--- 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: UniProtKB: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: REMOVE reason: >- The IBA annotation suggests nuclear localization from phylogenetic inference, with UBE2Z as the supporting with/from sequence, but the direct human BIRC6 localization evidence supports trans-Golgi network, endosomes, cytosol, centrosome/spindle-pole, midbody, and Flemming-body localizations rather than nucleus. The extensive localization studies in PMID:18329369 do not report nuclear localization, and UniProt does not annotate BIRC6 to the nucleus, so this propagation should not be retained for human BIRC6. supported_by: - reference_id: UniProtKB: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: UniProtKB: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: MODIFY reason: >- Ubiquitin-protein transferase activity is a core function of BIRC6, but it is a broad parent. The PN projection to GO:0061630 ubiquitin protein ligase activity is the more specific molecular-function term for the E3 component of BIRC6's dual E2/E3 activity. proposed_replacement_terms: - id: GO:0061630 label: ubiquitin protein ligase 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: UniProtKB: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: UniProtKB: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: UniProtKB: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: UniProtKB: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: UniProtKB: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, but the more specific term is GO:0061630 ubiquitin protein ligase activity. action: MODIFY reason: >- Direct biochemical demonstration of E2/E3 ubiquitin ligase activity supports a core molecular function of BIRC6. The broad parent term should be replaced by the PN-supported specific term GO:0061630. proposed_replacement_terms: - id: GO:0061630 label: ubiquitin protein ligase 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: 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: UniProtKB: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: UniProtKB: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: UniProtKB: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: UniProtKB: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. - id: file:human/BIRC6/BIRC6-notes.md title: Manual PROTEOSTASIS PN review notes for BIRC6 findings: - statement: >- PN review supports replacing the broad BIRC6 ubiquitin-protein transferase activity annotation with GO:0061630 ubiquitin protein ligase activity. - statement: >- BIRC6 autophagy evidence concerns LC3 ubiquitination and autophagy suppression, not lysosome-autophagosome SNARE or docking/fusion activity. 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:0061630 label: ubiquitin protein ligase 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.