","title":"[Physiological and Psychological Data influencing Pregnant Women Smoking Behavior - CNGOF-SFT Expert Report and 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[\n    {\n      \"year\": 2024,\n      \"finding\": \"UBE2D1 (UbcH5) is a promiscuous E2 ubiquitin-conjugating enzyme that functions as the midpoint of the E1-E2-E3 ubiquitin conjugation cascade; a multivalent engineered protein inhibitor targeting simultaneously the RING- and backside-binding sites of UBE2D was developed and shown in HeLa cells to phenocopy UBE2D knockdown by reducing cisplatin IC50 and increasing abundance of ~20% of identified proteins, consistent with reduced ubiquitin-mediated degradation and proteotoxic stress.\",\n      \"method\": \"Engineered protein inhibitor design targeting RING- and backside-binding sites; HeLa cell KD/inhibitor treatment with whole-cell proteomics and cisplatin sensitivity assay\",\n      \"journal\": \"bioRxiv\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — clean cellular inhibitor with defined binding sites and two orthogonal readouts (proteomics + drug sensitivity), single lab, preprint only\",\n      \"pmids\": [\"bio_10.1101_2024.09.02.610852\"],\n      \"is_preprint\": true\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"TCF25 imposes K48 polyubiquitin-linkage specificity on Listerin-mediated ubiquitination of nascent chains by physically interacting with the RING domain of Listerin and the acceptor ubiquitin (UbA), orienting UbA so that its K48 is directly positioned to attack the thioester bond of the UBE2D1~Ub conjugate; TCF25 itself is also K48-specifically ubiquitinated by Listerin via UBE2D1.\",\n      \"method\": \"Functional biochemical reconstitution assay; AlphaFold3 structural modeling; identification of TCF25–Listerin RING and TCF25–acceptor Ub interactions by binding studies\",\n      \"journal\": \"bioRxiv\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 / Weak — in vitro biochemical reconstitution with structural modeling, single lab, preprint only\",\n      \"pmids\": [\"bio_10.1101_2024.10.17.618946\"],\n      \"is_preprint\": true\n    },\n    {\n      \"year\": 2002,\n      \"finding\": \"The previously reported iron-transport stimulator SFT corresponds to intron 6/exon 7 of UBE2D1 (UbcH5A), an E2 ubiquitin-conjugating enzyme involved in iron-dependent ubiquitination of HIF-1α by the VHL E3 ligase complex; in vitro studies on HepG2 cells failed to demonstrate UbcH5A regulation in response to iron loading or chelation, indicating prior SFT expression data reflect UbcH5A mRNA.\",\n      \"method\": \"Sequence analysis of SFT cDNA vs. UbcH5A genomic locus; RT-PCR expression assay; in vitro iron loading/chelation in HepG2 cells\",\n      \"journal\": \"Blood\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — sequence/molecular identity established by multiple methods (sequencing, RT-PCR, cell assay), single lab; negative functional result for iron regulation is clearly stated\",\n      \"pmids\": [\"12480712\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"UBE2D1 (UbcH5A) is a promiscuous E2 ubiquitin-conjugating enzyme that occupies the central position of the E1–E2–E3 ubiquitin cascade, transferring ubiquitin to substrates via its RING-binding and backside surfaces; when paired with the RING E3 Listerin in ribosome-associated quality control, the adaptor TCF25 binds simultaneously to Listerin's RING domain and the acceptor ubiquitin to orient K48 for chain-linkage specificity on the UBE2D1~Ub thioester, and selective inhibition of UBE2D1 in cells broadly impairs ubiquitin-mediated protein degradation.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"UBE2D1 (UbcH5A) is a promiscuous E2 ubiquitin-conjugating enzyme that occupies the midpoint of the E1\\u2013E2\\u2013E3 conjugation cascade and broadly supports ubiquitin-mediated protein degradation [#0]. It engages E3 ligases and substrates through both its RING-binding and backside surfaces, and an engineered inhibitor blocking both sites simultaneously phenocopies UBE2D knockdown in HeLa cells, increasing the abundance of ~20% of detected proteins and sensitizing cells to cisplatin\\u2014consistent with impaired degradation and proteotoxic stress [#0]. In ribosome-associated quality control, UBE2D1 charged with ubiquitin acts with the RING E3 Listerin, where the adaptor TCF25 binds Listerin's RING domain and the acceptor ubiquitin to orient its K48 for nucleophilic attack on the UBE2D1~Ub thioester, thereby imposing K48-linkage specificity on nascent-chain ubiquitination [#1]. The gene was also shown to correspond to the previously reported iron-transport stimulator SFT, clarifying that those data reflect UbcH5A mRNA, although iron loading or chelation did not regulate UbcH5A in HepG2 cells [#2].\",\n  \"teleology\": [\n    {\n      \"year\": 2002,\n      \"claim\": \"Resolved the molecular identity of the putative iron-transport factor SFT, establishing that the relevant sequence is UBE2D1 (UbcH5A) rather than a distinct iron transporter.\",\n      \"evidence\": \"Sequence analysis of SFT cDNA against the UbcH5A locus, RT-PCR, and iron loading/chelation in HepG2 cells\",\n      \"pmids\": [\"12480712\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"No demonstration that UbcH5A is regulated by iron status\",\n        \"Does not define UBE2D1's catalytic role in HIF-1\\u03b1 ubiquitination directly\",\n        \"Single-lab molecular identity assignment\"\n      ]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Defined how E3-adaptor context confers chain-linkage specificity on a promiscuous E2, showing TCF25 orients the acceptor ubiquitin's K48 toward the UBE2D1~Ub thioester during Listerin-mediated quality-control ubiquitination.\",\n      \"evidence\": \"In vitro biochemical reconstitution with AlphaFold3 modeling and binding studies of TCF25\\u2013Listerin RING and TCF25\\u2013acceptor Ub interactions (preprint)\",\n      \"pmids\": [\"bio_10.1101_2024.10.17.618946\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Preprint, single lab; awaits peer review and experimental structure\",\n        \"Specificity mechanism shown for the Listerin/RQC context only\",\n        \"Cellular relevance of the modeled orientation not tested in vivo\"\n      ]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Established that simultaneous blockade of UBE2D1's RING- and backside-binding surfaces is sufficient to impair bulk ubiquitin-dependent degradation, validating the dual-surface engagement model of E2 function.\",\n      \"evidence\": \"Engineered multivalent protein inhibitor with defined binding sites; HeLa knockdown/inhibitor treatment with whole-cell proteomics and cisplatin sensitivity (preprint)\",\n      \"pmids\": [\"bio_10.1101_2024.09.02.610852\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Preprint, single lab; not independently replicated\",\n        \"Cross-reactivity across the UBE2D family not fully resolved\",\n        \"Specific substrates driving the ~20% proteome increase not enumerated\"\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"The full spectrum of E3 partners, substrates, and linkage outcomes that UBE2D1 mediates beyond the Listerin/RQC pathway remains undefined.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"No comprehensive E3 partner map in the corpus\",\n        \"Chain-type preferences outside K48/Listerin context uncharacterized\",\n        \"No experimental structure of UBE2D1 in the corpus\"\n      ]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0140096\", \"supporting_discovery_ids\": [0, 1]},\n      {\"term_id\": \"GO:0016740\", \"supporting_discovery_ids\": [0, 1]}\n    ],\n    \"localization\": [],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-392499\", \"supporting_discovery_ids\": [0, 1]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\"TCF25\", \"LTN1\"]\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":1,"faith_total":1,"faith_pct":100.0}}