id: Q9NUQ7 gene_symbol: UFSP2 product_type: PROTEIN status: COMPLETE taxon: id: NCBITaxon:9606 label: Homo sapiens description: >- UFSP2 (UFM1-specific protease 2) is the principal human UFM1-specific cysteine (thiol-dependent) isopeptidase of the peptidase C78 family (catalytic Cys302). It acts in the UFM1 (ubiquitin-fold modifier 1) conjugation system, where it both processes pro-UFM1 to expose the activating C-terminal glycine and, predominantly, removes UFM1 from conjugated target proteins (deUFMylation). Documented substrates include the ribosomal protein RPL26/uL24, CYB5R3, DDRGK1, MRE11, TRIP4 and CD274/PD-L1. At the cytoplasmic surface of the endoplasmic reticulum, UFSP2 deUFMylates RPL26 on 60S ribosomal subunits, a step required to release the UFM1 E3 ligase complex and recycle 60S subunits after ribosome-associated quality control of stalled ER-translocating ribosomes. Through deUFMylation of CYB5R3 it modulates ER-phagy, and through TRIP4 it influences nuclear-receptor (estrogen receptor) transactivation. Loss-of-function and missense UFSP2 variants cause autosomal-dominant skeletal dysplasias (Beukes hip dysplasia, spondyloepimetaphyseal dysplasia) and a recessive neurodevelopmental/epileptic encephalopathy. existing_annotations: - term: id: GO:0005783 label: endoplasmic reticulum evidence_type: IBA original_reference_id: GO_REF:0000033 qualifier: is_active_in review: summary: Phylogenetic inference that UFSP2 acts at the endoplasmic reticulum, where it deUFMylates RPL26 on ER-associated 60S ribosomes. Consistent with direct experimental evidence. action: ACCEPT reason: UFSP2 is an ER-membrane-tethered deUFMylase; the IBA localization is corroborated by direct IDA evidence. supported_by: - reference_id: PMID:38383785 supporting_text: ER-membrane-tethered deUFMylase UFSP2 - term: id: GO:0071567 label: deUFMylase activity evidence_type: IBA original_reference_id: GO_REF:0000033 qualifier: enables review: summary: Phylogenetic inference of UFM1-specific protease (deUFMylase) activity, the core molecular function of UFSP2, directly supported by extensive biochemistry. action: ACCEPT reason: deUFMylase activity is the central, repeatedly demonstrated function of UFSP2. supported_by: - reference_id: file:human/UFSP2/UFSP2-uniprot.txt supporting_text: Thiol-dependent isopeptidase that specifically cleaves UFM1 - term: id: GO:0005634 label: nucleus evidence_type: IBA original_reference_id: GO_REF:0000033 qualifier: is_active_in review: summary: Phylogenetic inference of nuclear localization. Nuclear localization for human UFSP2 is supported only by sequence similarity to the mouse ortholog, not by direct human data; the dominant functional pool is at the ER/cytosol. action: KEEP_AS_NON_CORE reason: Possible minor nuclear pool (e.g. TRIP4-related nuclear-receptor regulation) but not the core site of UFSP2's deUFMylase function; retained as non-core. supported_by: - reference_id: file:human/UFSP2/UFSP2-uniprot.txt supporting_text: Nucleus {ECO:0000250|UniProtKB:Q99K23} - term: id: GO:0006508 label: proteolysis evidence_type: IBA original_reference_id: GO_REF:0000033 qualifier: involved_in review: summary: Generic proteolysis term reflecting the peptidase activity of UFSP2. The specific activity is UFM1-specific isopeptide/peptide cleavage, better captured by deUFMylase activity and protein maturation. action: KEEP_AS_NON_CORE reason: Technically correct (UFSP2 is a protease) but uninformative compared with the specific deUFMylase activity; retained as non-core parent process. supported_by: - reference_id: file:human/UFSP2/UFSP2-uniprot.txt supporting_text: Thiol-dependent isopeptidase that specifically cleaves UFM1 - term: id: GO:0005634 label: nucleus evidence_type: IEA original_reference_id: GO_REF:0000120 qualifier: located_in review: summary: Electronic localization to nucleus, inherited from the mouse ortholog; see the IBA/ISS nucleus annotations. action: KEEP_AS_NON_CORE reason: Not the core site of action; supported only by orthology, retained as non-core. supported_by: - reference_id: file:human/UFSP2/UFSP2-uniprot.txt supporting_text: Nucleus {ECO:0000250|UniProtKB:Q99K23} - term: id: GO:0005737 label: cytoplasm evidence_type: IEA original_reference_id: GO_REF:0000120 qualifier: located_in review: summary: Electronic localization to cytoplasm, consistent with the cytoplasmic/ER-surface site where UFSP2 acts on ribosomal and other substrates. action: ACCEPT reason: Cytoplasm (including the cytoplasmic face of the ER) is a documented compartment for UFSP2 activity. supported_by: - reference_id: file:human/UFSP2/UFSP2-uniprot.txt supporting_text: Cytoplasm {ECO:0000250|UniProtKB:Q99K23} - term: id: GO:0005783 label: endoplasmic reticulum evidence_type: IEA original_reference_id: GO_REF:0000120 qualifier: located_in review: summary: Electronic localization to ER, consistent with the experimentally established ER-membrane-tethered localization of UFSP2. action: ACCEPT reason: ER is the principal functional site of UFSP2 (RPL26 deUFMylation); agrees with direct evidence. supported_by: - reference_id: PMID:38383785 supporting_text: ER-membrane-tethered deUFMylase UFSP2 - term: id: GO:0005515 label: protein binding evidence_type: IPI original_reference_id: PMID:32296183 qualifier: enables review: summary: High-throughput binary interactome screen recording UFSP2 interactions with APOBEC1 and LMO1; the bare protein binding term is uninformative and these partners do not inform UFSP2's deUFMylase function. action: KEEP_AS_NON_CORE reason: Records real interactions but the generic term is uninformative per curation guidelines; partners are not part of the core function. supported_by: - reference_id: file:human/UFSP2/UFSP2-goa.tsv supporting_text: GO:0005515 - 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: Ortholog-based (Ensembl) electronic annotation transferring an interferon-gamma production phenotype from the mouse gene. No direct human evidence; not part of the characterized UFM1-protease function. action: MARK_AS_OVER_ANNOTATED reason: Phenotype-based orthology transfer with no mechanistic link to UFSP2's deUFMylase activity in human; likely an indirect downstream consequence rather than a core function. supported_by: - reference_id: file:human/UFSP2/UFSP2-goa.tsv supporting_text: GO:0032649 - term: id: GO:0071567 label: deUFMylase activity evidence_type: IEA original_reference_id: GO_REF:0000120 qualifier: enables review: summary: Automated electronic annotation of deUFMylase activity, redundant with and consistent with extensive experimental support. action: ACCEPT reason: Correct core molecular function. supported_by: - reference_id: file:human/UFSP2/UFSP2-uniprot.txt supporting_text: Thiol-dependent isopeptidase that specifically cleaves UFM1 - term: id: GO:0005634 label: nucleus evidence_type: ISS original_reference_id: GO_REF:0000024 qualifier: located_in review: summary: Sequence-similarity-based nuclear localization transferred from the mouse ortholog (Q99K23). See the IBA/IEA nucleus annotations. action: KEEP_AS_NON_CORE reason: Orthology-only support; not the core functional compartment. supported_by: - reference_id: file:human/UFSP2/UFSP2-uniprot.txt supporting_text: Nucleus {ECO:0000250|UniProtKB:Q99K23} - term: id: GO:0005737 label: cytoplasm evidence_type: ISS original_reference_id: GO_REF:0000024 qualifier: located_in review: summary: Sequence-similarity-based cytoplasmic localization, consistent with the cytoplasmic/ER-surface site of UFSP2 action. action: ACCEPT reason: Cytoplasmic localization is well supported, including by direct human data. supported_by: - reference_id: file:human/UFSP2/UFSP2-uniprot.txt supporting_text: Cytoplasm {ECO:0000250|UniProtKB:Q99K23} - term: id: GO:0071567 label: deUFMylase activity evidence_type: IDA original_reference_id: PMID:37795761 qualifier: enables review: summary: Direct evidence for UFSP2 deUFMylase activity in the context of HRD1 UFMylation and ER homeostasis. action: ACCEPT reason: Direct experimental support for the core deUFMylase activity. supported_by: - reference_id: file:human/UFSP2/UFSP2-uniprot.txt supporting_text: Thiol-dependent isopeptidase that specifically cleaves UFM1 - term: id: GO:0071567 label: deUFMylase activity evidence_type: IDA original_reference_id: PMID:36893266 qualifier: enables review: summary: Direct evidence for UFSP2 deUFMylase activity. action: ACCEPT reason: Direct experimental support for the core deUFMylase activity. supported_by: - reference_id: file:human/UFSP2/UFSP2-uniprot.txt supporting_text: Thiol-dependent isopeptidase that specifically cleaves UFM1 - term: id: GO:0042177 label: negative regulation of protein catabolic process evidence_type: IDA original_reference_id: PMID:36543799 qualifier: involved_in review: summary: UFSP2 deUFMylates CYB5R3; because CYB5R3 UFMylation signals ER-phagy (degradation), UFSP2 activity opposes this catabolic route. The negative regulation of a degradation process is a downstream consequence of its deUFMylase activity. action: KEEP_AS_NON_CORE reason: Plausible process outcome of UFSP2 reversing CYB5R3 UFMylation, but a downstream/context-specific effect rather than the core molecular function. supported_by: - reference_id: PMID:36543799 supporting_text: overexpression of UFSP2 but not the active-site mutant UFSP2C302A decreased the amount of the UFM1~CYB5R3 conjugate - term: id: GO:0071567 label: deUFMylase activity evidence_type: IDA original_reference_id: PMID:31595041 qualifier: enables review: summary: Direct evidence for UFSP2 deUFMylase activity on a target substrate. action: ACCEPT reason: Direct experimental support for the core deUFMylase activity. supported_by: - reference_id: file:human/UFSP2/UFSP2-uniprot.txt supporting_text: Thiol-dependent isopeptidase that specifically cleaves UFM1 - term: id: GO:0071567 label: deUFMylase activity evidence_type: IDA original_reference_id: PMID:36543799 qualifier: enables review: summary: Direct demonstration that wild-type UFSP2, but not the catalytic Cys302Ala mutant, removes UFM1 from CYB5R3, establishing UFSP2 deUFMylase activity on this ER substrate. action: ACCEPT reason: Active-site-dependent removal of UFM1 from a defined substrate; strong direct support for the core function. supported_by: - reference_id: PMID:36543799 supporting_text: overexpression of UFSP2 but not the active-site mutant UFSP2C302A decreased the amount of the UFM1~CYB5R3 conjugate - term: id: GO:0072344 label: rescue of stalled cytosolic ribosome evidence_type: IDA original_reference_id: PMID:38383785 qualifier: involved_in review: summary: UFSP2 deUFMylation of RPL26/uL24 is required to release the UFM1 E3 ligase from UFMylated 60S subunits, enabling 60S recycling after RQC-mediated splitting of ribosomes stalled during co-translational ER translocation. action: ACCEPT reason: Directly supported role in the ribosome-rescue/recycling arm of ER-associated RQC; this is a key biological process for UFSP2. supported_by: - reference_id: PMID:38383785 supporting_text: UFMylation facilitates the rescue of 60S ribosomal subunits (60S) that are released after ribosome-associated quality-control-mediated splitting of ribosomes that stall during co-translational translocation of secretory proteins into the ER - term: id: GO:0005783 label: endoplasmic reticulum evidence_type: IDA original_reference_id: PMID:35926457 qualifier: is_active_in review: summary: Direct evidence that UFSP2 acts at the ER (in contrast to cytosolic UFSP1), where it removes UFM1 from the ribosomal subunit RPL26. action: ACCEPT reason: Establishes the ER as the functional compartment for UFSP2's RPL26 deUFMylation. supported_by: - reference_id: PMID:35926457 supporting_text: While UFSP2, but not UFSP1, removes UFM1 from the ribosomal subunit RPL26 - term: id: GO:0032790 label: ribosome disassembly evidence_type: IDA original_reference_id: PMID:38383785 qualifier: involved_in review: summary: UFSP2-mediated deUFMylation of RPL26 releases the UFM1 E3 ligase clamp from the 60S subunit, contributing to disassembly/recycling of post-RQC 60S ribosomal subunits. action: ACCEPT reason: Directly supported role in releasing the E3-UFM1 clamp to allow 60S recycling. supported_by: - reference_id: PMID:38383785 supporting_text: UFM1 E3 ligase promotes recycling of 60S ribosomal subunits from the ER - term: id: GO:0071567 label: deUFMylase activity evidence_type: IMP original_reference_id: PMID:27926783 qualifier: enables review: summary: Mutational/phenotypic evidence supporting UFSP2 as the active deUFMylase mediating deconjugation of UFM1 from target proteins. action: ACCEPT reason: Supports the core deUFMylase activity; UFSP2 mainly acts as a protein deUFMylase. supported_by: - reference_id: file:human/UFSP2/UFSP2-uniprot.txt supporting_text: UFSP2 mainly acts as a protein deUFMylase that mediates deconjugation of UFM1 from target proteins - term: id: GO:0071567 label: deUFMylase activity evidence_type: IDA original_reference_id: PMID:35926457 qualifier: enables review: summary: Direct evidence that UFSP2 removes UFM1 from RPL26, confirming deUFMylase activity. action: ACCEPT reason: Direct experimental support for the core deUFMylase activity. supported_by: - reference_id: PMID:35926457 supporting_text: While UFSP2, but not UFSP1, removes UFM1 from the ribosomal subunit RPL26 - term: id: GO:0071567 label: deUFMylase activity evidence_type: IDA original_reference_id: PMID:38383785 qualifier: enables review: summary: UFSP2 deUFMylates RPL26 on 60S subunits, the activity underlying 60S recycling. action: ACCEPT reason: Direct support for the core deUFMylase activity in the ribosome-recycling context. supported_by: - reference_id: PMID:38383785 supporting_text: ER-membrane-tethered deUFMylase UFSP2 - term: id: GO:0071567 label: deUFMylase activity evidence_type: IMP original_reference_id: PMID:33473208 qualifier: enables review: summary: A pathogenic UFSP2 variant impairs UFMylation homeostasis, consistent with UFSP2 functioning as the active UFM1-specific peptidase; mutant phenotype supports the enzymatic role. action: ACCEPT reason: Disease-variant evidence supports UFSP2's deUFMylase/UFM1-protease function. supported_by: - reference_id: PMID:33473208 supporting_text: UFM1-specific peptidase 2 (UFSP2), which participates in the UFMylation pathway - term: id: GO:0071567 label: deUFMylase activity evidence_type: IMP original_reference_id: PMID:32160526 qualifier: enables review: summary: Mutational evidence supporting UFSP2 deUFMylase activity. action: ACCEPT reason: Supports the core deUFMylase activity. supported_by: - reference_id: file:human/UFSP2/UFSP2-uniprot.txt supporting_text: Thiol-dependent isopeptidase that specifically cleaves UFM1 - 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: UFSP2 deUFMylates the coactivator TRIP4/ASC-1, regulating nuclear-receptor (including estrogen receptor) transactivation. A context-specific downstream role of UFSP2's deUFMylase activity. action: KEEP_AS_NON_CORE reason: A genuine but context-specific regulatory process downstream of UFSP2 deUFMylating TRIP4; not the core molecular function. supported_by: - reference_id: file:human/UFSP2/UFSP2-uniprot.txt supporting_text: Catalyzes deUFMylation of TRIP4, regulating intracellular nuclear receptors transactivation - term: id: GO:0006508 label: proteolysis evidence_type: IMP original_reference_id: PMID:25219498 qualifier: involved_in review: summary: Generic proteolysis term reflecting UFSP2's peptidase activity (here in the TRIP4 deUFMylation study). The specific activity is UFM1-specific cleavage. action: KEEP_AS_NON_CORE reason: Correct but uninformative parent term relative to deUFMylase activity. supported_by: - reference_id: file:human/UFSP2/UFSP2-uniprot.txt supporting_text: Thiol-dependent isopeptidase that specifically cleaves UFM1 - term: id: GO:0071567 label: deUFMylase activity evidence_type: IMP original_reference_id: PMID:25219498 qualifier: enables review: summary: UFSP2 deUFMylates TRIP4; mutational/functional evidence supports the deUFMylase activity on this substrate. action: ACCEPT reason: Supports the core deUFMylase activity with a defined substrate (TRIP4). supported_by: - reference_id: file:human/UFSP2/UFSP2-uniprot.txt supporting_text: Catalyzes deUFMylation of TRIP4, regulating intracellular nuclear receptors transactivation - term: id: GO:0005515 label: protein binding evidence_type: IPI original_reference_id: PMID:25219498 qualifier: enables review: summary: Records a UFSP2-TRIP4 (Q15650) interaction (the substrate it deUFMylates). The bare protein binding term is uninformative; the functionally meaningful relationship is enzyme-substrate. action: KEEP_AS_NON_CORE reason: Reflects the UFSP2-TRIP4 substrate interaction but the generic term is uninformative per curation guidelines. supported_by: - reference_id: file:human/UFSP2/UFSP2-uniprot.txt supporting_text: Catalyzes deUFMylation of TRIP4, regulating intracellular nuclear receptors transactivation core_functions: - description: UFM1-specific cysteine (thiol-dependent) protease that removes UFM1 from conjugated substrates (deUFMylation), most prominently RPL26/uL24 on ER-associated 60S ribosomal subunits, and also processes pro-UFM1; catalytic residue Cys302. molecular_function: id: GO:0071567 label: deUFMylase activity locations: - id: GO:0005783 label: endoplasmic reticulum supported_by: - reference_id: file:human/UFSP2/UFSP2-uniprot.txt supporting_text: UFSP2 mainly acts as a protein deUFMylase that mediates deconjugation of UFM1 from target proteins - reference_id: PMID:35926457 supporting_text: While UFSP2, but not UFSP1, removes UFM1 from the ribosomal subunit RPL26 - description: deUFMylation of RPL26/uL24 releases the UFM1 E3 ligase from UFMylated 60S subunits, enabling recycling of 60S ribosomal subunits after ribosome-associated quality control of ribosomes that stall during co-translational ER translocation. molecular_function: id: GO:0071567 label: deUFMylase activity locations: - id: GO:0005783 label: endoplasmic reticulum supported_by: - reference_id: PMID:38383785 supporting_text: UFMylation facilitates the rescue of 60S ribosomal subunits (60S) that are released after ribosome-associated quality-control-mediated splitting of ribosomes that stall during co-translational translocation of secretory proteins into the ER - reference_id: PMID:38383785 supporting_text: ER-membrane-tethered deUFMylase UFSP2 proposed_new_terms: [] suggested_questions: - question: How is the choice between UFSP2 pro-UFM1 maturation and substrate deUFMylation regulated, and what determines its substrate selectivity (RPL26 vs CYB5R3 vs TRIP4)? - question: How do the skeletal-dysplasia missense variants versus the recessive neurodevelopmental variant differ mechanistically in their effect on UFSP2 catalysis and the resulting UFMylation balance? suggested_experiments: - description: Substrate-resolved UFM1-conjugate proteomics in UFSP2-knockout versus catalytically dead (C302A) rescue cells to map the in vivo deUFMylation substrate repertoire. - description: Reconstitute UFMylated 60S recycling in vitro with purified UFSP2 to test whether RPL26 deUFMylation is necessary and sufficient to release the UFM1 E3 ligase clamp. references: - 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: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:25219498 title: Modification of ASC1 by UFM1 is crucial for ERĪ± transactivation and breast cancer development. findings: - statement: UFSP2 deUFMylates the coactivator TRIP4, regulating nuclear-receptor (including estrogen receptor) transactivation. reference_section_type: RESULTS reference_review: relevance: MEDIUM correctness: UNVERIFIED review_notes: Not cached; supporting facts taken from the UniProt FUNCTION summary citing this PMID. - id: PMID:27926783 title: 'A novel approach to assess the ubiquitin-fold modifier 1-system in cells.' findings: - statement: UFSP2 mainly acts as a protein deUFMylase deconjugating UFM1 from target proteins. reference_section_type: RESULTS reference_review: relevance: MEDIUM correctness: UNVERIFIED review_notes: Not cached; supporting facts taken from the UniProt FUNCTION summary citing this PMID. - id: PMID:31595041 title: 'UFMylation of RPL26 links translocation-associated quality control to endoplasmic reticulum protein homeostasis.' findings: [] reference_review: relevance: MEDIUM correctness: UNVERIFIED review_notes: Not cached; cited by UniProt for UFSP2 deUFMylase activity. - id: PMID:32160526 title: A Genome-wide ER-phagy Screen Highlights Key Roles of Mitochondrial Metabolism and ER-Resident UFMylation. findings: [] reference_review: relevance: MEDIUM correctness: UNVERIFIED review_notes: Not cached; cited by UniProt for UFSP2 deUFMylase activity. - id: PMID:32296183 title: A reference map of the human binary protein interactome. findings: [] reference_review: relevance: LOW correctness: VERIFIED review_notes: High-throughput binary interactome; partners (APOBEC1, LMO1) do not inform UFSP2 function. - id: PMID:33473208 title: A pathogenic UFSP2 variant in an autosomal recessive form of pediatric neurodevelopmental anomalies and epilepsy. findings: - statement: A homozygous UFSP2 variant in the UFM1-specific peptidase 2 causes a recessive pediatric neurodevelopmental disorder with epilepsy, affecting UFMylation. reference_section_type: ABSTRACT reference_review: relevance: HIGH correctness: VERIFIED review_notes: PubMed-verified; links UFSP2 enzymatic function to neurodevelopmental disease. - id: PMID:35926457 title: Human UFSP1 is an active protease that regulates UFM1 maturation and UFMylation. findings: - statement: UFSP2, but not UFSP1, removes UFM1 from the ribosomal subunit RPL26; UFSP2 acts at the ER. reference_section_type: ABSTRACT reference_review: relevance: HIGH correctness: VERIFIED review_notes: PubMed-verified; distinguishes UFSP2 (ER, RPL26) from UFSP1. - id: PMID:36543799 title: The UFM1 system regulates ER-phagy through the ufmylation of CYB5R3. findings: - statement: Wild-type UFSP2, but not the active-site mutant UFSP2C302A, removes UFM1 from CYB5R3; CYB5R3 UFMylation signals ER-phagy required for neuronal development. reference_section_type: RESULTS reference_review: relevance: HIGH correctness: VERIFIED review_notes: PubMed-verified; CYB5R3 deUFMylation by UFSP2 (Cys302-dependent). - id: PMID:36893266 title: Dysregulation of PD-L1 by UFMylation imparts tumor immune evasion and identified as a potential therapeutic target. findings: [] reference_review: relevance: MEDIUM correctness: UNVERIFIED review_notes: Not cached; cited by UniProt/GOA for UFSP2 deUFMylase activity (IDA). - id: PMID:37795761 title: UFMylation of HRD1 regulates endoplasmic reticulum homeostasis. findings: - statement: UFSP2 deUFMylase activity acts in the context of HRD1 UFMylation and ER homeostasis. reference_section_type: RESULTS reference_review: relevance: MEDIUM correctness: VERIFIED review_notes: PubMed-verified title; cited for UFSP2 deUFMylase activity (IDA). - id: PMID:38383785 title: UFM1 E3 ligase promotes recycling of 60S ribosomal subunits from the ER. findings: - statement: UFM1 modifies RPL26/uL24 on ER ribosomes to facilitate rescue/recycling of 60S subunits after RQC splitting; UFSP2 is the ER-membrane-tethered deUFMylase that removes this mark. reference_section_type: ABSTRACT reference_review: relevance: HIGH correctness: VERIFIED review_notes: PubMed-verified; defines UFSP2's role in 60S recycling / ribosome disassembly.