id: Q9GZZ9 gene_symbol: UBA5 product_type: PROTEIN status: COMPLETE taxon: id: NCBITaxon:9606 label: Homo sapiens description: >- UBA5 (ubiquitin-like modifier-activating enzyme 5) is the E1-activating enzyme of the ufmylation pathway, the first and rate-limiting step in conjugation of the ubiquitin-like modifier UFM1 to substrate proteins. UBA5 is a minimalistic, single-domain (ThiF/MoeB-type adenylation domain) E1 that functions as a homodimer. It activates mature UFM1 by adenylating UFM1's C-terminal glycine with ATP and then forming a high-energy thioester between that glycine and the catalytic cysteine (Cys250), releasing AMP. UFM1 is bound in trans across the two subunits of the UBA5 homodimer, and activated UFM1 is then transferred to the E2-conjugating enzyme UFC1 via UBA5's C-terminal UFC1-binding sequence. UBA5 binds zinc and uses a UFM1-interacting sequence (UIS) that also engages GABARAP/LC3 family proteins, which recruit UBA5 to the ER membrane. Acting at the cytosol and ER, UBA5-initiated ufmylation supports ribosome recycling, the response to ER stress, reticulophagy, the DNA-damage response, innate-immune (RIG-I/interferon) signaling, and erythroid/megakaryocyte differentiation. Biallelic UBA5 loss-of-function variants cause developmental and epileptic encephalopathy (DEE44) and autosomal-recessive spinocerebellar ataxia (SCAR24). alternative_products: - name: 1 (UBE1DC1A {ECO:0000303|PubMed:18442052}) id: Q9GZZ9-1 - name: 2 (UBE1DC1B {ECO:0000303|PubMed:18442052}) id: Q9GZZ9-2 sequence_note: VSP_038528 existing_annotations: - term: id: GO:0005829 label: cytosol evidence_type: IBA original_reference_id: GO_REF:0000033 qualifier: is_active_in review: summary: >- UBA5 acts in the cytosol, where it activates UFM1. Supported by direct evidence (HPA IDA cytosol) and phylogenetic inference. action: ACCEPT reason: >- Cytosol is the principal site where UBA5 activates UFM1; well supported. supported_by: - reference_id: file:human/UBA5/UBA5-uniprot.txt supporting_text: 'SUBCELLULAR LOCATION: Cytoplasm' - term: id: GO:0071569 label: protein ufmylation evidence_type: IBA original_reference_id: GO_REF:0000033 qualifier: involved_in review: summary: >- UBA5 is the E1 that initiates protein ufmylation; the process annotation is core and strongly supported across many studies. action: ACCEPT reason: >- Ufmylation is the central process UBA5 enables; well supported by direct and phylogenetic evidence. supported_by: - reference_id: file:human/UBA5/UBA5-uniprot.txt supporting_text: E1-like enzyme which specifically catalyzes the first step in - term: id: GO:0071566 label: UFM1 activating enzyme activity evidence_type: IBA original_reference_id: GO_REF:0000033 qualifier: enables review: summary: >- UFM1 activating enzyme activity is UBA5's core molecular function: ATP-dependent adenylation and thioester formation with UFM1's C-terminal glycine. Strongly supported. action: ACCEPT reason: >- This is the defining catalytic activity of UBA5 (the UFM1 E1); supported by direct biochemistry and phylogenetic inference. supported_by: - reference_id: file:human/UBA5/UBA5-uniprot.txt supporting_text: UFM1-activating enzyme - term: id: GO:0005634 label: nucleus evidence_type: IEA original_reference_id: GO_REF:0000044 qualifier: located_in review: summary: >- UBA5 can localize to the nucleus (notably in the presence of SUMO2). Supported experimentally but a minor pool relative to its cytosolic site of action. action: KEEP_AS_NON_CORE reason: >- Nuclear localization is documented but secondary; UBA5 mainly acts in the cytoplasm. supported_by: - reference_id: file:human/UBA5/UBA5-uniprot.txt supporting_text: Nucleus - term: id: GO:0005737 label: cytoplasm evidence_type: IEA original_reference_id: GO_REF:0000044 qualifier: located_in review: summary: >- Cytoplasmic localization, consistent with the experimentally supported cytoplasm/cytosol annotations. action: ACCEPT reason: Correct primary compartment for UBA5; agrees with direct evidence. supported_by: - reference_id: file:human/UBA5/UBA5-uniprot.txt supporting_text: 'SUBCELLULAR LOCATION: Cytoplasm' - term: id: GO:0005789 label: endoplasmic reticulum membrane evidence_type: IEA original_reference_id: GO_REF:0000044 qualifier: located_in review: summary: >- UBA5 localizes to the ER membrane through its GABARAPL2 interaction, consistent with ufmylation acting at ER-bound ribosomes. action: ACCEPT reason: >- ER-membrane localization is directly supported (IDA, PMID:30990354) and functionally relevant to ER-associated ufmylation. supported_by: - reference_id: file:human/UBA5/UBA5-uniprot.txt supporting_text: Endoplasmic reticulum membrane - term: id: GO:0005794 label: Golgi apparatus evidence_type: IEA original_reference_id: GO_REF:0000044 qualifier: located_in review: summary: >- Golgi localization reported in one study (PMID:26872069). Minor and not clearly tied to UBA5's core ufmylation function. action: KEEP_AS_NON_CORE reason: >- Documented but peripheral localization; not central to UBA5's UFM1-E1 function. supported_by: - reference_id: file:human/UBA5/UBA5-uniprot.txt supporting_text: Golgi apparatus - term: id: GO:0008641 label: ubiquitin-like modifier activating enzyme activity evidence_type: IEA original_reference_id: GO_REF:0000002 qualifier: enables review: summary: >- Family-level (InterPro) annotation of UBL-activating enzyme activity. This is correct but less precise than the specific UFM1-activating enzyme activity term. action: MODIFY reason: >- UBA5 is specific for UFM1; the general E1 term should be replaced by the precise UFM1 activating enzyme activity (GO:0071566). proposed_replacement_terms: - id: GO:0071566 label: UFM1 activating enzyme activity supported_by: - reference_id: file:human/UBA5/UBA5-uniprot.txt supporting_text: it is specific for UFM1 - term: id: GO:0005515 label: protein binding evidence_type: IPI original_reference_id: PMID:16189514 qualifier: enables review: summary: >- High-throughput interaction (WITH GABARAPL2, P60520). The GABARAP/LC3 interactions recruit UBA5 to ER membranes; the generic term is uninformative. action: KEEP_AS_NON_CORE reason: >- Records a real GABARAPL2 interaction (relevant to ER localization), but the generic protein binding term is uninformative and non-core. supported_by: - reference_id: file:human/UBA5/UBA5-uniprot.txt supporting_text: Interacts (via UIS motif) with - term: id: GO:0005515 label: protein binding evidence_type: IPI original_reference_id: PMID:20562859 qualifier: enables review: summary: >- Autophagy interaction network capturing UBA5 interactions with UFM1 (P61960) and GABARAP-family members. Generic protein binding term. action: KEEP_AS_NON_CORE reason: >- Captures real cascade/recruitment interactions (UFM1, GABARAPs) but the generic MF term is uninformative. supported_by: - reference_id: file:human/UBA5/UBA5-goa.tsv supporting_text: UniProtKB:P61960 - term: id: GO:0005515 label: protein binding evidence_type: IPI original_reference_id: PMID:21900206 qualifier: enables review: summary: >- High-throughput interaction (WITH GABARAPL2, P60520). Generic protein binding term. action: KEEP_AS_NON_CORE reason: >- Real GABARAPL2 interaction but the generic MF term is uninformative and non-core. supported_by: - reference_id: file:human/UBA5/UBA5-uniprot.txt supporting_text: Interacts (via UIS motif) with - term: id: GO:0005515 label: protein binding evidence_type: IPI original_reference_id: PMID:25416956 qualifier: enables review: summary: >- Y2H interactome (WITH GABARAPL2, P60520). Generic protein binding term. action: KEEP_AS_NON_CORE reason: Real GABARAPL2 interaction; generic MF term uninformative and non-core. supported_by: - reference_id: file:human/UBA5/UBA5-uniprot.txt supporting_text: Interacts (via UIS motif) with - term: id: GO:0005515 label: protein binding evidence_type: IPI original_reference_id: PMID:26496610 qualifier: enables review: summary: >- Quantitative interactome capturing UBA5-UFM1 (P61960). Generic protein binding term; the meaningful partner is the UFM1 substrate of activation. action: KEEP_AS_NON_CORE reason: >- Real, mechanistically relevant UFM1 interaction, but the generic MF term is uninformative. supported_by: - reference_id: file:human/UBA5/UBA5-goa.tsv supporting_text: UniProtKB:P61960 - term: id: GO:0005515 label: protein binding evidence_type: IPI original_reference_id: PMID:26872069 qualifier: enables review: summary: >- SCAR24 disease study reporting UBA5-UFM1 (P61960) interaction. Generic term; UFM1 binding is the functionally meaningful interaction. action: KEEP_AS_NON_CORE reason: >- Real UFM1 interaction underlying activation, but the generic MF term is uninformative. supported_by: - reference_id: file:human/UBA5/UBA5-goa.tsv supporting_text: UniProtKB:P61960 - term: id: GO:0005515 label: protein binding evidence_type: IPI original_reference_id: PMID:28514442 qualifier: enables review: summary: >- BioPlex interactome capturing UBA5 interactions with GABARAPL2 (P60520) and UFM1 (P61960). Generic protein binding term. action: KEEP_AS_NON_CORE reason: >- Captures real cascade/recruitment interactions but the generic MF term is uninformative. supported_by: - reference_id: file:human/UBA5/UBA5-goa.tsv supporting_text: UniProtKB:P61960 - term: id: GO:0005515 label: protein binding evidence_type: IPI original_reference_id: PMID:32296183 qualifier: enables review: summary: >- HuRI binary interactome (WITH GABARAPL2, P60520). Generic protein binding term. action: KEEP_AS_NON_CORE reason: Real GABARAPL2 interaction; generic MF term uninformative and non-core. supported_by: - reference_id: file:human/UBA5/UBA5-uniprot.txt supporting_text: Interacts (via UIS motif) with - term: id: GO:0005515 label: protein binding evidence_type: IPI original_reference_id: PMID:33961781 qualifier: enables review: summary: >- BioPlex interactome capturing UBA5 interactions with GABARAPL2 (P60520) and UFM1 (P61960). Generic protein binding term. action: KEEP_AS_NON_CORE reason: >- Captures real cascade/recruitment interactions but the generic MF term is uninformative. supported_by: - reference_id: file:human/UBA5/UBA5-goa.tsv supporting_text: UniProtKB:P61960 - term: id: GO:0005515 label: protein binding evidence_type: IPI original_reference_id: PMID:35271311 qualifier: enables review: summary: >- OpenCell interactome capturing UBA5-UFM1 (P61960). Generic protein binding term. action: KEEP_AS_NON_CORE reason: Real UFM1 interaction; generic MF term uninformative and non-core. supported_by: - reference_id: file:human/UBA5/UBA5-goa.tsv supporting_text: UniProtKB:P61960 - term: id: GO:0005515 label: protein binding evidence_type: IPI original_reference_id: PMID:38225382 qualifier: enables review: summary: >- High-throughput interaction (WITH GABARAPL2, P60520). Generic protein binding term. action: KEEP_AS_NON_CORE reason: Real GABARAPL2 interaction; generic MF term uninformative and non-core. supported_by: - reference_id: file:human/UBA5/UBA5-uniprot.txt supporting_text: Interacts (via UIS motif) with - term: id: GO:0005515 label: protein binding evidence_type: IPI original_reference_id: PMID:40205054 qualifier: enables review: summary: >- Multimodal cell-maps interactome capturing UBA5 interactions with GABARAPL2 (P60520), UFM1 (P61960) and GABARAPL1 (Q9H0R8). Generic protein binding term. action: KEEP_AS_NON_CORE reason: >- Captures real cascade/recruitment interactions but the generic MF term is uninformative. supported_by: - reference_id: file:human/UBA5/UBA5-goa.tsv supporting_text: UniProtKB:P61960 - term: id: GO:0030218 label: erythrocyte differentiation evidence_type: IEA original_reference_id: GO_REF:0000107 qualifier: involved_in review: summary: >- Orthology-transferred role in erythroid differentiation, consistent with ufmylation being essential for erythroid/megakaryocyte differentiation in mouse. A downstream developmental consequence of ufmylation. action: KEEP_AS_NON_CORE reason: >- Genuine ufmylation-dependent developmental process, but downstream of and non-core relative to UBA5's E1 activity. supported_by: - reference_id: file:human/UBA5/UBA5-uniprot.txt supporting_text: essential for erythroid differentiation of both megakaryocytes and - term: id: GO:0030219 label: megakaryocyte differentiation evidence_type: IEA original_reference_id: GO_REF:0000107 qualifier: involved_in review: summary: >- Orthology-transferred role in megakaryocyte differentiation, consistent with the essential role of ufmylation in hematopoiesis. Downstream developmental consequence. action: KEEP_AS_NON_CORE reason: >- Genuine ufmylation-dependent developmental process, but downstream of and non-core relative to UBA5's E1 activity. supported_by: - reference_id: file:human/UBA5/UBA5-uniprot.txt supporting_text: essential for erythroid differentiation of both megakaryocytes and - term: id: GO:0032649 label: regulation of type II interferon production evidence_type: IEA original_reference_id: GO_REF:0000107 qualifier: involved_in review: summary: >- Orthology-transferred role in interferon production, consistent with ufmylation regulating RIG-I/interferon innate-immune signaling. Downstream signaling consequence. action: KEEP_AS_NON_CORE reason: >- Genuine ufmylation-associated innate-immune process, but downstream of and non-core relative to UBA5's E1 activity. supported_by: - reference_id: file:human/UBA5/UBA5-uniprot.txt supporting_text: interferon response - term: id: GO:0071566 label: UFM1 activating enzyme activity evidence_type: IEA original_reference_id: GO_REF:0000120 qualifier: enables review: summary: >- Automated annotation of the core UFM1-activating enzyme activity, redundant with strong experimental support. action: ACCEPT reason: Core molecular function; redundant with direct experimental evidence. supported_by: - reference_id: file:human/UBA5/UBA5-uniprot.txt supporting_text: UFM1-activating enzyme - term: id: GO:0071569 label: protein ufmylation evidence_type: IEA original_reference_id: GO_REF:0000120 qualifier: involved_in review: summary: >- Automated annotation of the core ufmylation process, redundant with strong experimental support. action: ACCEPT reason: Core biological process; redundant with direct experimental evidence. supported_by: - reference_id: file:human/UBA5/UBA5-uniprot.txt supporting_text: E1-like enzyme which specifically catalyzes the first step in - term: id: GO:0005829 label: cytosol evidence_type: IDA original_reference_id: GO_REF:0000052 qualifier: located_in review: summary: >- Direct immunofluorescence (HPA) cytosolic localization, consistent with UBA5's principal site of action. action: ACCEPT reason: IDA-supported cytosolic localization; correct compartment. supported_by: - reference_id: file:human/UBA5/UBA5-uniprot.txt supporting_text: 'SUBCELLULAR LOCATION: Cytoplasm' - term: id: GO:0005634 label: nucleus evidence_type: EXP original_reference_id: PMID:18442052 qualifier: located_in review: summary: >- Experimental nuclear localization (induced in the presence of SUMO2). Documented but a minor pool. action: KEEP_AS_NON_CORE reason: >- Supported nuclear localization but secondary to the cytoplasmic site of action. supported_by: - reference_id: file:human/UBA5/UBA5-uniprot.txt supporting_text: it localizes to the nucleus in presence of SUMO2 - term: id: GO:0005737 label: cytoplasm evidence_type: EXP original_reference_id: PMID:18442052 qualifier: located_in review: summary: >- Experimental cytoplasmic localization, the principal compartment where UBA5 acts. action: ACCEPT reason: Correct primary compartment; experimentally supported. supported_by: - reference_id: file:human/UBA5/UBA5-uniprot.txt supporting_text: Localizes mainly in the - term: id: GO:0005794 label: Golgi apparatus evidence_type: EXP original_reference_id: PMID:26872069 qualifier: located_in review: summary: >- Experimental Golgi localization from one study. Minor and not central to the ufmylation function. action: KEEP_AS_NON_CORE reason: Documented but peripheral localization; non-core. supported_by: - reference_id: file:human/UBA5/UBA5-uniprot.txt supporting_text: Golgi apparatus - term: id: GO:0071566 label: UFM1 activating enzyme activity evidence_type: IDA original_reference_id: PMID:34588452 qualifier: enables review: summary: >- Direct demonstration of UBA5's UFM1-activating enzyme activity in the context of UFM1 transfer from UBA5 to UFC1. Core MF. action: ACCEPT reason: Core molecular function directly demonstrated. supported_by: - reference_id: file:human/UBA5/UBA5-uniprot.txt supporting_text: UFM1-activating enzyme - term: id: GO:0071569 label: protein ufmylation evidence_type: IDA original_reference_id: PMID:34588452 qualifier: involved_in review: summary: >- Direct evidence for UBA5's role in ufmylation (UFM1 transfer to UFC1). Core process. action: ACCEPT reason: Core biological process; directly supported. supported_by: - reference_id: file:human/UBA5/UBA5-uniprot.txt supporting_text: E1-like enzyme which specifically catalyzes the first step in - term: id: GO:0071569 label: protein ufmylation evidence_type: IMP original_reference_id: PMID:30626644 qualifier: involved_in review: summary: >- Functional genetics (RPL26-UFMylation study) implicating UBA5 in ufmylation. Core process. action: ACCEPT reason: Core process; supported by functional perturbation. supported_by: - reference_id: PMID:30626644 supporting_text: RPL26 is the principal target of UFM1 conjugation - term: id: GO:0005515 label: protein binding evidence_type: IPI original_reference_id: PMID:26929408 qualifier: enables review: summary: >- Structural/functional study of the UBA5 UIS motif, capturing interactions with UFM1 (P61960) and GABARAP-family proteins (GABARAP, GABARAPL1, GABARAPL2). Generic term; the interactions are mechanistically meaningful. action: KEEP_AS_NON_CORE reason: >- Real UFM1/GABARAP interactions via the UIS motif, but the generic MF term is uninformative. supported_by: - reference_id: file:human/UBA5/UBA5-uniprot.txt supporting_text: Interacts (via UIS motif) with - term: id: GO:0005515 label: protein binding evidence_type: IPI original_reference_id: PMID:30990354 qualifier: enables review: summary: >- Study of the atypical LIR motif in UBA5 mediating GABARAPL2 (P60520) binding and ER-membrane localization. Generic term; interaction is functionally relevant. action: KEEP_AS_NON_CORE reason: >- Real GABARAPL2 interaction underlying ER localization, but the generic MF term is uninformative. supported_by: - reference_id: file:human/UBA5/UBA5-uniprot.txt supporting_text: mediates membrane - term: id: GO:0071569 label: protein ufmylation evidence_type: IDA original_reference_id: PMID:26929408 qualifier: involved_in review: summary: >- Direct evidence that the UBA5 UIS motif is required for ufmylation. Core process. action: ACCEPT reason: Core process; directly supported. supported_by: - reference_id: file:human/UBA5/UBA5-uniprot.txt supporting_text: required for binding to ubiquitin-like - term: id: GO:0005515 label: protein binding evidence_type: IPI original_reference_id: PMID:34299007 qualifier: enables review: summary: >- Study of UBA5 C-terminal regions in UFM1 transfer to UFC1, capturing UFM1 (P61960), UFC1 (Q9Y3C8) and GABARAP-family interactions. Generic term. action: KEEP_AS_NON_CORE reason: >- Real, mechanistically central UFC1/UFM1 interactions, but the generic MF term is uninformative. supported_by: - reference_id: file:human/UBA5/UBA5-uniprot.txt supporting_text: Interacts (via C-terminus) with UFC1 - term: id: GO:0005515 label: protein binding evidence_type: IPI original_reference_id: PMID:27653677 qualifier: enables review: summary: >- Structure of the UBA5-UFM1 complex (WITH UFM1, P61960) revealing the trans-binding activation mechanism. Generic term; interaction is central. action: KEEP_AS_NON_CORE reason: >- Mechanistically central UFM1 interaction, but the generic MF term is uninformative. supported_by: - reference_id: file:human/UBA5/UBA5-uniprot.txt supporting_text: binds UFM1 via a trans-binding mechanism - term: id: GO:0005515 label: protein binding evidence_type: IPI original_reference_id: PMID:29295865 qualifier: enables review: summary: >- Study showing UFM1 trans-binding stimulates UBA5 homodimerization and ATP binding (WITH UFM1, P61960). Generic term; mechanistically meaningful. action: KEEP_AS_NON_CORE reason: Real UFM1 interaction underlying activation; generic MF term uninformative. supported_by: - reference_id: file:human/UBA5/UBA5-uniprot.txt supporting_text: binds UFM1 via a trans-binding mechanism - term: id: GO:0005515 label: protein binding evidence_type: IPI original_reference_id: PMID:30412706 qualifier: enables review: summary: >- Structural study of UBA5 N-terminal extension and UFM1 activation (WITH UFM1, P61960). Generic term; interaction is central. action: KEEP_AS_NON_CORE reason: Real UFM1 interaction underlying activation; generic MF term uninformative. supported_by: - reference_id: file:human/UBA5/UBA5-uniprot.txt supporting_text: binds UFM1 via a trans-binding mechanism - term: id: GO:0005789 label: endoplasmic reticulum membrane evidence_type: IDA original_reference_id: PMID:30990354 qualifier: located_in review: summary: >- Direct evidence that the GABARAPL2 interaction localizes UBA5 to the ER membrane, where ER-associated ufmylation occurs. action: ACCEPT reason: >- IDA-supported ER-membrane localization, functionally relevant to ER-associated ufmylation. supported_by: - reference_id: file:human/UBA5/UBA5-uniprot.txt supporting_text: mediates membrane - term: id: GO:0008270 label: zinc ion binding evidence_type: IDA original_reference_id: PMID:27653677 qualifier: enables review: summary: >- UBA5 binds a structural zinc ion (coordinated by Cys/His residues), a conserved feature of its adenylation domain. Directly demonstrated. action: ACCEPT reason: >- Zinc binding is a directly supported structural molecular function of UBA5's E1 domain. supported_by: - reference_id: file:human/UBA5/UBA5-uniprot.txt supporting_text: Zn(2+) - term: id: GO:0008270 label: zinc ion binding evidence_type: IDA original_reference_id: PMID:30412706 qualifier: enables review: summary: >- Independent structural confirmation of zinc binding in UBA5's adenylation domain. action: ACCEPT reason: Directly supported structural zinc binding. supported_by: - reference_id: file:human/UBA5/UBA5-uniprot.txt supporting_text: Zn(2+) - term: id: GO:0030218 label: erythrocyte differentiation evidence_type: ISS original_reference_id: GO_REF:0000024 qualifier: involved_in review: summary: >- Sequence/orthology-based erythroid differentiation role, redundant with the IEA annotation. Downstream developmental consequence of ufmylation. action: KEEP_AS_NON_CORE reason: >- Genuine ufmylation-dependent developmental process; non-core relative to UBA5's E1 activity. supported_by: - reference_id: file:human/UBA5/UBA5-uniprot.txt supporting_text: essential for erythroid differentiation of both megakaryocytes and - term: id: GO:0030219 label: megakaryocyte differentiation evidence_type: ISS original_reference_id: GO_REF:0000024 qualifier: involved_in review: summary: >- Sequence/orthology-based megakaryocyte differentiation role, redundant with the IEA annotation. Downstream developmental consequence. action: KEEP_AS_NON_CORE reason: >- Genuine ufmylation-dependent developmental process; non-core relative to UBA5's E1 activity. supported_by: - reference_id: file:human/UBA5/UBA5-uniprot.txt supporting_text: essential for erythroid differentiation of both megakaryocytes and - term: id: GO:0034976 label: response to endoplasmic reticulum stress evidence_type: IMP original_reference_id: PMID:32160526 qualifier: involved_in review: summary: >- Genome-wide ER-phagy screen implicating UBA5-initiated ufmylation in the ER-stress response. Downstream process of ufmylation. action: KEEP_AS_NON_CORE reason: >- Genuine ufmylation-dependent process, but downstream of and non-core relative to UBA5's E1 activity. supported_by: - reference_id: PMID:32160526 supporting_text: ER-Resident UFMylation - term: id: GO:0042803 label: protein homodimerization activity evidence_type: IDA original_reference_id: PMID:27653677 qualifier: enables review: summary: >- UBA5 forms a homodimer, which is required for UFM1 activation via the trans-binding mechanism. Directly demonstrated and mechanistically core. action: ACCEPT reason: >- Homodimerization is a directly supported molecular function essential for UBA5's UFM1-activating activity. supported_by: - reference_id: file:human/UBA5/UBA5-uniprot.txt supporting_text: Homodimer; homodimerization is required for UFM1 activation - term: id: GO:0042803 label: protein homodimerization activity evidence_type: IDA original_reference_id: PMID:29295865 qualifier: enables review: summary: >- UFM1 trans-binding promotes UBA5 homodimerization; directly demonstrated. action: ACCEPT reason: >- Directly supported homodimerization activity required for UFM1 activation. supported_by: - reference_id: file:human/UBA5/UBA5-uniprot.txt supporting_text: Trans-binding also promotes stabilization of the - term: id: GO:0061709 label: reticulophagy evidence_type: IMP original_reference_id: PMID:32160526 qualifier: involved_in review: summary: >- Genome-wide ER-phagy screen implicating UBA5-initiated ufmylation in reticulophagy. Downstream process. action: KEEP_AS_NON_CORE reason: >- Genuine ufmylation-dependent process; non-core relative to UBA5's E1 activity. supported_by: - reference_id: PMID:32160526 supporting_text: ER-Resident UFMylation - term: id: GO:0071566 label: UFM1 activating enzyme activity evidence_type: IDA original_reference_id: PMID:27653677 qualifier: enables review: summary: >- Direct biochemical/structural demonstration of UFM1 activation (adenylation and thioester formation). Core MF. action: ACCEPT reason: Core molecular function directly demonstrated. supported_by: - reference_id: file:human/UBA5/UBA5-uniprot.txt supporting_text: yielding a UFM1-E1 thioester and free AMP - term: id: GO:0071566 label: UFM1 activating enzyme activity evidence_type: IDA original_reference_id: PMID:29295865 qualifier: enables review: summary: >- Direct demonstration of UFM1 activation (enhanced ATP binding upon UFM1 trans-binding). Core MF. action: ACCEPT reason: Core molecular function directly demonstrated. supported_by: - reference_id: file:human/UBA5/UBA5-uniprot.txt supporting_text: enhances ATP-binding - term: id: GO:0071566 label: UFM1 activating enzyme activity evidence_type: IDA original_reference_id: PMID:30412706 qualifier: enables review: summary: >- Direct demonstration that the UBA5 N-terminal extension boosts UFM1 activation. Core MF. action: ACCEPT reason: Core molecular function directly demonstrated. supported_by: - reference_id: file:human/UBA5/UBA5-uniprot.txt supporting_text: UFM1-activating enzyme - term: id: GO:0071569 label: protein ufmylation evidence_type: IDA original_reference_id: PMID:27653677 qualifier: involved_in review: summary: >- Direct evidence for UBA5's role in ufmylation via UFM1 activation. Core process. action: ACCEPT reason: Core process; directly supported. supported_by: - reference_id: file:human/UBA5/UBA5-uniprot.txt supporting_text: E1-like enzyme which specifically catalyzes the first step in - term: id: GO:0071569 label: protein ufmylation evidence_type: IDA original_reference_id: PMID:29295865 qualifier: involved_in review: summary: Direct evidence for UBA5's role in ufmylation. Core process. action: ACCEPT reason: Core process; directly supported. supported_by: - reference_id: file:human/UBA5/UBA5-uniprot.txt supporting_text: E1-like enzyme which specifically catalyzes the first step in - term: id: GO:0071569 label: protein ufmylation evidence_type: IDA original_reference_id: PMID:30412706 qualifier: involved_in review: summary: Direct evidence for UBA5's role in ufmylation. Core process. action: ACCEPT reason: Core process; directly supported. supported_by: - reference_id: file:human/UBA5/UBA5-uniprot.txt supporting_text: E1-like enzyme which specifically catalyzes the first step in - term: id: GO:0071569 label: protein ufmylation evidence_type: IMP original_reference_id: PMID:32160526 qualifier: involved_in review: summary: >- Functional perturbation in the ER-phagy screen implicating UBA5 in ufmylation. Core process. action: ACCEPT reason: Core process; supported by functional perturbation. supported_by: - reference_id: PMID:32160526 supporting_text: ER-Resident UFMylation - term: id: GO:0005515 label: protein binding evidence_type: IPI original_reference_id: PMID:29868776 qualifier: enables review: summary: >- HLD14 study reporting UBA5 interaction with UFC1 (Q9Y3C8, the E2). Generic term; mechanistically central cascade interaction. action: KEEP_AS_NON_CORE reason: >- Real UFC1 interaction underlying UFM1 transfer, but the generic MF term is uninformative. supported_by: - reference_id: file:human/UBA5/UBA5-uniprot.txt supporting_text: Interacts (via C-terminus) with UFC1 - term: id: GO:0050905 label: neuromuscular process evidence_type: IGI original_reference_id: PMID:26872069 qualifier: involved_in review: summary: >- Genetic-interaction-based annotation (with a Drosophila gene) of a neuromuscular process in the SCAR24 ataxia study. Indirect organismal phenotype. action: KEEP_AS_NON_CORE reason: >- Reflects an organismal/neuromuscular phenotype of UBA5 dysfunction; downstream and non-core relative to its E1 activity. supported_by: - reference_id: file:human/UBA5/UBA5-goa.tsv supporting_text: neuromuscular process - term: id: GO:0005737 label: cytoplasm evidence_type: IDA original_reference_id: PMID:26872069 qualifier: located_in review: summary: >- Direct cytoplasmic localization, the principal compartment where UBA5 acts. action: ACCEPT reason: Correct primary compartment; directly supported. supported_by: - reference_id: file:human/UBA5/UBA5-uniprot.txt supporting_text: 'SUBCELLULAR LOCATION: Cytoplasm' - term: id: GO:0071566 label: UFM1 activating enzyme activity evidence_type: IMP original_reference_id: PMID:27545681 qualifier: enables review: summary: >- DEE44 disease variants reduce/abolish UFM1 activating enzyme activity, directly implicating UBA5's catalytic function. Core MF. action: ACCEPT reason: >- Core molecular function supported by disease-variant functional characterization. supported_by: - reference_id: file:human/UBA5/UBA5-uniprot.txt supporting_text: reduces UFM1 activating enzyme - term: id: GO:0071569 label: protein ufmylation evidence_type: IMP original_reference_id: PMID:27545681 qualifier: involved_in review: summary: >- DEE44 disease variants disrupt the UFM1 cascade, implicating UBA5 in ufmylation. Core process. action: ACCEPT reason: Core process; supported by disease-variant functional characterization. supported_by: - reference_id: file:human/UBA5/UBA5-uniprot.txt supporting_text: E1-like enzyme which specifically catalyzes the first step in - term: id: GO:1990592 label: protein K69-linked ufmylation evidence_type: IDA original_reference_id: PMID:25219498 qualifier: involved_in review: summary: >- UBA5 supports formation of K69-linked poly-UFM1 chains as the activating enzyme. A specific aspect of the core ufmylation process. action: ACCEPT reason: >- Specific ufmylation chain-linkage process that UBA5 enables as the E1; supported. supported_by: - reference_id: file:human/UBA5/UBA5-uniprot.txt supporting_text: UFM1-activating enzyme - term: id: GO:0033146 label: regulation of intracellular estrogen receptor signaling pathway evidence_type: IMP original_reference_id: PMID:25219498 qualifier: involved_in review: summary: >- Ufmylation of ASC1 (substrate) regulates ERalpha signaling; UBA5 is required as the E1. Substrate-specific downstream signaling consequence. action: KEEP_AS_NON_CORE reason: >- Substrate-specific downstream signaling outcome of ufmylation; non-core relative to UBA5's E1 activity. supported_by: - reference_id: file:human/UBA5/UBA5-goa.tsv supporting_text: regulation of intracellular estrogen receptor signaling pathway - term: id: GO:0034976 label: response to endoplasmic reticulum stress evidence_type: IDA original_reference_id: PMID:23152784 qualifier: acts_upstream_of_or_within review: summary: >- The UFM1 conjugation system (including UBA5) is induced by ER-stress and acts in the ER-stress response. Downstream process. action: KEEP_AS_NON_CORE reason: >- Genuine ufmylation-associated process; downstream and non-core relative to UBA5's E1 activity. supported_by: - reference_id: file:human/UBA5/UBA5-goa.tsv supporting_text: response to endoplasmic reticulum stress - term: id: GO:0071569 label: protein ufmylation evidence_type: IMP original_reference_id: PMID:23152784 qualifier: acts_upstream_of_or_within review: summary: >- UBA5 acts upstream within the ufmylation process; the conjugation system is transcriptionally regulated by ER stress. Core process. action: ACCEPT reason: Core process; UBA5 is the initiating E1. supported_by: - reference_id: file:human/UBA5/UBA5-uniprot.txt supporting_text: E1-like enzyme which specifically catalyzes the first step in - term: id: GO:0005737 label: cytoplasm evidence_type: IDA original_reference_id: GO_REF:0000054 qualifier: located_in review: summary: >- Localization-database (LIFEdb) cytoplasmic localization, consistent with UBA5's principal compartment. action: ACCEPT reason: Correct primary compartment; supported by direct localization data. supported_by: - reference_id: file:human/UBA5/UBA5-uniprot.txt supporting_text: 'SUBCELLULAR LOCATION: Cytoplasm' - term: id: GO:0071566 label: UFM1 activating enzyme activity evidence_type: IDA original_reference_id: PMID:15071506 qualifier: enables review: summary: >- The founding study established UBA5 (Uba5) as the E1 that activates UFM1 by forming a high-energy thioester. Core MF. action: ACCEPT reason: Core molecular function demonstrated in the defining ufmylation paper. supported_by: - reference_id: PMID:15071506 supporting_text: activated by a novel E1-like enzyme, Uba5, by forming a - term: id: GO:0071569 label: protein ufmylation evidence_type: IDA original_reference_id: PMID:15071506 qualifier: involved_in review: summary: >- The founding study established UBA5 as the activating enzyme of the UFM1 conjugation system. Core process. action: ACCEPT reason: Core process; demonstrated in the defining ufmylation paper. supported_by: - reference_id: PMID:15071506 supporting_text: activated by a novel E1-like enzyme, Uba5, by forming a core_functions: - description: >- UBA5 is the E1-activating enzyme of the ufmylation cascade. As a homodimer it adenylates the C-terminal glycine of mature UFM1 with ATP and forms a high-energy thioester between that glycine and its catalytic Cys250 (releasing AMP), then transfers activated UFM1 to the E2 enzyme UFC1. molecular_function: id: GO:0071566 label: UFM1 activating enzyme activity locations: - id: GO:0005829 label: cytosol - id: GO:0005789 label: endoplasmic reticulum membrane supported_by: - reference_id: file:human/UBA5/UBA5-uniprot.txt supporting_text: Activates UFM1 by first adenylating its C-terminal glycine residue with - reference_id: file:human/UBA5/UBA5-uniprot.txt supporting_text: yielding a UFM1-E1 thioester and free AMP - description: >- UBA5 homodimerization is an integral part of its catalytic mechanism. The two subunits cooperate in a trans-binding mechanism in which UFM1 contacts distinct sites on both protomers, and dimerization is required for UFM1 activation. molecular_function: id: GO:0042803 label: protein homodimerization activity locations: - id: GO:0005829 label: cytosol supported_by: - reference_id: file:human/UBA5/UBA5-uniprot.txt supporting_text: Homodimer; homodimerization is required for UFM1 activation proposed_new_terms: [] suggested_questions: - question: >- How is UBA5 activity and UFM1 charging regulated in different subcellular/stress contexts (e.g. ER-membrane recruitment via GABARAP/LC3 versus cytosolic activity)? - question: >- Why do specific DEE44 versus SCAR24 UBA5 variants produce distinct neurological phenotypes despite both impairing UFM1 activation? - question: >- What is the functional significance of UBA5 phosphorylation (Ser45, Ser358) for its E1 activity or its interactions with UFM1/UFC1? suggested_experiments: - description: >- Quantitative in vitro UFM1-charging assays (adenylation and thioester formation) comparing wild-type UBA5 with DEE44/SCAR24 disease variants to rank residual E1 activity against clinical severity. - description: >- Structure-guided mutagenesis of the UIS and UFC motifs combined with cell-based ufmylation readouts (RPL26 UFMylation) to dissect UFM1 binding, GABARAP recruitment, and UFM1 handoff to UFC1. - description: >- Proximity-labeling (BioID/TurboID) of UBA5 across resting and ER-stress conditions to map context-dependent localization and partners at the ER membrane. references: - id: GO_REF:0000002 title: Gene Ontology annotation through association of InterPro records with GO terms findings: [] - id: GO_REF:0000024 title: >- Manual transfer of experimentally-verified manual GO annotation data to orthologs using Ensembl Compara findings: [] - id: GO_REF:0000033 title: Annotation inferences using phylogenetic trees findings: [] - id: GO_REF:0000044 title: Gene Ontology annotation based on UniProtKB/Swiss-Prot Subcellular Location vocabulary mapping findings: [] - id: GO_REF:0000052 title: Gene Ontology annotation based on curation of immunofluorescence data findings: [] - id: GO_REF:0000054 title: Gene Ontology annotation based on LIFEdb localization data findings: [] - id: GO_REF:0000107 title: >- Automatic transfer of experimentally verified manual GO annotation data to orthologs using Ensembl Compara findings: [] - id: GO_REF:0000120 title: Combined Automated Annotation using Multiple IEA Methods findings: [] - id: PMID:15071506 title: A novel protein-conjugating system for Ufm1, a ubiquitin-fold modifier. findings: - statement: >- Established UBA5 (Uba5) as the E1-like enzyme that activates UFM1 by forming a high-energy thioester, and UFC1 as the cognate E2. reference_section_type: ABSTRACT reference_review: relevance: HIGH correctness: VERIFIED review_notes: Founding paper defining UBA5 as the UFM1 E1; PubMed-verified. - id: PMID:16189514 title: Towards a proteome-scale map of the human protein-protein interaction network. findings: [] - id: PMID:18442052 title: UBE1DC1, an ubiquitin-activating enzyme, activates two different ubiquitin-like proteins. findings: - statement: >- Characterized UBA5 (UBE1DC1) subcellular localization (cytoplasm and, with SUMO2, nucleus) and its activating-enzyme activity; the SUMO2 claim was later superseded (UBA5 is specific for UFM1). reference_section_type: RESULTS - id: PMID:20562859 title: Network organization of the human autophagy system. findings: [] - id: PMID:21900206 title: A directed protein interaction network for investigating intracellular signal transduction. findings: [] - id: PMID:23152784 title: >- Transcriptional regulation of the Ufm1 conjugation system in response to disturbance of the endoplasmic reticulum homeostasis and inhibition of vesicle trafficking. findings: - statement: >- The UFM1 conjugation system (including UBA5) is induced by ER stress, linking ufmylation to ER homeostasis. reference_section_type: ABSTRACT - id: PMID:25219498 title: >- Modification of ASC1 by UFM1 is crucial for ERĪ± transactivation and breast cancer development. findings: - statement: >- Ufmylation of ASC1 (requiring the UBA5 E1) regulates ERalpha signaling. reference_section_type: ABSTRACT - id: PMID:25416956 title: A proteome-scale map of the human interactome network. findings: [] - id: PMID:26496610 title: >- A human interactome in three quantitative dimensions organized by stoichiometries and abundances. findings: [] - id: PMID:26872069 title: UBA5 mutations cause a new form of autosomal recessive cerebellar ataxia. findings: - statement: >- Biallelic UBA5 variants cause SCAR24; a truncating variant delocalizes UBA5 and disrupts its interaction with UFM1. reference_section_type: ABSTRACT reference_review: relevance: HIGH correctness: VERIFIED review_notes: SCAR24 disease genetics; PubMed-verified. - id: PMID:26929408 title: >- Structural and functional analysis of a novel interaction motif within UFM1-activating enzyme 5 (UBA5) required for binding to ubiquitin-like proteins and ufmylation. findings: - statement: >- Defined the UBA5 UIS motif that binds UFM1 and LC3/GABARAP proteins and is required for ufmylation. reference_section_type: ABSTRACT - id: PMID:27545681 title: >- Biallelic variants in UBA5 reveal that disruption of the UFM1 cascade can result in early-onset encephalopathy. findings: - statement: >- DEE44-causing UBA5 variants reduce or abolish UFM1 activating enzyme activity. reference_section_type: RESULTS reference_review: relevance: HIGH correctness: VERIFIED review_notes: DEE44 disease genetics with functional E1-activity readouts. - id: PMID:27653677 title: >- Trans-binding mechanism of ubiquitin-like protein activation revealed by a UBA5-UFM1 Complex. findings: - statement: >- Structural basis of UFM1 activation by UBA5 via a trans-binding mechanism across the homodimer; defines the catalytic Cys250 thioester and Zn site. reference_section_type: ABSTRACT reference_review: relevance: HIGH correctness: VERIFIED review_notes: Key mechanistic structure of the UBA5-UFM1 E1 reaction. - id: PMID:28514442 title: >- Architecture of the human interactome defines protein communities and disease networks. findings: [] - id: PMID:29295865 title: >- Trans-binding of UFM1 to UBA5 stimulates UBA5 homodimerization and ATP binding. findings: - statement: >- UFM1 trans-binding stimulates UBA5 homodimerization and enhances ATP binding, promoting UFM1 activation. reference_section_type: ABSTRACT - id: PMID:29868776 title: >- Biallelic UFM1 and UFC1 mutations expand the essential role of ufmylation in brain development. findings: - statement: UBA5 interacts with UFC1 as part of the UFM1 transfer cascade. reference_section_type: RESULTS - id: PMID:30412706 title: >- An N-terminal extension to UBA5 adenylation domain boosts UFM1 activation: isoform-specific differences in ubiquitin-like protein activation. findings: - statement: >- The UBA5 N-terminal extension boosts UFM1 activation; structural characterization of the UBA5-UFM1 complex and zinc site. reference_section_type: ABSTRACT - id: PMID:30626644 title: Ribosomal protein RPL26 is the principal target of UFMylation. findings: - statement: >- RPL26 is the principal UFM1 target; the UBA5/UFC1/UFL1 machinery acts on ER-bound ribosomes. reference_section_type: ABSTRACT - id: PMID:30990354 title: 'An atypical LIR motif within UBA5 (ubiquitin like modifier activating enzyme 5) interacts with GABARAP proteins and mediates membrane localization of UBA5.' findings: - statement: >- An atypical LIR motif in UBA5 binds GABARAP-family proteins and recruits UBA5 to the ER membrane. reference_section_type: ABSTRACT - id: PMID:32160526 title: >- A genome-wide ER-phagy screen highlights key roles of mitochondrial metabolism and ER-Resident UFMylation. findings: - statement: >- ER-resident UFMylation (initiated by UBA5) is required for reticulophagy and ER homeostasis. reference_section_type: ABSTRACT - id: PMID:32296183 title: A reference map of the human binary protein interactome. findings: [] - id: PMID:33961781 title: >- Dual proteome-scale networks reveal cell-specific remodeling of the human interactome. findings: [] - id: PMID:34299007 title: >- A concerted action of UBA5 C-terminal unstructured regions is important for transfer of activated UFM1 to UFC1. findings: - statement: >- UBA5 C-terminal regions mediate transfer of activated UFM1 to the E2 UFC1. reference_section_type: ABSTRACT - id: PMID:34588452 title: Structural basis for UFM1 transfer from UBA5 to UFC1. findings: - statement: >- Defined the UBA5 UFC-binding sequence and the structural mechanism of UFM1 transfer from UBA5 to UFC1, including activation of the UFC1 active site. reference_section_type: ABSTRACT reference_review: relevance: HIGH correctness: VERIFIED review_notes: Mechanism of E1-to-E2 UFM1 handoff. - id: PMID:35271311 title: 'OpenCell: Endogenous tagging for the cartography of human cellular organization.' findings: [] - id: PMID:38225382 title: Systematic discovery of protein interaction interfaces using AlphaFold and experimental validation. findings: [] - id: PMID:40205054 title: Multimodal cell maps as a foundation for structural and functional genomics. findings: []