# USP21 (Q9UK80, UBP21_HUMAN) review notes NOTE: This is the CORRECT USP21 (UniProt Q9UK80). An earlier batch-6 fetch under the symbol "USP21" mis-resolved (UniProt synonym collision) to USP25 and was relabeled; this review is freshly fetched for Q9UK80. ## Identity / overview - Ubiquitin carboxyl-terminal hydrolase 21 (USP21), a deubiquitinating enzyme (DUB) of the peptidase C19 / USP family. EC 3.4.19.12. 565 aa. Gene on chr 1q21. HGNC:12620. [file:human/USP21/USP21-uniprot.txt "Belongs to the peptidase C19 family. USP21 subfamily."] - Catalytic USP domain spans residues 212-558; catalytic nucleophile Cys-221 (mutating to A/S abolishes activity); proton-acceptor His-518; a structural Zn(2+) site (C384/C387/C437/C440). [file:human/USP21/USP21-uniprot.txt "MUTAGEN 221 ... C->A,S: Abolishes ubiquitin thioesterase activity."] - Dual subcellular localization: cytoplasm and nucleus; has a CRM1-dependent nuclear export signal (motif 134-152). [PMID:21888622 — "A global survey of CRM1-dependent nuclear export sequences in the human deubiquitinase family"] ## Core molecular function: cysteine-type deubiquitinase (GO:0004843) - Originally identified as an isopeptidase with DUAL specificity, removing ubiquitin from ubiquitinated proteins AND NEDD8 from NEDD8 conjugates (but NOT SUMO/Sentrin-1). Cys-221 required. [PMID:10799498 "USP21 is capable of removing ubiquitin from ubiquitinated proteins as expected. Furthermore, USP21 is capable of removing NEDD8 from NEDD8 conjugates but has no effect on Sentrin-1 conjugates."] -> supports both GO:0004843 (deubiquitinase) and GO:0019784 (deNEDDylase activity), both IDA. - Catalytic activity re-confirmed with active-site mapping and Cys-221 mutagenesis. [PMID:32011234 — active site, mutagenesis of Cys-221] - USP21 USP domain crystallized in complex with ubiquitin (PDB 3I3T/2Y5B/3MTN); structural Zn site. [PMID:21399617 "Polyubiquitin binding and cross-reactivity in the USP domain deubiquitinase USP21."] ## Substrate / process contexts (BP) 1. **Ribosome-associated quality control (RQC), negative regulator.** USP21 (with OTUD3) deubiquitinates 40S ribosomal proteins eS10/RPS10 and uS10/RPS20, antagonizing ZNF598-mediated 40S ubiquitylation and limiting RQC activation. [PMID:32011234 "we identify OTUD3 and USP21 as deubiquitylating enzymes that antagonize ZNF598-mediated 40S ubiquitylation and can limit RQC activation"] [PMID:32011234 "cells lacking USP21 or OTUD3 have altered RQC activity and delayed eS10 deubiquitylation indicating a functional role for deubiquitylating enzymes within the RQC pathway"] This is the IDA-supported BP behind GO:0016579 protein deubiquitination (PMID:32011234). 2. **rDNA silencing / NoRC stabilization.** USP21 deubiquitinates and stabilizes BAZ2A/TIP5 (a NoRC component), acting with BEND3 to repress rRNA gene transcription. [PMID:26100909 "USP21 can interact with and deubiquitinate Tip5, thereby stabilizing the total levels of Tip5."] Supports GO:0016579 (IMP/IPI; substrate BAZ2A/TIP5). 3. **Histone H2A deubiquitination / transcription coactivation.** UniProt (By similarity, from mouse Q9QZL6) describes deubiquitination of histone H2A relieving repression, acting as a transcriptional coactivator and regulating transcription initiation. This underlies the ISS terms GO:0003713 (transcription coactivator activity), GO:0045815 (transcription initiation-coupled chromatin remodeling) and the GOC IEA GO:0045893 (positive regulation of DNA-templated transcription). These are ortholog-transferred (mouse) / inferred, not direct human experimental evidence. [file:human/USP21/USP21-uniprot.txt "Deubiquitinates histone H2A ... thereby acting as a coactivator (By similarity)."] 4. Reported but not in this GOA set: deubiquitination of RIPK1/RIP1 (TNF/NF-kB signaling), RIG-I, GATA3, MARK3, ACLY, microtubule/centrosome regulation. Mentioned as prior work in PMID:26100909 ("regulate the deubiquitination of several other substrates including RIG-1, RIP1, and GATA-3"). These broaden the substrate range but the specific GO BP terms for them are not in the seeded GOA. ## Interactions (IPI protein binding annotations) - All bare GO:0005515 protein binding annotations from high-throughput interactome screens: - PMID:19615732 (Sowa et al. DUB interaction landscape) WITH UCHL1 (P09936) - PMID:25416956 (HuRI/CCSB Y2H) WITH KRT40 (Q6A162) - PMID:32296183 (binary interactome HuRI) WITH EFEMP2/O95967, CPSF6/Q16630-2, ADAMTSL4/Q6UY14-3, KCTD9/Q7L273, HOXC10/Q9NYD6 - PMID:32814053 (neurodegeneration interactome) WITH UCHL1 (P09936) - PMID:26100909 IPI WITH BEND3 (Q5T5X7) and BAZ2A (Q9UIF9) — these two are functionally meaningful (BEND3 = interactor; BAZ2A/TIP5 = substrate), unlike the generic screen hits. - Per curation guidelines, bare "protein binding" is uninformative and should not be elevated to core. The BEND3/BAZ2A interactions (PMID:26100909) are biologically meaningful but are still recorded as bare GO:0005515; they are best captured via the deubiquitination BP context. ## Localization annotations - Cytoplasm + nucleus, both experimentally supported (PMID:21888622, EXP). HPA IDA: cytosol (GO:0005829) and nucleoplasm (GO:0005654). IBA cytoplasm. These are consistent. - Centrosome (CD-CODE Centrosome cross-ref in UniProt) consistent with reported microtubule/centrosome role, but no centrosome GO term is in the seeded GOA. ## Reactome TAS - Reactome annotations (R-HSA-5688426, -5690157, -5690159, -6783177) place USP21 DUB activity in Ub-specific processing protease and TNFR1 signaling pathways (consistent with RIPK1 deubiquitination role). These are TAS general DUB-activity / localization terms — acceptable as curated but non-specific. ## Curation decisions summary - Core MF: cysteine-type deubiquitinase activity (GO:0004843) — strong IDA/IMP human evidence. - Secondary MF: deNEDDylase activity (GO:0019784) — IDA, accept (genuine dual specificity). - BP: protein deubiquitination (GO:0016579) — accept as core process (multiple direct substrates: 40S RPs, BAZ2A). - GO:0008234 cysteine-type peptidase activity — parent of GO:0004843; KEEP_AS_NON_CORE (less precise). - Transcription-related terms (GO:0003713, GO:0045815, GO:0045893) — mouse ISS / inferred; KEEP_AS_NON_CORE (real but ortholog-transferred / indirect, not the primary human-demonstrated function). - protein binding (GO:0005515) IPI — KEEP_AS_NON_CORE (records real interactions) or MARK_AS_OVER_ANNOTATED for generic screen hits unrelated to function; never core. - Localizations — ACCEPT (cytosol, nucleoplasm, nucleus, cytoplasm all supported).