FBXO21 (FBX21, KIAA0875; also reported as SIP/FBXO3B) is a 628-residue F-box protein that serves as the substrate-recognition subunit of a multi-subunit SCF (SKP1-CUL1-F-box protein)-type E3 ubiquitin ligase complex. Through its N-terminal F-box domain (residues 28-84) it binds SKP1, coupling to CUL1 and the catalytic RING subunit RBX1, while its central and C-terminal regions provide substrate specificity. The best-characterized substrate is EID1 (EP300-interacting inhibitor of differentiation 1): FBXO21 binds the C-terminal region of EID1 and SCF(FBXO21) directly ubiquitylates EID1 to drive its proteasomal degradation predominantly in the cytoplasm (EID1 accumulates in both cytoplasm and nucleus upon FBXO21 loss), thereby influencing EID1-dependent transcriptional repression; a peptidic modular degron in EID1 is necessary and sufficient for SCF(FBXO21)-dependent polyubiquitylation. FBXO21 operates in two mechanistic modes. In the canonical proteolytic mode it directs K48-type proteasomal degradation of substrates including EID1, the PI3K regulatory subunit p85alpha (PIK3R1; degradation in acute myeloid leukemia shapes PI3K/AKT versus ERK signaling and AML cell survival/differentiation), and the multidrug-resistance transporter ABCB1/P-glycoprotein (whose turnover is blocked by Ser291-phosphorylated CD44). In a non-proteolytic signaling mode, SCF(FBXO21) catalyzes Lys29-linked ubiquitination of the kinase ASK1 (MAP3K5) that promotes ASK1 activation rather than degradation, driving ASK1-JNK/p38 and IRF3-dependent antiviral innate immune signaling and type I interferon (IFN-beta) and IL-6 induction after viral or nucleic-acid challenge. As an SCF adaptor, FBXO21 thus acts in the ubiquitin-proteasome system to mediate ubiquitin-dependent, SCF-type protein catabolism and, via atypical chain linkages, ubiquitin-dependent signal transduction. It is broadly expressed (tissue-enhanced in fallopian tube).
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0003677 DNA binding | IEA GO_REF:0000002 | REMOVE | Summary: InterPro domain-based electronic assignment of DNA binding, propagated from a hemimethylated-DNA-binding-like (YccV-like) domain match; FBXO21 is an SCF substrate adaptor with no established DNA-binding function. Reason: This is an over-propagated IEA. FBXO21's UniProt-curated function is purely as the substrate-recognition subunit of an SCF E3 ubiquitin ligase, binding SKP1/CUL1 and substrates (EID1). The DNA binding term derives from an InterPro signature (IPR011722 hemimethylated-DNA-binding/YccV-like, TIGR02097 yccV) detected in the protein's C-terminal region; there is no experimental or curated evidence that FBXO21 binds DNA sequence-specifically or functions in DNA metabolism. The annotation conflates a remote domain-fold match with a molecular function and is biologically misleading for a cytoplasmic/nuclear ubiquitin-ligase adaptor. Supporting Evidence: file:human/FBXO21/FBXO21-uniprot.txt Substrate-recognition component of the SCF (SKP1-CUL1-F-box protein)-type E3 ubiquitin ligase complex. |
| GO:0005515 protein binding | IPI PMID:26085330 FBXO21 mediates the ubiquitylation and proteasomal degradati... | KEEP AS NON CORE | Summary: IPI interaction underpinning the functionally meaningful FBXO21-EID1 substrate relationship (FBXO21 binds the C-terminal region of EID1 and targets it for ubiquitylation). The bare protein binding term is uninformative, but this records a real substrate interaction. Reason: Records the substrate-recognition interaction with EID1, which is biologically central, but bare protein binding (GO:0005515) is uninformative per curation guidelines; the substrate relationship is better captured by the SCF/catabolism process annotations and core functions. Supporting Evidence: PMID:26085330 The central and COOH-terminal portion of FBXO21 was found to interact with the COOH-terminal region of EID1 in transfected cells. |
| GO:0005515 protein binding | IPI PMID:27705803 A High-Density Map for Navigating the Human Polycomb Complex... | KEEP AS NON CORE | Summary: Interaction captured in a high-throughput affinity-purification map of the human Polycomb complexome. Bare protein binding is uninformative. Reason: High-throughput AP-MS interaction; bare protein binding (GO:0005515) is uninformative and not a core function. |
| GO:0005515 protein binding | IPI PMID:33961781 Dual proteome-scale networks reveal cell-specific remodeling... | KEEP AS NON CORE | Summary: Interaction captured in the BioPlex proteome-scale AP-MS interactome (cell-specific remodeling study). Bare protein binding is uninformative. Reason: High-throughput AP-MS interactome; bare protein binding (GO:0005515) is uninformative and not a core function. Supporting Evidence: PMID:33961781 BioPlex 3.0, results from affinity purification of 10,128 human proteins-half the proteome-in 293T cells and includes 118,162 interactions among 14,586 proteins. |
| GO:0005515 protein binding | IPI PMID:40205054 Multimodal cell maps as a foundation for structural and func... | KEEP AS NON CORE | Summary: Interaction captured in a multimodal AP-MS/immunofluorescence cell map of U2OS cells. Bare protein binding is uninformative. Reason: High-throughput AP-MS interactome; bare protein binding (GO:0005515) is uninformative and not a core function. Supporting Evidence: PMID:40205054 through joint measurement of biophysical interactions and immunofluorescence images for over 5,100 proteins in U2OS osteosarcoma cells |
| GO:0019005 SCF ubiquitin ligase complex | NAS PMID:34445249 The SCF Complex Is Essential to Maintain Genome and Chromoso... | ACCEPT | Summary: FBXO21 is the variable F-box substrate-recognition subunit of an SCF (SKP1-CUL1-F-box) E3 ubiquitin ligase complex, binding SKP1 and CUL1. This is a core localization/complex-membership annotation. Reason: Directly supported by UniProt curation (interacts with SKP1 and CUL1) and by a dedicated ComplexPortal entry (CPX-7930, SCF E3 ubiquitin ligase complex, FBXO21 variant). Core to FBXO21's molecular role. Supporting Evidence: file:human/FBXO21/FBXO21-uniprot.txt Directly interacts with SKP1 and CUL1. |
| GO:0031146 SCF-dependent proteasomal ubiquitin-dependent protein catabolic process | NAS PMID:34445249 The SCF Complex Is Essential to Maintain Genome and Chromoso... | ACCEPT | Summary: As the substrate-recognition subunit of an SCF complex, FBXO21 drives SCF-dependent, proteasome-mediated degradation of its substrates (demonstrated for EID1). This is the core biological process. Reason: Core biological process. SCF complexes target substrates with poly-ubiquitin chains for proteasomal degradation (PMID:34445249), and FBXO21 was shown to drive proteasomal degradation of EID1 (PMID:26085330). Specific and well-supported. Supporting Evidence: PMID:34445249 encompasses a group of 69 SCF E3 ubiquitin ligase complexes that primarily modify protein substrates with poly-ubiquitin chains to target them for proteasomal degradation |
| GO:0005829 cytosol | TAS Reactome:R-HSA-8952618 | KEEP AS NON CORE | Summary: Reactome TAS localization to cytosol assigned via a generic CRL1 (cullin-RING ligase) neddylation/cycle reaction. Correct compartment but generic and inherited from pathway context. Reason: Cytosolic localization is consistent with FBXO21 acting in cytoplasmic SCF complexes (and EID1 is degraded in cytoplasm and nucleus), but this annotation is a generic CRL-cycle pathway assignment, redundant across many reactions; non-core. |
| GO:0005829 cytosol | TAS Reactome:R-HSA-8952620 | KEEP AS NON CORE | Summary: Reactome TAS localization to cytosol from a generic CRL1 neddylation/cycle reaction. Reason: Generic CRL-cycle localization; correct but redundant and non-core. |
| GO:0005829 cytosol | TAS Reactome:R-HSA-8955241 | KEEP AS NON CORE | Summary: Reactome TAS localization to cytosol from a generic cytosolic CRL E3 ligase (CAND1-binding) reaction. Reason: Generic CRL-cycle localization; correct but redundant and non-core. |
| GO:0005829 cytosol | TAS Reactome:R-HSA-8955289 | KEEP AS NON CORE | Summary: Reactome TAS localization to cytosol from a generic cytosolic CRL E3 ligase (COMMD/CAND1) reaction. Reason: Generic CRL-cycle localization; correct but redundant and non-core. |
| GO:0005829 cytosol | TAS Reactome:R-HSA-8956040 | KEEP AS NON CORE | Summary: Reactome TAS localization to cytosol from the COP9-signalosome deneddylation reaction on cytosolic CRL complexes. Reason: Generic CRL-cycle localization; correct but redundant and non-core. |
| GO:0005829 cytosol | TAS Reactome:R-HSA-8956200 | KEEP AS NON CORE | Summary: Reactome TAS localization to cytosol from a generic CRL1 (DCUN1D3-binding) reaction. Reason: Generic CRL-cycle localization; correct but redundant and non-core. |
| GO:0005829 cytosol | TAS Reactome:R-HSA-983140 | KEEP AS NON CORE | Summary: Reactome TAS localization to cytosol from a generic ubiquitin-transfer (E2-to-substrate) reaction in the antigen-processing/proteasome pathway. Reason: Generic ubiquitination-cycle localization; correct but redundant and non-core. |
| GO:0005829 cytosol | TAS Reactome:R-HSA-983147 | KEEP AS NON CORE | Summary: Reactome TAS localization to cytosol from a generic reaction (release of E3 from polyubiquitinated substrate). Reason: Generic ubiquitination-cycle localization; correct but redundant and non-core. |
| GO:0005829 cytosol | TAS Reactome:R-HSA-983156 | KEEP AS NON CORE | Summary: Reactome TAS localization to cytosol from a generic polyubiquitination-of-substrate reaction. Reason: Generic ubiquitination-cycle localization; correct but redundant and non-core. |
| GO:0005829 cytosol | TAS Reactome:R-HSA-983157 | KEEP AS NON CORE | Summary: Reactome TAS localization to cytosol from a generic reaction (interaction of E3 with substrate and E2-Ub complex). Reason: Generic ubiquitination-cycle localization; correct but redundant and non-core. |
| GO:0000151 ubiquitin ligase complex | NAS PMID:10531035 Identification of a family of human F-box proteins. | KEEP AS NON CORE | Summary: FBXO21 is a subunit of a ubiquitin ligase (SCF) complex, the general parent of the more specific SCF ubiquitin ligase complex annotation. Supported by the founding F-box protein family paper. Reason: Correct but generic; the more specific GO:0019005 (SCF ubiquitin ligase complex) better captures FBXO21's complex membership. F-box proteins are one of the four subunits of SCF ubiquitin ligases. Supporting Evidence: PMID:10531035 F-box proteins are one of the four subunits of ubiquitin protein ligases called SCFs. |
| GO:0004842 ubiquitin-protein transferase activity | NAS PMID:10531035 Identification of a family of human F-box proteins. | MODIFY | Summary: NAS assignment of ubiquitin-protein transferase activity from the founding F-box family paper. However, within the SCF complex the catalytic ubiquitin-transfer activity resides in the RING subunit (RBX1); the F-box protein FBXO21 functions as the substrate-recruiting adaptor, not the catalytic transferase. Reason: F-box proteins do not themselves catalyse ubiquitin transfer; they are the substrate-recognition adaptors that recruit substrates to the SCF, whose catalytic activity is provided by the RING subunit RBX1 (with the E2). The NAS source (PMID:10531035) describes SCF complexes (not FBXO21 itself) as ubiquitin ligases. The more accurate molecular function for an F-box protein is ubiquitin-like ligase-substrate adaptor activity (GO:1990756). Proposed replacements: ubiquitin-like ligase-substrate adaptor activity Supporting Evidence: file:human/FBXO21/FBXO21-uniprot.txt Substrate-recognition component of the SCF (SKP1-CUL1-F-box protein)-type E3 ubiquitin ligase complex. |
| GO:0006511 ubiquitin-dependent protein catabolic process | NAS PMID:10531035 Identification of a family of human F-box proteins. | KEEP AS NON CORE | Summary: FBXO21, as an SCF substrate adaptor, mediates ubiquitin-dependent protein catabolism (directly demonstrated for EID1). General parent of the SCF-dependent catabolism term. Reason: Correct and supported (FBXO21 drives ubiquitin-dependent proteasomal degradation of EID1), but the more specific GO:0031146 (SCF-dependent proteasomal ubiquitin-dependent protein catabolic process) better captures the role; retained as non-core to avoid redundancy. Supporting Evidence: PMID:26085330 FBXO21 mediates the ubiquitylation and proteasomal degradation of EID1. |
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Download this section (compressed HTML)Q: Beyond EID1, what is the full substrate repertoire of SCF(FBXO21), and which substrate-recognition surface (central vs C-terminal region) engages each substrate?
Q: Is the reported antiviral/innate-immune signalling role of FBXO21 dependent on its SCF ligase activity and substrate ubiquitylation, or does it act through a ligase-independent mechanism?
Q: What governs the subcellular partitioning of SCF(FBXO21) activity between cytoplasm and nucleus, given that EID1 accumulates in both compartments upon FBXO21 loss?
Experiment: Perform DiPIUS or quantitative ubiquitinome/proteome profiling in FBXO21-knockout versus wild-type cells (with and without proteasome inhibition) to define the endogenous SCF(FBXO21) substrate repertoire.
Experiment: Reconstitute SCF(FBXO21)-mediated ubiquitylation of EID1 in vitro with purified SKP1, CUL1, RBX1, an E2, and an F-box-domain mutant of FBXO21 to confirm that adaptor (SKP1-binding) function is required and to map EID1 ubiquitylation sites and chain linkage.
Experiment: Test whether FBXO21's reported antiviral signalling function requires SCF assembly by comparing wild-type FBXO21 with an F-box-deletion (SKP1-binding-defective) mutant in interferon-pathway reporter and viral-challenge assays.
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