id: Q9UK80 gene_symbol: USP21 product_type: PROTEIN status: COMPLETE taxon: id: NCBITaxon:9606 label: Homo sapiens description: >- USP21 (ubiquitin carboxyl-terminal hydrolase 21) is a cysteine-protease deubiquitinating enzyme (DUB) of the peptidase C19 / ubiquitin-specific protease (USP) family. Its catalytic USP domain (residues ~212-558) uses a Cys-221 nucleophile and a His-518 proton acceptor and contains a structural zinc site; mutation of Cys-221 abolishes activity. USP21 hydrolyzes isopeptide and peptide bonds at the C-terminal Gly of ubiquitin to remove ubiquitin from conjugated substrates, and it has dual specificity, also removing the ubiquitin-like modifier NEDD8 (but not SUMO/Sentrin-1). It localizes to both the cytoplasm and the nucleus and carries a CRM1-dependent nuclear export signal. Through its DUB activity USP21 antagonizes ubiquitin-dependent signaling and degradation of diverse substrates. It deubiquitinates 40S ribosomal proteins RPS10/eS10 and RPS20/uS10 to counteract ZNF598-mediated ribosomal ubiquitylation and limit ribosome-associated quality control (RQC); it deubiquitinates and stabilizes the NoRC component BAZ2A/TIP5 to promote rDNA silencing together with BEND3; and (by similarity to the mouse ortholog) it deubiquitinates histone H2A to relieve transcriptional repression and act as a transcriptional coactivator. Additional reported substrates include RIPK1, RIG-I, GATA3, MARK3 and ACLY, consistent with broad roles in innate immune signaling, transcription and metabolism. alternative_products: - name: '1' id: Q9UK80-1 - name: '2' id: Q9UK80-2 sequence_note: VSP_036717, VSP_036718 - name: '3' id: Q9UK80-3 sequence_note: VSP_036719 existing_annotations: - term: id: GO:0005737 label: cytoplasm evidence_type: IBA original_reference_id: GO_REF:0000033 qualifier: is_active_in review: summary: Phylogenetically inferred cytoplasmic localization. USP21 is experimentally documented in the cytoplasm and acts on cytoplasmic substrates (e.g. 40S ribosomal proteins), so this is well supported. action: ACCEPT reason: Cytoplasmic localization is corroborated by direct experimental evidence (EXP, PMID:21888622) and HPA cytosol IDA, and is where USP21 deubiquitinates ribosomal substrates. supported_by: - reference_id: file:human/USP21/USP21-uniprot.txt supporting_text: 'SUBCELLULAR LOCATION: Cytoplasm' - term: id: GO:0004843 label: cysteine-type deubiquitinase activity evidence_type: IEA original_reference_id: GO_REF:0000120 qualifier: enables review: summary: Electronic (InterPro/EC-based) assignment of the core DUB activity. This is the central, experimentally proven molecular function of USP21. action: ACCEPT reason: The cysteine-type deubiquitinase activity is directly demonstrated in human cells (IDA, PMID:10799498; PMID:32011234) with Cys-221 as the catalytic nucleophile; the IEA assignment is correct and corroborated by experiment. supported_by: - reference_id: PMID:10799498 supporting_text: USP21 is capable of removing ubiquitin from ubiquitinated proteins as expected. - term: id: GO:0005634 label: nucleus evidence_type: IEA original_reference_id: GO_REF:0000044 qualifier: located_in review: summary: Automated subcellular-location assignment of nuclear localization, consistent with USP21's documented nuclear pool and nuclear substrates (BAZ2A/TIP5, histone H2A). action: ACCEPT reason: Nuclear localization is experimentally supported (EXP, PMID:21888622) and consistent with nucleoplasm IDA; USP21 shuttles via a CRM1-dependent NES. supported_by: - reference_id: file:human/USP21/USP21-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: Automated subcellular-location assignment of cytoplasmic localization, redundant with but consistent with the IBA and experimental cytoplasm annotations. action: ACCEPT reason: Correct compartment; agrees with stronger experimental (EXP) and IBA evidence for the same location. supported_by: - reference_id: file:human/USP21/USP21-uniprot.txt supporting_text: 'SUBCELLULAR LOCATION: Cytoplasm' - term: id: GO:0008234 label: cysteine-type peptidase activity evidence_type: IEA original_reference_id: GO_REF:0000117 qualifier: enables review: summary: Family-level (ARBA) assignment of cysteine-type peptidase activity, a parent of the more specific deubiquitinase activity that USP21 actually performs. action: KEEP_AS_NON_CORE reason: Correct but less precise than GO:0004843 cysteine-type deubiquitinase activity, which is the experimentally established function. Retained as a true but non-core (general) molecular-function annotation. supported_by: - reference_id: file:human/USP21/USP21-uniprot.txt supporting_text: Belongs to the peptidase C19 family. USP21 subfamily. - term: id: GO:0016579 label: protein deubiquitination evidence_type: IEA original_reference_id: GO_REF:0000002 qualifier: involved_in review: summary: InterPro-based assignment of the protein deubiquitination process, which is the direct biological outcome of USP21's DUB activity. Beyond the cache-verified substrates (40S ribosomal proteins, BAZ2A/TIP5), the Falcon deep-research report compiles a broad reported substrate repertoire (e.g. RIG-I, MEK2, Nanog, histone H2A, MARK3, TCF7) processed via multiple ubiquitin chain types, all of which fall under this general process term. action: ACCEPT reason: Protein deubiquitination is directly demonstrated for multiple human substrates (40S ribosomal proteins, BAZ2A/TIP5); this process annotation is well supported. The Falcon report (UNVERIFIED LLM synthesis; primary substrate papers not in cache) further supports breadth of substrate processing and chain-type promiscuity but does not alter this annotation. supported_by: - reference_id: PMID:32011234 supporting_text: cells lacking USP21 or OTUD3 have altered RQC activity and delayed eS10 deubiquitylation - reference_id: file:human/USP21/USP21-deep-research-falcon.md supporting_text: The enzyme exhibits promiscuous activity toward multiple ubiquitin chain types, including K6-, K11-, K29-, K48-, K63-linked, and linear ubiquitin conjugates - term: id: GO:0045893 label: positive regulation of DNA-templated transcription evidence_type: IEA original_reference_id: GO_REF:0000108 qualifier: involved_in review: summary: Automated inference (from the transcription coactivator activity term) that USP21 positively regulates transcription. This derives ultimately from the mouse "by similarity" histone H2A deubiquitination / coactivator role rather than direct human experimental evidence. action: KEEP_AS_NON_CORE reason: A plausible downstream process inherited from the ortholog-transferred coactivator role (histone H2A deubiquitination relieving repression), but not directly demonstrated for human USP21 and peripheral to its core DUB function. USP21 acts as both a coactivator (H2A) and a repressor (rDNA via BAZ2A), so a single positive-regulation term is an oversimplification. The Falcon report adds (UNVERIFIED) that USP21 removes the repressive H2AK119ub mark with specificity for nucleosomal substrate, consistent with a transcriptional-activation role, though the primary paper is not cached. supported_by: - reference_id: file:human/USP21/USP21-uniprot.txt supporting_text: resulting in regulation of transcriptional initiation - reference_id: file:human/USP21/USP21-deep-research-falcon.md supporting_text: USP21 removes monoubiquitin from histone H2A at lysine 119 (H2AK119ub) in nucleosomal contexts, with strong specificity for nucleosomal rather than free histone substrates - term: id: GO:0005515 label: protein binding evidence_type: IPI original_reference_id: PMID:19615732 qualifier: enables review: summary: High-throughput DUB interaction-landscape screen (Sowa et al.) capturing a USP21-UCHL1 (P09936) interaction. The bare protein binding term is uninformative and the partner does not define a specific USP21 function. action: KEEP_AS_NON_CORE reason: Records a real physical interaction but bare protein binding (GO:0005515) is uninformative per curation guidelines; not a core function. The UCHL1 partner is an unrelated DUB from a global screen. supported_by: - reference_id: file:human/USP21/USP21-goa.tsv supporting_text: PMID:19615732 UniProtKB:P09936 - term: id: GO:0005515 label: protein binding evidence_type: IPI original_reference_id: PMID:25416956 qualifier: enables review: summary: Proteome-scale yeast two-hybrid interactome (HuRI) capturing a USP21-KRT40 (Q6A162) interaction. Bare protein binding from a global screen; uninformative. action: KEEP_AS_NON_CORE reason: Single high-throughput Y2H interaction with a keratin (KRT40) that has no established functional relationship to USP21; bare protein binding is uninformative and not part of the core function. supported_by: - reference_id: file:human/USP21/USP21-goa.tsv supporting_text: PMID:25416956 UniProtKB:Q6A162 - term: id: GO:0005515 label: protein binding evidence_type: IPI original_reference_id: PMID:32296183 qualifier: enables review: summary: Binary reference interactome (HuRI) capturing several USP21 interactions (EFEMP2, CPSF6, ADAMTSL4, KCTD9, HOXC10). These are bare protein binding hits from a systematic screen. action: KEEP_AS_NON_CORE reason: Records real binary interactions but bare protein binding (GO:0005515) is uninformative; the partners are from a global screen and do not individually define a specific USP21 molecular function. Not core. supported_by: - reference_id: file:human/USP21/USP21-goa.tsv supporting_text: PMID:32296183 UniProtKB:O95967 - term: id: GO:0005515 label: protein binding evidence_type: IPI original_reference_id: PMID:32814053 qualifier: enables review: summary: Neurodegeneration interactome screen capturing a USP21-UCHL1 (P09936) interaction. Bare protein binding from a high-throughput map. action: KEEP_AS_NON_CORE reason: Records a real interaction but bare protein binding (GO:0005515) is uninformative and the partner does not define a specific USP21 function; not core. supported_by: - reference_id: file:human/USP21/USP21-goa.tsv supporting_text: PMID:32814053 UniProtKB:P09936 - term: id: GO:0016579 label: protein deubiquitination evidence_type: TAS original_reference_id: Reactome:R-HSA-5688426 qualifier: involved_in review: summary: Reactome (TAS) curation of USP21 protein deubiquitination, here in the context of ubiquitin-specific processing protease pathways. Consistent with its core process. action: ACCEPT reason: Protein deubiquitination is the genuine process carried out by USP21 and is directly supported by experimental evidence elsewhere; the curated TAS term is appropriate. supported_by: - reference_id: file:human/USP21/USP21-goa.tsv supporting_text: GO:0016579 protein deubiquitination - term: id: GO:0004843 label: cysteine-type deubiquitinase activity evidence_type: TAS original_reference_id: Reactome:R-HSA-5690157 qualifier: enables review: summary: Reactome (TAS) annotation of the core DUB activity. Correct and experimentally corroborated. action: ACCEPT reason: Reflects USP21's experimentally proven cysteine-type deubiquitinase activity; curated TAS evidence is consistent with direct IDA evidence. supported_by: - reference_id: file:human/USP21/USP21-goa.tsv supporting_text: GO:0004843 cysteine-type deubiquitinase activity - term: id: GO:0004843 label: cysteine-type deubiquitinase activity evidence_type: TAS original_reference_id: Reactome:R-HSA-5690159 qualifier: enables review: summary: Reactome (TAS) annotation of the core cysteine-type deubiquitinase activity. action: ACCEPT reason: Correct core molecular function, corroborated by direct experimental evidence. supported_by: - reference_id: file:human/USP21/USP21-goa.tsv supporting_text: GO:0004843 cysteine-type deubiquitinase activity - term: id: GO:0004843 label: cysteine-type deubiquitinase activity evidence_type: TAS original_reference_id: Reactome:R-HSA-6783177 qualifier: enables review: summary: Reactome (TAS) annotation of the core cysteine-type deubiquitinase activity. action: ACCEPT reason: Correct core molecular function, corroborated by direct experimental evidence. supported_by: - reference_id: file:human/USP21/USP21-goa.tsv supporting_text: GO:0004843 cysteine-type deubiquitinase activity - term: id: GO:0005654 label: nucleoplasm evidence_type: IDA original_reference_id: GO_REF:0000052 qualifier: located_in review: summary: Direct immunofluorescence (HPA) evidence for nucleoplasmic localization, consistent with USP21's nuclear substrates (BAZ2A/TIP5, histone H2A). action: ACCEPT reason: IDA-supported nuclear localization agrees with the documented nuclear pool of USP21 and its nuclear functions. supported_by: - reference_id: file:human/USP21/USP21-goa.tsv supporting_text: GO:0005654 nucleoplasm cellular_component - term: id: GO:0005829 label: cytosol evidence_type: IDA original_reference_id: GO_REF:0000052 qualifier: located_in review: summary: Direct immunofluorescence (HPA) evidence for cytosolic localization, consistent with USP21's cytoplasmic role in ribosome quality control. action: ACCEPT reason: IDA-supported cytosolic localization agrees with the documented cytoplasmic site of action. supported_by: - reference_id: file:human/USP21/USP21-goa.tsv supporting_text: GO:0005829 cytosol cellular_component - term: id: GO:0005654 label: nucleoplasm evidence_type: TAS original_reference_id: Reactome:R-HSA-5690157 qualifier: located_in review: summary: Reactome (TAS) nucleoplasm localization, consistent with the experimentally supported nuclear pool. action: ACCEPT reason: Agrees with HPA IDA nucleoplasm and EXP nucleus evidence. supported_by: - reference_id: file:human/USP21/USP21-goa.tsv supporting_text: GO:0005654 nucleoplasm cellular_component - term: id: GO:0005654 label: nucleoplasm evidence_type: TAS original_reference_id: Reactome:R-HSA-6783177 qualifier: located_in review: summary: Reactome (TAS) nucleoplasm localization, redundant with the other nucleoplasm annotations and consistent with experimental evidence. action: ACCEPT reason: Agrees with HPA IDA nucleoplasm and EXP nucleus evidence. supported_by: - reference_id: file:human/USP21/USP21-goa.tsv supporting_text: GO:0005654 nucleoplasm cellular_component - term: id: GO:0005829 label: cytosol evidence_type: TAS original_reference_id: Reactome:R-HSA-5690159 qualifier: located_in review: summary: Reactome (TAS) cytosol localization, consistent with the experimentally supported cytoplasmic pool. action: ACCEPT reason: Agrees with HPA IDA cytosol and EXP cytoplasm evidence. supported_by: - reference_id: file:human/USP21/USP21-goa.tsv supporting_text: GO:0005829 cytosol cellular_component - term: id: GO:0005634 label: nucleus evidence_type: EXP original_reference_id: PMID:21888622 qualifier: located_in review: summary: Experimental (EXP) evidence for nuclear localization from a study of CRM1-dependent nuclear export signals across the human DUB family; USP21 has a functional NES. action: ACCEPT reason: Direct experimental evidence places USP21 in the nucleus with a CRM1-dependent export signal, consistent with its nuclear substrates. supported_by: - reference_id: file:human/USP21/USP21-uniprot.txt supporting_text: Nucleus {ECO:0000269|PubMed:21888622} - term: id: GO:0005737 label: cytoplasm evidence_type: EXP original_reference_id: PMID:21888622 qualifier: located_in review: summary: Experimental (EXP) evidence for cytoplasmic localization, consistent with USP21's CRM1-dependent nuclear export and cytoplasmic substrates. The Falcon deep-research report notes a more specific cytoplasmic distribution from a systematic DUB-localization survey (Urbe et al. 2012), in which USP21 uniquely associates with microtubules and centrosomes. action: ACCEPT reason: Direct experimental evidence supports cytoplasmic localization; consistent with IBA, IEA and HPA IDA cytosol. A more granular cytoplasmic localization (microtubule/centrosome) is reported in the Falcon synthesis but the primary paper is not in the cache, so no more-specific CC term is asserted here. supported_by: - reference_id: file:human/USP21/USP21-uniprot.txt supporting_text: Cytoplasm {ECO:0000269|PubMed:21888622} - reference_id: file:human/USP21/USP21-deep-research-falcon.md supporting_text: USP21 is the only deubiquitinase in a systematic survey of 66 mammalian DUBs to display clear association with both microtubules and centrosomes - term: id: GO:0004843 label: cysteine-type deubiquitinase activity evidence_type: IDA original_reference_id: PMID:32011234 qualifier: enables review: summary: Direct (IDA) demonstration that USP21 is a cysteine-type deubiquitinase acting on ubiquitylated 40S ribosomal proteins, with catalytic Cys-221 required. action: ACCEPT reason: Strong direct human experimental evidence for the core DUB activity; USP21 antagonizes ZNF598-mediated 40S ubiquitylation. This is a defining piece of evidence for the core molecular function. supported_by: - reference_id: PMID:32011234 supporting_text: we identify OTUD3 and USP21 as deubiquitylating enzymes that antagonize ZNF598-mediated 40S ubiquitylation and can limit RQC activation - term: id: GO:0016579 label: protein deubiquitination evidence_type: IDA original_reference_id: PMID:32011234 qualifier: involved_in review: summary: Direct (IDA) evidence that USP21 carries out protein deubiquitination of 40S ribosomal proteins (eS10/RPS10, uS10/RPS20) within the RQC pathway, acting as a negative regulator of RQC. action: ACCEPT reason: Directly demonstrated process; cells lacking USP21 show delayed eS10 deubiquitylation and altered RQC activity. This is a core, well-supported biological process for USP21. supported_by: - reference_id: PMID:32011234 supporting_text: cells lacking USP21 or OTUD3 have altered RQC activity and delayed eS10 deubiquitylation - term: id: GO:0045815 label: transcription initiation-coupled chromatin remodeling evidence_type: ISS original_reference_id: GO_REF:0000024 qualifier: involved_in review: summary: Sequence-similarity (ISS, from mouse Q9QZL6) transfer of a chromatin-remodeling / transcription-initiation role based on histone H2A deubiquitination. Not directly demonstrated for human USP21. action: KEEP_AS_NON_CORE reason: A plausible role inherited by ortholog transfer from mouse (histone H2A deubiquitination relieving H3K4 methylation repression), but not directly shown in human and secondary to USP21's core DUB function across multiple substrates. supported_by: - reference_id: file:human/USP21/USP21-uniprot.txt supporting_text: Deubiquitination of histone H2A releaves the repression of di- and trimethylation of histone H3 at 'Lys-4' - term: id: GO:0004843 label: cysteine-type deubiquitinase activity evidence_type: ISS original_reference_id: GO_REF:0000024 qualifier: enables review: summary: Sequence-similarity (ISS, from mouse Q9QZL6) assignment of the core DUB activity, which is independently proven by direct human experimental evidence. action: ACCEPT reason: The cysteine-type deubiquitinase activity is the core molecular function and is directly demonstrated in human (IDA); the ISS transfer is concordant. supported_by: - reference_id: PMID:10799498 supporting_text: USP21 is capable of removing ubiquitin from ubiquitinated proteins as expected. - term: id: GO:0004843 label: cysteine-type deubiquitinase activity evidence_type: IMP original_reference_id: PMID:26100909 qualifier: enables review: summary: Mutational/functional (IMP) evidence supporting USP21 deubiquitinase activity in the context of deubiquitinating and stabilizing the NoRC component BAZ2A/TIP5. action: ACCEPT reason: USP21 interacts with and deubiquitinates Tip5/BAZ2A, stabilizing it; this supports the core DUB activity acting on a defined nuclear substrate. supported_by: - reference_id: PMID:26100909 supporting_text: USP21 can interact with and deubiquitinate Tip5, thereby stabilizing the total levels of Tip5. - term: id: GO:0005515 label: protein binding evidence_type: IPI original_reference_id: PMID:26100909 qualifier: enables review: summary: IPI interactions (WITH BEND3/Q5T5X7 and BAZ2A/Q9UIF9) underlying the rDNA-silencing study. Unlike generic screen hits, these partners are functionally meaningful (BEND3 regulates USP21 stability; BAZ2A/TIP5 is a USP21 substrate), but the term itself is uninformative bare protein binding. action: KEEP_AS_NON_CORE reason: Records biologically meaningful interactions (BEND3 interactor and BAZ2A substrate), but bare protein binding (GO:0005515) is uninformative and the relevant biology is better captured by the deubiquitination process annotation; not core. supported_by: - reference_id: file:human/USP21/USP21-goa.tsv supporting_text: PMID:26100909 UniProtKB:Q9UIF9 - term: id: GO:0008234 label: cysteine-type peptidase activity evidence_type: IMP original_reference_id: PMID:10799498 qualifier: enables review: summary: Mutational (IMP) evidence (Cys-221 required) for cysteine-type peptidase activity, a parent of the specific deubiquitinase activity USP21 performs. action: KEEP_AS_NON_CORE reason: Correct but less precise than GO:0004843; the same Cys-221 mutagenesis supports the more specific deubiquitinase activity term, which should be the core MF. supported_by: - reference_id: file:human/USP21/USP21-uniprot.txt supporting_text: 'C->A,S: Abolishes ubiquitin thioesterase activity.' - term: id: GO:0004843 label: cysteine-type deubiquitinase activity evidence_type: IDA original_reference_id: PMID:10799498 qualifier: enables review: summary: Original direct (IDA) demonstration that USP21 removes ubiquitin from ubiquitinated proteins in cells. Defines the core molecular function. action: ACCEPT reason: First direct evidence of USP21's cysteine-type deubiquitinase activity; this is the gene's core molecular function. supported_by: - reference_id: PMID:10799498 supporting_text: USP21 is capable of removing ubiquitin from ubiquitinated proteins as expected. - term: id: GO:0019784 label: deNEDDylase activity evidence_type: IDA original_reference_id: PMID:10799498 qualifier: enables review: summary: Direct (IDA) evidence that USP21 also removes NEDD8 from NEDD8 conjugates (but not SUMO/Sentrin-1), giving it dual ubiquitin/NEDD8 isopeptidase specificity. action: ACCEPT reason: A genuine, experimentally demonstrated secondary catalytic activity; USP21 was the first USP shown to have dual ubiquitin/NEDD8 specificity. supported_by: - reference_id: PMID:10799498 supporting_text: USP21 is capable of removing NEDD8 from NEDD8 conjugates but has no effect on Sentrin-1 conjugates. - term: id: GO:0003713 label: transcription coactivator activity evidence_type: ISS original_reference_id: GO_REF:0000024 qualifier: enables review: summary: Sequence-similarity (ISS, from mouse Q9QZL6) assignment of transcription coactivator activity, based on histone H2A deubiquitination relieving repression. Not a direct catalytic/binding activity and not demonstrated in human. action: KEEP_AS_NON_CORE reason: Inherited by ortholog transfer; reflects an indirect (via H2A deubiquitination) coactivator role rather than USP21's core enzymatic function. USP21 can also repress transcription (rDNA via BAZ2A), so coactivator is context-specific. supported_by: - reference_id: file:human/USP21/USP21-uniprot.txt supporting_text: thereby acting as a coactivator - term: id: GO:0008234 label: cysteine-type peptidase activity evidence_type: ISS original_reference_id: GO_REF:0000024 qualifier: enables review: summary: Sequence-similarity (ISS, from mouse Q9QZL6) assignment of the general cysteine-type peptidase activity, a parent of the specific deubiquitinase activity. action: KEEP_AS_NON_CORE reason: Correct but less precise than GO:0004843 cysteine-type deubiquitinase activity; retained as a general non-core MF annotation. supported_by: - reference_id: file:human/USP21/USP21-uniprot.txt supporting_text: Belongs to the peptidase C19 family. USP21 subfamily. 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:0000108 title: Automatic assignment of GO terms using logical inference, based on inter-ontology links findings: [] - id: GO_REF:0000117 title: Electronic Gene Ontology annotations created by ARBA machine learning models findings: [] - id: GO_REF:0000120 title: Combined Automated Annotation using Multiple IEA Methods findings: [] - id: PMID:10799498 title: Identification of a novel isopeptidase with dual specificity for ubiquitin- and NEDD8-conjugated proteins. findings: - statement: USP21 is a cysteine-protease isopeptidase that removes ubiquitin from ubiquitinated proteins and removes NEDD8 from NEDD8 conjugates, but has no effect on Sentrin-1/SUMO conjugates (dual ubiquitin/NEDD8 specificity). reference_section_type: ABSTRACT - statement: Catalytic Cys-221 is required; its mutation abolishes ubiquitin thioesterase activity. reference_section_type: RESULTS reference_review: relevance: HIGH correctness: VERIFIED review_notes: "Cached PMID_10799498 title/body match; establishes USP21 as the founding dual ubiquitin/NEDD8 isopeptidase (supports GO:0004843 and GO:0019784, consistent with the GOA evidence rows for this PMID)." - id: PMID:19615732 title: Defining the human deubiquitinating enzyme interaction landscape. findings: [] - id: PMID:21888622 title: A global survey of CRM1-dependent nuclear export sequences in the human deubiquitinase family. findings: - statement: USP21 contains a functional CRM1-dependent nuclear export signal and localizes to both nucleus and cytoplasm. reference_section_type: RESULTS - id: PMID:25416956 title: A proteome-scale map of the human interactome network. findings: [] - id: PMID:26100909 title: BEND3 represses rDNA transcription by stabilizing a NoRC component via USP21 deubiquitinase. findings: - statement: USP21 interacts with and deubiquitinates BAZ2A/TIP5 (a NoRC component), stabilizing it; SUMOylated BEND3 stabilizes USP21, and together they promote rDNA silencing. reference_section_type: RESULTS reference_review: relevance: HIGH correctness: VERIFIED review_notes: "Cached PMID_26100909 title/body match; supports USP21's nuclear deubiquitination of BAZ2A/TIP5 substrate (a basis for the protein-deubiquitination core function)." - id: PMID:32011234 title: Distinct regulatory ribosomal ubiquitylation events are reversible and hierarchically organized. findings: - statement: USP21 (with OTUD3) is a deubiquitylating enzyme that antagonizes ZNF598-mediated 40S ribosomal ubiquitylation (on eS10/RPS10 and uS10/RPS20) and limits ribosome-associated quality control (RQC) activation. reference_section_type: ABSTRACT - statement: Cells lacking USP21 have altered RQC activity and delayed eS10 deubiquitylation, establishing a functional role for USP21 within the RQC pathway. reference_section_type: ABSTRACT reference_review: relevance: HIGH correctness: VERIFIED review_notes: "Cached PMID_32011234 title/body match; body explicitly names USP21 (with OTUD3) antagonizing ZNF598-mediated 40S ubiquitylation, supporting the RQC deubiquitination function." - id: PMID:32296183 title: A reference map of the human binary protein interactome. findings: [] - id: PMID:32814053 title: Interactome Mapping Provides a Network of Neurodegenerative Disease Proteins and Uncovers Widespread Protein Aggregation in Affected Brains. findings: [] - id: Reactome:R-HSA-5688426 title: Ub-specific processing proteases (protein deubiquitination) findings: [] - id: Reactome:R-HSA-5690157 title: Ub-specific processing proteases (USP21 deubiquitinase activity) findings: [] - id: Reactome:R-HSA-5690159 title: Ub-specific processing proteases (USP21 deubiquitinase activity) findings: [] - id: Reactome:R-HSA-6783177 title: Ub-specific processing proteases (USP21 deubiquitinase activity) findings: [] - id: file:human/USP21/USP21-deep-research-falcon.md title: Falcon deep research report for USP21 findings: - statement: USP21 is a broad-specificity DUB that processes multiple polyubiquitin chain types (K6, K11, K29, K48, K63, and linear) and cross-reacts with ISG15, with substrate-stabilizing deubiquitination reported for RIG-I (K63), MEK2 (K48), Nanog (K48), histone H2A (H2AK119ub), MARK3, TCF7, GATA3 and RIPK1. reference_section_type: OTHER reference_review: relevance: HIGH correctness: UNVERIFIED review_notes: >- LLM-synthesized (Edison/Falcon) literature report; useful for substrate breadth and chain-type/pathway context, but treated as UNVERIFIED. USP21-SPECIFIC substrate evidence that the report attributes to dedicated primary papers includes: RIG-I deubiquitination / negative regulation of antiviral RIG-I-IFN signaling (Fan et al. 2014, J Exp Med, doi:10.1084/jem.20122844), MEK2 stabilization driving ERK/MAPK signaling (Li et al. 2018, doi:10.1038/s41419-018-0523-z), Nanog stabilization in ESC pluripotency (Liu et al. 2016), histone H2A K119ub deubiquitination, MARK3/macropinocytosis in pancreatic cancer (Hou et al. 2021), TCF7, and microtubule/centrosome association (Urbe et al. 2012). These primary papers are NOT in the local publications cache and could not be verified here, so substrate identities and chain-type assignments are recorded but not used to change existing experimental annotations. DUB-FAMILY-LEVEL inference (broad chain-type promiscuity, ISG15 cross-reactivity, general USP catalytic mechanism) should not be over-read as USP21-specific physiological function. NOTE a conflict to flag for experts: this report (citing Ye et al. 2011 structural work) states USP21 is "inactive against NEDD8 conjugates", whereas the curated IDA annotation GO:0019784 (PMID:10799498) records deNEDDylase activity; the existing experimental deNEDDylase annotation is retained and NOT weakened on the basis of this report. core_functions: - description: Cysteine-type deubiquitinating enzyme that hydrolyzes isopeptide/peptide bonds at the C-terminal Gly of ubiquitin to remove ubiquitin from conjugated substrates, using a Cys-221 nucleophile within its USP domain. molecular_function: id: GO:0004843 label: cysteine-type deubiquitinase activity locations: - id: GO:0005829 label: cytosol - id: GO:0005654 label: nucleoplasm supported_by: - reference_id: PMID:10799498 supporting_text: USP21 is capable of removing ubiquitin from ubiquitinated proteins as expected. - reference_id: PMID:32011234 supporting_text: we identify OTUD3 and USP21 as deubiquitylating enzymes that antagonize ZNF598-mediated 40S ubiquitylation and can limit RQC activation - description: Removes the ubiquitin-like modifier NEDD8 from NEDD8-conjugated proteins (deNEDDylase activity), a genuine secondary isopeptidase specificity distinct from SUMO; USP21 was the first USP shown to act on both ubiquitin and NEDD8. molecular_function: id: GO:0019784 label: deNEDDylase activity supported_by: - reference_id: PMID:10799498 supporting_text: USP21 is capable of removing NEDD8 from NEDD8 conjugates but has no effect on Sentrin-1 conjugates. - description: Through its deubiquitinase activity USP21 carries out protein deubiquitination of specific substrates, including 40S ribosomal proteins (eS10/RPS10, uS10/RPS20) to negatively regulate ribosome-associated quality control, and BAZ2A/TIP5 to stabilize the NoRC complex and promote rDNA silencing. molecular_function: id: GO:0004843 label: cysteine-type deubiquitinase activity locations: - id: GO:0005829 label: cytosol - id: GO:0005654 label: nucleoplasm supported_by: - reference_id: PMID:32011234 supporting_text: cells lacking USP21 or OTUD3 have altered RQC activity and delayed eS10 deubiquitylation - reference_id: PMID:26100909 supporting_text: USP21 can interact with and deubiquitinate Tip5, thereby stabilizing the total levels of Tip5. directly_involved_in: - id: GO:0016579 label: protein deubiquitination proposed_new_terms: [] suggested_questions: - question: What is the in vivo substrate hierarchy and selectivity of USP21 across its reported targets (40S ribosomal proteins, BAZ2A/TIP5, histone H2A, RIPK1, RIG-I, GATA3, MARK3, ACLY), and which interactions reflect direct catalysis versus indirect stabilization? - question: How is USP21's dual ubiquitin/NEDD8 specificity regulated in cells, and does its deNEDDylase activity have a distinct physiological substrate set? - question: Does USP21 nucleocytoplasmic shuttling (via its CRM1-dependent NES) partition its ribosome-quality-control (cytoplasmic) versus chromatin/transcription (nuclear) functions? suggested_experiments: - description: Catalytically-dead (C221A) versus wild-type USP21 rescue in USP21-knockout cells combined with diGly-ubiquitin proteomics to define the direct, catalysis-dependent deubiquitinated substrate repertoire genome-wide. - description: Quantitative kinetic assays comparing USP21 activity on ubiquitin- versus NEDD8-isopeptide substrates (and on different polyubiquitin linkage types) to characterize its dual specificity and linkage preference. - description: Time-resolved measurement of eS10/uS10 (RPS10/RPS20) ubiquitylation and ribosome stalling / RQC reporter readouts upon USP21 depletion or overexpression to quantify its role as a negative regulator of RQC.