{"gene":"CDC16","run_date":"2026-06-09T22:57:18","timeline":{"discoveries":[{"year":1995,"finding":"CDC16 (APC6/ANAPC6) is a subunit of the 20S anaphase-promoting complex (APC), a regulated ubiquitin-protein ligase that catalyzes the mitosis-specific ubiquitination of cyclin B, targeting it for proteasomal destruction to enable anaphase progression.","method":"Biochemical fractionation of mitotic Xenopus egg extracts; immunodepletion with CDC27 antibodies; immunopurification of CDC27 complexes; in vitro ubiquitination assays reconstituted with UBC4 and E1","journal":"Cell","confidence":"High","confidence_rationale":"Tier 1 / Strong — reconstituted ubiquitin ligase activity in vitro, immunodepletion and complementation, replicated across labs","pmids":["7736580"],"is_preprint":false},{"year":1993,"finding":"S. pombe cdc16 (ortholog of human CDC16/APC6) is essential for limiting septum formation to once per cell cycle and for maintaining p34cdc2 kinase activity; deletion causes multiple septa without cytokinesis, establishing cdc16 as a negative regulator of septation.","method":"Gene cloning, gene deletion, temperature-sensitive mutant analysis, genetic interaction studies in S. pombe","journal":"The EMBO journal","confidence":"High","confidence_rationale":"Tier 2 / Strong — loss-of-function deletion with defined cellular phenotype, genetic epistasis, replicated findings on cdc16 function in septation","pmids":["8334988"],"is_preprint":false},{"year":1994,"finding":"S. pombe cut9 (ortholog of CDC16/APC6) encodes a 78-kDa TPR-repeat protein required for the onset of anaphase; cut9 temperature-sensitive mutants block anaphase while allowing post-anaphase events, and cut9 genetically interacts with nuc2, scn1, and scn2.","method":"Temperature-sensitive mutant characterization, gene cloning, TPR domain analysis, genetic suppressor analysis in S. pombe","journal":"The Journal of cell biology","confidence":"High","confidence_rationale":"Tier 2 / Strong — loss-of-function mutant with defined anaphase block phenotype, genetic epistasis with multiple interactors, consistent with role in APC/C","pmids":["7798319"],"is_preprint":false},{"year":1998,"finding":"S. pombe Cdc16 (APC6 ortholog) and Byr4 form a two-component GTPase-activating protein (GAP) for the Spg1 GTPase that controls septation; Cdc16 alone has no detectable GAP activity but together with Byr4 stimulates Spg1 GTP hydrolysis, negatively regulating septation.","method":"Yeast two-hybrid, in vitro coprecipitation, in vitro GTPase assays measuring GTP hydrolysis and dissociation, genetic interaction analysis in S. pombe","journal":"Current biology : CB","confidence":"High","confidence_rationale":"Tier 1 / Strong — in vitro reconstituted GAP activity with multiple orthogonal methods (biochemical, genetic, two-hybrid), specificity controls with seven Ypt GTPases","pmids":["9742395"],"is_preprint":false},{"year":1996,"finding":"S. cerevisiae CDC16 restricts DNA replication to once per cell cycle; cdc16 mutants accumulate up to 8C DNA through rereplication of all chromosomes within a single cell cycle despite elevated Clb2-Cdc28 kinase activity, implicating CDC16 in targeted proteolysis of an S-phase initiator.","method":"Genetic screen for DNA overreplication mutants, flow cytometry (DNA content analysis), conditional allele characterization in S. cerevisiae","journal":"Cell","confidence":"High","confidence_rationale":"Tier 2 / Strong — clean loss-of-function genetic analysis with defined cellular phenotype (DNA rereplication), replicated and extended in follow-up paper (PMID:9660930)","pmids":["8620535"],"is_preprint":false},{"year":1997,"finding":"PP5 serine/threonine phosphatase physically interacts with CDC16 and CDC27 (APC/C subunits) through TPR-TPR interactions; the N-terminal TPR domain of PP5 binds the C-terminal TPR block of CDC16, and PP5 co-localizes with the mitotic spindle apparatus, suggesting PP5 may regulate APC/C activity by dephosphorylating these subunits.","method":"Yeast two-hybrid analysis, in vitro binding assays, deletion mapping, indirect immunofluorescence localization","journal":"The Journal of biological chemistry","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — two-hybrid plus in vitro binding with deletion mapping (two methods), single lab; functional consequence of interaction not directly tested","pmids":["9405394"],"is_preprint":false},{"year":1998,"finding":"S. cerevisiae CDC16 is required to prevent reinitiation of DNA synthesis from normal chromosomal replication origins; cdc16 mutants reinitiate replication in a Cdc6p- and Cdc46/Mcm5p-dependent manner despite elevated Cdc28p kinase activity, placing CDC16 upstream of origin firing control.","method":"Two-dimensional DNA electrophoresis, density-transfer experiments, genetic analysis with cdc6 and cdc46/mcm5 mutations in S. cerevisiae","journal":"Molecular cell","confidence":"High","confidence_rationale":"Tier 2 / Strong — multiple orthogonal methods (2D gel electrophoresis, density transfer, genetic epistasis), clearly defines CDC16 role in origin firing control","pmids":["9660930"],"is_preprint":false},{"year":1999,"finding":"Byr4 contains one Cdc16-binding site and four Spg1-binding sites; the Cdc16-binding site plus a single Spg1-binding site (SBS4) is necessary and sufficient to reconstitute Cdc16-dependent Spg1 GAP activity comparable to wild-type Byr4, delineating the minimal functional unit of the two-component GAP.","method":"In vitro mutagenesis, in vitro GTPase assays, binding affinity measurements of Byr4 mutants in S. pombe","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1 / Strong — in vitro reconstitution with mutagenesis defining binding sites and GAP activity requirements","pmids":["10196225"],"is_preprint":false},{"year":2004,"finding":"Swm1/Apc13 stabilizes the association of Cdc16 and Cdc27 within the APC/C; deletion of SWM1 reduces Cdc16 and Cdc27 incorporation into the APC/C and abolishes ubiquitin ligase activity in vitro, placing Swm1/Apc13 as a structural stabilizer of CDC16 within the complex.","method":"Co-immunoprecipitation, in vitro ubiquitination assays, genetic complementation across species (human and S. pombe homologs complement S. cerevisiae swm1 deletion)","journal":"Molecular and cellular biology","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal Co-IP demonstrating reduced Cdc16 association, in vitro ubiquitination activity assay, cross-species complementation","pmids":["15060174"],"is_preprint":false},{"year":2004,"finding":"New temperature-sensitive alleles of S. pombe cut9 (CDC16/APC6 ortholog) cause defective rereplication in the absence of cyclin B (Cdc13), identifying cut9 as required for the rereplication process and linking APC/C function to DNA replication licensing in fission yeast.","method":"Genetic screen for rereplication-defective temperature-sensitive mutants, complementation cloning in S. pombe","journal":"Genetics","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — genetic loss-of-function with defined phenotype, single lab, screen-based identification without detailed mechanistic follow-up","pmids":["15466421"],"is_preprint":false},{"year":2009,"finding":"CDC26 stabilizes the structure of APC6 (CDC16) through an intermolecular TPR mimic composed of one helix from each protein; this interaction is required for APC assembly and integrity.","method":"Crystal structure determination, biophysical binding studies, genetic analysis of CDC26-APC6 interaction","journal":"Nature structural & molecular biology","confidence":"High","confidence_rationale":"Tier 1 / Strong — crystal structure with biophysical and genetic validation, defines molecular mechanism of CDC26-APC6 interaction","pmids":["19668213"],"is_preprint":false},{"year":2010,"finding":"The crystal structure of S. pombe Cut9 (Cdc16/Apc6) in complex with Hcn1 (Cdc26) reveals a contiguous TPR superhelix of 14 TPR units; the C-terminal TPR block interacts with Hcn1, while the N-terminal TPR block mediates Cdc16/Cut9 homo-dimerization through a conserved interface also present in Cdc27. The N-acetyl-Met residue of Hcn1 is enclosed within the Cut9 TPR chamber, protecting Hcn1/Cdc26 from Doa10-mediated ubiquitin-dependent degradation.","method":"X-ray crystallography of Cut9-Hcn1 complex, structural analysis of dimerization and binding interfaces","journal":"The EMBO journal","confidence":"High","confidence_rationale":"Tier 1 / Strong — high-resolution crystal structure defining domain architecture, homo-dimer interface, and substrate protection mechanism","pmids":["20924356"],"is_preprint":false},{"year":2022,"finding":"DEPDC1B competes with SCUBE3 for binding to CDC16 (as APC/C ubiquitin ligase subunit); by sequestering CDC16, DEPDC1B prevents CDC16-mediated ubiquitination and proteasomal degradation of SCUBE3, stabilizing SCUBE3 to promote melanoma angiogenesis and metastasis.","method":"Co-immunoprecipitation, ubiquitination assays, protein stability assays, gain/loss-of-function experiments in melanoma cells and mouse models","journal":"Advanced science (Weinheim, Baden-Wurttemberg, Germany)","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — reciprocal Co-IP, ubiquitination assay, in vivo mouse model, single lab with multiple orthogonal methods","pmids":["35088579"],"is_preprint":false},{"year":2025,"finding":"c-Jun competitively interacts with CDC16 (a key APC/C subunit) to reduce APC/C complex formation, inhibit cell cycle progression (G1 arrest), and suppress neuroblastoma cell proliferation and migration.","method":"Co-immunoprecipitation, flow cytometry cell cycle analysis, EdU proliferation assay, transwell migration/invasion assay in neuroblastoma cells","journal":"Biology direct","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — Co-IP demonstrating c-Jun–CDC16 interaction with functional readouts, single lab, no structural or in vitro reconstitution data","pmids":["40149013"],"is_preprint":false},{"year":2019,"finding":"CDC16 interacts with YDJC and overexpression of CDC16 suppresses EMT by increasing PP2A expression and reducing ERK2 activation; CDC16 overexpression also promotes ubiquitination of YDJC, suggesting CDC16 targets YDJC for degradation.","method":"Co-immunoprecipitation, overexpression and siRNA knockdown, ubiquitination assays, EMT marker analysis in lung cancer cells","journal":"Journal of oncology","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single lab, single Co-IP plus knockdown/overexpression without rigorous reconstitution or mechanistic pathway validation","pmids":["31485224"],"is_preprint":false},{"year":2018,"finding":"CDC16 physically binds YDJC (co-immunoprecipitation), and CDC16 siRNA promotes SPC-induced keratin reorganization, cell migration and invasion, while CDC16 overexpression blocks these events, placing CDC16 as a negative regulator of YDJC-driven cytoskeletal remodeling in lung cancer cells.","method":"Co-immunoprecipitation, siRNA knockdown, overexpression, migration/invasion assays in A549 lung cancer cells","journal":"Oncotarget","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single lab, single Co-IP with functional knockdown/overexpression data, no mechanistic reconstitution","pmids":["29796162"],"is_preprint":false}],"current_model":"CDC16 (APC6/ANAPC6) is a core TPR-repeat subunit of the anaphase-promoting complex/cyclosome (APC/C), an E3 ubiquitin ligase; it forms a contiguous 14-TPR superhelix that homo-dimerizes and scaffolds APC/C assembly (stabilized by CDC26/Hcn1 via an intermolecular TPR mimic and by Swm1/Apc13), and the assembled complex catalyzes mitosis-specific ubiquitination of cyclin B and securin to drive anaphase onset, restrict DNA replication to once per cell cycle, and limit septation — while in S. pombe it additionally participates as part of a two-component GAP (with Byr4) to inactivate the Spg1 GTPase and negatively regulate cytokinesis."},"narrative":{"mechanistic_narrative":"CDC16 (APC6/ANAPC6) is a core subunit of the anaphase-promoting complex/cyclosome (APC/C), a regulated ubiquitin-protein ligase that catalyzes mitosis-specific ubiquitination of cyclin B to drive its proteasomal destruction and enable anaphase progression [PMID:7736580]. Structurally, CDC16 is a TPR-repeat protein that folds into a contiguous 14-TPR superhelix: its N-terminal TPR block mediates homo-dimerization through an interface conserved with CDC27, while its C-terminal TPR block engages CDC26/Hcn1, which stabilizes APC6 through an intermolecular TPR mimic required for APC/C assembly and integrity and which simultaneously sequesters the CDC26 N-acetyl-Met to protect it from ubiquitin-dependent degradation [PMID:19668213, PMID:20924356]. Stable incorporation of CDC16 (and CDC27) into the APC/C is further reinforced by Swm1/Apc13, whose loss reduces CDC16 association and abolishes ligase activity [PMID:15060174]. Through this scaffolding role, CDC16 enforces several cell-cycle controls: it restricts DNA replication to once per cycle by directing targeted proteolysis upstream of origin firing, such that loss-of-function permits Cdc6- and Mcm5-dependent rereplication despite elevated mitotic CDK activity [PMID:8620535, PMID:9660930], and it is required for the onset of anaphase [PMID:7798319]. In fission yeast CDC16 has an additional APC/C-independent function: together with Byr4 it forms a two-component GTPase-activating protein for the Spg1 GTPase that negatively regulates septation, with CDC16 alone lacking GAP activity but cooperating through a defined Byr4 Cdc16-binding site to stimulate Spg1 GTP hydrolysis [PMID:8334988, PMID:9742395, PMID:10196225]. In human cancer contexts, CDC16's APC/C-associated ubiquitination activity is modulated by competitive binding: DEPDC1B competes with the substrate SCUBE3 for CDC16 to block its degradation in melanoma, and c-Jun competes for CDC16 to reduce APC/C formation and induce G1 arrest in neuroblastoma [PMID:35088579, PMID:40149013].","teleology":[{"year":1993,"claim":"Established the first cellular function for CDC16 by showing its fission-yeast ortholog limits septum formation and sustains mitotic CDK activity, framing it as a negative regulator of cytokinesis.","evidence":"Gene cloning, deletion and temperature-sensitive mutant analysis with genetic epistasis in S. pombe","pmids":["8334988"],"confidence":"High","gaps":["Molecular mechanism of septation control not defined","Connection to ubiquitination machinery not yet made"]},{"year":1994,"claim":"Identified CDC16/Cut9 as a TPR-repeat protein required for the onset of anaphase, providing the structural and phenotypic basis later unified with APC/C function.","evidence":"Temperature-sensitive mutant characterization, TPR domain analysis and genetic suppressor analysis in S. pombe","pmids":["7798319"],"confidence":"High","gaps":["Biochemical activity of the TPR protein not established","Anaphase substrate not identified"]},{"year":1995,"claim":"Placed CDC16 within the 20S APC and defined the complex's biochemical activity, showing it is a ubiquitin ligase that targets cyclin B for destruction to enable anaphase.","evidence":"Biochemical fractionation of mitotic Xenopus extracts, immunodepletion/immunopurification and in vitro reconstituted ubiquitination assays","pmids":["7736580"],"confidence":"High","gaps":["Specific catalytic contribution of CDC16 versus other subunits not resolved","Substrate-recognition mechanism not defined"]},{"year":1996,"claim":"Extended CDC16 function to genome stability by showing it restricts DNA replication to once per cell cycle, implicating it in proteolysis of an S-phase initiator.","evidence":"Genetic overreplication screen, flow cytometry DNA-content analysis and conditional allele characterization in S. cerevisiae","pmids":["8620535"],"confidence":"High","gaps":["Identity of the proteolytic target controlling rereplication not defined","Direct biochemical link to APC/C in this role not shown"]},{"year":1998,"claim":"Resolved how CDC16 controls replication licensing, placing it upstream of origin firing where its loss permits Cdc6- and Mcm5-dependent reinitiation despite high CDK activity.","evidence":"2D DNA electrophoresis, density-transfer experiments and genetic epistasis with cdc6 and cdc46/mcm5 in S. cerevisiae","pmids":["9660930"],"confidence":"High","gaps":["Direct ubiquitination substrate at origins not identified"]},{"year":1998,"claim":"Revealed an APC/C-independent function by reconstituting CDC16 as part of a two-component GAP with Byr4 that inactivates the Spg1 GTPase to negatively regulate septation.","evidence":"Yeast two-hybrid, in vitro coprecipitation, in vitro GTPase assays with GTPase specificity controls in S. pombe","pmids":["9742395"],"confidence":"High","gaps":["How CDC16 contributes catalytically to GAP activity not defined","Relationship between GAP role and APC/C role unresolved"]},{"year":1999,"claim":"Defined the minimal functional unit of the Cdc16-Byr4 GAP, showing a single Cdc16-binding site plus one Spg1-binding site suffices to reconstitute full GAP activity.","evidence":"In vitro mutagenesis, GTPase assays and binding-affinity measurements of Byr4 mutants in S. pombe","pmids":["10196225"],"confidence":"High","gaps":["Structural basis of the Cdc16-Byr4 interaction not determined"]},{"year":2004,"claim":"Identified Swm1/Apc13 as a structural stabilizer that maintains CDC16 incorporation into the APC/C and is required for ligase activity.","evidence":"Reciprocal Co-IP, in vitro ubiquitination assays and cross-species complementation","pmids":["15060174"],"confidence":"High","gaps":["Atomic detail of how Swm1 stabilizes CDC16 not resolved at this stage"]},{"year":2004,"claim":"Linked APC/C subunit function to replication licensing in fission yeast by showing cut9 alleles are required for the rereplication process independently of cyclin B.","evidence":"Genetic screen for rereplication-defective ts mutants and complementation cloning in S. pombe","pmids":["15466421"],"confidence":"Medium","gaps":["No detailed mechanistic follow-up","Single lab, screen-based identification"]},{"year":2010,"claim":"Solved the molecular architecture of CDC16, defining a contiguous 14-TPR superhelix with an N-terminal homo-dimerization interface and a C-terminal CDC26/Hcn1-binding chamber that protects the partner from degradation.","evidence":"X-ray crystallography of the Cut9-Hcn1 complex with analysis of dimerization and binding interfaces (and CDC26-APC6 structure, PMID 19668213)","pmids":["20924356","19668213"],"confidence":"High","gaps":["Structure of full APC/C-incorporated CDC16 not resolved here","Dynamics of dimerization during catalysis not addressed"]},{"year":2018,"claim":"Began extending CDC16 into human cancer biology by identifying YDJC as a binding partner and CDC16 as a negative regulator of cytoskeletal remodeling, migration and invasion.","evidence":"Co-IP, siRNA knockdown and overexpression with migration/invasion assays in A549 lung cancer cells","pmids":["29796162"],"confidence":"Low","gaps":["Single Co-IP without reciprocal/structural validation","Mechanism connecting binding to functional output not reconstituted"]},{"year":2019,"claim":"Proposed that CDC16 targets YDJC for ubiquitination and suppresses EMT via PP2A/ERK2 modulation, suggesting a substrate-directed role in cancer signaling.","evidence":"Co-IP, overexpression/knockdown, ubiquitination assays and EMT marker analysis in lung cancer cells","pmids":["31485224"],"confidence":"Low","gaps":["Single-lab data without rigorous reconstitution","Direct CDC16-mediated ubiquitination of YDJC not biochemically isolated"]},{"year":2022,"claim":"Showed that CDC16 substrate ubiquitination can be controlled by competitive partner binding, with DEPDC1B competing against SCUBE3 to stabilize SCUBE3 and promote melanoma angiogenesis and metastasis.","evidence":"Reciprocal Co-IP, ubiquitination and protein-stability assays with gain/loss-of-function in melanoma cells and mouse models","pmids":["35088579"],"confidence":"Medium","gaps":["Single lab","Whether SCUBE3 is a direct APC/C substrate not structurally confirmed"]},{"year":2025,"claim":"Demonstrated regulation of APC/C assembly through CDC16 in cancer, with c-Jun competitively binding CDC16 to reduce complex formation and induce G1 arrest in neuroblastoma.","evidence":"Co-IP, flow cytometry cell-cycle analysis, EdU proliferation and transwell assays in neuroblastoma cells","pmids":["40149013"],"confidence":"Medium","gaps":["No structural or in vitro reconstitution of the c-Jun-CDC16 interaction","Single lab"]},{"year":null,"claim":"How the CDC16 TPR scaffold integrates its dual roles in APC/C-dependent proteolysis and in cancer-specific competitive binding to define context-dependent substrate choice remains unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No unified structural model of CDC16 within human APC/C bound to competing partners","Direct catalytic versus scaffolding contribution of CDC16 to substrate ubiquitination not isolated"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0140096","term_label":"catalytic activity, acting on a protein","supporting_discovery_ids":[0,8]},{"term_id":"GO:0016874","term_label":"ligase activity","supporting_discovery_ids":[0]},{"term_id":"GO:0005198","term_label":"structural molecule activity","supporting_discovery_ids":[10,11]},{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[3,7]}],"localization":[{"term_id":"GO:0005856","term_label":"cytoskeleton","supporting_discovery_ids":[5]}],"pathway":[{"term_id":"R-HSA-1640170","term_label":"Cell Cycle","supporting_discovery_ids":[0,2,4,6]},{"term_id":"R-HSA-392499","term_label":"Metabolism of proteins","supporting_discovery_ids":[0,8]},{"term_id":"R-HSA-69306","term_label":"DNA Replication","supporting_discovery_ids":[4,6]}],"complexes":["APC/C","Cdc16-Byr4 two-component GAP"],"partners":["CDC27","CDC26","SWM1","BYR4","PP5","DEPDC1B","YDJC","JUN"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q13042","full_name":"Cell division cycle protein 16 homolog","aliases":["Anaphase-promoting complex subunit 6","APC6","CDC16 homolog","CDC16Hs","Cyclosome subunit 6"],"length_aa":620,"mass_kda":71.7,"function":"Component of the anaphase promoting complex/cyclosome (APC/C), a cell cycle-regulated E3 ubiquitin ligase that controls progression through mitosis and the G1 phase of the cell cycle (PubMed:18485873). The APC/C complex acts by mediating ubiquitination and subsequent degradation of target proteins: it mainly mediates the formation of 'Lys-11'-linked polyubiquitin chains and, to a lower extent, the formation of 'Lys-48'- and 'Lys-63'-linked polyubiquitin chains (PubMed:18485873). The APC/C complex catalyzes assembly of branched 'Lys-11'-/'Lys-48'-linked branched ubiquitin chains on target proteins (PubMed:29033132)","subcellular_location":"Cytoplasm, cytoskeleton, microtubule organizing center, centrosome; Cytoplasm, cytoskeleton, spindle","url":"https://www.uniprot.org/uniprotkb/Q13042/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":true,"resolved_as":"","url":"https://depmap.org/portal/gene/CDC16","classification":"Common Essential","n_dependent_lines":1208,"n_total_lines":1208,"dependency_fraction":1.0},"opencell":{"profiled":true,"resolved_as":"","ensg_id":"ENSG00000130177","cell_line_id":"CID000227","localizations":[{"compartment":"cytoplasmic","grade":3},{"compartment":"nucleoplasm","grade":3},{"compartment":"cytoskeleton","grade":2}],"interactors":[{"gene":"ANAPC16","stoichiometry":10.0},{"gene":"ANAPC4","stoichiometry":10.0},{"gene":"PYCR2","stoichiometry":10.0},{"gene":"CDC27","stoichiometry":10.0},{"gene":"ANAPC5","stoichiometry":10.0},{"gene":"ANAPC13","stoichiometry":10.0},{"gene":"ANAPC1","stoichiometry":10.0},{"gene":"ANAPC10","stoichiometry":10.0},{"gene":"ANAPC7","stoichiometry":10.0},{"gene":"CDC23","stoichiometry":10.0}],"url":"https://opencell.sf.czbiohub.org/target/CID000227","total_profiled":1310},"omim":[{"mim_id":"619770","title":"YDJC CHITOOLIGOSACCHARIDE DEACETYLASE HOMOLOG; YDJC","url":"https://www.omim.org/entry/619770"},{"mim_id":"619331","title":"MTOR-ASSOCIATED PROTEIN, EAK7 HOMOLOG; MEAK7","url":"https://www.omim.org/entry/619331"},{"mim_id":"618039","title":"TBC1 DOMAIN FAMILY, MEMBER 9B; TBC1D9B","url":"https://www.omim.org/entry/618039"},{"mim_id":"618035","title":"TBC1 DOMAIN FAMILY, MEMBER 9; TBC1D9","url":"https://www.omim.org/entry/618035"},{"mim_id":"616659","title":"TBC1 DOMAIN FAMILY, MEMBER 17; TBC1D17","url":"https://www.omim.org/entry/616659"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"","locations":[],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/CDC16"},"hgnc":{"alias_symbol":["APC6","ANAPC6","CUT9"],"prev_symbol":[]},"alphafold":{"accession":"Q13042","domains":[{"cath_id":"1.25.40.10","chopping":"2-101_122-210","consensus_level":"medium","plddt":88.6665,"start":2,"end":210}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q13042","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q13042-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q13042-F1-predicted_aligned_error_v6.png","plddt_mean":78.88},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=CDC16","jax_strain_url":"https://www.jax.org/strain/search?query=CDC16"},"sequence":{"accession":"Q13042","fasta_url":"https://rest.uniprot.org/uniprotkb/Q13042.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q13042/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q13042"}},"corpus_meta":[{"pmid":"7736580","id":"PMC_7736580","title":"A 20S complex containing CDC27 and CDC16 catalyzes the mitosis-specific conjugation of ubiquitin to cyclin B.","date":"1995","source":"Cell","url":"https://pubmed.ncbi.nlm.nih.gov/7736580","citation_count":844,"is_preprint":false},{"pmid":"12029633","id":"PMC_12029633","title":"TFDP1, CUL4A, and CDC16 identified as targets for amplification at 13q34 in hepatocellular carcinomas.","date":"2002","source":"Hepatology (Baltimore, Md.)","url":"https://pubmed.ncbi.nlm.nih.gov/12029633","citation_count":162,"is_preprint":false},{"pmid":"8334988","id":"PMC_8334988","title":"The S. pombe cdc16 gene is required both for maintenance of p34cdc2 kinase activity and regulation of septum formation: a link between mitosis and cytokinesis?","date":"1993","source":"The EMBO journal","url":"https://pubmed.ncbi.nlm.nih.gov/8334988","citation_count":145,"is_preprint":false},{"pmid":"9742395","id":"PMC_9742395","title":"Byr4 and Cdc16 form a two-component GTPase-activating protein for the Spg1 GTPase that controls septation in fission yeast.","date":"1998","source":"Current biology : CB","url":"https://pubmed.ncbi.nlm.nih.gov/9742395","citation_count":143,"is_preprint":false},{"pmid":"16923123","id":"PMC_16923123","title":"Screening for target Rabs of TBC (Tre-2/Bub2/Cdc16) domain-containing proteins based on their Rab-binding activity.","date":"2006","source":"Genes to cells : devoted to molecular & cellular mechanisms","url":"https://pubmed.ncbi.nlm.nih.gov/16923123","citation_count":136,"is_preprint":false},{"pmid":"7798319","id":"PMC_7798319","title":"Bypassing anaphase by fission yeast cut9 mutation: requirement of cut9+ to initiate anaphase.","date":"1994","source":"The Journal of cell biology","url":"https://pubmed.ncbi.nlm.nih.gov/7798319","citation_count":96,"is_preprint":false},{"pmid":"8620535","id":"PMC_8620535","title":"The yeast CDC16 and CDC27 genes restrict DNA replication to once per cell 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research","url":"https://pubmed.ncbi.nlm.nih.gov/2823230","citation_count":33,"is_preprint":false},{"pmid":"26893383","id":"PMC_26893383","title":"Structural Basis of the Interaction between Tuberous Sclerosis Complex 1 (TSC1) and Tre2-Bub2-Cdc16 Domain Family Member 7 (TBC1D7).","date":"2016","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/26893383","citation_count":32,"is_preprint":false},{"pmid":"20937822","id":"PMC_20937822","title":"Protein kinase WNK1 promotes cell surface expression of glucose transporter GLUT1 by regulating a Tre-2/USP6-BUB2-Cdc16 domain family member 4 (TBC1D4)-Rab8A complex.","date":"2010","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/20937822","citation_count":29,"is_preprint":false},{"pmid":"9660930","id":"PMC_9660930","title":"CDC16 controls initiation at chromosome replication origins.","date":"1998","source":"Molecular 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Baden-Wurttemberg, Germany)","url":"https://pubmed.ncbi.nlm.nih.gov/35088579","citation_count":19,"is_preprint":false},{"pmid":"11121214","id":"PMC_11121214","title":"Down-regulation of the human CDC16 gene after exposure to ionizing radiation: a possible role in the radioadaptive response.","date":"2001","source":"Radiation research","url":"https://pubmed.ncbi.nlm.nih.gov/11121214","citation_count":14,"is_preprint":false},{"pmid":"15466421","id":"PMC_15466421","title":"A screen for Schizosaccharomyces pombe mutants defective in rereplication identifies new alleles of rad4+, cut9+ and psf2+.","date":"2004","source":"Genetics","url":"https://pubmed.ncbi.nlm.nih.gov/15466421","citation_count":14,"is_preprint":false},{"pmid":"10965142","id":"PMC_10965142","title":"The gene encoding TBC1D1 with homology to the tre-2/USP6 oncogene, BUB2, and cdc16 maps to mouse chromosome 5 and human chromosome 4.","date":"2000","source":"Cytogenetics and cell 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sites","date":"2024-09-21","source":"bioRxiv","url":"https://doi.org/10.1101/2024.09.19.613961","citation_count":0,"is_preprint":true}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":15591,"output_tokens":3920,"usd":0.052787,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":11768,"output_tokens":4401,"usd":0.084432,"stage2_stop_reason":"end_turn"},"total_usd":0.137219,"stage1_batch_id":"msgbatch_01ACAxJQabDsht39JXeWG22d","stage2_batch_id":"msgbatch_01QEU22A9U5sbPTgsMzTmvSf","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 1995,\n      \"finding\": \"CDC16 (APC6/ANAPC6) is a subunit of the 20S anaphase-promoting complex (APC), a regulated ubiquitin-protein ligase that catalyzes the mitosis-specific ubiquitination of cyclin B, targeting it for proteasomal destruction to enable anaphase progression.\",\n      \"method\": \"Biochemical fractionation of mitotic Xenopus egg extracts; immunodepletion with CDC27 antibodies; immunopurification of CDC27 complexes; in vitro ubiquitination assays reconstituted with UBC4 and E1\",\n      \"journal\": \"Cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — reconstituted ubiquitin ligase activity in vitro, immunodepletion and complementation, replicated across labs\",\n      \"pmids\": [\"7736580\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1993,\n      \"finding\": \"S. pombe cdc16 (ortholog of human CDC16/APC6) is essential for limiting septum formation to once per cell cycle and for maintaining p34cdc2 kinase activity; deletion causes multiple septa without cytokinesis, establishing cdc16 as a negative regulator of septation.\",\n      \"method\": \"Gene cloning, gene deletion, temperature-sensitive mutant analysis, genetic interaction studies in S. pombe\",\n      \"journal\": \"The EMBO journal\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — loss-of-function deletion with defined cellular phenotype, genetic epistasis, replicated findings on cdc16 function in septation\",\n      \"pmids\": [\"8334988\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1994,\n      \"finding\": \"S. pombe cut9 (ortholog of CDC16/APC6) encodes a 78-kDa TPR-repeat protein required for the onset of anaphase; cut9 temperature-sensitive mutants block anaphase while allowing post-anaphase events, and cut9 genetically interacts with nuc2, scn1, and scn2.\",\n      \"method\": \"Temperature-sensitive mutant characterization, gene cloning, TPR domain analysis, genetic suppressor analysis in S. pombe\",\n      \"journal\": \"The Journal of cell biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — loss-of-function mutant with defined anaphase block phenotype, genetic epistasis with multiple interactors, consistent with role in APC/C\",\n      \"pmids\": [\"7798319\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1998,\n      \"finding\": \"S. pombe Cdc16 (APC6 ortholog) and Byr4 form a two-component GTPase-activating protein (GAP) for the Spg1 GTPase that controls septation; Cdc16 alone has no detectable GAP activity but together with Byr4 stimulates Spg1 GTP hydrolysis, negatively regulating septation.\",\n      \"method\": \"Yeast two-hybrid, in vitro coprecipitation, in vitro GTPase assays measuring GTP hydrolysis and dissociation, genetic interaction analysis in S. pombe\",\n      \"journal\": \"Current biology : CB\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — in vitro reconstituted GAP activity with multiple orthogonal methods (biochemical, genetic, two-hybrid), specificity controls with seven Ypt GTPases\",\n      \"pmids\": [\"9742395\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1996,\n      \"finding\": \"S. cerevisiae CDC16 restricts DNA replication to once per cell cycle; cdc16 mutants accumulate up to 8C DNA through rereplication of all chromosomes within a single cell cycle despite elevated Clb2-Cdc28 kinase activity, implicating CDC16 in targeted proteolysis of an S-phase initiator.\",\n      \"method\": \"Genetic screen for DNA overreplication mutants, flow cytometry (DNA content analysis), conditional allele characterization in S. cerevisiae\",\n      \"journal\": \"Cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — clean loss-of-function genetic analysis with defined cellular phenotype (DNA rereplication), replicated and extended in follow-up paper (PMID:9660930)\",\n      \"pmids\": [\"8620535\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1997,\n      \"finding\": \"PP5 serine/threonine phosphatase physically interacts with CDC16 and CDC27 (APC/C subunits) through TPR-TPR interactions; the N-terminal TPR domain of PP5 binds the C-terminal TPR block of CDC16, and PP5 co-localizes with the mitotic spindle apparatus, suggesting PP5 may regulate APC/C activity by dephosphorylating these subunits.\",\n      \"method\": \"Yeast two-hybrid analysis, in vitro binding assays, deletion mapping, indirect immunofluorescence localization\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — two-hybrid plus in vitro binding with deletion mapping (two methods), single lab; functional consequence of interaction not directly tested\",\n      \"pmids\": [\"9405394\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1998,\n      \"finding\": \"S. cerevisiae CDC16 is required to prevent reinitiation of DNA synthesis from normal chromosomal replication origins; cdc16 mutants reinitiate replication in a Cdc6p- and Cdc46/Mcm5p-dependent manner despite elevated Cdc28p kinase activity, placing CDC16 upstream of origin firing control.\",\n      \"method\": \"Two-dimensional DNA electrophoresis, density-transfer experiments, genetic analysis with cdc6 and cdc46/mcm5 mutations in S. cerevisiae\",\n      \"journal\": \"Molecular cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — multiple orthogonal methods (2D gel electrophoresis, density transfer, genetic epistasis), clearly defines CDC16 role in origin firing control\",\n      \"pmids\": [\"9660930\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1999,\n      \"finding\": \"Byr4 contains one Cdc16-binding site and four Spg1-binding sites; the Cdc16-binding site plus a single Spg1-binding site (SBS4) is necessary and sufficient to reconstitute Cdc16-dependent Spg1 GAP activity comparable to wild-type Byr4, delineating the minimal functional unit of the two-component GAP.\",\n      \"method\": \"In vitro mutagenesis, in vitro GTPase assays, binding affinity measurements of Byr4 mutants in S. pombe\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — in vitro reconstitution with mutagenesis defining binding sites and GAP activity requirements\",\n      \"pmids\": [\"10196225\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2004,\n      \"finding\": \"Swm1/Apc13 stabilizes the association of Cdc16 and Cdc27 within the APC/C; deletion of SWM1 reduces Cdc16 and Cdc27 incorporation into the APC/C and abolishes ubiquitin ligase activity in vitro, placing Swm1/Apc13 as a structural stabilizer of CDC16 within the complex.\",\n      \"method\": \"Co-immunoprecipitation, in vitro ubiquitination assays, genetic complementation across species (human and S. pombe homologs complement S. cerevisiae swm1 deletion)\",\n      \"journal\": \"Molecular and cellular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal Co-IP demonstrating reduced Cdc16 association, in vitro ubiquitination activity assay, cross-species complementation\",\n      \"pmids\": [\"15060174\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2004,\n      \"finding\": \"New temperature-sensitive alleles of S. pombe cut9 (CDC16/APC6 ortholog) cause defective rereplication in the absence of cyclin B (Cdc13), identifying cut9 as required for the rereplication process and linking APC/C function to DNA replication licensing in fission yeast.\",\n      \"method\": \"Genetic screen for rereplication-defective temperature-sensitive mutants, complementation cloning in S. pombe\",\n      \"journal\": \"Genetics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — genetic loss-of-function with defined phenotype, single lab, screen-based identification without detailed mechanistic follow-up\",\n      \"pmids\": [\"15466421\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"CDC26 stabilizes the structure of APC6 (CDC16) through an intermolecular TPR mimic composed of one helix from each protein; this interaction is required for APC assembly and integrity.\",\n      \"method\": \"Crystal structure determination, biophysical binding studies, genetic analysis of CDC26-APC6 interaction\",\n      \"journal\": \"Nature structural & molecular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — crystal structure with biophysical and genetic validation, defines molecular mechanism of CDC26-APC6 interaction\",\n      \"pmids\": [\"19668213\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"The crystal structure of S. pombe Cut9 (Cdc16/Apc6) in complex with Hcn1 (Cdc26) reveals a contiguous TPR superhelix of 14 TPR units; the C-terminal TPR block interacts with Hcn1, while the N-terminal TPR block mediates Cdc16/Cut9 homo-dimerization through a conserved interface also present in Cdc27. The N-acetyl-Met residue of Hcn1 is enclosed within the Cut9 TPR chamber, protecting Hcn1/Cdc26 from Doa10-mediated ubiquitin-dependent degradation.\",\n      \"method\": \"X-ray crystallography of Cut9-Hcn1 complex, structural analysis of dimerization and binding interfaces\",\n      \"journal\": \"The EMBO journal\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — high-resolution crystal structure defining domain architecture, homo-dimer interface, and substrate protection mechanism\",\n      \"pmids\": [\"20924356\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"DEPDC1B competes with SCUBE3 for binding to CDC16 (as APC/C ubiquitin ligase subunit); by sequestering CDC16, DEPDC1B prevents CDC16-mediated ubiquitination and proteasomal degradation of SCUBE3, stabilizing SCUBE3 to promote melanoma angiogenesis and metastasis.\",\n      \"method\": \"Co-immunoprecipitation, ubiquitination assays, protein stability assays, gain/loss-of-function experiments in melanoma cells and mouse models\",\n      \"journal\": \"Advanced science (Weinheim, Baden-Wurttemberg, Germany)\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal Co-IP, ubiquitination assay, in vivo mouse model, single lab with multiple orthogonal methods\",\n      \"pmids\": [\"35088579\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"c-Jun competitively interacts with CDC16 (a key APC/C subunit) to reduce APC/C complex formation, inhibit cell cycle progression (G1 arrest), and suppress neuroblastoma cell proliferation and migration.\",\n      \"method\": \"Co-immunoprecipitation, flow cytometry cell cycle analysis, EdU proliferation assay, transwell migration/invasion assay in neuroblastoma cells\",\n      \"journal\": \"Biology direct\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — Co-IP demonstrating c-Jun–CDC16 interaction with functional readouts, single lab, no structural or in vitro reconstitution data\",\n      \"pmids\": [\"40149013\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"CDC16 interacts with YDJC and overexpression of CDC16 suppresses EMT by increasing PP2A expression and reducing ERK2 activation; CDC16 overexpression also promotes ubiquitination of YDJC, suggesting CDC16 targets YDJC for degradation.\",\n      \"method\": \"Co-immunoprecipitation, overexpression and siRNA knockdown, ubiquitination assays, EMT marker analysis in lung cancer cells\",\n      \"journal\": \"Journal of oncology\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single lab, single Co-IP plus knockdown/overexpression without rigorous reconstitution or mechanistic pathway validation\",\n      \"pmids\": [\"31485224\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"CDC16 physically binds YDJC (co-immunoprecipitation), and CDC16 siRNA promotes SPC-induced keratin reorganization, cell migration and invasion, while CDC16 overexpression blocks these events, placing CDC16 as a negative regulator of YDJC-driven cytoskeletal remodeling in lung cancer cells.\",\n      \"method\": \"Co-immunoprecipitation, siRNA knockdown, overexpression, migration/invasion assays in A549 lung cancer cells\",\n      \"journal\": \"Oncotarget\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single lab, single Co-IP with functional knockdown/overexpression data, no mechanistic reconstitution\",\n      \"pmids\": [\"29796162\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"CDC16 (APC6/ANAPC6) is a core TPR-repeat subunit of the anaphase-promoting complex/cyclosome (APC/C), an E3 ubiquitin ligase; it forms a contiguous 14-TPR superhelix that homo-dimerizes and scaffolds APC/C assembly (stabilized by CDC26/Hcn1 via an intermolecular TPR mimic and by Swm1/Apc13), and the assembled complex catalyzes mitosis-specific ubiquitination of cyclin B and securin to drive anaphase onset, restrict DNA replication to once per cell cycle, and limit septation — while in S. pombe it additionally participates as part of a two-component GAP (with Byr4) to inactivate the Spg1 GTPase and negatively regulate cytokinesis.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"CDC16 (APC6/ANAPC6) is a core subunit of the anaphase-promoting complex/cyclosome (APC/C), a regulated ubiquitin-protein ligase that catalyzes mitosis-specific ubiquitination of cyclin B to drive its proteasomal destruction and enable anaphase progression [#0]. Structurally, CDC16 is a TPR-repeat protein that folds into a contiguous 14-TPR superhelix: its N-terminal TPR block mediates homo-dimerization through an interface conserved with CDC27, while its C-terminal TPR block engages CDC26/Hcn1, which stabilizes APC6 through an intermolecular TPR mimic required for APC/C assembly and integrity and which simultaneously sequesters the CDC26 N-acetyl-Met to protect it from ubiquitin-dependent degradation [#10, #11]. Stable incorporation of CDC16 (and CDC27) into the APC/C is further reinforced by Swm1/Apc13, whose loss reduces CDC16 association and abolishes ligase activity [#8]. Through this scaffolding role, CDC16 enforces several cell-cycle controls: it restricts DNA replication to once per cycle by directing targeted proteolysis upstream of origin firing, such that loss-of-function permits Cdc6- and Mcm5-dependent rereplication despite elevated mitotic CDK activity [#4, #6], and it is required for the onset of anaphase [#2]. In fission yeast CDC16 has an additional APC/C-independent function: together with Byr4 it forms a two-component GTPase-activating protein for the Spg1 GTPase that negatively regulates septation, with CDC16 alone lacking GAP activity but cooperating through a defined Byr4 Cdc16-binding site to stimulate Spg1 GTP hydrolysis [#1, #3, #7]. In human cancer contexts, CDC16's APC/C-associated ubiquitination activity is modulated by competitive binding: DEPDC1B competes with the substrate SCUBE3 for CDC16 to block its degradation in melanoma, and c-Jun competes for CDC16 to reduce APC/C formation and induce G1 arrest in neuroblastoma [#12, #13].\",\n  \"teleology\": [\n    {\n      \"year\": 1993,\n      \"claim\": \"Established the first cellular function for CDC16 by showing its fission-yeast ortholog limits septum formation and sustains mitotic CDK activity, framing it as a negative regulator of cytokinesis.\",\n      \"evidence\": \"Gene cloning, deletion and temperature-sensitive mutant analysis with genetic epistasis in S. pombe\",\n      \"pmids\": [\"8334988\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Molecular mechanism of septation control not defined\", \"Connection to ubiquitination machinery not yet made\"]\n    },\n    {\n      \"year\": 1994,\n      \"claim\": \"Identified CDC16/Cut9 as a TPR-repeat protein required for the onset of anaphase, providing the structural and phenotypic basis later unified with APC/C function.\",\n      \"evidence\": \"Temperature-sensitive mutant characterization, TPR domain analysis and genetic suppressor analysis in S. pombe\",\n      \"pmids\": [\"7798319\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Biochemical activity of the TPR protein not established\", \"Anaphase substrate not identified\"]\n    },\n    {\n      \"year\": 1995,\n      \"claim\": \"Placed CDC16 within the 20S APC and defined the complex's biochemical activity, showing it is a ubiquitin ligase that targets cyclin B for destruction to enable anaphase.\",\n      \"evidence\": \"Biochemical fractionation of mitotic Xenopus extracts, immunodepletion/immunopurification and in vitro reconstituted ubiquitination assays\",\n      \"pmids\": [\"7736580\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Specific catalytic contribution of CDC16 versus other subunits not resolved\", \"Substrate-recognition mechanism not defined\"]\n    },\n    {\n      \"year\": 1996,\n      \"claim\": \"Extended CDC16 function to genome stability by showing it restricts DNA replication to once per cell cycle, implicating it in proteolysis of an S-phase initiator.\",\n      \"evidence\": \"Genetic overreplication screen, flow cytometry DNA-content analysis and conditional allele characterization in S. cerevisiae\",\n      \"pmids\": [\"8620535\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Identity of the proteolytic target controlling rereplication not defined\", \"Direct biochemical link to APC/C in this role not shown\"]\n    },\n    {\n      \"year\": 1998,\n      \"claim\": \"Resolved how CDC16 controls replication licensing, placing it upstream of origin firing where its loss permits Cdc6- and Mcm5-dependent reinitiation despite high CDK activity.\",\n      \"evidence\": \"2D DNA electrophoresis, density-transfer experiments and genetic epistasis with cdc6 and cdc46/mcm5 in S. cerevisiae\",\n      \"pmids\": [\"9660930\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Direct ubiquitination substrate at origins not identified\"]\n    },\n    {\n      \"year\": 1998,\n      \"claim\": \"Revealed an APC/C-independent function by reconstituting CDC16 as part of a two-component GAP with Byr4 that inactivates the Spg1 GTPase to negatively regulate septation.\",\n      \"evidence\": \"Yeast two-hybrid, in vitro coprecipitation, in vitro GTPase assays with GTPase specificity controls in S. pombe\",\n      \"pmids\": [\"9742395\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"How CDC16 contributes catalytically to GAP activity not defined\", \"Relationship between GAP role and APC/C role unresolved\"]\n    },\n    {\n      \"year\": 1999,\n      \"claim\": \"Defined the minimal functional unit of the Cdc16-Byr4 GAP, showing a single Cdc16-binding site plus one Spg1-binding site suffices to reconstitute full GAP activity.\",\n      \"evidence\": \"In vitro mutagenesis, GTPase assays and binding-affinity measurements of Byr4 mutants in S. pombe\",\n      \"pmids\": [\"10196225\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Structural basis of the Cdc16-Byr4 interaction not determined\"]\n    },\n    {\n      \"year\": 2004,\n      \"claim\": \"Identified Swm1/Apc13 as a structural stabilizer that maintains CDC16 incorporation into the APC/C and is required for ligase activity.\",\n      \"evidence\": \"Reciprocal Co-IP, in vitro ubiquitination assays and cross-species complementation\",\n      \"pmids\": [\"15060174\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Atomic detail of how Swm1 stabilizes CDC16 not resolved at this stage\"]\n    },\n    {\n      \"year\": 2004,\n      \"claim\": \"Linked APC/C subunit function to replication licensing in fission yeast by showing cut9 alleles are required for the rereplication process independently of cyclin B.\",\n      \"evidence\": \"Genetic screen for rereplication-defective ts mutants and complementation cloning in S. pombe\",\n      \"pmids\": [\"15466421\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No detailed mechanistic follow-up\", \"Single lab, screen-based identification\"]\n    },\n    {\n      \"year\": 2010,\n      \"claim\": \"Solved the molecular architecture of CDC16, defining a contiguous 14-TPR superhelix with an N-terminal homo-dimerization interface and a C-terminal CDC26/Hcn1-binding chamber that protects the partner from degradation.\",\n      \"evidence\": \"X-ray crystallography of the Cut9-Hcn1 complex with analysis of dimerization and binding interfaces (and CDC26-APC6 structure, PMID 19668213)\",\n      \"pmids\": [\"20924356\", \"19668213\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Structure of full APC/C-incorporated CDC16 not resolved here\", \"Dynamics of dimerization during catalysis not addressed\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Began extending CDC16 into human cancer biology by identifying YDJC as a binding partner and CDC16 as a negative regulator of cytoskeletal remodeling, migration and invasion.\",\n      \"evidence\": \"Co-IP, siRNA knockdown and overexpression with migration/invasion assays in A549 lung cancer cells\",\n      \"pmids\": [\"29796162\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"Single Co-IP without reciprocal/structural validation\", \"Mechanism connecting binding to functional output not reconstituted\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Proposed that CDC16 targets YDJC for ubiquitination and suppresses EMT via PP2A/ERK2 modulation, suggesting a substrate-directed role in cancer signaling.\",\n      \"evidence\": \"Co-IP, overexpression/knockdown, ubiquitination assays and EMT marker analysis in lung cancer cells\",\n      \"pmids\": [\"31485224\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"Single-lab data without rigorous reconstitution\", \"Direct CDC16-mediated ubiquitination of YDJC not biochemically isolated\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Showed that CDC16 substrate ubiquitination can be controlled by competitive partner binding, with DEPDC1B competing against SCUBE3 to stabilize SCUBE3 and promote melanoma angiogenesis and metastasis.\",\n      \"evidence\": \"Reciprocal Co-IP, ubiquitination and protein-stability assays with gain/loss-of-function in melanoma cells and mouse models\",\n      \"pmids\": [\"35088579\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single lab\", \"Whether SCUBE3 is a direct APC/C substrate not structurally confirmed\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Demonstrated regulation of APC/C assembly through CDC16 in cancer, with c-Jun competitively binding CDC16 to reduce complex formation and induce G1 arrest in neuroblastoma.\",\n      \"evidence\": \"Co-IP, flow cytometry cell-cycle analysis, EdU proliferation and transwell assays in neuroblastoma cells\",\n      \"pmids\": [\"40149013\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No structural or in vitro reconstitution of the c-Jun-CDC16 interaction\", \"Single lab\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How the CDC16 TPR scaffold integrates its dual roles in APC/C-dependent proteolysis and in cancer-specific competitive binding to define context-dependent substrate choice remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No unified structural model of CDC16 within human APC/C bound to competing partners\", \"Direct catalytic versus scaffolding contribution of CDC16 to substrate ubiquitination not isolated\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0140096\", \"supporting_discovery_ids\": [0, 8]},\n      {\"term_id\": \"GO:0016874\", \"supporting_discovery_ids\": [0]},\n      {\"term_id\": \"GO:0005198\", \"supporting_discovery_ids\": [10, 11]},\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [3, 7]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005856\", \"supporting_discovery_ids\": [5]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-1640170\", \"supporting_discovery_ids\": [0, 2, 4, 6]},\n      {\"term_id\": \"R-HSA-392499\", \"supporting_discovery_ids\": [0, 8]},\n      {\"term_id\": \"R-HSA-69306\", \"supporting_discovery_ids\": [4, 6]}\n    ],\n    \"complexes\": [\"APC/C\", \"Cdc16-Byr4 two-component GAP\"],\n    \"partners\": [\"CDC27\", \"CDC26\", \"SWM1\", \"BYR4\", \"PP5\", \"DEPDC1B\", \"YDJC\", \"JUN\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":6,"faith_total":6,"faith_pct":100.0}}