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.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0005737 cytoplasm | IBA GO_REF:0000033 | ACCEPT | 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. Reason: Cytoplasmic localization is corroborated by direct experimental evidence (EXP, PMID:21888622) and HPA cytosol IDA, and is where USP21 deubiquitinates ribosomal substrates. Supporting Evidence: file:human/USP21/USP21-uniprot.txt SUBCELLULAR LOCATION: Cytoplasm |
| GO:0004843 cysteine-type deubiquitinase activity | IEA GO_REF:0000120 | ACCEPT | Summary: Electronic (InterPro/EC-based) assignment of the core DUB activity. This is the central, experimentally proven molecular function of USP21. 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. Supporting Evidence: PMID:10799498 USP21 is capable of removing ubiquitin from ubiquitinated proteins as expected. |
| GO:0005634 nucleus | IEA GO_REF:0000044 | ACCEPT | Summary: Automated subcellular-location assignment of nuclear localization, consistent with USP21's documented nuclear pool and nuclear substrates (BAZ2A/TIP5, histone H2A). Reason: Nuclear localization is experimentally supported (EXP, PMID:21888622) and consistent with nucleoplasm IDA; USP21 shuttles via a CRM1-dependent NES. Supporting Evidence: file:human/USP21/USP21-uniprot.txt Nucleus |
| GO:0005737 cytoplasm | IEA GO_REF:0000044 | ACCEPT | Summary: Automated subcellular-location assignment of cytoplasmic localization, redundant with but consistent with the IBA and experimental cytoplasm annotations. Reason: Correct compartment; agrees with stronger experimental (EXP) and IBA evidence for the same location. Supporting Evidence: file:human/USP21/USP21-uniprot.txt SUBCELLULAR LOCATION: Cytoplasm |
| GO:0008234 cysteine-type peptidase activity | IEA GO_REF:0000117 | KEEP AS NON CORE | Summary: Family-level (ARBA) assignment of cysteine-type peptidase activity, a parent of the more specific deubiquitinase activity that USP21 actually performs. 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. Supporting Evidence: file:human/USP21/USP21-uniprot.txt Belongs to the peptidase C19 family. USP21 subfamily. |
| GO:0016579 protein deubiquitination | IEA GO_REF:0000002 | ACCEPT | 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. 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. Supporting Evidence: PMID:32011234 cells lacking USP21 or OTUD3 have altered RQC activity and delayed eS10 deubiquitylation file:human/USP21/USP21-deep-research-falcon.md The enzyme exhibits promiscuous activity toward multiple ubiquitin chain types, including K6-, K11-, K29-, K48-, K63-linked, and linear ubiquitin conjugates |
| GO:0045893 positive regulation of DNA-templated transcription | IEA GO_REF:0000108 | KEEP AS NON CORE | 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. 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. Supporting Evidence: file:human/USP21/USP21-uniprot.txt resulting in regulation of transcriptional initiation file:human/USP21/USP21-deep-research-falcon.md USP21 removes monoubiquitin from histone H2A at lysine 119 (H2AK119ub) in nucleosomal contexts, with strong specificity for nucleosomal rather than free histone substrates |
| GO:0005515 protein binding | IPI PMID:19615732 Defining the human deubiquitinating enzyme interaction lands... | KEEP AS NON CORE | 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. 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. Supporting Evidence: file:human/USP21/USP21-goa.tsv PMID:19615732 UniProtKB:P09936 |
| GO:0005515 protein binding | IPI PMID:25416956 A proteome-scale map of the human interactome network. | KEEP AS NON CORE | Summary: Proteome-scale yeast two-hybrid interactome (HuRI) capturing a USP21-KRT40 (Q6A162) interaction. Bare protein binding from a global screen; uninformative. 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. Supporting Evidence: file:human/USP21/USP21-goa.tsv PMID:25416956 UniProtKB:Q6A162 |
| GO:0005515 protein binding | IPI PMID:32296183 A reference map of the human binary protein interactome. | KEEP AS NON CORE | Summary: Binary reference interactome (HuRI) capturing several USP21 interactions (EFEMP2, CPSF6, ADAMTSL4, KCTD9, HOXC10). These are bare protein binding hits from a systematic screen. 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. Supporting Evidence: file:human/USP21/USP21-goa.tsv PMID:32296183 UniProtKB:O95967 |
| GO:0005515 protein binding | IPI PMID:32814053 Interactome Mapping Provides a Network of Neurodegenerative ... | KEEP AS NON CORE | Summary: Neurodegeneration interactome screen capturing a USP21-UCHL1 (P09936) interaction. Bare protein binding from a high-throughput map. 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. Supporting Evidence: file:human/USP21/USP21-goa.tsv PMID:32814053 UniProtKB:P09936 |
| GO:0016579 protein deubiquitination | TAS Reactome:R-HSA-5688426 | ACCEPT | Summary: Reactome (TAS) curation of USP21 protein deubiquitination, here in the context of ubiquitin-specific processing protease pathways. Consistent with its core process. 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. Supporting Evidence: file:human/USP21/USP21-goa.tsv GO:0016579 protein deubiquitination |
| GO:0004843 cysteine-type deubiquitinase activity | TAS Reactome:R-HSA-5690157 | ACCEPT | Summary: Reactome (TAS) annotation of the core DUB activity. Correct and experimentally corroborated. Reason: Reflects USP21's experimentally proven cysteine-type deubiquitinase activity; curated TAS evidence is consistent with direct IDA evidence. Supporting Evidence: file:human/USP21/USP21-goa.tsv GO:0004843 cysteine-type deubiquitinase activity |
| GO:0004843 cysteine-type deubiquitinase activity | TAS Reactome:R-HSA-5690159 | ACCEPT | Summary: Reactome (TAS) annotation of the core cysteine-type deubiquitinase activity. Reason: Correct core molecular function, corroborated by direct experimental evidence. Supporting Evidence: file:human/USP21/USP21-goa.tsv GO:0004843 cysteine-type deubiquitinase activity |
| GO:0004843 cysteine-type deubiquitinase activity | TAS Reactome:R-HSA-6783177 | ACCEPT | Summary: Reactome (TAS) annotation of the core cysteine-type deubiquitinase activity. Reason: Correct core molecular function, corroborated by direct experimental evidence. Supporting Evidence: file:human/USP21/USP21-goa.tsv GO:0004843 cysteine-type deubiquitinase activity |
| GO:0005654 nucleoplasm | IDA GO_REF:0000052 | ACCEPT | Summary: Direct immunofluorescence (HPA) evidence for nucleoplasmic localization, consistent with USP21's nuclear substrates (BAZ2A/TIP5, histone H2A). Reason: IDA-supported nuclear localization agrees with the documented nuclear pool of USP21 and its nuclear functions. Supporting Evidence: file:human/USP21/USP21-goa.tsv GO:0005654 nucleoplasm cellular_component |
| GO:0005829 cytosol | IDA GO_REF:0000052 | ACCEPT | Summary: Direct immunofluorescence (HPA) evidence for cytosolic localization, consistent with USP21's cytoplasmic role in ribosome quality control. Reason: IDA-supported cytosolic localization agrees with the documented cytoplasmic site of action. Supporting Evidence: file:human/USP21/USP21-goa.tsv GO:0005829 cytosol cellular_component |
| GO:0005654 nucleoplasm | TAS Reactome:R-HSA-5690157 | ACCEPT | Summary: Reactome (TAS) nucleoplasm localization, consistent with the experimentally supported nuclear pool. Reason: Agrees with HPA IDA nucleoplasm and EXP nucleus evidence. Supporting Evidence: file:human/USP21/USP21-goa.tsv GO:0005654 nucleoplasm cellular_component |
| GO:0005654 nucleoplasm | TAS Reactome:R-HSA-6783177 | ACCEPT | Summary: Reactome (TAS) nucleoplasm localization, redundant with the other nucleoplasm annotations and consistent with experimental evidence. Reason: Agrees with HPA IDA nucleoplasm and EXP nucleus evidence. Supporting Evidence: file:human/USP21/USP21-goa.tsv GO:0005654 nucleoplasm cellular_component |
| GO:0005829 cytosol | TAS Reactome:R-HSA-5690159 | ACCEPT | Summary: Reactome (TAS) cytosol localization, consistent with the experimentally supported cytoplasmic pool. Reason: Agrees with HPA IDA cytosol and EXP cytoplasm evidence. Supporting Evidence: file:human/USP21/USP21-goa.tsv GO:0005829 cytosol cellular_component |
| GO:0005634 nucleus | EXP PMID:21888622 A global survey of CRM1-dependent nuclear export sequences i... | ACCEPT | 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. Reason: Direct experimental evidence places USP21 in the nucleus with a CRM1-dependent export signal, consistent with its nuclear substrates. Supporting Evidence: file:human/USP21/USP21-uniprot.txt Nucleus {ECO:0000269|PubMed:21888622} |
| GO:0005737 cytoplasm | EXP PMID:21888622 A global survey of CRM1-dependent nuclear export sequences i... | ACCEPT | 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. 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. Supporting Evidence: file:human/USP21/USP21-uniprot.txt Cytoplasm {ECO:0000269|PubMed:21888622} file:human/USP21/USP21-deep-research-falcon.md USP21 is the only deubiquitinase in a systematic survey of 66 mammalian DUBs to display clear association with both microtubules and centrosomes |
| GO:0004843 cysteine-type deubiquitinase activity | IDA PMID:32011234 Distinct regulatory ribosomal ubiquitylation events are reve... | ACCEPT | Summary: Direct (IDA) demonstration that USP21 is a cysteine-type deubiquitinase acting on ubiquitylated 40S ribosomal proteins, with catalytic Cys-221 required. 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. Supporting Evidence: PMID:32011234 we identify OTUD3 and USP21 as deubiquitylating enzymes that antagonize ZNF598-mediated 40S ubiquitylation and can limit RQC activation |
| GO:0016579 protein deubiquitination | IDA PMID:32011234 Distinct regulatory ribosomal ubiquitylation events are reve... | ACCEPT | 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. 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. Supporting Evidence: PMID:32011234 cells lacking USP21 or OTUD3 have altered RQC activity and delayed eS10 deubiquitylation |
| GO:0045815 transcription initiation-coupled chromatin remodeling | ISS GO_REF:0000024 | KEEP AS NON CORE | 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. 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. Supporting Evidence: file:human/USP21/USP21-uniprot.txt Deubiquitination of histone H2A releaves the repression of di- and trimethylation of histone H3 at 'Lys-4' |
| GO:0004843 cysteine-type deubiquitinase activity | ISS GO_REF:0000024 | ACCEPT | Summary: Sequence-similarity (ISS, from mouse Q9QZL6) assignment of the core DUB activity, which is independently proven by direct human experimental evidence. Reason: The cysteine-type deubiquitinase activity is the core molecular function and is directly demonstrated in human (IDA); the ISS transfer is concordant. Supporting Evidence: PMID:10799498 USP21 is capable of removing ubiquitin from ubiquitinated proteins as expected. |
| GO:0004843 cysteine-type deubiquitinase activity | IMP PMID:26100909 BEND3 represses rDNA transcription by stabilizing a NoRC com... | ACCEPT | Summary: Mutational/functional (IMP) evidence supporting USP21 deubiquitinase activity in the context of deubiquitinating and stabilizing the NoRC component BAZ2A/TIP5. Reason: USP21 interacts with and deubiquitinates Tip5/BAZ2A, stabilizing it; this supports the core DUB activity acting on a defined nuclear substrate. Supporting Evidence: PMID:26100909 USP21 can interact with and deubiquitinate Tip5, thereby stabilizing the total levels of Tip5. |
| GO:0005515 protein binding | IPI PMID:26100909 BEND3 represses rDNA transcription by stabilizing a NoRC com... | KEEP AS NON CORE | 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. 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. Supporting Evidence: file:human/USP21/USP21-goa.tsv PMID:26100909 UniProtKB:Q9UIF9 |
| GO:0008234 cysteine-type peptidase activity | IMP PMID:10799498 Identification of a novel isopeptidase with dual specificity... | KEEP AS NON CORE | Summary: Mutational (IMP) evidence (Cys-221 required) for cysteine-type peptidase activity, a parent of the specific deubiquitinase activity USP21 performs. 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. Supporting Evidence: file:human/USP21/USP21-uniprot.txt C->A,S: Abolishes ubiquitin thioesterase activity. |
| GO:0004843 cysteine-type deubiquitinase activity | IDA PMID:10799498 Identification of a novel isopeptidase with dual specificity... | ACCEPT | Summary: Original direct (IDA) demonstration that USP21 removes ubiquitin from ubiquitinated proteins in cells. Defines the core molecular function. Reason: First direct evidence of USP21's cysteine-type deubiquitinase activity; this is the gene's core molecular function. Supporting Evidence: PMID:10799498 USP21 is capable of removing ubiquitin from ubiquitinated proteins as expected. |
| GO:0019784 deNEDDylase activity | IDA PMID:10799498 Identification of a novel isopeptidase with dual specificity... | ACCEPT | Summary: Direct (IDA) evidence that USP21 also removes NEDD8 from NEDD8 conjugates (but not SUMO/Sentrin-1), giving it dual ubiquitin/NEDD8 isopeptidase specificity. Reason: A genuine, experimentally demonstrated secondary catalytic activity; USP21 was the first USP shown to have dual ubiquitin/NEDD8 specificity. Supporting Evidence: PMID:10799498 USP21 is capable of removing NEDD8 from NEDD8 conjugates but has no effect on Sentrin-1 conjugates. |
| GO:0003713 transcription coactivator activity | ISS GO_REF:0000024 | KEEP AS NON CORE | 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. 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. Supporting Evidence: file:human/USP21/USP21-uniprot.txt thereby acting as a coactivator |
| GO:0008234 cysteine-type peptidase activity | ISS GO_REF:0000024 | KEEP AS NON CORE | Summary: Sequence-similarity (ISS, from mouse Q9QZL6) assignment of the general cysteine-type peptidase activity, a parent of the specific deubiquitinase activity. Reason: Correct but less precise than GO:0004843 cysteine-type deubiquitinase activity; retained as a general non-core MF annotation. Supporting Evidence: file:human/USP21/USP21-uniprot.txt Belongs to the peptidase C19 family. USP21 subfamily. |
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Download this section (compressed HTML)Q: 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?
Q: How is USP21's dual ubiquitin/NEDD8 specificity regulated in cells, and does its deNEDDylase activity have a distinct physiological substrate set?
Q: Does USP21 nucleocytoplasmic shuttling (via its CRM1-dependent NES) partition its ribosome-quality-control (cytoplasmic) versus chromatin/transcription (nuclear) functions?
Experiment: 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.
Experiment: 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.
Experiment: 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.
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