FBXW4

UniProt ID: P57775
Organism: Homo sapiens
Review Status: COMPLETE
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Gene Description

FBXW4 (dactylin; SHFM3) is a member of the F-box/WD40 (FBXW) family of proteins. Its 412-residue product contains an N-terminal F-box motif (approximately residues 25-71) and a C-terminal beta-propeller built from roughly six WD40 repeats. F-box proteins function as the interchangeable substrate-recognition subunits of SCF (SKP1-CUL1-F-box)-type cullin-RING E3 ubiquitin ligase complexes: the F-box motif docks the protein onto SKP1/CUL1, while the WD40 propeller recognizes (typically phosphorylated) substrate proteins and presents them for ubiquitination by the RBX1-bound E2, committing them to proteasomal degradation. Affinity-purification studies confirm that FBXW4 assembles, in an F-box-dependent manner, with the canonical SCF core subunits SKP1, CUL1 and RBX1 and with COP9 signalosome subunits (which deneddylate and regulate cullin-RING ligases), and that FBXW4 associates with ubiquitinated cellular proteins in a manner enhanced by proteasome inhibition - establishing it as a bona fide SCF substrate receptor engaged in ubiquitin-dependent turnover. Its physiological substrates, however, remain undefined. FBXW4 is broadly expressed (including brain, kidney, lung and liver) and is recurrently mutated, deleted, or under-expressed across human cancers, suggesting a candidate tumor-suppressor role. The human gene maps to chromosome 10q24.3 within the critical region for split-hand/foot malformation type 3 (SHFM3), and the orthologous gene is disrupted in the mouse dactylaplasia (Dac) mutant, which fails to maintain the apical ectodermal ridge and truncates the autopod. SHFM3 is most often associated with tandem/discontinuous genomic duplications at 10q24 that perturb a shared cis-regulatory neighborhood and alter expression of FBXW4 and several neighboring genes (e.g. BTRC, POLL, LBX1) rather than with coding mutations in FBXW4 itself, so FBXW4's precise contribution to limb development and its physiological ubiquitination substrates remain incompletely defined.

Proposed New Ontology Terms

ubiquitin-like ligase-substrate adaptor activity

Definition: Bridging a substrate to a ubiquitin-like protein ligase, as performed by an SCF F-box substrate-recognition subunit that binds both SKP1/the ligase scaffold and the substrate to facilitate the substrate's ubiquitination. This corresponds to the existing GO term GO:1990756, which is not currently in FBXW4's annotation set.

Justification: FBXW4 assembles with the SCF core (SKP1/CUL1/RBX1) and the COP9 signalosome in an F-box-dependent manner and associates with ubiquitinated proteins in a proteasome-inhibitor-dependent way, consistent with a substrate-adaptor molecular function rather than catalysis (which is RBX1's). Adding GO:1990756 would give FBXW4 an informative molecular-function term in place of the uninformative bare protein binding annotations.

Parent term: ubiquitin-like ligase-substrate adaptor activity

Supporting Evidence:

Existing Annotations Review

GO Term Evidence Action Reason
GO:0019005 SCF ubiquitin ligase complex
IBA
GO_REF:0000033
ACCEPT
Summary: Phylogenetic (PAN-GO) assignment of SCF complex membership, consistent with FBXW4's F-box motif that docks F-box proteins onto SKP1/CUL1. Now directly corroborated by FBXW4-specific affinity-purification data showing F-box-dependent assembly with SKP1, CUL1 and RBX1.
Reason: Core localization/assembly role for an F-box protein; supported by the F-box domain, the documented SKP1 interaction, and direct biochemical co-purification of FBXW4 with the SCF core (SKP1/CUL1/RBX1) and COP9 signalosome in an F-box-dependent manner.
Supporting Evidence:
file:human/FBXW4/FBXW4-uniprot.txt
Part of a SCF (SKP1-cullin-F-box) protein ligase complex
file:human/FBXW4/FBXW4-deep-research-falcon.md
FBXW4 co-purifies/interacts with **SKP1, CUL1, RBX1** and multiple **COP9 signalosome (COPS)** subunits, and these interactions are **F-box dependent**
GO:0031146 SCF-dependent proteasomal ubiquitin-dependent protein catabolic process
IBA
GO_REF:0000033
ACCEPT
Summary: Phylogenetic assignment of involvement in SCF-dependent proteasomal degradation, the canonical process for F-box substrate-receptor proteins. FBXW4-specific data show it engages ubiquitinated proteins in a proteasome-inhibitor- and F-box-dependent manner, supporting genuine participation in ubiquitin-dependent turnover.
Reason: Core biological process for an F-box protein acting as an SCF substrate receptor; consistent with the UniProt function statement and with direct evidence that FBXW4 associates with ubiquitinated cellular proteins (increased by MG132) in an F-box-dependent manner.
Supporting Evidence:
file:human/FBXW4/FBXW4-uniprot.txt
Probably recognizes and binds to some phosphorylated proteins and promotes their ubiquitination and degradation
file:human/FBXW4/FBXW4-deep-research-falcon.md
FBXW4 interacts with **ubiquitinated cellular proteins**, and the interaction increases with **proteasome inhibition (MG132)** in an **F-box-dependent** manner, consistent with substrate engagement in ubiquitin-dependent turnover pathways
GO:0005515 protein binding
IPI
PMID:22632967
Cyclin F-mediated degradation of ribonucleotide reductase M2...
KEEP AS NON CORE
Summary: IntAct interaction captured against SKP1 (UniProtKB:P63208) in a cyclin F/SCF study; records the functionally important FBXW4-SKP1 association. Bare protein binding is uninformative.
Reason: Records the real FBXW4-SKP1 interaction (the WITH/FROM target is P63208/SKP1), which underpins SCF assembly, but bare protein binding is uninformative per curation guidelines.
Supporting Evidence:
file:human/FBXW4/FBXW4-uniprot.txt
P57775; P63208: SKP1; NbExp=3; IntAct=EBI-2372268, EBI-307486
GO:0005515 protein binding
IPI
PMID:27705803
A High-Density Map for Navigating the Human Polycomb Complex...
KEEP AS NON CORE
Summary: IntAct interaction against SKP1 (UniProtKB:P63208) from a Polycomb complexome map; supports FBXW4-SKP1 association. Bare protein binding is uninformative.
Reason: Records the FBXW4-SKP1 interaction (WITH/FROM P63208/SKP1) relevant to SCF assembly, but bare protein binding is uninformative.
Supporting Evidence:
file:human/FBXW4/FBXW4-uniprot.txt
P57775; P63208: SKP1; NbExp=3; IntAct=EBI-2372268, EBI-307486
GO:0005515 protein binding
IPI
PMID:32814053
Interactome Mapping Provides a Network of Neurodegenerative ...
KEEP AS NON CORE
Summary: High-throughput interactome interaction against PRKN/Parkin isoform (UniProtKB:O60260-5) from a neurodegenerative-disease interactome study. Bare protein binding is uninformative.
Reason: Records a high-throughput interaction (WITH/FROM O60260-5/PRKN); bare protein binding is uninformative and not a core function.
Supporting Evidence:
file:human/FBXW4/FBXW4-uniprot.txt
P57775; O60260-5: PRKN; NbExp=3; IntAct=EBI-2372268, EBI-21251460
GO:0005515 protein binding
IPI
PMID:33961781
Dual proteome-scale networks reveal cell-specific remodeling...
KEEP AS NON CORE
Summary: IntAct interaction against SKP1 (UniProtKB:P63208) from a cell-specific interactome map; supports FBXW4-SKP1 association. Bare protein binding is uninformative.
Reason: Records the FBXW4-SKP1 interaction (WITH/FROM P63208/SKP1) relevant to SCF assembly, but bare protein binding is uninformative.
Supporting Evidence:
file:human/FBXW4/FBXW4-uniprot.txt
P57775; P63208: SKP1; NbExp=3; IntAct=EBI-2372268, EBI-307486
GO:0019005 SCF ubiquitin ligase complex
NAS
PMID:34445249
The SCF Complex Is Essential to Maintain Genome and Chromoso...
ACCEPT
Summary: ComplexPortal (CPX-7761) curated assignment of FBXW4 to an SCF E3 ubiquitin ligase complex variant.
Reason: Correct core assembly annotation; FBXW4 is the substrate-receptor subunit of an SCF complex variant (ComplexPortal CPX-7761), consistent with SKP1 binding.
Supporting Evidence:
file:human/FBXW4/FBXW4-uniprot.txt
Part of a SCF (SKP1-cullin-F-box) protein ligase complex
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: ComplexPortal-derived assignment of involvement in SCF-dependent proteasomal degradation, the canonical process for an SCF substrate receptor.
Reason: Correct core biological process; redundant with the IBA assignment of the same term.
Supporting Evidence:
file:human/FBXW4/FBXW4-uniprot.txt
promotes their ubiquitination and degradation
GO:0060173 limb development
NAS
PMID:10471509
A novel member of the F-box/WD40 gene family, encoding dacty...
KEEP AS NON CORE
Summary: Author-stated involvement in limb development, based on disruption of the orthologous gene (dactylin) in the mouse dactylaplasia mutant, which truncates the autopod via failure to maintain the apical ectodermal ridge.
Reason: Genetically well-supported developmental association (dactylaplasia mouse; SHFM3 locus) but the molecular mechanism and direct FBXW4 substrates in limb patterning are not established; this is a pleiotropic developmental role rather than a demonstrated direct molecular function.
Supporting Evidence:
PMID:10471509
this report demonstrates the importance of this gene family in vertebrate embryonic development
GO:0005829 cytosol
TAS
Reactome:R-HSA-8952618
KEEP AS NON CORE
Summary: Reactome pathway-level cytosol localization for FBXW4 within generic CRL1/SCF neddylation and ubiquitination reactions.
Reason: Plausible cytosolic localization for an SCF subunit, but derived from generic CRL pathway reactions rather than FBXW4-specific localization data; the dactylin/SHFM3 literature implies action in developing tissues without resolving compartment.
Supporting Evidence:
file:human/FBXW4/FBXW4-uniprot.txt
Part of a SCF (SKP1-cullin-F-box) protein ligase complex
GO:0005829 cytosol
TAS
Reactome:R-HSA-8952620
KEEP AS NON CORE
Summary: Reactome pathway-level cytosol localization (NEDD8:AcM-UBE2M binds CRL1) propagated to FBXW4 as an SCF subunit.
Reason: Generic CRL pathway-derived localization; plausible but not FBXW4-specific.
Supporting Evidence:
file:human/FBXW4/FBXW4-uniprot.txt
Part of a SCF (SKP1-cullin-F-box) protein ligase complex
GO:0005829 cytosol
TAS
Reactome:R-HSA-8955241
KEEP AS NON CORE
Summary: Reactome pathway-level cytosol localization (CAND1 binds cytosolic CRL ligases) propagated to FBXW4.
Reason: Generic CRL pathway-derived localization; plausible but not FBXW4-specific.
Supporting Evidence:
file:human/FBXW4/FBXW4-uniprot.txt
Part of a SCF (SKP1-cullin-F-box) protein ligase complex
GO:0005829 cytosol
TAS
Reactome:R-HSA-8955289
KEEP AS NON CORE
Summary: Reactome pathway-level cytosol localization (COMMDs displace CAND1) propagated to FBXW4.
Reason: Generic CRL pathway-derived localization; plausible but not FBXW4-specific.
Supporting Evidence:
file:human/FBXW4/FBXW4-uniprot.txt
Part of a SCF (SKP1-cullin-F-box) protein ligase complex
GO:0005829 cytosol
TAS
Reactome:R-HSA-8956040
KEEP AS NON CORE
Summary: Reactome pathway-level cytosol localization (COP9 signalosome deneddylates CRLs) propagated to FBXW4.
Reason: Generic CRL pathway-derived localization; plausible but not FBXW4-specific.
Supporting Evidence:
file:human/FBXW4/FBXW4-uniprot.txt
Part of a SCF (SKP1-cullin-F-box) protein ligase complex
GO:0005829 cytosol
TAS
Reactome:R-HSA-8956200
KEEP AS NON CORE
Summary: Reactome pathway-level cytosol localization (MyrG-DCUN1D3 binds CRL1) propagated to FBXW4.
Reason: Generic CRL pathway-derived localization; plausible but not FBXW4-specific.
Supporting Evidence:
file:human/FBXW4/FBXW4-uniprot.txt
Part of a SCF (SKP1-cullin-F-box) protein ligase complex
GO:0005829 cytosol
TAS
Reactome:R-HSA-983140
KEEP AS NON CORE
Summary: Reactome pathway-level cytosol localization (transfer of Ub from E2 to substrate) propagated to FBXW4.
Reason: Generic CRL pathway-derived localization; plausible but not FBXW4-specific.
Supporting Evidence:
file:human/FBXW4/FBXW4-uniprot.txt
Part of a SCF (SKP1-cullin-F-box) protein ligase complex
GO:0005829 cytosol
TAS
Reactome:R-HSA-983147
KEEP AS NON CORE
Summary: Reactome pathway-level cytosol localization (release of E3 from polyubiquitinated substrate) propagated to FBXW4.
Reason: Generic CRL pathway-derived localization; plausible but not FBXW4-specific.
Supporting Evidence:
file:human/FBXW4/FBXW4-uniprot.txt
Part of a SCF (SKP1-cullin-F-box) protein ligase complex
GO:0005829 cytosol
TAS
Reactome:R-HSA-983156
KEEP AS NON CORE
Summary: Reactome pathway-level cytosol localization (polyubiquitination of substrate) propagated to FBXW4.
Reason: Generic CRL pathway-derived localization; plausible but not FBXW4-specific.
Supporting Evidence:
file:human/FBXW4/FBXW4-uniprot.txt
Part of a SCF (SKP1-cullin-F-box) protein ligase complex
GO:0005829 cytosol
TAS
Reactome:R-HSA-983157
KEEP AS NON CORE
Summary: Reactome pathway-level cytosol localization (interaction of E3 with substrate and E2-Ub complex) propagated to FBXW4.
Reason: Generic CRL pathway-derived localization; plausible but not FBXW4-specific.
Supporting Evidence:
file:human/FBXW4/FBXW4-uniprot.txt
Part of a SCF (SKP1-cullin-F-box) protein ligase complex
GO:0030326 embryonic limb morphogenesis
NAS
PMID:10405324
A novel human gene encoding an F-box/WD40 containing protein...
KEEP AS NON CORE
Summary: Author-stated putative involvement in limb morphogenesis from the original cloning paper, based on FBXW4 mapping to the SHFM3 critical region at 10q24.3.
Reason: Reflects a candidate-gene/positional inference (SHFM3 critical region) rather than a demonstrated molecular mechanism; developmental role is non-core and the direct substrates in limb morphogenesis are unknown.
Supporting Evidence:
PMID:10405324
likely to be involved in key signaling pathways crucial for normal limb development, make it a promising candidate gene for SHFM3
GO:0000151 ubiquitin ligase complex
NAS
PMID:10945468
cDNA cloning and expression analysis of new members of the m...
ACCEPT
Summary: Author-stated membership in a ubiquitin ligase complex, based on FBXW4 being an F-box/WD40 protein of the SCF family. A more general parent of the specific SCF complex term.
Reason: Correct but generic; subsumed by the more specific GO:0019005 (SCF ubiquitin ligase complex). Consistent with the F-box family role.
Supporting Evidence:
PMID:10945468
F-box proteins are critical components of the SCF ubiquitin-protein ligase complex and are involved in substrate recognition and recruitment for ubiquitination
GO:0006511 ubiquitin-dependent protein catabolic process
NAS
PMID:10945468
cDNA cloning and expression analysis of new members of the m...
ACCEPT
Summary: Author-stated involvement in ubiquitin-dependent protein catabolism, a parent of the specific SCF-dependent proteasomal process.
Reason: Correct but generic; the more specific GO:0031146 better captures FBXW4's role as an SCF substrate receptor.
Supporting Evidence:
PMID:10945468
their distinct role in ubiquitin-dependent protein degradation

Core Functions

Substrate-recognition (substrate-adaptor) subunit of an SCF (SKP1-CUL1-F-box) cullin-RING E3 ubiquitin ligase complex, docking via its F-box motif onto SKP1/CUL1 and using its WD40 propeller to recruit substrates and bridge them to the ligase for SCF-dependent proteasomal degradation. FBXW4 itself is not catalytic; the ubiquitin-transfer/RING activity resides on the RBX1 subunit of the assembled SCF complex. Direct physiological substrates of SCF(FBXW4) remain undefined.

Supporting Evidence:
  • file:human/FBXW4/FBXW4-uniprot.txt
    Part of a SCF (SKP1-cullin-F-box) protein ligase complex
  • PMID:10945468
    F-box proteins are critical components of the SCF ubiquitin-protein ligase complex and are involved in substrate recognition and recruitment for ubiquitination
  • file:human/FBXW4/FBXW4-deep-research-falcon.md
    FBXW4 co-purifies/interacts with **SKP1, CUL1, RBX1** and multiple **COP9 signalosome (COPS)** subunits, and these interactions are **F-box dependent**

References

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Suggested Questions for Experts

Q: What are the direct, phosphorylation-dependent ubiquitination substrates recognized by the FBXW4 WD40 propeller, and which signaling pathways (e.g. Wnt) do they belong to?

Q: Given that SHFM3 is associated with a tandem duplication at 10q24 rather than FBXW4 coding mutations, is the limb phenotype due to altered FBXW4 dosage, a neighboring gene, or a regulatory element, and what is FBXW4's direct molecular contribution?

Suggested Experiments

Experiment: Affinity purification of tagged FBXW4 with SKP1/CUL1/RBX1 followed by mass spectrometry of co-purifying and ubiquitinated proteins, in limb-bud-derived or epithelial cells, to identify physiological SCF(FBXW4) substrates.

Experiment: Reconstitute SCF(FBXW4) in vitro with SKP1, CUL1, RBX1 and an E2 and test ubiquitination of candidate developmental-signaling substrates, comparing wild-type to F-box-deletion FBXW4 to confirm substrate-adaptor activity.

Deep Research

Falcon

(FBXW4-deep-research-falcon.md)

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πŸ“š Additional Documentation

Pn Notes

(FBXW4-pn-notes.md)

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