id: Q80UW2
gene_symbol: Fbxo2
product_type: PROTEIN
status: IN_PROGRESS
taxon:
  id: NCBITaxon:10090
  label: Mus musculus
description: >-
  Fbxo2 (also known as Fbs1, Fbx2, NFB42) is the substrate-recognition component of the
  SCF(Fbxo2) E3 ubiquitin-protein ligase complex (SKP1-CUL1-FBXO2-RBX1). It functions
  primarily in the endoplasmic reticulum-associated degradation (ERAD) pathway, where it
  recognizes and binds N-linked high-mannose oligosaccharides on misfolded glycoproteins
  that have been retrotranslocated from the ER to the cytosol. The sugar-binding domain
  (FBA domain) recognizes Man3GlcNAc2 (the innermost chitobiose core of N-glycans), and
  binding is enhanced when glycoproteins are denatured because denaturation exposes the
  normally buried chitobiose structure (PMID:15723043, PMID:14990996). Fbxo2 is NOT a
  chaperone; it is a glycoprotein sensor that targets substrates for ubiquitination and
  proteasomal degradation. It also prevents cytosolic aggregation of retrotranslocated
  glycoproteins (PMID:17215248). In neurons, Fbxo2 mediates activity-dependent degradation
  of NMDA receptor NR1 subunits at glutamatergic synapses (PMID:15809437). Expression is
  enriched in brain and cochlea; Fbxo2 knockout mice develop progressive hearing loss due
  to cochlear cell degeneration (PMID:17494702). Fbxo2 also associates with p97/VCP AAA
  ATPase for substrate extraction from the ER membrane (PMID:15723043).
existing_annotations:
# ============================================================
# IBA annotations (phylogenetically inferred, GO_REF:0000033)
# ============================================================
- term:
    id: GO:0036503
    label: ERAD pathway
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    summary: >-
      IBA annotation for involvement in the ERAD pathway. This is a core function of Fbxo2,
      well-established by multiple experimental papers. Fbxo2 recognizes N-glycans on
      misfolded glycoproteins retrotranslocated from the ER and promotes their ubiquitination
      and proteasomal degradation (PMID:12140560, PMID:15723043).
    action: ACCEPT
    reason: >-
      ERAD is the central biological pathway in which Fbxo2 operates. The IBA annotation is
      consistent with direct experimental evidence from PMID:12140560 and PMID:15723043. The
      phylogenetic inference is well-supported.
    supported_by:
      - reference_id: PMID:12140560
        supporting_text: >-
          expression of the mutant Fbx2 Delta F, which lacks the F-box domain that is
          essential for forming the SCF complex, appreciably blocks degradation of typical
          substrates of the ER-associated degradation pathway
      - reference_id: PMID:15723043
        supporting_text: >-
          the SCF(Fbs1,2) ubiquitin-ligase complexes that contribute to ubiquitination of
          glycoproteins are involved in the ER-associated degradation pathway

- term:
    id: GO:0005737
    label: cytoplasm
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    summary: >-
      IBA annotation for cytoplasm localization. Fbxo2 operates in the cytosol, where it
      recognizes retrotranslocated glycoproteins from the ER. More specifically it localizes
      to the cytosol and to microsome membrane peripheral cytoplasmic side (UniProt).
    action: ACCEPT
    reason: >-
      Cytoplasm is a correct general localization. The IBA is consistent with IDA evidence
      for cytosol (PMID:12140560). The broader term cytoplasm is acceptable for an IBA.
    supported_by:
      - reference_id: PMID:12140560
        supporting_text: >-
          Pre-integrin beta 1 is a target of Fbx2; these two proteins interact in the
          cytosol after inhibition of the proteasome

- term:
    id: GO:0006516
    label: glycoprotein catabolic process
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    summary: >-
      IBA annotation for involvement in glycoprotein catabolic process. This is a core
      function. Fbxo2 promotes ubiquitination and subsequent proteasomal degradation of
      N-glycosylated proteins (PMID:12140560, PMID:15723043).
    action: ACCEPT
    reason: >-
      Glycoprotein catabolism is the downstream consequence of Fbxo2-mediated substrate
      recognition and ubiquitination. Well-supported by direct experimental evidence.
    supported_by:
      - reference_id: PMID:12140560
        supporting_text: >-
          SCF(Fbx2) ubiquitinates N-glycosylated proteins that are translocated from the
          ER to the cytosol by the quality control mechanism

- term:
    id: GO:0019005
    label: SCF ubiquitin ligase complex
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    summary: >-
      IBA annotation for membership in the SCF ubiquitin ligase complex. Fbxo2 is the F-box
      substrate recognition subunit of the SCF(Fbxo2) complex consisting of CUL1, RBX1,
      SKP1, and FBXO2 (PMID:12140560, PMID:17389369).
    action: ACCEPT
    reason: >-
      SCF complex membership is a core structural aspect of Fbxo2 function, extensively
      validated by crystal structures (PMID:17389369) and biochemical data (PMID:12140560).
    supported_by:
      - reference_id: PMID:12140560
        supporting_text: >-
          N-glycan serves as a signal for degradation by the Skp1-Cullin1-Fbx2-Roc1
          (SCF(Fbx2)) ubiquitin ligase complex

- term:
    id: GO:0031146
    label: SCF-dependent proteasomal ubiquitin-dependent protein catabolic process
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    summary: >-
      IBA annotation for involvement in SCF-dependent proteasomal ubiquitin-dependent
      protein catabolic process. This describes the pathway Fbxo2 participates in.
    action: ACCEPT
    reason: >-
      This is the specific proteasomal degradation pathway that SCF(Fbxo2) mediates.
      Well-supported by PMID:12140560 demonstrating that SCF(Fbxo2) ubiquitinates
      glycoproteins for proteasomal degradation.
    supported_by:
      - reference_id: PMID:12140560
        supporting_text: >-
          The F-box protein Fbx2 (ref. 4) binds specifically to proteins attached to
          N-linked high-mannose oligosaccharides and subsequently contributes to
          ubiquitination of N-glycosylated proteins

- term:
    id: GO:0061630
    label: ubiquitin protein ligase activity
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    summary: >-
      IBA annotation for ubiquitin protein ligase activity with qualifier "contributes_to".
      Fbxo2 is the substrate recognition component of the SCF(Fbxo2) E3 ligase complex; it
      does not itself possess catalytic E3 ligase activity but contributes to the complex's
      activity by conferring substrate specificity (PMID:12140560, PMID:17389369).
    action: MODIFY
    reason: >-
      While "contributes_to" ubiquitin protein ligase activity is technically defensible as
      Fbxo2 is a subunit of an active E3 ligase complex, the more precise molecular function
      of Fbxo2 is as a ubiquitin ligase substrate adaptor. GO:1990756 "ubiquitin-like
      ligase-substrate adaptor activity" better captures Fbxo2's actual role: bringing
      together the E3 ligase and its substrate through glycan recognition.
    proposed_replacement_terms:
      - id: GO:1990756
        label: ubiquitin-like ligase-substrate adaptor activity
    supported_by:
      - reference_id: PMID:17389369
        supporting_text: >-
          In SCF ubiquitin ligases, a diverse array of F-box proteins confers substrate
          specificity. Fbs1/Fbx2, a member of the F-box protein family, recognizes
          high-mannose oligosaccharides

# ============================================================
# IEA annotations (electronic annotations)
# ============================================================
- term:
    id: GO:0005737
    label: cytoplasm
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  review:
    summary: >-
      IEA annotation for cytoplasm localization. Redundant with IBA and IDA evidence
      for cytoplasm/cytosol localization.
    action: ACCEPT
    reason: >-
      Correct and consistent with experimental evidence. IEA is broader than the IDA
      cytosol annotation but not incorrect.

- term:
    id: GO:0006516
    label: glycoprotein catabolic process
  evidence_type: IEA
  original_reference_id: GO_REF:0000117
  review:
    summary: >-
      IEA annotation for glycoprotein catabolic process, inferred by ARBA machine learning.
      Redundant with IBA and IDA evidence for the same term.
    action: ACCEPT
    reason: >-
      Correct and consistent with experimental data from PMID:12140560 and PMID:15723043.

- term:
    id: GO:0019005
    label: SCF ubiquitin ligase complex
  evidence_type: IEA
  original_reference_id: GO_REF:0000117
  review:
    summary: >-
      IEA annotation for SCF ubiquitin ligase complex membership. Redundant with IBA and
      IDA evidence.
    action: ACCEPT
    reason: >-
      Correct. Fbxo2 is a well-characterized component of the SCF(Fbxo2) complex.

- term:
    id: GO:0030246
    label: carbohydrate binding
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  review:
    summary: >-
      IEA annotation for carbohydrate binding, inferred from UniProt keyword "Lectin".
      Carbohydrate binding is a core molecular function of Fbxo2. The FBA (F-box associated)
      domain specifically binds high-mannose N-glycans (PMID:14990996, PMID:17389369).
    action: ACCEPT
    reason: >-
      Correct and a core function. Carbohydrate binding is well-established experimentally.
      While a more specific term like oligosaccharide binding (GO:0070492) might be more
      precise, carbohydrate binding is not incorrect for an IEA annotation.

- term:
    id: GO:0031146
    label: SCF-dependent proteasomal ubiquitin-dependent protein catabolic process
  evidence_type: IEA
  original_reference_id: GO_REF:0000117
  review:
    summary: >-
      IEA annotation for SCF-dependent proteasomal degradation. Redundant with IBA and IDA
      evidence for the same term.
    action: ACCEPT
    reason: >-
      Correct and consistent with experimental evidence from PMID:12140560.

- term:
    id: GO:0036503
    label: ERAD pathway
  evidence_type: IEA
  original_reference_id: GO_REF:0000117
  review:
    summary: >-
      IEA annotation for ERAD pathway involvement. Redundant with IBA and IDA evidence.
    action: ACCEPT
    reason: >-
      Correct. ERAD is the core biological pathway of Fbxo2 function.

# ============================================================
# IPI annotations (protein binding, various references)
# ============================================================
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:17389369
  review:
    summary: >-
      IPI annotation for protein binding based on crystal structure of SCF(Fbs1) with
      glycoprotein substrate RNase1 (PMID:17389369). The interaction partner is
      UniProtKB:P61823 (bovine RNase1). The crystal structure revealed the structural
      basis for how the sugar-binding domain selects glycosylated substrates.
    action: MODIFY
    reason: >-
      "Protein binding" is uninformative. The interaction demonstrated in PMID:17389369 is
      actually glycan-mediated binding of a glycoprotein substrate. The correct MF annotation
      is carbohydrate binding or more specifically oligosaccharide binding, or the substrate
      adaptor activity. Since these are already captured by other annotations, this particular
      "protein binding" annotation should be modified to the more informative substrate adaptor
      term.
    proposed_replacement_terms:
      - id: GO:1990756
        label: ubiquitin-like ligase-substrate adaptor activity
    supported_by:
      - reference_id: PMID:17389369
        supporting_text: >-
          The structure of the SBD-glycoprotein complex indicates that the SBD primarily
          recognizes Man(3)GlcNAc(2), thereby explaining the broad activity of the enzyme
          against various glycoproteins

- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:17389369
  review:
    summary: >-
      Second IPI annotation for protein binding from PMID:17389369, this time with
      UniProtKB:P63208-1 (Skp1). The crystal structure showed the Skp1-Fbs1 complex
      architecture with the F-box domain mediating Skp1 interaction.
    action: MODIFY
    reason: >-
      "Protein binding" is uninformative. The interaction with Skp1 is an obligate
      structural interaction within the SCF complex. This is better captured by the
      existing SCF complex membership annotation (GO:0019005) and the substrate adaptor
      activity (GO:1990756).
    proposed_replacement_terms:
      - id: GO:1990756
        label: ubiquitin-like ligase-substrate adaptor activity
    supported_by:
      - reference_id: PMID:17389369
        supporting_text: >-
          we determined the crystal structures of the Skp1-Fbs1 complex and the
          sugar-binding domain (SBD) of the Fbs1-glycoprotein complex

- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:15809437
  review:
    summary: >-
      IPI annotation for protein binding based on PMID:15809437, with interaction partner
      PR:P35438 (NR1/GRIN1 NMDA receptor subunit). Fbxo2 binds to high-mannose glycans
      of the NR1 ectodomain and promotes NR1 ubiquitination.
    action: MODIFY
    reason: >-
      "Protein binding" is uninformative. The binding to NR1 is glycan-mediated (Fbxo2
      binds the high-mannose glycans on the NR1 ectodomain) and represents substrate
      recognition for ubiquitination. This is better captured by carbohydrate binding
      (GO:0030246) and/or ubiquitin-like ligase-substrate adaptor activity (GO:1990756).
    proposed_replacement_terms:
      - id: GO:1990756
        label: ubiquitin-like ligase-substrate adaptor activity
    supported_by:
      - reference_id: PMID:15809437
        supporting_text: >-
          the F-box protein, Fbx2, bound to high-mannose glycans of the NR1 ectodomain.
          F-box proteins specify ubiquitination by linking protein substrates to the
          terminal E3 ligase

- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:15723043
  review:
    summary: >-
      IPI annotation for protein binding from PMID:15723043, with interaction partner
      PR:P09055 (integrin beta-1). Fbxo2 interacts with integrin-beta1 (an ERAD substrate)
      in the cytosol in a manner dependent on p97 ATPase activity.
    action: MODIFY
    reason: >-
      "Protein binding" is uninformative. The interaction with integrin-beta1 represents
      glycan-mediated substrate recognition. This is better captured by the substrate
      adaptor activity term and the ERAD pathway annotation.
    proposed_replacement_terms:
      - id: GO:1990756
        label: ubiquitin-like ligase-substrate adaptor activity
    supported_by:
      - reference_id: PMID:15723043
        supporting_text: >-
          The SCF(Fbs1) complex was associated with p97/VCP AAA ATPase and bound to
          integrin-beta1, one of the SCF(Fbs1) substrates, in the cytosol in a manner
          dependent on p97 ATPase activity

- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:15723043
  review:
    summary: >-
      Second IPI annotation for protein binding from PMID:15723043 (with PR:Q01853, VCP/p97).
      This is a separate entry from the same reference, representing the VCP/p97 interaction
      partner.
    action: MODIFY
    reason: >-
      Same reasoning as the other PMID:15723043 protein binding annotation. The VCP/p97
      interaction is part of the ERAD machinery. "Protein binding" is uninformative; the
      ERAD pathway annotation already captures this functional context.
    proposed_replacement_terms:
      - id: GO:1990756
        label: ubiquitin-like ligase-substrate adaptor activity
    supported_by:
      - reference_id: PMID:15723043
        supporting_text: >-
          The SCF(Fbs1) complex was associated with p97/VCP AAA ATPase

# ============================================================
# ISO annotations (ortholog-based transfer)
# ============================================================
- term:
    id: GO:0005737
    label: cytoplasm
  evidence_type: ISO
  original_reference_id: GO_REF:0000119
  review:
    summary: >-
      ISO annotation for cytoplasm localization, transferred from human ortholog
      UniProtKB:Q9UK22 (FBXO2). Redundant with IBA and IDA evidence.
    action: ACCEPT
    reason: >-
      Correct and consistent with experimental evidence for cytoplasm/cytosol localization.

- term:
    id: GO:0008285
    label: negative regulation of cell population proliferation
  evidence_type: ISO
  original_reference_id: GO_REF:0000096
  review:
    summary: >-
      ISO annotation for negative regulation of cell population proliferation, transferred
      from rat ortholog RGD:621751. This is not a well-characterized function of Fbxo2.
      The core function of Fbxo2 is ERAD-linked glycoprotein degradation, not cell
      proliferation regulation.
    action: KEEP_AS_NON_CORE
    reason: >-
      While Fbxo2-mediated degradation of glycoprotein substrates could indirectly affect
      cell proliferation, this is not a core evolved function. The annotation is based on
      ortholog transfer from rat and may reflect a secondary/downstream consequence of
      Fbxo2's ubiquitin ligase activity rather than a specific proliferation-regulatory role.
      Keeping as non-core since the evidence is indirect.

- term:
    id: GO:0098890
    label: extrinsic component of postsynaptic membrane
  evidence_type: ISO
  original_reference_id: GO_REF:0000096
  review:
    summary: >-
      ISO annotation for extrinsic component of postsynaptic membrane, transferred from
      rat ortholog. This is consistent with Fbxo2's role in degrading NMDA receptor NR1
      subunits at the postsynapse (PMID:15809437).
    action: ACCEPT
    reason: >-
      This localization is consistent with the experimentally demonstrated role of Fbxo2
      at glutamatergic synapses (PMID:15809437). Fbxo2 acts on NR1 subunits at the
      postsynaptic membrane, and being a cytoplasmic peripheral protein would make it an
      extrinsic component of the postsynaptic membrane.
    supported_by:
      - reference_id: PMID:15809437
        supporting_text: >-
          the F-box protein, Fbx2, bound to high-mannose glycans of the NR1 ectodomain

- term:
    id: GO:0098978
    label: glutamatergic synapse
  evidence_type: ISO
  original_reference_id: GO_REF:0000096
  review:
    summary: >-
      ISO annotation for glutamatergic synapse localization, transferred from rat ortholog.
      Redundant with IDA evidence from SynGO (PMID:15809437).
    action: ACCEPT
    reason: >-
      Correct. Fbxo2 localizes to glutamatergic synapses where it mediates NMDA receptor
      degradation. Consistent with direct experimental evidence from PMID:15809437.

# ============================================================
# IDA annotations from SynGO (PMID:15809437) - glutamatergic synapse
# Multiple ECO codes for the same term represent different evidence types
# ============================================================
- term:
    id: GO:0098978
    label: glutamatergic synapse
  evidence_type: IDA
  original_reference_id: PMID:15809437
  review:
    summary: >-
      IDA annotation from SynGO for glutamatergic synapse localization based on
      PMID:15809437. Kato et al. showed Fbxo2 localizes to hippocampal neurons and
      specifically targets NR1 at glutamatergic synapses. Multiple evidence lines
      (ECO:0000314, ECO:0005589, ECO:0007695, ECO:0007719) all support this.
    action: ACCEPT
    reason: >-
      Well-supported by PMID:15809437 which demonstrated Fbxo2 localization and function
      at glutamatergic synapses in hippocampal neurons.
    supported_by:
      - reference_id: PMID:15809437
        supporting_text: >-
          When expressed in hippocampal neurons, this Fbx2 dominant-negative mutant
          augmented NR1 subunit levels and NMDA receptor-mediated currents in an
          activity-dependent fashion

- term:
    id: GO:0098978
    label: glutamatergic synapse
  evidence_type: IMP
  original_reference_id: PMID:15809437
  review:
    summary: >-
      IMP annotation from SynGO for glutamatergic synapse localization based on mutant
      phenotype analysis (dominant-negative Fbxo2) in PMID:15809437.
    action: ACCEPT
    reason: >-
      The dominant-negative Fbxo2 mutant increased NR1 levels and NMDA receptor currents
      at glutamatergic synapses, demonstrating that endogenous Fbxo2 functions at these
      synapses (PMID:15809437).
    supported_by:
      - reference_id: PMID:15809437
        supporting_text: >-
          this Fbx2 dominant-negative mutant augmented NR1 subunit levels and NMDA
          receptor-mediated currents in an activity-dependent fashion

# ============================================================
# IDA annotations from SynGO (PMID:15809437) - synaptic protein catabolism
# ============================================================
- term:
    id: GO:0099576
    label: regulation of protein catabolic process at postsynapse, modulating synaptic
      transmission
  evidence_type: IDA
  original_reference_id: PMID:15809437
  review:
    summary: >-
      IDA annotation from SynGO for regulation of postsynaptic protein catabolism. Fbxo2
      promotes ubiquitination and degradation of NMDA receptor NR1 subunits at the
      postsynapse, thereby modulating synaptic transmission (PMID:15809437).
    action: ACCEPT
    reason: >-
      This is a well-supported neuronal-specific function of Fbxo2. Kato et al. showed that
      Fbxo2 mediates activity-dependent NR1 degradation at postsynaptic sites, directly
      modulating NMDA receptor-mediated currents.
    supported_by:
      - reference_id: PMID:15809437
        supporting_text: >-
          ubiquitination of NR1 was increased by Fbx2 and diminished by an Fbx2
          dominant-negative mutant

- term:
    id: GO:0099576
    label: regulation of protein catabolic process at postsynapse, modulating synaptic
      transmission
  evidence_type: IMP
  original_reference_id: PMID:15809437
  review:
    summary: >-
      IMP annotation from SynGO for postsynaptic protein catabolism regulation, based on
      mutant phenotype evidence. The dominant-negative Fbxo2 augmented NR1 levels and
      NMDA receptor currents.
    action: ACCEPT
    reason: >-
      Well-supported by the dominant-negative experiment in PMID:15809437 showing
      that blocking Fbxo2 function increased NR1 levels and NMDA receptor currents.
    supported_by:
      - reference_id: PMID:15809437
        supporting_text: >-
          this Fbx2 dominant-negative mutant augmented NR1 subunit levels and NMDA
          receptor-mediated currents in an activity-dependent fashion

# ============================================================
# IEA annotation - protein ubiquitination (UniPathway)
# ============================================================
- term:
    id: GO:0016567
    label: protein ubiquitination
  evidence_type: IEA
  original_reference_id: GO_REF:0000041
  review:
    summary: >-
      IEA annotation for protein ubiquitination, based on UniPathway vocabulary mapping.
      Fbxo2 participates in protein ubiquitination as part of the SCF(Fbxo2) complex.
    action: ACCEPT
    reason: >-
      Correct. Fbxo2 is integral to the SCF(Fbxo2) E3 ubiquitin ligase complex that
      ubiquitinates glycoprotein substrates. Consistent with IDA evidence from PMID:12140560.

# ============================================================
# IPI annotation - protein binding (PMID:15809437, from MGI)
# ============================================================
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:15809437
  review:
    summary: >-
      IPI annotation for protein binding from PMID:15809437, with interaction partner
      PR:P35438 (NR1/GRIN1). This is the MGI-curated version of the NR1 interaction.
      Redundant with the SynGO-curated IPI annotation from the same paper.
    action: MODIFY
    reason: >-
      "Protein binding" is uninformative. The NR1 interaction is glycan-mediated and
      represents substrate recognition for ubiquitination. Better captured by
      GO:1990756 ubiquitin-like ligase-substrate adaptor activity.
    proposed_replacement_terms:
      - id: GO:1990756
        label: ubiquitin-like ligase-substrate adaptor activity
    supported_by:
      - reference_id: PMID:15809437
        supporting_text: >-
          the F-box protein, Fbx2, bound to high-mannose glycans of the NR1 ectodomain

# ============================================================
# IDA annotations from UniProtKB (PMID:12140560) - original Yoshida 2002 paper
# ============================================================
- term:
    id: GO:0005829
    label: cytosol
  evidence_type: IDA
  original_reference_id: PMID:12140560
  review:
    summary: >-
      IDA annotation for cytosol localization from the landmark paper identifying
      SCF(Fbxo2) (PMID:12140560). Fbxo2 interacts with its glycoprotein substrate
      pre-integrin beta-1 in the cytosol after proteasome inhibition.
    action: ACCEPT
    reason: >-
      Well-supported. Yoshida et al. demonstrated cytosolic localization of Fbxo2 and
      its interaction with substrates in the cytosol (PMID:12140560). UniProt also lists
      cytoplasm and microsome membrane (cytoplasmic side) as subcellular locations.
    supported_by:
      - reference_id: PMID:12140560
        supporting_text: >-
          Pre-integrin beta 1 is a target of Fbx2; these two proteins interact in the
          cytosol after inhibition of the proteasome

- term:
    id: GO:0006516
    label: glycoprotein catabolic process
  evidence_type: IDA
  original_reference_id: PMID:12140560
  review:
    summary: >-
      IDA annotation for glycoprotein catabolic process from PMID:12140560. SCF(Fbxo2)
      ubiquitinates N-glycosylated proteins translocated from the ER, promoting their
      proteasomal degradation.
    action: ACCEPT
    reason: >-
      Core function. Directly demonstrated in PMID:12140560 that Fbxo2 targets glycoproteins
      for degradation.
    supported_by:
      - reference_id: PMID:12140560
        supporting_text: >-
          SCF(Fbx2) ubiquitinates N-glycosylated proteins that are translocated from the
          ER to the cytosol by the quality control mechanism

- term:
    id: GO:0016567
    label: protein ubiquitination
  evidence_type: IDA
  original_reference_id: PMID:12140560
  review:
    summary: >-
      IDA annotation for protein ubiquitination from PMID:12140560. Fbxo2 contributes to
      ubiquitination of N-glycosylated proteins as part of the SCF(Fbxo2) complex.
    action: ACCEPT
    reason: >-
      Core function. Directly demonstrated in PMID:12140560.
    supported_by:
      - reference_id: PMID:12140560
        supporting_text: >-
          The F-box protein Fbx2 (ref. 4) binds specifically to proteins attached to
          N-linked high-mannose oligosaccharides and subsequently contributes to
          ubiquitination of N-glycosylated proteins

- term:
    id: GO:0019005
    label: SCF ubiquitin ligase complex
  evidence_type: IDA
  original_reference_id: PMID:12140560
  review:
    summary: >-
      IDA annotation for SCF ubiquitin ligase complex membership from PMID:12140560.
      Fbxo2 was identified as the F-box protein forming the SCF(Fbxo2) complex
      (SKP1-CUL1-FBXO2-ROC1).
    action: ACCEPT
    reason: >-
      Core structural annotation. The SCF(Fbxo2) complex was originally identified in
      PMID:12140560 and confirmed by crystal structures (PMID:17389369).
    supported_by:
      - reference_id: PMID:12140560
        supporting_text: >-
          N-glycan serves as a signal for degradation by the Skp1-Cullin1-Fbx2-Roc1
          (SCF(Fbx2)) ubiquitin ligase complex

- term:
    id: GO:0031146
    label: SCF-dependent proteasomal ubiquitin-dependent protein catabolic process
  evidence_type: IDA
  original_reference_id: PMID:12140560
  review:
    summary: >-
      IDA annotation for SCF-dependent proteasomal degradation from PMID:12140560.
      SCF(Fbxo2) mediates ubiquitin-dependent proteasomal degradation of glycoprotein
      substrates.
    action: ACCEPT
    reason: >-
      Core function. The dominant-negative Fbxo2 Delta-F blocked ERAD substrate
      degradation (PMID:12140560), directly demonstrating SCF-dependent proteasomal
      degradation.
    supported_by:
      - reference_id: PMID:12140560
        supporting_text: >-
          expression of the mutant Fbx2 Delta F, which lacks the F-box domain that is
          essential for forming the SCF complex, appreciably blocks degradation of typical
          substrates of the ER-associated degradation pathway

# ============================================================
# IDA annotations from MGI (PMID:15723043) - Yoshida 2005
# ============================================================
- term:
    id: GO:0006511
    label: ubiquitin-dependent protein catabolic process
  evidence_type: IDA
  original_reference_id: PMID:15723043
  review:
    summary: >-
      IDA annotation for ubiquitin-dependent protein catabolic process from PMID:15723043.
      This is a parent term of the more specific SCF-dependent proteasomal degradation
      annotation. Fbxo2 mediates ubiquitin-dependent degradation of glycoprotein substrates.
    action: ACCEPT
    reason: >-
      Correct, though redundant with the more specific GO:0031146 annotation. Keeping as
      the evidence from PMID:15723043 demonstrated ubiquitin-dependent degradation.
    supported_by:
      - reference_id: PMID:15723043
        supporting_text: >-
          the SCF(Fbs1,2) ubiquitin-ligase complexes that contribute to ubiquitination of
          glycoproteins are involved in the ER-associated degradation pathway

# ============================================================
# IDA annotations from MGI (PMID:15809437) - Kato 2005
# ============================================================
- term:
    id: GO:0031396
    label: regulation of protein ubiquitination
  evidence_type: IDA
  original_reference_id: PMID:15809437
  review:
    summary: >-
      IDA annotation for regulation of protein ubiquitination from PMID:15809437. Fbxo2
      increased NR1 ubiquitination, and the dominant-negative mutant diminished it.
    action: ACCEPT
    reason: >-
      Well-supported. PMID:15809437 showed that Fbxo2 expression increased NR1
      ubiquitination and the dominant-negative form decreased it, demonstrating regulation
      of ubiquitination at the synapse.
    supported_by:
      - reference_id: PMID:15809437
        supporting_text: >-
          ubiquitination of NR1 was increased by Fbx2 and diminished by an Fbx2
          dominant-negative mutant

- term:
    id: GO:0043197
    label: dendritic spine
  evidence_type: IDA
  original_reference_id: PMID:15809437
  review:
    summary: >-
      IDA annotation for dendritic spine localization from PMID:15809437. Fbxo2 was shown
      to localize to hippocampal neurons including dendritic spines where it targets NMDA
      receptors for degradation.
    action: ACCEPT
    reason: >-
      Consistent with the synaptic function of Fbxo2 in degrading NR1 subunits. Dendritic
      spines are the postsynaptic compartment of glutamatergic synapses.
    supported_by:
      - reference_id: PMID:15809437
        supporting_text: >-
          When expressed in hippocampal neurons, this Fbx2 dominant-negative mutant
          augmented NR1 subunit levels and NMDA receptor-mediated currents

# ============================================================
# TAS and IDA annotations from MGI (PMID:15723043)
# ============================================================
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:15723043
  review:
    summary: >-
      IPI annotation for protein binding from PMID:15723043, with interaction partner
      PR:Q01853 (VCP/p97). This is the MGI-curated record of Fbxo2 interaction with
      VCP/p97 AAA ATPase.
    action: MODIFY
    reason: >-
      "Protein binding" is uninformative. The VCP/p97 interaction is part of the ERAD
      machinery coordination. Better captured by ERAD pathway annotation.
    proposed_replacement_terms:
      - id: GO:1990756
        label: ubiquitin-like ligase-substrate adaptor activity
    supported_by:
      - reference_id: PMID:15723043
        supporting_text: >-
          The SCF(Fbs1) complex was associated with p97/VCP AAA ATPase and bound to
          integrin-beta1, one of the SCF(Fbs1) substrates, in the cytosol in a manner
          dependent on p97 ATPase activity

- term:
    id: GO:0005829
    label: cytosol
  evidence_type: TAS
  original_reference_id: PMID:15723043
  review:
    summary: >-
      TAS annotation for cytosol localization from PMID:15723043. Yoshida et al. showed
      Fbxo2 binds integrin-beta1 in the cytosol dependent on p97 ATPase activity.
    action: ACCEPT
    reason: >-
      Correct and consistent with IDA evidence from PMID:12140560. Redundant but valid.
    supported_by:
      - reference_id: PMID:15723043
        supporting_text: >-
          The SCF(Fbs1) complex was associated with p97/VCP AAA ATPase and bound to
          integrin-beta1, one of the SCF(Fbs1) substrates, in the cytosol

- term:
    id: GO:0006516
    label: glycoprotein catabolic process
  evidence_type: IDA
  original_reference_id: PMID:15723043
  review:
    summary: >-
      IDA annotation for glycoprotein catabolic process from PMID:15723043. Redundant with
      the same annotation from PMID:12140560, but independently supported by this paper
      which demonstrated Fbs1/Fbs2 interaction with denatured glycoproteins.
    action: ACCEPT
    reason: >-
      Core function, independently confirmed in PMID:15723043.
    supported_by:
      - reference_id: PMID:15723043
        supporting_text: >-
          the SCF(Fbs1,2) ubiquitin-ligase complexes that contribute to ubiquitination
          of glycoproteins are involved in the ER-associated degradation pathway

# ============================================================
# KEY ANNOTATION: denatured protein binding (GO:0031249)
# This is the annotation being obsoleted as part of this project
# ============================================================
- term:
    id: GO:0031249
    label: denatured protein binding
  evidence_type: IDA
  original_reference_id: PMID:15723043
  review:
    summary: >-
      IDA annotation for denatured protein binding. GO:0031249 is being obsoleted. Yoshida
      et al. (PMID:15723043) showed that Fbs1 and Fbs2 "interacted with denatured
      glycoproteins...more efficiently than native proteins" and proposed that "Fbs proteins
      distinguish native from unfolded glycoproteins by sensing the exposed chitobiose
      structure." Critically, this is NOT general denatured protein binding. Fbxo2 recognizes
      the N-glycan (chitobiose core) that becomes exposed upon glycoprotein denaturation.
      It does not bind non-glycosylated denatured proteins and is not a chaperone.
    action: MODIFY
    reason: >-
      GO:0031249 is being obsoleted and is inaccurate for Fbxo2 regardless. Fbxo2 does not
      bind denatured proteins in general -- it binds the N-glycan moiety on denatured
      glycoproteins. The enhanced binding to denatured vs native glycoproteins is because
      denaturation exposes the normally protein-buried chitobiose core of N-glycans. The
      actual molecular function is carbohydrate/oligosaccharide binding (already annotated
      as GO:0030246) and ubiquitin-like ligase-substrate adaptor activity (GO:1990756).
      Alternatively, GO:0051787 "misfolded protein binding" could apply in a loose sense,
      but this also misrepresents the mechanism since Fbxo2 recognizes the glycan, not the
      protein moiety. The best replacement is the oligosaccharide binding term combined with
      the substrate adaptor activity.
    proposed_replacement_terms:
      - id: GO:0070492
        label: oligosaccharide binding
      - id: GO:1990756
        label: ubiquitin-like ligase-substrate adaptor activity
    supported_by:
      - reference_id: PMID:15723043
        supporting_text: >-
          Both Fbs1 and Fbs2 proteins interacted with denatured glycoproteins, which were
          modified with not only high-mannose but also complex-type oligosaccharides, more
          efficiently than native proteins. Given that Fbs proteins interact with innermost
          chitobiose in N-glycans, we propose that Fbs proteins distinguish native from
          unfolded glycoproteins by sensing the exposed chitobiose structure

# ============================================================
# IDA annotation for ERAD pathway from MGI (PMID:15723043)
# ============================================================
- term:
    id: GO:0036503
    label: ERAD pathway
  evidence_type: IDA
  original_reference_id: PMID:15723043
  review:
    summary: >-
      IDA annotation for ERAD pathway from PMID:15723043. Redundant with IBA and IDA
      evidence from PMID:12140560, but independently confirmed.
    action: ACCEPT
    reason: >-
      Core function. PMID:15723043 confirmed ERAD involvement and additionally demonstrated
      the p97/VCP interaction that links Fbxo2 to the ERAD retrotranslocation machinery.
    supported_by:
      - reference_id: PMID:15723043
        supporting_text: >-
          the SCF(Fbs1,2) ubiquitin-ligase complexes that contribute to ubiquitination of
          glycoproteins are involved in the ER-associated degradation pathway

# ============================================================
# IDA annotation for amyloid-beta binding (PMID:9173930)
# ============================================================
- term:
    id: GO:0001540
    label: amyloid-beta binding
  evidence_type: IDA
  original_reference_id: PMID:9173930
  review:
    summary: >-
      IDA annotation for amyloid-beta binding from PMID:9173930 (Yehiely et al. 1997).
      This paper screened a lambdagt11 mouse brain cDNA library using a PrP-alkaline
      phosphatase fusion probe to find candidate prion protein binding partners. Six
      clones were isolated, four of which were novel. The paper identified Fbxo2 as a
      candidate prion protein binding partner, not specifically as an amyloid-beta binder.
      The annotation appears to be a misinterpretation of the screening result. The binding
      was to prion protein (PrP), not to amyloid-beta peptide.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      PMID:9173930 was a candidate screen for PrP binding partners using a PrP-AP probe,
      not a specific amyloid-beta binding assay. The paper states it identified "candidate
      proteins binding to prion protein," not amyloid-beta. Given what is now known about
      Fbxo2's glycan-binding specificity, any interaction with PrP would most likely be
      mediated through PrP's N-glycans rather than specific amyloid-beta recognition. The
      annotation of "amyloid-beta binding" appears to be an overinterpretation. It is
      plausible that Fbxo2 could bind glycosylated forms of amyloid precursor protein (APP)
      family members through their N-glycans, but this would be glycan binding, not
      amyloid-beta peptide binding.
    supported_by:
      - reference_id: PMID:9173930
        supporting_text: >-
          PrP-AP was used to screen a lambdagt11 mouse brain cDNA library, and six clones
          were isolated. Four cDNAs are novel while two clones are fragments of Nrf2
          (NF-E2 related factor 2) transcription factor and Aplp1 (amyloid precursor-like
          protein 1)

# ============================================================
# IDA annotation for carbohydrate binding (PMID:12939278)
# ============================================================
- term:
    id: GO:0030246
    label: carbohydrate binding
  evidence_type: IDA
  original_reference_id: PMID:12939278
  review:
    summary: >-
      IDA annotation for carbohydrate binding from PMID:12939278 (Yoshida et al. 2003).
      This paper primarily characterized Fbs2 (Fbxo6b) as a new family member, but also
      confirmed that Fbs1 (Fbxo2) binds specifically to proteins with high-mannose
      oligosaccharides. The paper demonstrated that Man3-9GlcNAc2 glycans are required for
      efficient binding.
    action: ACCEPT
    reason: >-
      Core molecular function. Carbohydrate binding (specifically N-glycan/oligosaccharide
      binding) is the primary mechanism by which Fbxo2 recognizes substrates. Well-supported
      by multiple papers including PMID:12140560, PMID:12939278, and structural studies
      (PMID:14990996, PMID:17389369).
    supported_by:
      - reference_id: PMID:12939278
        supporting_text: >-
          Fbs1 (F-box protein that recognizes sugar chains; equivalent to Fbx2 or NFB42)
          binds specifically to proteins attached with high mannose oligosaccharides and
          subsequently contributes to elimination of N-glycoproteins in cytosol

# ============================================================
# NEW annotations suggested based on literature review
# ============================================================
- term:
    id: GO:1990756
    label: ubiquitin-like ligase-substrate adaptor activity
  evidence_type: IDA
  original_reference_id: PMID:12140560
  review:
    summary: >-
      NEW annotation. Fbxo2 is the substrate-recognition (F-box) subunit of the SCF(Fbxo2)
      E3 ubiquitin ligase complex. It brings together the E3 ligase (via Skp1 binding through
      its F-box domain) and the glycoprotein substrate (via N-glycan binding through its FBA
      domain). This is the canonical function of F-box proteins. GO:1990756 is defined as
      "The binding activity of a molecule that brings together a ubiquitin-like ligase and its
      substrate. Usually mediated by F-box BTB/POZ domain proteins" -- this precisely describes
      Fbxo2.
    action: NEW
    reason: >-
      This term is not currently annotated for Fbxo2 but is the most accurate molecular
      function descriptor. It captures the substrate adaptor role that is the core molecular
      function of Fbxo2, bridging the SCF complex catalytic machinery with glycoprotein
      substrates via N-glycan recognition. Supported by crystal structures (PMID:17389369)
      and biochemical data (PMID:12140560).
    supported_by:
      - reference_id: PMID:17389369
        supporting_text: >-
          In SCF ubiquitin ligases, a diverse array of F-box proteins confers substrate
          specificity. Fbs1/Fbx2, a member of the F-box protein family, recognizes
          high-mannose oligosaccharides
      - reference_id: PMID:12140560
        supporting_text: >-
          The F-box protein Fbx2 (ref. 4) binds specifically to proteins attached to
          N-linked high-mannose oligosaccharides and subsequently contributes to
          ubiquitination of N-glycosylated proteins

- term:
    id: GO:0070492
    label: oligosaccharide binding
  evidence_type: IDA
  original_reference_id: PMID:14990996
  review:
    summary: >-
      NEW annotation. Fbxo2 specifically binds oligosaccharides, particularly
      Man3GlcNAc2 (the innermost core of N-glycans). This is more specific than the
      existing "carbohydrate binding" annotation. The crystal structure of Fbxo2 with
      chitobiose (PMID:14990996) and with glycoprotein substrate (PMID:17389369)
      demonstrated the oligosaccharide binding specificity.
    action: NEW
    reason: >-
      GO:0070492 "oligosaccharide binding" is more specific than GO:0030246 "carbohydrate
      binding" and accurately describes Fbxo2's binding to N-glycan oligosaccharides.
      Mutagenesis of key residues (F177A, Y279A, W280A) abolished glycoprotein binding
      (PMID:14990996), confirming the structural basis of oligosaccharide recognition.
    additional_reference_ids:
      - PMID:17389369
    supported_by:
      - reference_id: PMID:17389369
        supporting_text: >-
          The structure of the SBD-glycoprotein complex indicates that the SBD primarily
          recognizes Man(3)GlcNAc(2), thereby explaining the broad activity of the enzyme
          against various glycoproteins

references:
- id: GO_REF:0000033
  title: Annotation inferences using phylogenetic trees
  findings: []
- id: GO_REF:0000041
  title: Gene Ontology annotation based on UniPathway vocabulary mapping
  findings: []
- id: GO_REF:0000096
  title: Automated transfer of experimentally-verified manual GO annotation data to
    mouse-rat orthologs
  findings: []
- id: GO_REF:0000117
  title: Electronic Gene Ontology annotations created by ARBA machine learning models
  findings: []
- id: GO_REF:0000119
  title: Automated transfer of experimentally-verified manual GO annotation data to
    mouse-human orthologs
  findings: []
- id: GO_REF:0000120
  title: Combined Automated Annotation using Multiple IEA Methods
  findings: []
- id: PMID:12140560
  title: E3 ubiquitin ligase that recognizes sugar chains.
  findings:
    - statement: >-
        SCF(Fbxo2) ubiquitin ligase complex identified as recognizing N-glycan sugar chains
        on retrotranslocated glycoproteins for ERAD-mediated proteasomal degradation.
      supporting_text: >-
        N-glycan serves as a signal for degradation by the Skp1-Cullin1-Fbx2-Roc1
        (SCF(Fbx2)) ubiquitin ligase complex
    - statement: >-
        Pre-integrin beta-1 identified as substrate of SCF(Fbxo2); interaction occurs in
        cytosol after proteasome inhibition.
      supporting_text: >-
        Pre-integrin beta 1 is a target of Fbx2; these two proteins interact in the
        cytosol after inhibition of the proteasome
    - statement: >-
        Dominant-negative Fbxo2 (lacking F-box domain) blocks typical ERAD substrate
        degradation.
      supporting_text: >-
        expression of the mutant Fbx2 Delta F, which lacks the F-box domain that is
        essential for forming the SCF complex, appreciably blocks degradation of typical
        substrates of the ER-associated degradation pathway
- id: PMID:12939278
  title: Fbs2 is a new member of the E3 ubiquitin ligase family that recognizes sugar
    chains.
  findings:
    - statement: >-
        Fbs2 (Fbxo6b) identified as second F-box protein recognizing N-glycans. Both Fbs1 and
        Fbs2 require Man3-9GlcNAc2 for binding. Fbs1 expression restricted to brain and testis
        while Fbs2 is ubiquitous.
      supporting_text: >-
        Although the expression of Fbs1 was restricted to the adult brain and testis,
        the Fbs2 transcript was widely expressed
- id: PMID:14990996
  title: Structural basis of sugar-recognizing ubiquitin ligase.
  findings:
    - statement: >-
        Crystal structure of Fbxo2 FBA domain with chitobiose at 1.7 angstroms.
        Mutagenesis of F177, Y279, W280 abolished glycoprotein binding.
      supporting_text: >-
        Efficient binding to an N-glycan requires di-N-acetylchitobiose (chitobiose).
        Here we report the crystal structures of the sugar-binding domain (SBD) of Fbs1
        alone and in complex with chitobiose
- id: PMID:15723043
  title: Glycoprotein-specific ubiquitin ligases recognize N-glycans in unfolded substrates.
  findings:
    - statement: >-
        Fbs1/Fbs2 interact preferentially with denatured glycoproteins by sensing exposed
        chitobiose. SCF(Fbs1) associates with p97/VCP AAA ATPase.
      supporting_text: >-
        Both Fbs1 and Fbs2 proteins interacted with denatured glycoproteins, which were
        modified with not only high-mannose but also complex-type oligosaccharides, more
        efficiently than native proteins. Given that Fbs proteins interact with innermost
        chitobiose in N-glycans, we propose that Fbs proteins distinguish native from
        unfolded glycoproteins by sensing the exposed chitobiose structure
- id: PMID:15809437
  title: Activity-dependent NMDA receptor degradation mediated by retrotranslocation
    and ubiquitination.
  findings:
    - statement: >-
        Fbxo2 binds high-mannose glycans of NR1 ectodomain and promotes NR1 ubiquitination.
        Dominant-negative Fbxo2 augments NR1 levels and NMDA receptor currents at
        glutamatergic synapses in an activity-dependent manner.
      supporting_text: >-
        the F-box protein, Fbx2, bound to high-mannose glycans of the NR1 ectodomain.
        F-box proteins specify ubiquitination by linking protein substrates to the
        terminal E3 ligase. Indeed, ubiquitination of NR1 was increased by Fbx2 and
        diminished by an Fbx2 dominant-negative mutant
- id: PMID:17215248
  title: A neural-specific F-box protein Fbs1 functions as a chaperone suppressing glycoprotein
    aggregation.
  findings:
    - statement: >-
        Fbxo2 prevents formation of cytosolic aggregates of retrotranslocated unfolded
        glycoproteins. Functions as both ubiquitin ligase component and anti-aggregation
        factor. Predominantly detected as heterodimer with Skp1.
      supporting_text: >-
        In vitro, Fbs1 prevented the aggregation of the glycoprotein through the
        N-terminal unique sequence of Fbs1
- id: PMID:17389369
  title: Structural basis for the selection of glycosylated substrates by SCF(Fbs1)
    ubiquitin ligase.
  findings:
    - statement: >-
        Crystal structures of Skp1-Fbs1 complex and SBD-glycoprotein complex reveal that
        the sugar-binding domain primarily recognizes Man3GlcNAc2, explaining broad
        glycoprotein substrate specificity.
      supporting_text: >-
        The structure of the SBD-glycoprotein complex indicates that the SBD primarily
        recognizes Man(3)GlcNAc(2), thereby explaining the broad activity of the enzyme
        against various glycoproteins
- id: PMID:17494702
  title: Selective cochlear degeneration in mice lacking the F-box protein, Fbx2, a
    glycoprotein-specific ubiquitin ligase subunit.
  findings:
    - statement: >-
        Fbxo2 knockout mice develop progressive hearing loss due to degeneration of cochlear
        epithelial support cells, hair cells, and spiral ganglion neurons. Expression enriched
        in brain and cochlea.
      supporting_text: >-
        Mice with targeted deletion of Fbxo2 develop age-related hearing loss beginning at 2
        months. Cellular degeneration begins in the epithelial support cells of the organ of
        Corti
- id: PMID:9173930
  title: Identification of candidate proteins binding to prion protein.
  findings:
    - statement: >-
        Fbxo2 (then unnamed) identified as candidate prion protein binding partner using
        PrP-AP probe to screen mouse brain cDNA library. Four of six isolated clones were
        novel and expressed preferentially in brain.
      supporting_text: >-
        PrP-AP was used to screen a lambdagt11 mouse brain cDNA library, and six clones
        were isolated. Four cDNAs are novel while two clones are fragments of Nrf2
        (NF-E2 related factor 2) transcription factor and Aplp1 (amyloid precursor-like
        protein 1)
core_functions:
  - description: >-
      Substrate-recognition component of the SCF(Fbxo2) E3 ubiquitin-protein ligase complex
      that recognizes N-linked high-mannose oligosaccharides on misfolded glycoproteins
      retrotranslocated from the ER to the cytosol, promoting their ubiquitination and
      proteasomal degradation via the ERAD pathway.
    molecular_function:
      id: GO:1990756
      label: ubiquitin-like ligase-substrate adaptor activity
    directly_involved_in:
      - id: GO:0036503
        label: ERAD pathway
      - id: GO:0006516
        label: glycoprotein catabolic process
    locations:
      - id: GO:0005829
        label: cytosol
    in_complex:
      id: GO:0019005
      label: SCF ubiquitin ligase complex
    supported_by:
      - reference_id: PMID:12140560
        supporting_text: >-
          N-glycan serves as a signal for degradation by the Skp1-Cullin1-Fbx2-Roc1
          (SCF(Fbx2)) ubiquitin ligase complex
      - reference_id: PMID:17389369
        supporting_text: >-
          In SCF ubiquitin ligases, a diverse array of F-box proteins confers substrate
          specificity. Fbs1/Fbx2, a member of the F-box protein family, recognizes
          high-mannose oligosaccharides
  - description: >-
      Binds N-linked high-mannose oligosaccharides, specifically recognizing the innermost
      chitobiose (Man3GlcNAc2) core of N-glycans. This lectin-like activity is the basis
      for substrate recognition in ERAD. Binding is enhanced when glycoproteins are
      denatured because denaturation exposes the normally buried chitobiose structure.
    molecular_function:
      id: GO:0030246
      label: carbohydrate binding
    supported_by:
      - reference_id: PMID:15723043
        supporting_text: >-
          Fbs proteins interact with innermost chitobiose in N-glycans
      - reference_id: PMID:17389369
        supporting_text: >-
          The structure of the SBD-glycoprotein complex indicates that the SBD primarily
          recognizes Man(3)GlcNAc(2)
  - description: >-
      At glutamatergic synapses in the brain, Fbxo2 mediates activity-dependent degradation
      of NMDA receptor NR1 subunits by binding their high-mannose glycans and promoting
      ubiquitination, thereby regulating synaptic transmission.
    molecular_function:
      id: GO:1990756
      label: ubiquitin-like ligase-substrate adaptor activity
    directly_involved_in:
      - id: GO:0099576
        label: regulation of protein catabolic process at postsynapse, modulating synaptic
          transmission
    locations:
      - id: GO:0098978
        label: glutamatergic synapse
    supported_by:
      - reference_id: PMID:15809437
        supporting_text: >-
          the F-box protein, Fbx2, bound to high-mannose glycans of the NR1 ectodomain.
          F-box proteins specify ubiquitination by linking protein substrates to the
          terminal E3 ligase. Indeed, ubiquitination of NR1 was increased by Fbx2 and
          diminished by an Fbx2 dominant-negative mutant

proposed_new_terms:
  - proposed_name: misfolded glycoprotein sensor activity
    proposed_definition: >-
      Recognition of N-glycans on misfolded glycoproteins to target them for
      ubiquitin-dependent degradation. Distinct from chaperone activity (no protein
      refolding) and from general misfolded protein binding (recognition is glycan-mediated
      rather than via exposed hydrophobic patches). Examples include Fbxo2 (Fbs1) and
      Fbxo6 (Fbs2) in the ERAD pathway.
    justification: >-
      No existing GO term precisely captures the mechanism of Fbxo2. "Denatured protein
      binding" (GO:0031249, being obsoleted) is inaccurate because Fbxo2 binds glycans
      not the protein moiety. "Misfolded protein binding" (GO:0051787) implies direct
      recognition of misfolded protein conformation. "Carbohydrate binding" is correct
      but does not capture the quality-control context. A term for glycan-based misfolded
      glycoprotein recognition would fill this gap. See also the UNFOLDED_PROTEIN_BINDING
      project discussion of "misfolded protein sensor activity."

suggested_questions:
  - question: >-
      Is Fbxo2's anti-aggregation function (suppressing aggregation of retrotranslocated
      glycoproteins in the cytosol, PMID:17215248) independent of its ubiquitin ligase
      activity, and does it warrant a separate GO annotation?
  - question: >-
      Should the amyloid-beta binding annotation (GO:0001540, PMID:9173930) be removed
      entirely? The original paper identified Fbxo2 as a candidate PrP-binding protein,
      not an amyloid-beta binder. Any binding to PrP or APP family members is likely
      glycan-mediated.
  - question: >-
      Would a more specific MF term like "N-glycan binding" or "high-mannose oligosaccharide
      binding" be appropriate for Fbxo2, rather than the general "carbohydrate binding"?

suggested_experiments:
  - description: >-
      Test whether Fbxo2 binds non-glycosylated misfolded proteins to definitively
      distinguish glycan-dependent vs protein-conformation-dependent recognition. This
      would clarify whether GO:0051787 (misfolded protein binding) is ever appropriate
      for Fbxo2.
    hypothesis: >-
      Fbxo2 does not bind non-glycosylated misfolded proteins because its binding mechanism
      is entirely glycan-dependent via the FBA domain.
  - description: >-
      In Fbxo2 knockout cochlea, identify accumulated glycoprotein substrates by
      proteomics to better understand the ERAD substrates relevant to hearing loss
      pathogenesis (building on PMID:17494702).
    hypothesis: >-
      Specific cochlear glycoproteins accumulate in Fbxo2 knockout mice, revealing the
      ERAD substrates whose failed degradation causes cochlear degeneration.