{"gene":"UBXN7","run_date":"2026-06-10T10:51:56","timeline":{"discoveries":[{"year":2008,"finding":"UBXD7 (UBXN7) links p97 to the CUL2/VHL ubiquitin ligase and its substrate HIF1α; depletion of p97 leads to accumulation of endogenous HIF1α, establishing UBXN7 as a substrate-binding adaptor that connects p97 to CRL2-mediated protein turnover.","method":"Network proteomics (mass spectrometry of immunoprecipitates), co-immunoprecipitation, siRNA depletion with HIF1α accumulation readout","journal":"Cell","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal Co-IP and MS interactome with functional KD phenotype, widely replicated by subsequent independent labs","pmids":["18775313"],"is_preprint":false},{"year":2012,"finding":"UBXN7 directly engages NEDD8-modified cullins via its UIM (ubiquitin-interacting motif) domain, independent of its UBA ubiquitin-binding domain; this interaction is sufficient to shift CUL2 to its neddylated form and cause accumulation of non-ubiquitylated HIF1α, indicating that UBXN7 negatively regulates CRL2 ligase activity by sequestering neddylated CUL2.","method":"Mutagenesis of UIM and UBA domains, co-immunoprecipitation, over-expression assays, mass spectrometry of immunoprecipitates","journal":"BMC biology","confidence":"High","confidence_rationale":"Tier 1–2 / Moderate — domain mutagenesis combined with multiple orthogonal co-IP and functional assays in single focused study","pmids":["22537386"],"is_preprint":false},{"year":2020,"finding":"Mitochondrial MUL1 E3 ubiquitin ligase ubiquitinates UBXN7, leading to its proteasomal degradation; inactivation of MUL1 causes UBXN7 accumulation, which in turn increases HIF-1α protein levels, reduces oxidative phosphorylation, and increases glycolysis, placing MUL1 upstream of UBXN7 in the CRL2VHL pathway.","method":"siRNA knockdown of MUL1, Western blot for UBXN7 and HIF-1α, metabolic assays (OXPHOS vs. glycolysis), identification of UBXN7 as MUL1 substrate","journal":"Scientific reports","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — KD with defined biochemical and metabolic phenotype, single lab but multiple orthogonal readouts","pmids":["32005965"],"is_preprint":false},{"year":2021,"finding":"UBXN7 acts as a scaffold for both CRL3KEAP1 and CRL2VHL complexes, mediating reciprocal regulation of NRF2 and HIF-1α: high UBXN7 levels lead to HIF-1α accumulation and glycolysis, while low UBXN7 (regulated by MUL1-mediated ubiquitination) correlates with NRF2 activation and increased OXPHOS.","method":"siRNA knockdown and overexpression of UBXN7, Western blot for NRF2 and HIF-1α, metabolic assays, MUL1 inactivation experiments","journal":"Biochimica et biophysica acta. Molecular cell research","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — KD/OE with multiple biochemical phenotypes, single lab extending prior findings","pmids":["33444648"],"is_preprint":false},{"year":2022,"finding":"UBXN7 facilitates replisome disassembly during S-phase in vertebrates by coupling CUL2-LRR1-dependent ubiquitylation of MCM7 (replicative helicase) to p97-mediated unloading from chromatin; UBXN7 uses independent domains to interact with both CUL2LRR1 and p97, acting as the first substrate-specific p97 cofactor for this process.","method":"Xenopus laevis egg extract cell-free system, biochemical domain-interaction assays, depletion/add-back experiments monitoring replisome disassembly","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1–2 / Moderate — cell-free reconstitution in Xenopus extracts with biochemical domain mapping and functional rescue, single lab but multiple orthogonal approaches","pmids":["35798141"],"is_preprint":false},{"year":2022,"finding":"HBx protein of HBV interacts with UBXN7 to promote K48-linked ubiquitination of UBXN7 at lysine 99, leading to its proteasomal degradation; UBXN7 itself inhibits NF-κB signaling by binding the ULK domain of IKKβ via its UBA domain, facilitating IKKβ degradation.","method":"SILAC ubiquitinome analysis, Co-IP, mutagenesis (K99 site), Western blot, in vitro and in vivo HBV replication assays","journal":"Cellular and molecular gastroenterology and hepatology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — SILAC quantitative ubiquitinomics plus co-IP and site-specific mutagenesis, single lab","pmids":["36096451"],"is_preprint":false},{"year":2023,"finding":"The UAS thioredoxin-like domain of UBXN7 directly docks on the RING domain of E3 ligases RNF111/Arkadia, RNF165/ARK2C, and TOPORS, inhibiting their autoubiquitylation by preventing interaction of the RING domain with E2 conjugating enzymes; this stabilizes RNF111 and modulates degradation of its substrate SKIL/SnoN in TGF-β signaling.","method":"Co-IP, domain mutagenesis (UAS deletion mutant), overexpression and siRNA depletion, interactome analysis of UAS domain, TGF-β-stimulated SKIL degradation assay","journal":"BMC biology","confidence":"High","confidence_rationale":"Tier 1–2 / Moderate — domain mutagenesis with multiple E3 ligase targets, functional substrate degradation assay, and mechanistic E2-binding block demonstrated in a single focused study","pmids":["37024974"],"is_preprint":false},{"year":2026,"finding":"UBXN7 (along with FAF1 and FAF2) functions as an accessory p97 adapter that boosts p97-Ufd1-Npl4-mediated substrate unfolding, thereby accelerating proteasomal degradation; stimulation occurs by positioning the UT3 ubiquitin-binding module of Ufd1 for efficient substrate loading onto p97, demonstrated by mutations in the helix-Ufd1 interaction that reduced stimulation.","method":"In vitro reconstituted p97-Ufd1-Npl4 unfolding and proteasomal degradation assay, mutagenesis of helix-Ufd1 interface, biochemical rate measurements","journal":"Science advances","confidence":"High","confidence_rationale":"Tier 1 / Moderate — in vitro reconstitution with mutagenesis and quantitative unfolding/degradation assays, single lab but rigorous biochemical approach","pmids":["41790892"],"is_preprint":false},{"year":2025,"finding":"UBXN7 interacts with SARS-CoV-2 N protein via its UBX domain and inhibits K48-linked ubiquitination and proteasomal degradation of N protein at lysine K257, leading to N protein accumulation and promoting viral dsRNA production and genome assembly.","method":"Reverse genetics system, co-immunoprecipitation, ubiquitination assays, site-directed mutagenesis (K257), UBXN7 depletion/overexpression with viral replication readouts","journal":"PLoS pathogens","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — co-IP with domain mapping, site-specific mutagenesis, and functional viral replication assays, single lab","pmids":["41086194"],"is_preprint":false}],"current_model":"UBXN7 is a multifunctional UBA-UBX family adaptor protein that (1) recruits the p97 AAA-ATPase segregase to ubiquitylated substrates of cullin-RING ligases (especially CRL2VHL/HIF-1α and CRL2LRR1/MCM7) by simultaneously engaging neddylated cullins via its UIM domain and p97 via its UBX domain; (2) negatively regulates specific CRL and RING E3 ligases (CRL2, RNF111, RNF165, TOPORS) by sequestering neddylated cullins or blocking RING–E2 interactions through its UAS thioredoxin-like domain; (3) is itself a substrate of mitochondrial MUL1 E3 ligase, linking mitochondrial stress sensing to HIF-1α/NRF2 balance and metabolic reprogramming; and (4) acts as an accessory adapter that positions Ufd1 within the p97 complex to boost substrate unfolding and proteasomal degradation."},"narrative":{"mechanistic_narrative":"UBXN7 is a multi-domain UBA-UBX adaptor that couples the p97 (VCP) AAA-ATPase segregase to ubiquitylated substrates of cullin-RING ligases, governing the turnover of regulatory proteins and the disassembly of chromatin-bound machines [PMID:18775313, PMID:35798141]. It bridges substrate to segregase using independent modules: a substrate/ligase-engaging arm and a UBX domain that recruits p97, first defined for the CUL2/VHL ligase and its substrate HIF1α [PMID:18775313] and later for CUL2-LRR1-dependent ubiquitylation of the MCM7 replicative helicase, where UBXN7 serves as the substrate-specific p97 cofactor that drives replisome unloading from chromatin during S-phase [PMID:35798141]. Beyond delivering substrates, UBXN7 negatively regulates ligase activity: its UIM domain binds NEDD8-modified cullins to sequester neddylated CUL2 and stabilize non-ubiquitylated HIF1α [PMID:22537386], while its UAS thioredoxin-like domain docks directly onto the RING domains of RNF111/Arkadia, RNF165 and TOPORS to block RING-E2 interaction and inhibit their autoubiquitylation, thereby stabilizing RNF111 and modulating SKIL/SnoN degradation in TGF-β signaling [PMID:37024974]. As an accessory p97 adapter, UBXN7 also accelerates p97-Ufd1-Npl4-mediated substrate unfolding and proteasomal degradation by positioning the UT3 ubiquitin-binding module of Ufd1 for substrate loading [PMID:41790892]. UBXN7 is itself an E3 substrate: mitochondrial MUL1 ubiquitylates UBXN7 for degradation, and loss of MUL1 elevates UBXN7, raising HIF-1α and shifting metabolism toward glycolysis, linking UBXN7 to reciprocal NRF2/HIF-1α control of oxidative versus glycolytic states [PMID:32005965, PMID:33444648]. UBXN7 is additionally targeted and exploited by viral proteins, being degraded upon HBV HBx engagement and stabilizing SARS-CoV-2 N protein via its UBX domain [PMID:36096451, PMID:41086194].","teleology":[{"year":2008,"claim":"Established that UBXN7 is a substrate-binding adaptor connecting the p97 segregase to CRL2-mediated turnover, answering how p97 is targeted to specific ubiquitylated substrates such as HIF1α.","evidence":"Network proteomics, reciprocal co-IP, and siRNA depletion with HIF1α accumulation readout","pmids":["18775313"],"confidence":"High","gaps":["Did not map which domains engage cullin versus p97","No direct demonstration that UBXN7 promotes versus restrains HIF1α degradation"]},{"year":2012,"claim":"Resolved that UBXN7 binds NEDD8-modified cullins through its UIM domain independently of its UBA module, revealing a negative-regulatory role in which sequestering neddylated CUL2 stalls CRL2 and accumulates non-ubiquitylated HIF1α.","evidence":"UIM/UBA domain mutagenesis, co-IP, overexpression assays, and MS of immunoprecipitates","pmids":["22537386"],"confidence":"High","gaps":["Quantitative balance between adaptor (pro-degradation) and sequestration (anti-degradation) roles unresolved","Generality across other cullins not established here"]},{"year":2020,"claim":"Identified UBXN7 as a MUL1 substrate, placing mitochondrial ubiquitin signaling upstream of UBXN7 to control HIF-1α levels and the OXPHOS-to-glycolysis balance.","evidence":"MUL1 siRNA knockdown, Western blot for UBXN7/HIF-1α, and OXPHOS versus glycolysis metabolic assays","pmids":["32005965"],"confidence":"Medium","gaps":["Direct MUL1-UBXN7 ubiquitylation site not mapped","Mechanism connecting mitochondrial localization of MUL1 to nuclear/cytosolic UBXN7 pool unclear"]},{"year":2021,"claim":"Extended UBXN7 to a scaffold acting on both CRL3KEAP1 and CRL2VHL, providing a reciprocal switch between NRF2 and HIF-1α outputs tied to UBXN7 abundance.","evidence":"siRNA/overexpression of UBXN7, Western blot for NRF2/HIF-1α, metabolic assays, and MUL1 inactivation","pmids":["33444648"],"confidence":"Medium","gaps":["Direct structural basis for dual-CRL scaffolding not shown","Single-lab finding extending prior work without independent replication"]},{"year":2022,"claim":"Demonstrated that UBXN7 is the substrate-specific p97 cofactor coupling CUL2-LRR1 ubiquitylation of MCM7 to p97-driven replisome disassembly, defining a defined physiological substrate beyond HIF1α.","evidence":"Xenopus egg extract cell-free reconstitution, domain-interaction assays, and depletion/add-back monitoring replisome disassembly","pmids":["35798141"],"confidence":"High","gaps":["Whether the same adaptor mode operates on other replication substrates not tested","Role of NEDD8-cullin sequestration during this process not addressed"]},{"year":2022,"claim":"Showed UBXN7 inhibits NF-κB signaling by binding IKKβ via its UBA domain, while being degraded through HBx-promoted K99 ubiquitylation, linking UBXN7 to inflammatory signaling and viral antagonism.","evidence":"SILAC ubiquitinome, co-IP, K99 site mutagenesis, and HBV replication assays","pmids":["36096451"],"confidence":"Medium","gaps":["Identity of the E3 ligase ubiquitylating UBXN7 at K99 in the HBx context unresolved","Mechanism by which UBXN7 facilitates IKKβ degradation not detailed"]},{"year":2023,"claim":"Defined a distinct mechanism in which the UAS thioredoxin-like domain docks on RING E3 ligases (RNF111, RNF165, TOPORS) to block RING-E2 engagement, broadening UBXN7 from a CRL regulator to a direct RING-ligase inhibitor controlling TGF-β effector SKIL/SnoN.","evidence":"Co-IP, UAS deletion mutagenesis, UAS interactome analysis, and TGF-β-stimulated SKIL degradation assay","pmids":["37024974"],"confidence":"High","gaps":["Structural detail of the UAS-RING interface not resolved","Whether this domain function is competitive with p97 adaptor activity unknown"]},{"year":2025,"claim":"Revealed UBXN7 engages SARS-CoV-2 N protein via its UBX domain to block K48 ubiquitylation at K257, stabilizing N and promoting viral replication, identifying a proviral exploitation of the adaptor.","evidence":"Reverse genetics, co-IP with domain mapping, K257 mutagenesis, and depletion/overexpression viral replication readouts","pmids":["41086194"],"confidence":"Medium","gaps":["Whether host p97 recruitment is involved in N protein protection unclear","Single-lab finding without independent confirmation"]},{"year":2026,"claim":"Reconstituted that UBXN7 acts as an accessory p97 adapter that accelerates p97-Ufd1-Npl4 substrate unfolding and degradation by positioning the Ufd1 UT3 module, providing a biochemical mechanism for how it enhances segregase throughput.","evidence":"In vitro reconstituted p97-Ufd1-Npl4 unfolding/degradation assays with helix-Ufd1 interface mutagenesis and rate measurements","pmids":["41790892"],"confidence":"High","gaps":["Whether this stimulation operates on physiological CRL2 substrates in cells not shown","Relationship between this accessory role and substrate-specific adaptor role not integrated"]},{"year":null,"claim":"How UBXN7's competing activities — p97 substrate delivery, NEDD8-cullin sequestration, and direct RING-E2 blockade — are coordinated and selectively deployed across different ligases and substrates remains unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No structural model integrating UIM, UBA, UAS, and UBX functions on a single ligase","Switching logic between pro-degradation and inhibitory modes not defined","In vivo physiological hierarchy of these roles not established"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[0,4,7]},{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[1,6]},{"term_id":"GO:0140096","term_label":"catalytic activity, acting on a protein","supporting_discovery_ids":[4,7]}],"localization":[{"term_id":"GO:0000228","term_label":"nuclear chromosome","supporting_discovery_ids":[4]}],"pathway":[{"term_id":"R-HSA-392499","term_label":"Metabolism of proteins","supporting_discovery_ids":[0,7]},{"term_id":"R-HSA-69306","term_label":"DNA Replication","supporting_discovery_ids":[4]},{"term_id":"R-HSA-162582","term_label":"Signal Transduction","supporting_discovery_ids":[3,6]},{"term_id":"R-HSA-1430728","term_label":"Metabolism","supporting_discovery_ids":[2,3]}],"complexes":["p97-Ufd1-Npl4 complex","CRL2VHL","CRL2LRR1"],"partners":["VCP","CUL2","HIF1A","MUL1","RNF111","TOPORS","IKBKB","UFD1"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"O94888","full_name":"UBX domain-containing protein 7","aliases":[],"length_aa":489,"mass_kda":54.9,"function":"Ubiquitin-binding adapter that links a subset of NEDD8-associated cullin ring ligases (CRLs) to the segregase VCP/p97, to regulate turnover of their ubiquitination substrates","subcellular_location":"Nucleus","url":"https://www.uniprot.org/uniprotkb/O94888/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/UBXN7","classification":"Not Classified","n_dependent_lines":13,"n_total_lines":1208,"dependency_fraction":0.01076158940397351},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[{"gene":"VAPA","stoichiometry":0.2},{"gene":"VAPB","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/search/UBXN7","total_profiled":1310},"omim":[{"mim_id":"616379","title":"UBX DOMAIN PROTEIN 7; UBXN7","url":"https://www.omim.org/entry/616379"},{"mim_id":"603135","title":"CULLIN 2; CUL2","url":"https://www.omim.org/entry/603135"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Enhanced","locations":[{"location":"Nucleoplasm","reliability":"Enhanced"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/UBXN7"},"hgnc":{"alias_symbol":["KIAA0794"],"prev_symbol":["UBXD7"]},"alphafold":{"accession":"O94888","domains":[{"cath_id":"3.40.30.10","chopping":"139-260","consensus_level":"high","plddt":94.5047,"start":139,"end":260},{"cath_id":"3.10.20.90","chopping":"411-486","consensus_level":"high","plddt":94.1596,"start":411,"end":486},{"cath_id":"1.10.8","chopping":"12-51","consensus_level":"high","plddt":91.2978,"start":12,"end":51}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/O94888","model_url":"https://alphafold.ebi.ac.uk/files/AF-O94888-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-O94888-F1-predicted_aligned_error_v6.png","plddt_mean":72.94},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=UBXN7","jax_strain_url":"https://www.jax.org/strain/search?query=UBXN7"},"sequence":{"accession":"O94888","fasta_url":"https://rest.uniprot.org/uniprotkb/O94888.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/O94888/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/O94888"}},"corpus_meta":[{"pmid":"18775313","id":"PMC_18775313","title":"UBXD7 binds multiple ubiquitin ligases and implicates p97 in HIF1alpha turnover.","date":"2008","source":"Cell","url":"https://pubmed.ncbi.nlm.nih.gov/18775313","citation_count":278,"is_preprint":false},{"pmid":"22537386","id":"PMC_22537386","title":"UBXN7 docks on neddylated cullin complexes using its UIM motif and causes HIF1α accumulation.","date":"2012","source":"BMC biology","url":"https://pubmed.ncbi.nlm.nih.gov/22537386","citation_count":59,"is_preprint":false},{"pmid":"32005965","id":"PMC_32005965","title":"Mitochondrial MUL1 E3 ubiquitin ligase regulates Hypoxia Inducible Factor (HIF-1α) and metabolic reprogramming by modulating the UBXN7 cofactor protein.","date":"2020","source":"Scientific reports","url":"https://pubmed.ncbi.nlm.nih.gov/32005965","citation_count":25,"is_preprint":false},{"pmid":"33444648","id":"PMC_33444648","title":"UBXN7 cofactor of CRL3KEAP1 and CRL2VHL ubiquitin ligase complexes mediates reciprocal regulation of NRF2 and HIF-1α proteins.","date":"2021","source":"Biochimica et biophysica acta. Molecular cell research","url":"https://pubmed.ncbi.nlm.nih.gov/33444648","citation_count":20,"is_preprint":false},{"pmid":"35798141","id":"PMC_35798141","title":"The p97 segregase cofactor Ubxn7 facilitates replisome disassembly during S-phase.","date":"2022","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/35798141","citation_count":15,"is_preprint":false},{"pmid":"36096451","id":"PMC_36096451","title":"HBV X Protein Induces Degradation of UBXN7, a Novel Negative Regulator of NF-κB Signaling, to Promote HBV Replication.","date":"2022","source":"Cellular and molecular gastroenterology and hepatology","url":"https://pubmed.ncbi.nlm.nih.gov/36096451","citation_count":10,"is_preprint":false},{"pmid":"32536059","id":"PMC_32536059","title":"[Circular RNA-UBXN7 promotes proliferation, migration and suppresses apoptosis in hepatocellular cancer].","date":"2020","source":"Zhonghua gan zang bing za zhi = Zhonghua ganzangbing zazhi = Chinese journal of hepatology","url":"https://pubmed.ncbi.nlm.nih.gov/32536059","citation_count":3,"is_preprint":false},{"pmid":"37024974","id":"PMC_37024974","title":"The UAS thioredoxin-like domain of UBXN7 regulates E3 ubiquitin ligase activity of RNF111/Arkadia.","date":"2023","source":"BMC biology","url":"https://pubmed.ncbi.nlm.nih.gov/37024974","citation_count":3,"is_preprint":false},{"pmid":"41790892","id":"PMC_41790892","title":"The accessory adapters FAF1, FAF2, and UBXN7 accelerate proteasomal degradation by increasing prior p97-mediated substrate unfolding.","date":"2026","source":"Science advances","url":"https://pubmed.ncbi.nlm.nih.gov/41790892","citation_count":0,"is_preprint":false},{"pmid":"41086194","id":"PMC_41086194","title":"UBXN7 facilitates SARS-CoV-2 replication via inhibiting the K48-linked ubiquitination of viral N protein.","date":"2025","source":"PLoS pathogens","url":"https://pubmed.ncbi.nlm.nih.gov/41086194","citation_count":0,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":7949,"output_tokens":2638,"usd":0.031709,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":9767,"output_tokens":3878,"usd":0.072892,"stage2_stop_reason":"end_turn"},"total_usd":0.104601,"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\": 2008,\n      \"finding\": \"UBXD7 (UBXN7) links p97 to the CUL2/VHL ubiquitin ligase and its substrate HIF1α; depletion of p97 leads to accumulation of endogenous HIF1α, establishing UBXN7 as a substrate-binding adaptor that connects p97 to CRL2-mediated protein turnover.\",\n      \"method\": \"Network proteomics (mass spectrometry of immunoprecipitates), co-immunoprecipitation, siRNA depletion with HIF1α accumulation readout\",\n      \"journal\": \"Cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal Co-IP and MS interactome with functional KD phenotype, widely replicated by subsequent independent labs\",\n      \"pmids\": [\"18775313\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"UBXN7 directly engages NEDD8-modified cullins via its UIM (ubiquitin-interacting motif) domain, independent of its UBA ubiquitin-binding domain; this interaction is sufficient to shift CUL2 to its neddylated form and cause accumulation of non-ubiquitylated HIF1α, indicating that UBXN7 negatively regulates CRL2 ligase activity by sequestering neddylated CUL2.\",\n      \"method\": \"Mutagenesis of UIM and UBA domains, co-immunoprecipitation, over-expression assays, mass spectrometry of immunoprecipitates\",\n      \"journal\": \"BMC biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Moderate — domain mutagenesis combined with multiple orthogonal co-IP and functional assays in single focused study\",\n      \"pmids\": [\"22537386\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"Mitochondrial MUL1 E3 ubiquitin ligase ubiquitinates UBXN7, leading to its proteasomal degradation; inactivation of MUL1 causes UBXN7 accumulation, which in turn increases HIF-1α protein levels, reduces oxidative phosphorylation, and increases glycolysis, placing MUL1 upstream of UBXN7 in the CRL2VHL pathway.\",\n      \"method\": \"siRNA knockdown of MUL1, Western blot for UBXN7 and HIF-1α, metabolic assays (OXPHOS vs. glycolysis), identification of UBXN7 as MUL1 substrate\",\n      \"journal\": \"Scientific reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — KD with defined biochemical and metabolic phenotype, single lab but multiple orthogonal readouts\",\n      \"pmids\": [\"32005965\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"UBXN7 acts as a scaffold for both CRL3KEAP1 and CRL2VHL complexes, mediating reciprocal regulation of NRF2 and HIF-1α: high UBXN7 levels lead to HIF-1α accumulation and glycolysis, while low UBXN7 (regulated by MUL1-mediated ubiquitination) correlates with NRF2 activation and increased OXPHOS.\",\n      \"method\": \"siRNA knockdown and overexpression of UBXN7, Western blot for NRF2 and HIF-1α, metabolic assays, MUL1 inactivation experiments\",\n      \"journal\": \"Biochimica et biophysica acta. Molecular cell research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — KD/OE with multiple biochemical phenotypes, single lab extending prior findings\",\n      \"pmids\": [\"33444648\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"UBXN7 facilitates replisome disassembly during S-phase in vertebrates by coupling CUL2-LRR1-dependent ubiquitylation of MCM7 (replicative helicase) to p97-mediated unloading from chromatin; UBXN7 uses independent domains to interact with both CUL2LRR1 and p97, acting as the first substrate-specific p97 cofactor for this process.\",\n      \"method\": \"Xenopus laevis egg extract cell-free system, biochemical domain-interaction assays, depletion/add-back experiments monitoring replisome disassembly\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Moderate — cell-free reconstitution in Xenopus extracts with biochemical domain mapping and functional rescue, single lab but multiple orthogonal approaches\",\n      \"pmids\": [\"35798141\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"HBx protein of HBV interacts with UBXN7 to promote K48-linked ubiquitination of UBXN7 at lysine 99, leading to its proteasomal degradation; UBXN7 itself inhibits NF-κB signaling by binding the ULK domain of IKKβ via its UBA domain, facilitating IKKβ degradation.\",\n      \"method\": \"SILAC ubiquitinome analysis, Co-IP, mutagenesis (K99 site), Western blot, in vitro and in vivo HBV replication assays\",\n      \"journal\": \"Cellular and molecular gastroenterology and hepatology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — SILAC quantitative ubiquitinomics plus co-IP and site-specific mutagenesis, single lab\",\n      \"pmids\": [\"36096451\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"The UAS thioredoxin-like domain of UBXN7 directly docks on the RING domain of E3 ligases RNF111/Arkadia, RNF165/ARK2C, and TOPORS, inhibiting their autoubiquitylation by preventing interaction of the RING domain with E2 conjugating enzymes; this stabilizes RNF111 and modulates degradation of its substrate SKIL/SnoN in TGF-β signaling.\",\n      \"method\": \"Co-IP, domain mutagenesis (UAS deletion mutant), overexpression and siRNA depletion, interactome analysis of UAS domain, TGF-β-stimulated SKIL degradation assay\",\n      \"journal\": \"BMC biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Moderate — domain mutagenesis with multiple E3 ligase targets, functional substrate degradation assay, and mechanistic E2-binding block demonstrated in a single focused study\",\n      \"pmids\": [\"37024974\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"UBXN7 (along with FAF1 and FAF2) functions as an accessory p97 adapter that boosts p97-Ufd1-Npl4-mediated substrate unfolding, thereby accelerating proteasomal degradation; stimulation occurs by positioning the UT3 ubiquitin-binding module of Ufd1 for efficient substrate loading onto p97, demonstrated by mutations in the helix-Ufd1 interaction that reduced stimulation.\",\n      \"method\": \"In vitro reconstituted p97-Ufd1-Npl4 unfolding and proteasomal degradation assay, mutagenesis of helix-Ufd1 interface, biochemical rate measurements\",\n      \"journal\": \"Science advances\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — in vitro reconstitution with mutagenesis and quantitative unfolding/degradation assays, single lab but rigorous biochemical approach\",\n      \"pmids\": [\"41790892\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"UBXN7 interacts with SARS-CoV-2 N protein via its UBX domain and inhibits K48-linked ubiquitination and proteasomal degradation of N protein at lysine K257, leading to N protein accumulation and promoting viral dsRNA production and genome assembly.\",\n      \"method\": \"Reverse genetics system, co-immunoprecipitation, ubiquitination assays, site-directed mutagenesis (K257), UBXN7 depletion/overexpression with viral replication readouts\",\n      \"journal\": \"PLoS pathogens\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — co-IP with domain mapping, site-specific mutagenesis, and functional viral replication assays, single lab\",\n      \"pmids\": [\"41086194\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"UBXN7 is a multifunctional UBA-UBX family adaptor protein that (1) recruits the p97 AAA-ATPase segregase to ubiquitylated substrates of cullin-RING ligases (especially CRL2VHL/HIF-1α and CRL2LRR1/MCM7) by simultaneously engaging neddylated cullins via its UIM domain and p97 via its UBX domain; (2) negatively regulates specific CRL and RING E3 ligases (CRL2, RNF111, RNF165, TOPORS) by sequestering neddylated cullins or blocking RING–E2 interactions through its UAS thioredoxin-like domain; (3) is itself a substrate of mitochondrial MUL1 E3 ligase, linking mitochondrial stress sensing to HIF-1α/NRF2 balance and metabolic reprogramming; and (4) acts as an accessory adapter that positions Ufd1 within the p97 complex to boost substrate unfolding and proteasomal degradation.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"UBXN7 is a multi-domain UBA-UBX adaptor that couples the p97 (VCP) AAA-ATPase segregase to ubiquitylated substrates of cullin-RING ligases, governing the turnover of regulatory proteins and the disassembly of chromatin-bound machines [#0, #4]. It bridges substrate to segregase using independent modules: a substrate/ligase-engaging arm and a UBX domain that recruits p97, first defined for the CUL2/VHL ligase and its substrate HIF1\\u03b1 [#0] and later for CUL2-LRR1-dependent ubiquitylation of the MCM7 replicative helicase, where UBXN7 serves as the substrate-specific p97 cofactor that drives replisome unloading from chromatin during S-phase [#4]. Beyond delivering substrates, UBXN7 negatively regulates ligase activity: its UIM domain binds NEDD8-modified cullins to sequester neddylated CUL2 and stabilize non-ubiquitylated HIF1\\u03b1 [#1], while its UAS thioredoxin-like domain docks directly onto the RING domains of RNF111/Arkadia, RNF165 and TOPORS to block RING-E2 interaction and inhibit their autoubiquitylation, thereby stabilizing RNF111 and modulating SKIL/SnoN degradation in TGF-\\u03b2 signaling [#6]. As an accessory p97 adapter, UBXN7 also accelerates p97-Ufd1-Npl4-mediated substrate unfolding and proteasomal degradation by positioning the UT3 ubiquitin-binding module of Ufd1 for substrate loading [#7]. UBXN7 is itself an E3 substrate: mitochondrial MUL1 ubiquitylates UBXN7 for degradation, and loss of MUL1 elevates UBXN7, raising HIF-1\\u03b1 and shifting metabolism toward glycolysis, linking UBXN7 to reciprocal NRF2/HIF-1\\u03b1 control of oxidative versus glycolytic states [#2, #3]. UBXN7 is additionally targeted and exploited by viral proteins, being degraded upon HBV HBx engagement and stabilizing SARS-CoV-2 N protein via its UBX domain [#5, #8].\",\n  \"teleology\": [\n    {\n      \"year\": 2008,\n      \"claim\": \"Established that UBXN7 is a substrate-binding adaptor connecting the p97 segregase to CRL2-mediated turnover, answering how p97 is targeted to specific ubiquitylated substrates such as HIF1\\u03b1.\",\n      \"evidence\": \"Network proteomics, reciprocal co-IP, and siRNA depletion with HIF1\\u03b1 accumulation readout\",\n      \"pmids\": [\"18775313\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not map which domains engage cullin versus p97\", \"No direct demonstration that UBXN7 promotes versus restrains HIF1\\u03b1 degradation\"]\n    },\n    {\n      \"year\": 2012,\n      \"claim\": \"Resolved that UBXN7 binds NEDD8-modified cullins through its UIM domain independently of its UBA module, revealing a negative-regulatory role in which sequestering neddylated CUL2 stalls CRL2 and accumulates non-ubiquitylated HIF1\\u03b1.\",\n      \"evidence\": \"UIM/UBA domain mutagenesis, co-IP, overexpression assays, and MS of immunoprecipitates\",\n      \"pmids\": [\"22537386\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Quantitative balance between adaptor (pro-degradation) and sequestration (anti-degradation) roles unresolved\", \"Generality across other cullins not established here\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Identified UBXN7 as a MUL1 substrate, placing mitochondrial ubiquitin signaling upstream of UBXN7 to control HIF-1\\u03b1 levels and the OXPHOS-to-glycolysis balance.\",\n      \"evidence\": \"MUL1 siRNA knockdown, Western blot for UBXN7/HIF-1\\u03b1, and OXPHOS versus glycolysis metabolic assays\",\n      \"pmids\": [\"32005965\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct MUL1-UBXN7 ubiquitylation site not mapped\", \"Mechanism connecting mitochondrial localization of MUL1 to nuclear/cytosolic UBXN7 pool unclear\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Extended UBXN7 to a scaffold acting on both CRL3KEAP1 and CRL2VHL, providing a reciprocal switch between NRF2 and HIF-1\\u03b1 outputs tied to UBXN7 abundance.\",\n      \"evidence\": \"siRNA/overexpression of UBXN7, Western blot for NRF2/HIF-1\\u03b1, metabolic assays, and MUL1 inactivation\",\n      \"pmids\": [\"33444648\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct structural basis for dual-CRL scaffolding not shown\", \"Single-lab finding extending prior work without independent replication\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Demonstrated that UBXN7 is the substrate-specific p97 cofactor coupling CUL2-LRR1 ubiquitylation of MCM7 to p97-driven replisome disassembly, defining a defined physiological substrate beyond HIF1\\u03b1.\",\n      \"evidence\": \"Xenopus egg extract cell-free reconstitution, domain-interaction assays, and depletion/add-back monitoring replisome disassembly\",\n      \"pmids\": [\"35798141\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether the same adaptor mode operates on other replication substrates not tested\", \"Role of NEDD8-cullin sequestration during this process not addressed\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Showed UBXN7 inhibits NF-\\u03baB signaling by binding IKK\\u03b2 via its UBA domain, while being degraded through HBx-promoted K99 ubiquitylation, linking UBXN7 to inflammatory signaling and viral antagonism.\",\n      \"evidence\": \"SILAC ubiquitinome, co-IP, K99 site mutagenesis, and HBV replication assays\",\n      \"pmids\": [\"36096451\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Identity of the E3 ligase ubiquitylating UBXN7 at K99 in the HBx context unresolved\", \"Mechanism by which UBXN7 facilitates IKK\\u03b2 degradation not detailed\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Defined a distinct mechanism in which the UAS thioredoxin-like domain docks on RING E3 ligases (RNF111, RNF165, TOPORS) to block RING-E2 engagement, broadening UBXN7 from a CRL regulator to a direct RING-ligase inhibitor controlling TGF-\\u03b2 effector SKIL/SnoN.\",\n      \"evidence\": \"Co-IP, UAS deletion mutagenesis, UAS interactome analysis, and TGF-\\u03b2-stimulated SKIL degradation assay\",\n      \"pmids\": [\"37024974\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Structural detail of the UAS-RING interface not resolved\", \"Whether this domain function is competitive with p97 adaptor activity unknown\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Revealed UBXN7 engages SARS-CoV-2 N protein via its UBX domain to block K48 ubiquitylation at K257, stabilizing N and promoting viral replication, identifying a proviral exploitation of the adaptor.\",\n      \"evidence\": \"Reverse genetics, co-IP with domain mapping, K257 mutagenesis, and depletion/overexpression viral replication readouts\",\n      \"pmids\": [\"41086194\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether host p97 recruitment is involved in N protein protection unclear\", \"Single-lab finding without independent confirmation\"]\n    },\n    {\n      \"year\": 2026,\n      \"claim\": \"Reconstituted that UBXN7 acts as an accessory p97 adapter that accelerates p97-Ufd1-Npl4 substrate unfolding and degradation by positioning the Ufd1 UT3 module, providing a biochemical mechanism for how it enhances segregase throughput.\",\n      \"evidence\": \"In vitro reconstituted p97-Ufd1-Npl4 unfolding/degradation assays with helix-Ufd1 interface mutagenesis and rate measurements\",\n      \"pmids\": [\"41790892\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether this stimulation operates on physiological CRL2 substrates in cells not shown\", \"Relationship between this accessory role and substrate-specific adaptor role not integrated\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How UBXN7's competing activities \\u2014 p97 substrate delivery, NEDD8-cullin sequestration, and direct RING-E2 blockade \\u2014 are coordinated and selectively deployed across different ligases and substrates remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No structural model integrating UIM, UBA, UAS, and UBX functions on a single ligase\", \"Switching logic between pro-degradation and inhibitory modes not defined\", \"In vivo physiological hierarchy of these roles not established\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [0, 4, 7]},\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [1, 6]},\n      {\"term_id\": \"GO:0140096\", \"supporting_discovery_ids\": [4, 7]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0000228\", \"supporting_discovery_ids\": [4]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-392499\", \"supporting_discovery_ids\": [0, 7]},\n      {\"term_id\": \"R-HSA-69306\", \"supporting_discovery_ids\": [4]},\n      {\"term_id\": \"R-HSA-162582\", \"supporting_discovery_ids\": [3, 6]},\n      {\"term_id\": \"R-HSA-1430728\", \"supporting_discovery_ids\": [2, 3]}\n    ],\n    \"complexes\": [\n      \"p97-Ufd1-Npl4 complex\",\n      \"CRL2VHL\",\n      \"CRL2LRR1\"\n    ],\n    \"partners\": [\n      \"VCP\",\n      \"CUL2\",\n      \"HIF1A\",\n      \"MUL1\",\n      \"RNF111\",\n      \"TOPORS\",\n      \"IKBKB\",\n      \"UFD1\"\n    ],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":6,"faith_total":6,"faith_pct":100.0}}