id: Q9NR09
gene_symbol: BIRC6
product_type: PROTEIN
status: COMPLETE
taxon:
  id: NCBITaxon:9606
  label: Homo sapiens
description: >-
  BIRC6 (also known as BRUCE or Apollon) is a giant (~528 kDa) dual-function E2 ubiquitin-conjugating
  enzyme and E3 ubiquitin-protein ligase (EC 2.3.2.24) belonging to the inhibitor of apoptosis (IAP)
  protein family. It contains an N-terminal BIR (baculovirus IAP repeat) domain that mediates
  caspase binding and inhibition, and a C-terminal UBC (ubiquitin-conjugating enzyme) domain that
  confers chimeric E2/E3 ubiquitin ligase activity. BIRC6 functions as an antiparallel homodimer
  with a central substrate-binding cavity. Its primary molecular functions are (1) ubiquitination
  of pro-apoptotic factors (caspases-3, -7, -9, Smac/DIABLO, HtrA2) to inhibit apoptosis, (2)
  mono-ubiquitination of LC3 at K51 to suppress autophagy (in cooperation with E1 enzyme UBA6),
  and (3) regulation of cytokinesis by localizing to the midbody ring and coordinating vesicular
  targeting during abscission. BIRC6 exhibits cell cycle-dependent localization, concentrating
  at the trans-Golgi network and endosomes in interphase and relocating to spindle poles, the
  midzone, and the midbody during cell division. Smac/DIABLO antagonizes BIRC6 by competing
  for substrate binding sites. BIRC6 is itself regulated by RNF41/Nrdp1-mediated ubiquitination
  and proteasomal degradation, by deubiquitination via USP8, and by caspase-mediated cleavage.

existing_annotations:
  # === IBA ANNOTATIONS ===
  - term:
      id: GO:0005802
      label: trans-Golgi network
    evidence_type: IBA
    original_reference_id: GO_REF:0000033
    review:
      summary: >-
        BIRC6 localizes to the trans-Golgi network membrane in interphase cells, as demonstrated
        by immunofluorescence in PMID:18329369 and confirmed in the UniProt subcellular location
        annotation. This IBA annotation is consistent with both experimental and phylogenetic evidence.
      action: ACCEPT
      reason: >-
        Trans-Golgi network localization is experimentally established for BIRC6 (PMID:18329369)
        and is a core aspect of its interphase localization. The IBA annotation is well-supported
        by the phylogenetic inference and direct experimental data.
      supported_by:
        - reference_id: Q9NR09
          supporting_text: >-
            In interphase cells, localizes to the trans-Golgi network membrane and endosomes.
        - reference_id: PMID:15200957
          supporting_text: >-
            BRUCE, a conserved 528 kDa peripheral membrane protein of the trans-Golgi network

  - term:
      id: GO:0061631
      label: ubiquitin conjugating enzyme activity
    evidence_type: IBA
    original_reference_id: GO_REF:0000033
    review:
      summary: >-
        BIRC6 contains a C-terminal UBC domain and functions as a chimeric E2/E3 ubiquitin ligase,
        confirmed by multiple structural and biochemical studies (PMID:15200957, PMID:36758104,
        PMID:36758105, PMID:36758106). The IBA annotation accurately captures the E2 conjugating
        enzyme activity component.
      action: ACCEPT
      reason: >-
        Ubiquitin conjugating enzyme activity is a core molecular function of BIRC6, well
        established by the presence of the UBC domain and direct biochemical demonstration
        of E2 activity. The IBA annotation is at the correct level of specificity.
      supported_by:
        - reference_id: PMID:15200957
          supporting_text: >-
            BRUCE has the distinctive property of functioning as a chimeric E2/E3 ubiquitin ligase
            with Smac being a substrate.

  - term:
      id: GO:0043066
      label: negative regulation of apoptotic process
    evidence_type: IBA
    original_reference_id: GO_REF:0000033
    review:
      summary: >-
        BIRC6 is a member of the IAP family and inhibits apoptosis by ubiquitinating and promoting
        degradation of pro-apoptotic factors including caspases and Smac/DIABLO (PMID:15200957,
        PMID:10544019, PMID:14765125). This is a core evolved function.
      action: ACCEPT
      reason: >-
        Anti-apoptotic activity is one of the two primary evolved functions of BIRC6. The IBA
        annotation is well-supported by extensive experimental evidence from multiple studies.
      supported_by:
        - reference_id: PMID:15200957
          supporting_text: >-
            BRUCE inhibits caspase activity and apoptosis depending on its BIR domain.
        - reference_id: PMID:14765125
          supporting_text: >-
            BRUCE normally inhibits apoptosis, and Nrdp1 can be important in the initiation of
            apoptosis by catalyzing ubiquitination and degradation of BRUCE.

  - term:
      id: GO:0005634
      label: nucleus
    evidence_type: IBA
    original_reference_id: GO_REF:0000033
    review:
      summary: >-
        There is no strong experimental evidence for nuclear localization of BIRC6 in the
        published literature. UniProt does not annotate nuclear localization. The experimentally
        documented localizations are trans-Golgi network, endosomes, spindle poles, centrosome,
        midbody, and cytoplasm (PMID:18329369, PMID:15200957).
      action: UNDECIDED
      reason: >-
        The IBA annotation suggests nuclear localization from phylogenetic inference, but no
        direct experimental evidence supports this for human BIRC6. The extensive localization
        studies in PMID:18329369 do not report nuclear localization. However, given the protein's
        enormous size (528 kDa) and its presence in multiple compartments during cell cycle,
        some nuclear association during mitosis cannot be excluded.
      supported_by:
        - reference_id: Q9NR09
          supporting_text: >-
            Concentrates in a pericentriolar compartment in interphase, moves partially to spindle
            poles in metaphase, and finally localizes to the spindle midzone and the midbody in
            telophase and during cytokinesis.

  # === IEA ANNOTATIONS ===
  - term:
      id: GO:0000922
      label: spindle pole
    evidence_type: IEA
    original_reference_id: GO_REF:0000044
    review:
      summary: >-
        BIRC6 moves partially to spindle poles in metaphase as part of its cell cycle-dependent
        localization pattern (PMID:18329369). This IEA annotation is consistent with direct
        experimental evidence.
      action: ACCEPT
      reason: >-
        Spindle pole localization is experimentally established by immunofluorescence
        (PMID:18329369) and consistent with BIRC6's role in cytokinesis.
      supported_by:
        - reference_id: Q9NR09
          supporting_text: >-
            Concentrates in a pericentriolar compartment in interphase, moves partially to spindle
            poles in metaphase

  - term:
      id: GO:0004842
      label: ubiquitin-protein transferase activity
    evidence_type: IEA
    original_reference_id: GO_REF:0000120
    review:
      summary: >-
        BIRC6 has ubiquitin-protein transferase (E3 ligase) activity demonstrated biochemically
        with multiple substrates including Smac, caspases, and LC3 (PMID:15200957, PMID:36758104,
        PMID:36758105, PMID:36758106). This IEA annotation is well-supported by direct evidence.
      action: ACCEPT
      reason: >-
        Ubiquitin-protein transferase activity is a core function of BIRC6. The IEA correctly
        captures the E3 ligase component of its dual E2/E3 activity.
      supported_by:
        - reference_id: PMID:15200957
          supporting_text: >-
            BRUCE has the distinctive property of functioning as a chimeric E2/E3 ubiquitin ligase
            with Smac being a substrate.

  - term:
      id: GO:0004869
      label: cysteine-type endopeptidase inhibitor activity
    evidence_type: IEA
    original_reference_id: GO_REF:0000043
    review:
      summary: >-
        BIRC6 inhibits caspase activity through its BIR domain-mediated binding and through
        ubiquitination-dependent degradation of caspases (PMID:15200957). The inhibition of
        caspases-3, -6, -7, and -9 is well-established. This IEA annotation is consistent with
        experimental data.
      action: ACCEPT
      reason: >-
        Caspase inhibition is a core function of BIRC6 as an IAP family member. The BIR domain
        directly binds and inhibits active caspases, and the UBC domain promotes their ubiquitination
        and degradation.
      supported_by:
        - reference_id: PMID:15200957
          supporting_text: >-
            BRUCE inhibits caspase activity and apoptosis depending on its BIR domain.

  - term:
      id: GO:0005768
      label: endosome
    evidence_type: IEA
    original_reference_id: GO_REF:0000044
    review:
      summary: >-
        BIRC6 localizes to endosomes in interphase cells (PMID:18329369). This IEA annotation
        is consistent with direct immunofluorescence evidence.
      action: ACCEPT
      reason: >-
        Endosomal localization is part of the vesicular system localization of BIRC6 in interphase,
        as experimentally demonstrated.
      supported_by:
        - reference_id: Q9NR09
          supporting_text: >-
            In interphase cells, localizes to the trans-Golgi network membrane and endosomes.

  - term:
      id: GO:0005794
      label: Golgi apparatus
    evidence_type: IEA
    original_reference_id: GO_REF:0000044
    review:
      summary: >-
        BIRC6 localizes to the trans-Golgi network, which is part of the Golgi apparatus
        (PMID:18329369, PMID:15200957). This broader IEA annotation is consistent with
        experimental evidence, though trans-Golgi network (GO:0005802) is more specific.
      action: ACCEPT
      reason: >-
        The Golgi apparatus annotation is correct as a broader term encompassing the more
        specific trans-Golgi network localization. Both the IEA and more specific IDA/IBA
        annotations coexist appropriately.
      supported_by:
        - reference_id: PMID:15200957
          supporting_text: >-
            BRUCE, a conserved 528 kDa peripheral membrane protein of the trans-Golgi network

  - term:
      id: GO:0005813
      label: centrosome
    evidence_type: IEA
    original_reference_id: GO_REF:0000044
    review:
      summary: >-
        BIRC6 concentrates in a pericentriolar compartment in interphase (PMID:18329369),
        which corresponds to centrosome localization. The IEA annotation is consistent with
        direct experimental evidence.
      action: ACCEPT
      reason: >-
        Centrosomal/pericentriolar localization during interphase is experimentally established
        by immunofluorescence.
      supported_by:
        - reference_id: Q9NR09
          supporting_text: >-
            Concentrates in a pericentriolar compartment in interphase

  - term:
      id: GO:0006915
      label: apoptotic process
    evidence_type: IEA
    original_reference_id: GO_REF:0000120
    review:
      summary: >-
        BIRC6 is involved in apoptotic process as an anti-apoptotic IAP protein. However, the
        more specific term 'negative regulation of apoptotic process' (GO:0043066) is already
        annotated and more accurately describes BIRC6's role.
      action: ACCEPT
      reason: >-
        While the more specific annotation GO:0043066 (negative regulation of apoptotic process)
        better describes BIRC6's role, this broader IEA annotation is not incorrect. It is
        acceptable for IEA annotations to be broader than more specific experimental annotations.
      supported_by:
        - reference_id: PMID:15200957
          supporting_text: >-
            BRUCE inhibits caspase activity and apoptosis depending on its BIR domain.

  - term:
      id: GO:0016567
      label: protein ubiquitination
    evidence_type: IEA
    original_reference_id: GO_REF:0000117
    review:
      summary: >-
        BIRC6 catalyzes protein ubiquitination as a chimeric E2/E3 enzyme (PMID:15200957,
        PMID:36758104, PMID:36758105). Substrates include caspases, Smac/DIABLO, HtrA2,
        and LC3. This IEA annotation is well-supported.
      action: ACCEPT
      reason: >-
        Protein ubiquitination is a core biochemical process catalyzed by BIRC6. The IEA
        annotation accurately captures this function.
      supported_by:
        - reference_id: PMID:15200957
          supporting_text: >-
            BRUCE has the distinctive property of functioning as a chimeric E2/E3 ubiquitin ligase
            with Smac being a substrate.

  - term:
      id: GO:0016740
      label: transferase activity
    evidence_type: IEA
    original_reference_id: GO_REF:0000043
    review:
      summary: >-
        BIRC6 has transferase activity as a ubiquitin-conjugating/ligase enzyme. However, this
        is a very broad parent term; the more specific terms ubiquitin conjugating enzyme activity
        (GO:0061631) and ubiquitin-protein transferase activity (GO:0004842) are already annotated.
      action: ACCEPT
      reason: >-
        This is a correct but very general IEA annotation. It is acceptable for automated IEA
        annotations to capture broader terms when more specific annotations already exist.
      supported_by:
        - reference_id: PMID:15200957
          supporting_text: >-
            BRUCE has the distinctive property of functioning as a chimeric E2/E3 ubiquitin ligase

  - term:
      id: GO:0030414
      label: peptidase inhibitor activity
    evidence_type: IEA
    original_reference_id: GO_REF:0000043
    review:
      summary: >-
        BIRC6 inhibits caspase (peptidase) activity through its BIR domain. The more specific
        term cysteine-type endopeptidase inhibitor activity (GO:0004869) is already annotated.
        This broader IEA term is not wrong.
      action: ACCEPT
      reason: >-
        This broader IEA annotation is consistent with the more specific caspase inhibitor
        function. It is acceptable for IEA annotations to be broader.
      supported_by:
        - reference_id: PMID:15200957
          supporting_text: >-
            BRUCE inhibits caspase activity and apoptosis depending on its BIR domain.

  - term:
      id: GO:0032465
      label: regulation of cytokinesis
    evidence_type: IEA
    original_reference_id: GO_REF:0000002
    review:
      summary: >-
        BIRC6 is a major regulator of the final stages of cytokinesis, controlling abscission,
        midbody ring formation, and vesicular targeting (PMID:18329369). This IEA annotation
        is consistent with strong experimental evidence.
      action: ACCEPT
      reason: >-
        Regulation of cytokinesis is a core function of BIRC6, well-established by the detailed
        mechanistic study in PMID:18329369.
      supported_by:
        - reference_id: PMID:18329369
          supporting_text: >-
            we identify BRUCE, a 528 kDa multifunctional protein, which processes
            ubiquitin-conjugating activity, as a major regulator of abscission.

  - term:
      id: GO:0042127
      label: regulation of cell population proliferation
    evidence_type: IEA
    original_reference_id: GO_REF:0000117
    review:
      summary: >-
        BIRC6 is involved in cell proliferation indirectly through its anti-apoptotic and
        cytokinesis regulatory functions. The review by Dubrez-Daloz et al. (PMID:18414036)
        discusses IAP roles in cell proliferation. However, this is a broad and somewhat
        indirect annotation for BIRC6.
      action: KEEP_AS_NON_CORE
      reason: >-
        Regulation of cell proliferation is not a direct core function of BIRC6 but rather an
        indirect consequence of its anti-apoptotic and cytokinesis roles. It should be kept
        as non-core.
      supported_by:
        - reference_id: PMID:18414036
          supporting_text: >-
            IAPs are also known as BIR-containing proteins (BIRCs). Most of them display
            anti-apoptotic properties when overexpressed.

  - term:
      id: GO:0043066
      label: negative regulation of apoptotic process
    evidence_type: IEA
    original_reference_id: GO_REF:0000117
    review:
      summary: >-
        Duplicate IEA annotation of negative regulation of apoptotic process. This is a core
        function of BIRC6 as an IAP family member, supported by multiple experimental studies.
      action: ACCEPT
      reason: >-
        This IEA annotation duplicates the IBA and IMP annotations for the same term. The
        function is well-established as a core role of BIRC6.
      supported_by:
        - reference_id: PMID:15200957
          supporting_text: >-
            BRUCE inhibits caspase activity and apoptosis depending on its BIR domain.

  - term:
      id: GO:0046872
      label: metal ion binding
    evidence_type: IEA
    original_reference_id: GO_REF:0000043
    review:
      summary: >-
        BIRC6 contains a BIR domain that coordinates zinc ions, as is characteristic of BIR
        domains across IAP family members. The cryo-EM structure (PMID:36758105) was solved
        in complex with zinc. This IEA annotation is consistent with the structural data.
      action: ACCEPT
      reason: >-
        Metal (zinc) ion binding is a structural feature of the BIR domain. While not a core
        functional annotation per se, it is an accurate molecular property of the protein.
      supported_by:
        - reference_id: file:human/BIRC6/BIRC6-deep-research-falcon.md
          supporting_text: >-
            BIRC6 forms an anti-parallel U-shaped dimer with a central substrate-binding cavity
            that accommodates Smac/DIABLO, and includes multiple domains (including a ubiquitin-like
            domain, N-terminal WD40 beta-propeller, a small BIR domain, and a UBC domain).

  - term:
      id: GO:0051301
      label: cell division
    evidence_type: IEA
    original_reference_id: GO_REF:0000043
    review:
      summary: >-
        BIRC6 is involved in cell division through its critical role in cytokinesis
        (PMID:18329369). The more specific term 'regulation of cytokinesis' (GO:0032465)
        is already annotated.
      action: ACCEPT
      reason: >-
        Cell division is a broader term that encompasses cytokinesis. This IEA annotation
        is acceptable as a parent of the more specific cytokinesis annotation.
      supported_by:
        - reference_id: PMID:18329369
          supporting_text: >-
            Depletion of BRUCE in cell cultures causes defective abscission and
            cytokinesis-associated apoptosis

  - term:
      id: GO:0061631
      label: ubiquitin conjugating enzyme activity
    evidence_type: IEA
    original_reference_id: GO_REF:0000120
    review:
      summary: >-
        Duplicate IEA annotation of ubiquitin conjugating enzyme activity, also annotated
        by IBA. BIRC6 has a UBC domain and functions as a chimeric E2/E3 enzyme.
      action: ACCEPT
      reason: >-
        This duplicates the IBA annotation for the same GO term. The E2 conjugating enzyme
        activity is a core function of BIRC6, well-established by structural and biochemical data.
      supported_by:
        - reference_id: PMID:15200957
          supporting_text: >-
            BRUCE has the distinctive property of functioning as a chimeric E2/E3 ubiquitin ligase

  - term:
      id: GO:0090543
      label: Flemming body
    evidence_type: IEA
    original_reference_id: GO_REF:0000044
    review:
      summary: >-
        BIRC6 localizes to the midbody ring (also called the Flemming body) during cytokinesis,
        as demonstrated by immunofluorescence (PMID:18329369). The UniProt subcellular location
        annotation explicitly mentions this.
      action: ACCEPT
      reason: >-
        Flemming body (midbody ring) localization is experimentally established and is central
        to BIRC6's role in cytokinesis regulation.
      supported_by:
        - reference_id: Q9NR09
          supporting_text: >-
            On the midbody, localizes to the midbody ring, also called Flemming body.

  # === IPI PROTEIN BINDING ANNOTATIONS ===
  - term:
      id: GO:0005515
      label: protein binding
    evidence_type: IPI
    original_reference_id: PMID:18329369
    review:
      summary: >-
        BIRC6 interacts with multiple proteins during cytokinesis including KIF23/MKLP1,
        USP8/UBPY, survivin, MEK1, RAB8, RAB11, PLK1, SEC6, and SEC8 (PMID:18329369).
        However, 'protein binding' is uninformative as a molecular function term.
      action: REMOVE
      reason: >-
        The term 'protein binding' (GO:0005515) provides no specific information about
        BIRC6's actual molecular function. The interactions are biologically meaningful
        but better captured by process annotations (regulation of cytokinesis) and more
        specific molecular function terms.
      supported_by:
        - reference_id: PMID:18329369
          supporting_text: >-
            BRUCE moves from the vesicular system to the midbody ring and serves as a platform
            for the membrane delivery machinery and mitotic regulators.

  - term:
      id: GO:0005515
      label: protein binding
    evidence_type: IPI
    original_reference_id: PMID:26496610
    review:
      summary: >-
        High-throughput interactome study. 'Protein binding' is uninformative.
      action: REMOVE
      reason: >-
        The term 'protein binding' (GO:0005515) is uninformative. High-throughput
        interaction data should be captured by more specific interaction types when possible.
      supported_by:
        - reference_id: PMID:26496610
          supporting_text: >-
            A human interactome in three quantitative dimensions organized by stoichiometries
            and abundances.

  - term:
      id: GO:0005515
      label: protein binding
    evidence_type: IPI
    original_reference_id: PMID:33961781
    review:
      summary: >-
        High-throughput interactome study. 'Protein binding' is uninformative.
      action: REMOVE
      reason: >-
        The term 'protein binding' (GO:0005515) is uninformative. These high-throughput
        data do not provide functional insight beyond what is captured by more specific
        annotations.
      supported_by:
        - reference_id: PMID:33961781
          supporting_text: >-
            Dual proteome-scale networks reveal cell-specific remodeling of the human interactome.

  # === IEA FROM ENSEMBL COMPARA ===
  - term:
      id: GO:0001890
      label: placenta development
    evidence_type: IEA
    original_reference_id: GO_REF:0000107
    review:
      summary: >-
        This annotation is transferred from mouse ortholog data. BIRC6-knockout mice show
        placental defects (labyrinthine layer development issues), which could be a consequence
        of the general anti-apoptotic and cytokinesis functions of BIRC6 rather than a
        placenta-specific function.
      action: KEEP_AS_NON_CORE
      reason: >-
        Placenta development is likely a pleiotropic consequence of BIRC6's core anti-apoptotic
        and cytokinesis functions rather than a specific evolved function for placental biology.
        The annotation should be kept but marked as non-core.
      supported_by:
        - reference_id: file:human/BIRC6/BIRC6-deep-research-falcon.md
          supporting_text: >-
            BIRC6 is a giant dual-function E2/E3 ubiquitin enzyme with a BIR domain that
            binds caspase regulators and a UBC domain enabling ubiquitin transfer.

  - term:
      id: GO:0016020
      label: membrane
    evidence_type: IEA
    original_reference_id: GO_REF:0000107
    review:
      summary: >-
        BIRC6 is described as a peripheral membrane protein of the trans-Golgi network
        (PMID:15200957). The 'membrane' annotation is very broad but not incorrect.
      action: ACCEPT
      reason: >-
        BIRC6 is a peripheral membrane protein associated with the trans-Golgi network
        membrane. This broad IEA annotation is acceptable alongside the more specific
        trans-Golgi network annotation.
      supported_by:
        - reference_id: PMID:15200957
          supporting_text: >-
            BRUCE, a conserved 528 kDa peripheral membrane protein of the trans-Golgi network

  # === IDA FROM IMMUNOFLUORESCENCE ===
  - term:
      id: GO:0005794
      label: Golgi apparatus
    evidence_type: IDA
    original_reference_id: GO_REF:0000052
    review:
      summary: >-
        BIRC6 localizes to the Golgi apparatus (specifically the trans-Golgi network) based on
        immunofluorescence data (GO_REF:0000052). Consistent with PMID:18329369 and PMID:15200957.
      action: ACCEPT
      reason: >-
        Golgi apparatus localization is experimentally established by immunofluorescence and
        consistent with the more specific trans-Golgi network localization.
      supported_by:
        - reference_id: PMID:15200957
          supporting_text: >-
            BRUCE, a conserved 528 kDa peripheral membrane protein of the trans-Golgi network

  - term:
      id: GO:0072686
      label: mitotic spindle
    evidence_type: IDA
    original_reference_id: GO_REF:0000052
    review:
      summary: >-
        BIRC6 localizes to the spindle midzone during telophase as part of its cell
        cycle-dependent localization (PMID:18329369). Immunofluorescence data supports
        mitotic spindle localization.
      action: ACCEPT
      reason: >-
        Mitotic spindle localization is experimentally established and is part of BIRC6's
        dynamic cell cycle-dependent localization pattern relevant to its cytokinesis function.
      supported_by:
        - reference_id: Q9NR09
          supporting_text: >-
            moves partially to spindle poles in metaphase, and finally localizes to the spindle
            midzone and the midbody in telophase

  # === TAS/HDA ===
  - term:
      id: GO:0005829
      label: cytosol
    evidence_type: TAS
    original_reference_id: Reactome:R-HSA-9700131
    review:
      summary: >-
        The Reactome pathway R-HSA-9700131 (ALK mutants bind type I TKIs) seems unrelated
        to BIRC6's primary biology. However, BIRC6 is a cytoplasmic/cytosolic protein that
        functions in the cytoplasm. Cytosol localization is reasonable given the protein's
        known distribution.
      action: ACCEPT
      reason: >-
        While the Reactome reference seems tangential, cytosolic localization of BIRC6 is
        consistent with its known function as a cytoplasmic protein that associates with
        membranes and cytoskeletal structures.
      supported_by:
        - reference_id: file:human/BIRC6/BIRC6-deep-research-falcon.md
          supporting_text: >-
            BIRC6 and Axin are reported to colocalize in the cytoplasm

  - term:
      id: GO:0016020
      label: membrane
    evidence_type: HDA
    original_reference_id: PMID:19946888
    review:
      summary: >-
        BIRC6 was identified in the membrane proteome of NK cells by high-throughput mass
        spectrometry (PMID:19946888). This is consistent with BIRC6 being a peripheral
        membrane protein of the trans-Golgi network.
      action: ACCEPT
      reason: >-
        Membrane association is consistent with BIRC6's established localization at the
        trans-Golgi network membrane. The HDA evidence supports the known biology.
      supported_by:
        - reference_id: PMID:15200957
          supporting_text: >-
            BRUCE, a conserved 528 kDa peripheral membrane protein of the trans-Golgi network

  # === IMP ANNOTATIONS ===
  - term:
      id: GO:2001237
      label: negative regulation of extrinsic apoptotic signaling pathway
    evidence_type: IMP
    original_reference_id: PMID:14765125
    review:
      summary: >-
        Qiu et al. (PMID:14765125) showed that decreasing BRUCE content by RNAi promotes
        apoptosis, and that Nrdp1-mediated degradation of BRUCE triggers apoptosis. This
        demonstrates that BIRC6 negatively regulates the extrinsic apoptotic signaling pathway.
      action: ACCEPT
      reason: >-
        The IMP evidence from PMID:14765125 directly demonstrates that BIRC6 loss promotes
        apoptosis, consistent with its role as an IAP. This annotation captures the specific
        pathway (extrinsic apoptotic signaling) that BIRC6 negatively regulates.
      supported_by:
        - reference_id: PMID:14765125
          supporting_text: >-
            decreasing BRUCE content by RNA interference or overexpression of Nrdp1 promotes
            apoptosis. Thus, BRUCE normally inhibits apoptosis

  # === IDA FROM PMID:18329369 ===
  - term:
      id: GO:0000922
      label: spindle pole
    evidence_type: IDA
    original_reference_id: PMID:18329369
    review:
      summary: >-
        BIRC6 moves to spindle poles in metaphase as demonstrated by immunofluorescence
        (PMID:18329369). Direct experimental evidence for this localization.
      action: ACCEPT
      reason: >-
        Spindle pole localization is directly demonstrated by immunofluorescence in
        PMID:18329369 as part of BIRC6's cell cycle-dependent localization.
      supported_by:
        - reference_id: Q9NR09
          supporting_text: >-
            moves partially to spindle poles in metaphase

  # === IDA FROM PMID:15200957 ===
  - term:
      id: GO:0004842
      label: ubiquitin-protein transferase activity
    evidence_type: IDA
    original_reference_id: PMID:15200957
    review:
      summary: >-
        Bartke et al. (PMID:15200957) directly demonstrated that BIRC6 functions as a chimeric
        E2/E3 ubiquitin ligase with Smac as a substrate. This is core experimental evidence
        for ubiquitin-protein transferase activity.
      action: ACCEPT
      reason: >-
        Direct biochemical demonstration of E2/E3 ubiquitin ligase activity. This is a core
        molecular function of BIRC6.
      supported_by:
        - reference_id: PMID:15200957
          supporting_text: >-
            BRUCE has the distinctive property of functioning as a chimeric E2/E3 ubiquitin ligase
            with Smac being a substrate.

  - term:
      id: GO:0004869
      label: cysteine-type endopeptidase inhibitor activity
    evidence_type: IMP
    original_reference_id: PMID:15200957
    review:
      summary: >-
        Bartke et al. (PMID:15200957) showed that BIRC6 inhibits caspase activity in a
        BIR domain-dependent manner. BIRC6 strongly inhibits caspase-9 and more weakly
        inhibits caspase-3 activity.
      action: ACCEPT
      reason: >-
        Caspase inhibition is a core function of BIRC6 as an IAP. The IMP evidence from
        PMID:15200957 directly demonstrates this activity.
      supported_by:
        - reference_id: PMID:15200957
          supporting_text: >-
            BRUCE inhibits caspase activity and apoptosis depending on its BIR domain.

  - term:
      id: GO:0005515
      label: protein binding
    evidence_type: IPI
    original_reference_id: PMID:15200957
    review:
      summary: >-
        BIRC6 interacts with Smac, HtrA2, caspases-3, -6, -7, and -9 (PMID:15200957).
        However, 'protein binding' is uninformative. These interactions are better captured
        by the caspase inhibitor activity and ubiquitin ligase annotations.
      action: REMOVE
      reason: >-
        The term 'protein binding' is uninformative. The specific interactions with Smac and
        caspases are better represented by the cysteine-type endopeptidase inhibitor activity
        (GO:0004869) and ubiquitin-protein transferase activity (GO:0004842) annotations.
      supported_by:
        - reference_id: PMID:15200957
          supporting_text: >-
            BRUCE inhibits caspase activity and apoptosis depending on its BIR domain. Upon
            apoptosis induction, BRUCE is antagonized by three mechanisms: first, through
            binding to Smac

  - term:
      id: GO:0005768
      label: endosome
    evidence_type: IDA
    original_reference_id: PMID:18329369
    review:
      summary: >-
        BIRC6 localizes to endosomes in interphase cells (PMID:18329369). Direct
        immunofluorescence evidence.
      action: ACCEPT
      reason: >-
        Endosomal localization is experimentally established by immunofluorescence and
        is part of BIRC6's vesicular system localization pattern.
      supported_by:
        - reference_id: Q9NR09
          supporting_text: >-
            In interphase cells, localizes to the trans-Golgi network membrane and endosomes.

  - term:
      id: GO:0005802
      label: trans-Golgi network
    evidence_type: IDA
    original_reference_id: PMID:18329369
    review:
      summary: >-
        BIRC6 localizes to the trans-Golgi network membrane in interphase cells
        (PMID:18329369). Direct experimental evidence by immunofluorescence.
      action: ACCEPT
      reason: >-
        Trans-Golgi network localization is a core localization of BIRC6, established by
        multiple studies.
      supported_by:
        - reference_id: Q9NR09
          supporting_text: >-
            In interphase cells, localizes to the trans-Golgi network membrane and endosomes.

  - term:
      id: GO:0005815
      label: microtubule organizing center
    evidence_type: IDA
    original_reference_id: PMID:18329369
    review:
      summary: >-
        BIRC6 concentrates in a pericentriolar compartment (microtubule organizing center)
        in interphase (PMID:18329369). Direct immunofluorescence evidence.
      action: ACCEPT
      reason: >-
        Microtubule organizing center (pericentriolar) localization during interphase is
        experimentally demonstrated and consistent with BIRC6's dynamic cell cycle-dependent
        localization.
      supported_by:
        - reference_id: Q9NR09
          supporting_text: >-
            Concentrates in a pericentriolar compartment in interphase

  - term:
      id: GO:0006468
      label: protein phosphorylation
    evidence_type: TAS
    original_reference_id: PMID:18329369
    review:
      summary: >-
        MISANNOTATION: BIRC6 (BRUCE/Apollon) is a ubiquitin-conjugating E2/E3 enzyme
        (EC 2.3.2.24), NOT a protein kinase. PMID:18329369 describes BRUCE's ubiquitin-conjugating
        activity in cytokinesis - "BRUCE...processes ubiquitin-conjugating activity"
        - there
        is no mention of phosphorylation activity. UniProt shows BIRC6 is PHOSPHORYLATED
        at multiple sites (Ser-480, Ser-581, etc.) making it a SUBSTRATE of kinases,
        not
        an enzyme that performs phosphorylation.
      action: REMOVE
      reason: >-
        BIRC6 does not catalyze protein phosphorylation. It is a substrate of kinases
        (phosphorylated at multiple sites), not a kinase itself. The cited reference
        PMID:18329369 describes ubiquitin-conjugating activity, not phosphorylation.
        This appears to be a misannotation.
      supported_by:
        - reference_id: PMID:18329369
          supporting_text: >-
            we identify BRUCE, a 528 kDa multifunctional protein, which processes
            ubiquitin-conjugating activity, as a major regulator of abscission.

  - term:
      id: GO:0016567
      label: protein ubiquitination
    evidence_type: TAS
    original_reference_id: PMID:18329369
    review:
      summary: >-
        BIRC6 catalyzes protein ubiquitination during cytokinesis, and ubiquitin relocalizes
        from midbody microtubules to the midbody ring in a BRUCE-dependent manner
        (PMID:18329369). TAS evidence from a well-characterized study.
      action: ACCEPT
      reason: >-
        Protein ubiquitination is a core biochemical activity of BIRC6, directly supported
        by PMID:18329369 and multiple other studies.
      supported_by:
        - reference_id: PMID:18329369
          supporting_text: >-
            ubiquitin relocalizes from midbody microtubules to the midbody ring during
            cytokinesis, and depletion of BRUCE disrupts this process.

  - term:
      id: GO:0030496
      label: midbody
    evidence_type: IDA
    original_reference_id: PMID:18329369
    review:
      summary: >-
        BIRC6 localizes to the midbody during telophase and cytokinesis, specifically to the
        midbody ring (PMID:18329369). Direct immunofluorescence evidence.
      action: ACCEPT
      reason: >-
        Midbody localization is experimentally established and central to BIRC6's role in
        cytokinesis.
      supported_by:
        - reference_id: Q9NR09
          supporting_text: >-
            finally localizes to the spindle midzone and the midbody in telophase and during
            cytokinesis.

  - term:
      id: GO:0032465
      label: regulation of cytokinesis
    evidence_type: IMP
    original_reference_id: PMID:18329369
    review:
      summary: >-
        Pohl and Jentsch (PMID:18329369) demonstrated that BIRC6 depletion causes defective
        abscission and cytokinesis-associated apoptosis. BIRC6 coordinates vesicular targeting
        to the abscission site and midbody ring formation.
      action: ACCEPT
      reason: >-
        Regulation of cytokinesis is a core function of BIRC6, demonstrated by IMP evidence
        showing that BIRC6 depletion causes cytokinesis defects.
      supported_by:
        - reference_id: PMID:18329369
          supporting_text: >-
            Depletion of BRUCE in cell cultures causes defective abscission and
            cytokinesis-associated apoptosis, accompanied by a block of vesicular targeting
            and defective formation of the midbody and the midbody ring.

  - term:
      id: GO:0043066
      label: negative regulation of apoptotic process
    evidence_type: IMP
    original_reference_id: PMID:15200957
    review:
      summary: >-
        Bartke et al. (PMID:15200957) showed that BIRC6 inhibits caspase activity and apoptosis
        through its BIR domain. Wild-type and mutant forms were used to demonstrate
        BIR domain-dependent anti-apoptotic activity.
      action: ACCEPT
      reason: >-
        IMP evidence from PMID:15200957 directly demonstrates that BIRC6 negatively regulates
        apoptosis. This is a core function of BIRC6.
      supported_by:
        - reference_id: PMID:15200957
          supporting_text: >-
            BRUCE inhibits caspase activity and apoptosis depending on its BIR domain.

  - term:
      id: GO:0042127
      label: regulation of cell population proliferation
    evidence_type: TAS
    original_reference_id: PMID:18414036
    review:
      summary: >-
        Dubrez-Daloz et al. (PMID:18414036) is a review discussing IAP family roles in cell
        proliferation, differentiation, and signaling. This is an indirect and broad annotation.
      action: KEEP_AS_NON_CORE
      reason: >-
        Regulation of cell proliferation is a secondary/indirect consequence of BIRC6's
        anti-apoptotic and cytokinesis functions, not a direct core function. The review
        reference discusses IAPs generally, not BIRC6 specifically.
      supported_by:
        - reference_id: PMID:18414036
          supporting_text: >-
            research of protein partners have revealed the importance of IAPs in adaptive
            response to cellular stress, in cell proliferation, differentiation, signaling,
            motility and in immune response.

  - term:
      id: GO:0005515
      label: protein binding
    evidence_type: IPI
    original_reference_id: PMID:14765125
    review:
      summary: >-
        BIRC6 interacts with RNF41/Nrdp1, which mediates BIRC6 ubiquitination and degradation
        (PMID:14765125). However, 'protein binding' is uninformative.
      action: REMOVE
      reason: >-
        The term 'protein binding' (GO:0005515) is uninformative. The interaction with RNF41
        is a regulatory mechanism (BIRC6 being a substrate of RNF41 E3 ligase) and does not
        describe BIRC6's molecular function.
      supported_by:
        - reference_id: PMID:14765125
          supporting_text: >-
            Nrdp1 associates with BRUCE/apollon, a 530 kDa membrane-associated IAP

  - term:
      id: GO:0043066
      label: negative regulation of apoptotic process
    evidence_type: TAS
    original_reference_id: PMID:10544019
    review:
      summary: >-
        Chen et al. (PMID:10544019) identified BIRC6/Apollon as a human IAP family member
        and showed that antisense knockdown sensitizes cells to apoptosis, indicating an
        anti-apoptotic function. This is the original identification paper.
      action: ACCEPT
      reason: >-
        The original identification paper demonstrates that BIRC6/Apollon protects cells
        from apoptosis. TAS evidence from the foundational paper for this gene.
      supported_by:
        - reference_id: PMID:10544019
          supporting_text: >-
            Treating SNB-78 cells with antisense oligonucleotide against Apollon reduced the
            expression of Apollon protein, and significantly sensitized the cells to apoptosis
            induced by cisplatin and camptothecin.

references:
  - id: GO_REF:0000002
    title: Gene Ontology annotation through association of InterPro records with
      GO terms
    findings: []
  - id: GO_REF:0000033
    title: Annotation inferences using phylogenetic trees
    findings: []
  - id: GO_REF:0000043
    title: Gene Ontology annotation based on UniProtKB/Swiss-Prot keyword
      mapping
    findings: []
  - id: GO_REF:0000044
    title: Gene Ontology annotation based on UniProtKB/Swiss-Prot Subcellular
      Location vocabulary mapping, accompanied by conservative changes to GO
      terms applied by UniProt
    findings: []
  - id: GO_REF:0000052
    title: Gene Ontology annotation based on curation of immunofluorescence data
    findings: []
  - id: GO_REF:0000107
    title: Automatic transfer of experimentally verified manual GO annotation
      data to orthologs using Ensembl Compara
    findings: []
  - id: GO_REF:0000117
    title: Electronic Gene Ontology annotations created by ARBA machine learning
      models
    findings: []
  - id: GO_REF:0000120
    title: Combined Automated Annotation using Multiple IEA Methods
    findings: []
  - id: PMID:10544019
    title: A human IAP-family gene, apollon, expressed in human brain cancer
      cells.
    findings:
      - statement: >-
          Identified Apollon/BIRC6 as a human IAP family member with a BIR domain and
          UBC domain, expressed in brain cancer cells.
      - statement: >-
          Antisense knockdown of Apollon sensitizes SNB-78 brain cancer cells to
          cisplatin and camptothecin-induced apoptosis.
  - id: PMID:14765125
    title: Nrdp1-mediated degradation of the gigantic IAP, BRUCE, is a novel
      pathway for triggering apoptosis.
    findings:
      - statement: >-
          Nrdp1/RNF41 associates with BRUCE and catalyzes its ubiquitination and
          proteasomal degradation.
      - statement: >-
          BRUCE normally inhibits apoptosis; decreasing BRUCE by RNAi or Nrdp1
          overexpression promotes apoptosis.
      - statement: >-
          Apoptotic stimuli induce proteasomal degradation of BRUCE but not XIAP or c-IAP1.
  - id: PMID:15200957
    title: Dual role of BRUCE as an antiapoptotic IAP and a chimeric E2/E3
      ubiquitin ligase.
    findings:
      - statement: >-
          BRUCE inhibits caspase activity and apoptosis in a BIR domain-dependent manner.
      - statement: >-
          BRUCE functions as a chimeric E2/E3 ubiquitin ligase with Smac as a substrate.
      - statement: >-
          BRUCE is antagonized by Smac binding, HtrA2 protease, and caspase-mediated
          cleavage.
      - statement: >-
          BRUCE is a 528 kDa peripheral membrane protein of the trans-Golgi network.
  - id: PMID:18329369
    title: Final stages of cytokinesis and midbody ring formation are controlled
      by BRUCE.
    findings:
      - statement: >-
          BRUCE is a major regulator of abscission during cytokinesis.
      - statement: >-
          BRUCE exhibits cell cycle-dependent localization: pericentriolar in interphase,
          spindle poles in metaphase, midbody/midbody ring in telophase/cytokinesis.
      - statement: >-
          BRUCE depletion causes defective abscission, cytokinesis-associated apoptosis,
          and disrupts midbody ring formation and ubiquitin relocalization.
      - statement: >-
          BRUCE interacts with KIF23/MKLP1, USP8/UBPY, survivin, MEK1, RAB8, RAB11,
          PLK1, SEC6, and SEC8.
  - id: PMID:18414036
    title: 'IAPs: more than just inhibitors of apoptosis proteins.'
    findings:
      - statement: >-
          Review discussing IAP family roles beyond apoptosis inhibition, including cell
          proliferation, differentiation, signaling, and immune response.
  - id: PMID:19946888
    title: Defining the membrane proteome of NK cells.
    findings:
      - statement: >-
          BIRC6 identified in NK cell membrane proteome by high-throughput mass spectrometry.
  - id: PMID:26496610
    title: A human interactome in three quantitative dimensions organized by
      stoichiometries and abundances.
    findings: []
  - id: PMID:33961781
    title: Dual proteome-scale networks reveal cell-specific remodeling of the
      human interactome.
    findings: []
  - id: PMID:36758104
    title: Structures of BIRC6-client complexes provide a mechanism of SMAC-mediated
      release of caspases.
    findings:
      - statement: >-
          Cryo-EM structure of BIRC6 reveals antiparallel homodimer with central
          substrate-binding cavity accommodating Smac/DIABLO.
      - statement: >-
          BIRC6 ubiquitinates caspases-3, -7, -9 and their procaspases via UBA6 as E1.
  - id: PMID:36758105
    title: Structural basis for regulation of apoptosis and autophagy by the
      BIRC6/SMAC complex.
    findings:
      - statement: >-
          BIRC6 ubiquitinates the autophagy protein MAP1LC3B; inhibited by Smac.
      - statement: >-
          Cryo-EM structure reveals multiple domains including WD40, BIR, and UBC.
  - id: PMID:36758106
    title: Structural basis for SMAC-mediated antagonism of caspase inhibition by the
      giant ubiquitin ligase BIRC6.
    findings:
      - statement: >-
          Smac competes with caspases for BIRC6 binding, providing mechanism for
          antagonism of caspase inhibition.
  - id: Reactome:R-HSA-9700131
    title: ALK mutants bind type I TKIs
    findings: []
  - id: file:human/BIRC6/BIRC6-deep-research-falcon.md
    title: Deep research on BIRC6 function (Falcon)
    findings:
      - statement: >-
          BIRC6 is a cell-fate rheostat coordinating apoptosis-autophagy balance through
          caspase-9 regulation and LC3 K51 ubiquitylation.
      - statement: >-
          BIRC6 mono-ubiquitinates LC3 at K51 in cooperation with UBA6, suppressing autophagy.
      - statement: >-
          BIRC6 ubiquitinates Axin to activate Wnt/beta-catenin signaling in RCC cells.

core_functions:
  - molecular_function:
      id: GO:0061631
      label: ubiquitin conjugating enzyme activity
    description: >-
      BIRC6 functions as a dual E2 ubiquitin-conjugating enzyme and E3 ubiquitin-protein ligase
      (EC 2.3.2.24). It combines E2 conjugating and E3 ligase activities in a single polypeptide,
      using UBA6 as the E1 activating enzyme. BIRC6 ubiquitinates pro-apoptotic factors (caspases-3,
      -7, -9, Smac/DIABLO, HtrA2) to promote their degradation and inhibit apoptosis. It also
      mono-ubiquitinates LC3 at K51 to suppress autophagy. BIRC6 forms an antiparallel homodimer
      with a central substrate-binding cavity. Its activity is antagonized by Smac/DIABLO, which
      competes for substrate binding sites.
    directly_involved_in:
      - id: GO:0016567
        label: protein ubiquitination
      - id: GO:0043066
        label: negative regulation of apoptotic process
    locations:
      - id: GO:0005802
        label: trans-Golgi network
      - id: GO:0005829
        label: cytosol
    supported_by:
      - reference_id: PMID:15200957
        supporting_text: >-
          BRUCE has the distinctive property of functioning as a chimeric E2/E3 ubiquitin ligase
          with Smac being a substrate.
      - reference_id: PMID:36758104
        supporting_text: >-
          Structures of BIRC6-client complexes provide a mechanism of SMAC-mediated release of
          caspases.

  - molecular_function:
      id: GO:0004869
      label: cysteine-type endopeptidase inhibitor activity
    description: >-
      BIRC6 directly inhibits caspase activity through its BIR domain. The BIR domain mediates
      binding to active caspases (caspase-3, -6, -7, -9), with strongest inhibition of caspase-9.
      This caspase-inhibitory activity works in concert with the E2/E3 ubiquitin ligase activity
      to suppress apoptosis: BIRC6 both directly inhibits caspases and promotes their
      ubiquitination-dependent degradation.
    directly_involved_in:
      - id: GO:0043066
        label: negative regulation of apoptotic process
      - id: GO:2001237
        label: negative regulation of extrinsic apoptotic signaling pathway
    locations:
      - id: GO:0005829
        label: cytosol
    supported_by:
      - reference_id: PMID:15200957
        supporting_text: >-
          BRUCE inhibits caspase activity and apoptosis depending on its BIR domain.

  - molecular_function:
      id: GO:0004842
      label: ubiquitin-protein transferase activity
    description: >-
      During cytokinesis, BIRC6 coordinates the final stages of abscission by functioning as a
      platform for membrane delivery machinery and mitotic regulators at the midbody ring. Its
      ubiquitin-conjugating/ligase activity is crucial for ubiquitin relocalization from midbody
      microtubules to the midbody ring. BIRC6 depletion causes defective abscission, disrupted
      midbody ring formation, and cytokinesis-associated apoptosis.
    directly_involved_in:
      - id: GO:0032465
        label: regulation of cytokinesis
      - id: GO:0051301
        label: cell division
    locations:
      - id: GO:0030496
        label: midbody
      - id: GO:0090543
        label: Flemming body
      - id: GO:0000922
        label: spindle pole
    supported_by:
      - reference_id: PMID:18329369
        supporting_text: >-
          we identify BRUCE, a 528 kDa multifunctional protein, which processes
          ubiquitin-conjugating activity, as a major regulator of abscission.

proposed_new_terms: []

suggested_questions:
  - question: >-
      What are the specific substrates ubiquitinated by BIRC6 during cytokinesis at the midbody
      ring? While BIRC6 is known to ubiquitinate apoptotic regulators (caspases, Smac) and
      autophagy proteins (LC3), the cytokinesis-relevant substrates at the midbody remain
      poorly defined.
  - question: >-
      Is the Wnt/beta-catenin signaling axis (through Axin ubiquitination) a conserved normal
      function of BIRC6 or a cancer-specific gain of function? Current evidence is limited
      to renal cell carcinoma models.
  - question: >-
      What determines the substrate selectivity between BIRC6's apoptotic (caspases, Smac),
      autophagy (LC3), and cytokinesis substrates? Is this regulated by localization,
      post-translational modifications, or interaction partners?

suggested_experiments:
  - description: >-
      Proximity labeling (BioID/TurboID) with BIRC6 at the midbody during cytokinesis to
      identify the specific ubiquitination substrates and interaction partners that mediate
      its cytokinesis function, as distinct from its apoptotic substrates.
    hypothesis: >-
      BIRC6 has a set of cytokinesis-specific substrates at the midbody ring that are distinct
      from its known apoptotic substrates.
  - description: >-
      Systematic comparison of BIRC6-mediated LC3 K51 ubiquitination across cell types and
      stress conditions to determine whether this autophagy-regulatory function is constitutive
      or context-dependent.
    hypothesis: >-
      BIRC6's autophagy-suppressive function through LC3 ubiquitination is dynamically
      regulated by cellular stress status and BIRC6's own turnover state.