Affinage

CDC16

Cell division cycle protein 16 homolog · UniProt Q13042

Round 2 corrected
Length
620 aa
Mass
71.7 kDa
Annotated
2026-04-28
59 papers in source corpus 15 papers cited in narrative 15 extracted findings

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

CDC16 (APC6) is a TPR-repeat scaffold subunit of the anaphase-promoting complex/cyclosome (APC/C), an E3 ubiquitin ligase essential for mitotic progression, anaphase onset, and prevention of DNA re-replication (PMID:7736580, PMID:8620535). CDC16 forms a contiguous 14-TPR superhelix that homo-dimerizes via its N-terminal TPR block; its C-terminal TPR domain binds CDC26 through an intermolecular TPR mimic that stabilizes overall APC/C integrity (PMID:20924356, PMID:19668213). Mitosis-specific phosphorylation of CDC16 and other TPR subunits by Cdk1 promotes CDC20 recruitment and APC/C activation, enabling cyclin B ubiquitination and the metaphase-to-anaphase transition (PMID:14657031, PMID:7736578). CDC16 also restricts DNA replication to once per cell cycle by preventing re-firing of replication origins through a pathway that requires Cdc6 and Mcm5, acting independently of CDK-mediated origin suppression (PMID:9660930).

Mechanistic history

Synthesis pass · year-by-year structured walk · 8 steps
  1. 1994 High

    Identification of the fission yeast ortholog Cut9 as a TPR protein essential for anaphase initiation established that CDC16-family genes are required for the metaphase-to-anaphase transition.

    Evidence Temperature-sensitive cut9 mutants in S. pombe arrest at anaphase onset; genetic epistasis with nuc2+, scn1, scn2

    PMID:7798319

    Open questions at the time
    • Biochemical function of Cut9/CDC16 unknown
    • No direct connection to ubiquitin-dependent proteolysis at this stage
  2. 1995 High

    Biochemical purification of the APC/C as a cyclin B ubiquitin ligase containing CDC16 and localization of CDC16 to the centrosome and mitotic spindle established CDC16 as a core subunit of the mitosis-specific E3 ligase driving anaphase.

    Evidence Immunopurification and reconstituted ubiquitination from Xenopus extracts; immunofluorescence and antibody microinjection arrest in HeLa cells

    PMID:7736578 PMID:7736580

    Open questions at the time
    • Direct enzymatic contribution of CDC16 versus other subunits not resolved
    • Structural basis of CDC16 incorporation into APC/C unknown
  3. 1996 High

    Demonstration that cdc16 mutants undergo genome-wide re-replication from normal origins revealed that CDC16/APC/C enforces the once-per-cell-cycle rule for DNA replication, independently of CDK-mediated inhibition.

    Evidence Flow cytometry showing up to 8C DNA content in S. cerevisiae cdc16 mutants; 2D gel and density-transfer confirmation of origin re-firing requiring Cdc6 and Mcm5

    PMID:8620535 PMID:9660930

    Open questions at the time
    • Identity of the APC/C substrate(s) whose stabilization permits re-replication not determined
    • Whether this function is conserved in metazoans not tested
  4. 1997 Medium

    Discovery that phosphatase PP5 physically interacts with CDC16's C-terminal TPR block and colocalizes at the mitotic spindle suggested a dephosphorylation-based regulatory input to APC/C activity.

    Evidence Yeast two-hybrid, in vitro binding, deletion mapping, and immunofluorescence colocalization

    PMID:9405394

    Open questions at the time
    • Functional consequence of PP5–CDC16 interaction on APC/C activity not demonstrated
    • No in vivo validation of dephosphorylation
  5. 2003 High

    Phosphoproteomics revealed CDC16 as a major target of Cdk1-dependent mitotic phosphorylation, and showed that Cdk1 (not Plk1) phosphorylation of APC/C TPR subunits is sufficient for CDC20 binding and APC/C activation.

    Evidence Mass spectrometry phospho-site mapping, in vitro kinase assays with Cdk1 and Plk1, co-immunoprecipitation for CDC20 binding

    PMID:14657031

    Open questions at the time
    • Individual contribution of CDC16 phosphorylation sites versus other TPR subunit sites not resolved
    • No phospho-site mutagenesis on CDC16 alone
  6. 2004 High

    Identification of Swm1/Apc13 as a subunit required for stable CDC16 and CDC27 incorporation into the APC/C revealed a hierarchy of accessory subunits that maintain complex integrity and ligase activity.

    Evidence Affinity purification–mass spectrometry, in vitro ubiquitin ligase assay, in vivo cell cycle delay upon SWM1 deletion in S. cerevisiae

    PMID:15060174

    Open questions at the time
    • Structural basis of Swm1-mediated CDC16 incorporation unknown at this time
  7. 2009 High

    Crystal structures of CDC16/CDC26 complexes resolved the molecular architecture: CDC16 is a 14-TPR superhelix that homo-dimerizes via its N-terminal block, and CDC26 stabilizes APC/C integrity by forming an intermolecular TPR mimic with CDC16's C-terminal domain.

    Evidence X-ray crystallography of S. pombe Cut9–Hcn1 complex, biophysical binding assays, genetic complementation

    PMID:19668213 PMID:20924356

    Open questions at the time
    • Full atomic model of CDC16 within the intact human APC/C not yet available at this stage
    • Mechanism by which N-terminal dimerization contributes to APC/C function not tested in vivo
  8. 2022 Medium

    Evidence that non-APC/C proteins (DEPDC1B, c-Jun) can competitively sequester CDC16, disrupting APC/C complex formation, suggested CDC16 availability may be a regulatory node exploited in cancer contexts.

    Evidence Co-immunoprecipitation and ubiquitination assays in melanoma (DEPDC1B–CDC16) and neuroblastoma (c-Jun–CDC16) cell lines, in vivo tumor models

    PMID:35088579 PMID:40149013

    Open questions at the time
    • Stoichiometry of sequestration relative to total cellular CDC16 pool unclear
    • Physiological relevance of competitive CDC16 binding outside overexpression settings not established
    • Independent replication needed

Open questions

Synthesis pass · forward-looking unresolved questions
  • The individual functional contribution of each CDC16 Cdk1-phosphorylation site, the structural basis of CDC16 within the complete human APC/C holoenzyme at high resolution, and whether CDC16 sequestration by non-APC/C partners represents a physiologically significant regulatory mechanism remain open questions.
  • No single-site phosphomutant analysis of CDC16
  • No cryo-EM structure of human APC/C focused on CDC16-specific contacts at sub-3Å resolution
  • Physiological relevance of DEPDC1B/c-Jun-mediated CDC16 sequestration not validated in non-cancer settings

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0005198 structural molecule activity 2 GO:0140096 catalytic activity, acting on a protein 2
Localization
GO:0005815 microtubule organizing center 2 GO:0005856 cytoskeleton 2
Pathway
R-HSA-1640170 Cell Cycle 6 R-HSA-392499 Metabolism of proteins 3 R-HSA-69306 DNA Replication 2
Partners
APC13CDC20CDC26CDC27DEPDC1BPP5
Complex memberships
APC/C

Evidence

Reading pass · 15 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
1995 CDC16 (human homolog of S. cerevisiae Cdc16) is a subunit of the 20S anaphase-promoting complex (APC), a mitosis-specific ubiquitin-protein ligase that catalyzes conjugation of ubiquitin to cyclin B, targeting it for proteasomal degradation at the onset of anaphase. Immunopurified CDC27-containing complexes (which include CDC16) are sufficient to reconstitute cyclin B ubiquitination activity. Biochemical fractionation of mitotic Xenopus egg extracts, immunodepletion with CDC27 antibodies, immunopurification, in vitro ubiquitination reconstitution assay Cell High 7736580
1995 Human CDC16Hs (encoded by a cDNA homologous to S. cerevisiae CDC16) colocalizes with CDC27Hs to the centrosome throughout the mammalian cell cycle and to the mitotic spindle. Microinjection of anti-CDC27Hs antibodies arrests HeLa cells in metaphase, demonstrating that the CDC16/CDC27-containing complex is essential for the metaphase-to-anaphase transition. Immunofluorescence microscopy, antibody microinjection into HeLa cells, cell cycle arrest assay Cell High 7736578
1994 The fission yeast cut9+ gene (encoding the S. pombe ortholog of Cdc16/APC6) is required for the initiation of anaphase; temperature-sensitive cut9 mutants enter mitosis and form short spindles but block at anaphase onset, while postanaphase events (spindle disassembly, septation, cytokinesis) continue inappropriately. Cut9 is a 78-kDa TPR-containing protein essential for viability. Temperature-sensitive mutant analysis, genetic epistasis (suppressor genes nuc2+, scn1, scn2), microscopy of cell cycle progression The Journal of cell biology High 7798319
1996 CDC16 and CDC27 in S. cerevisiae are required to restrict DNA replication to once per cell cycle; conditional cdc16 mutants rereplicate all chromosomes (up to 8C DNA content) within a single cell cycle without passing through mitosis, despite persistently elevated Clb2-Cdc28 (CDK) kinase activity, indicating CDC16 prevents rereplication independently of CDK-mediated inhibition of re-initiation. Conditional mutant analysis (temperature-sensitive alleles), flow cytometry (DNA content), genetic screen Cell High 8620535
1997 The serine/threonine phosphatase PP5 physically interacts with CDC16 and CDC27, two TPR-containing subunits of the APC/C. The interaction requires only the N-terminal TPR-containing domain of PP5, while the binding site on CDC16 and CDC27 maps to their C-terminal TPR block. PP5 colocalizes with CDC16/CDC27 at the mitotic spindle apparatus, suggesting it may regulate APC/C activity through dephosphorylation. Yeast two-hybrid analysis, in vitro binding assay, deletion mapping, indirect immunofluorescence microscopy The Journal of biological chemistry Medium 9405394
1998 In S. cerevisiae cdc16 mutants, rereplication initiates specifically from normal chromosomal replication origins, and requires both the initiation proteins Cdc6p and Cdc46/Mcm5p — proteins thought to be inactivated by CDK. This establishes that CDC16 is required to prevent inappropriate firing of replication origins after S-phase, acting independently of CDK-mediated origin suppression. Two-dimensional DNA gel electrophoresis, density-transfer experiments, genetic epistasis (cdc6 and cdc46 double mutants) Molecular cell High 9660930
2003 The Arabidopsis NOMEGA gene encodes the plant ortholog of APC6/CDC16; nomega mutant embryo sacs arrest at the two-nucleate stage and are unable to degrade Cyclin B, directly demonstrating that the CDC16-containing APC/C is required for Cyclin B proteolysis during cell cycle progression in plant gametophyte development. Genetic mutant characterization, cyclin B degradation assay in vivo, complementation The Plant journal Medium 14675450
2004 Swm1/Apc13 is an evolutionarily conserved APC/C subunit that promotes stable association of CDC16 and CDC27 with the complex; deletion of SWM1 reduces the incorporation of Cdc16 and Cdc27 into the APC/C, abolishes ubiquitin ligase activity in vitro, and delays APC/C-dependent cell cycle events in vivo. Affinity purification, mass spectrometry, in vitro ubiquitin ligase activity assay, in vivo cell cycle analysis Molecular and cellular biology High 15060174
2003 At least 34 mitosis-specific phosphorylation sites exist on human APC/C subunits; 32 of these cluster in Apc1 and TPR subunits including CDC16 (Cdc16), CDC27, CDC23, and Apc7. Cdk1 can generate at least 15 mitotic phospho-sites in vitro. APC phosphorylation by Cdk1 (but not Plk1) is sufficient for increased CDC20 binding and APC activation. Phospho-APC accumulates at centrosomes in prometaphase where cyclin B ubiquitination initiates. Mass spectrometry phospho-site mapping, in vitro kinase assays (Cdk1, Plk1), co-immunoprecipitation, immunofluorescence with phospho-specific antibodies The EMBO journal High 14657031
2010 The crystal structure of S. pombe Cut9 (Cdc16/Apc6) in complex with Hcn1 (Cdc26) reveals that Cdc16/Cut9 is a contiguous superhelix of 14 TPR units. The C-terminal TPR block interacts with Hcn1/Cdc26, while the N-terminal TPR block mediates CDC16 self-association through a homotypic dimer interface structurally related to the Cdc27 dimerization domain. The acetylated N-terminal Met of Hcn1 is enclosed within the Cut9 TPR chamber, protecting Hcn1 from Doa10-mediated ubiquitin-dependent degradation. X-ray crystallography, biochemical characterization The EMBO journal High 20924356
2009 Biophysical and structural studies show that CDC26 stabilizes the structure of APC6 (CDC16) through an intermolecular TPR mimic composed of one helix from each protein; genetic studies confirm that this interaction is required for APC integrity. X-ray crystallography, biophysical binding assays, genetic complementation Nature structural & molecular biology High 19668213
2022 DEPDC1B competitively associates with human CDC16 (an APC/C ubiquitin ligase subunit) to sequester it, thereby preventing CDC16-mediated ubiquitination and proteasomal degradation of the secreted protein SCUBE3. This stabilization of SCUBE3 promotes melanoma angiogenesis and metastasis. Co-immunoprecipitation, ubiquitination assay, siRNA knockdown, overexpression rescue, in vivo tumor/angiogenesis models Advanced science Medium 35088579
2018 YDJC physically interacts with CDC16 as shown by co-immunoprecipitation; CDC16 siRNA knockdown induces sphingosylphosphorylcholine-triggered keratin reorganization, migration, and invasion in A549 lung cancer cells, while CDC16 overexpression blocks these events, suggesting CDC16 suppresses EMT-related signaling. Co-immunoprecipitation, siRNA knockdown, overexpression, migration/invasion assays Oncotarget Low 29796162
2019 CDC16 overexpression induces ubiquitination of YDJC protein and increases PP2A expression; YDJC overexpression escapes CDC16-mediated ubiquitination (dependent on YDJC deacetylase activity) and promotes PP2A ubiquitination, leading to EMT in lung cancer cells. This places CDC16 as a ubiquitin ligase regulator in a YDJC-PP2A-ERK2-EMT axis. Co-immunoprecipitation, ubiquitination assay, siRNA knockdown, overexpression with deacetylase-dead mutant (YDJCD13A), in vivo orthotopic mouse model Journal of oncology Low 31485224
2025 c-Jun competitively interacts with CDC16, a key APC/C subunit, reducing APC complex formation and inhibiting cell cycle progression from G1 in neuroblastoma cells. c-Jun overexpression inhibits neuroblastoma cell proliferation and migration via sequestration of CDC16. Co-immunoprecipitation, flow cytometry (cell cycle), EdU proliferation assay, transwell migration assay, retinoic acid treatment Biology direct Low 40149013

Source papers

Stage 0 corpus · 59 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
2012 Insights into RNA biology from an atlas of mammalian mRNA-binding proteins. Cell 1718 22658674
2002 Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Proceedings of the National Academy of Sciences of the United States of America 1479 12477932
2006 A probability-based approach for high-throughput protein phosphorylation analysis and site localization. Nature biotechnology 1336 16964243
2015 The BioPlex Network: A Systematic Exploration of the Human Interactome. Cell 1118 26186194
2017 Architecture of the human interactome defines protein communities and disease networks. Nature 1085 28514442
2015 A human interactome in three quantitative dimensions organized by stoichiometries and abundances. Cell 1015 26496610
2014 A proteome-scale map of the human interactome network. Cell 977 25416956
2020 A reference map of the human binary protein interactome. Nature 849 32296183
2009 A genome-wide RNAi screen identifies multiple synthetic lethal interactions with the Ras oncogene. Cell 843 19490893
1995 A 20S complex containing CDC27 and CDC16 catalyzes the mitosis-specific conjugation of ubiquitin to cyclin B. Cell 843 7736580
2003 Complete sequencing and characterization of 21,243 full-length human cDNAs. Nature genetics 754 14702039
2001 Checkpoint inhibition of the APC/C in HeLa cells is mediated by a complex of BUBR1, BUB3, CDC20, and MAD2. The Journal of cell biology 726 11535616
2021 Dual proteome-scale networks reveal cell-specific remodeling of the human interactome. Cell 705 33961781
2012 A census of human soluble protein complexes. Cell 689 22939629
2011 Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Briefings in bioinformatics 656 21873635
2008 Mechanism of ubiquitin-chain formation by the human anaphase-promoting complex. Cell 442 18485873
2011 SIRT2 maintains genome integrity and suppresses tumorigenesis through regulating APC/C activity. Cancer cell 441 22014574
2004 The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). Genome research 438 15489334
2022 OpenCell: Endogenous tagging for the cartography of human cellular organization. Science (New York, N.Y.) 432 35271311
2010 Systematic analysis of human protein complexes identifies chromosome segregation proteins. Science (New York, N.Y.) 421 20360068
2015 Panorama of ancient metazoan macromolecular complexes. Nature 407 26344197
1996 Normalization and subtraction: two approaches to facilitate gene discovery. Genome research 401 8889548
2001 Anaphase-promoting complex/cyclosome-dependent proteolysis of human cyclin A starts at the beginning of mitosis and is not subject to the spindle assembly checkpoint. The Journal of cell biology 372 11285280
2000 Mitotic regulation of the APC activator proteins CDC20 and CDH1. Molecular biology of the cell 363 10793135
2000 Characterization of vertebrate cohesin complexes and their regulation in prophase. The Journal of cell biology 358 11076961
2003 Mitotic regulation of the human anaphase-promoting complex by phosphorylation. The EMBO journal 341 14657031
2021 A proximity-dependent biotinylation map of a human cell. Nature 339 34079125
1995 CDC27Hs colocalizes with CDC16Hs to the centrosome and mitotic spindle and is essential for the metaphase to anaphase transition. Cell 335 7736578
1999 Human BUBR1 is a mitotic checkpoint kinase that monitors CENP-E functions at kinetochores and binds the cyclosome/APC. The Journal of cell biology 314 10477750
2006 Phosphoproteome analysis of the human mitotic spindle. Proceedings of the National Academy of Sciences of the United States of America 281 16565220
2000 Systematic subcellular localization of novel proteins identified by large-scale cDNA sequencing. EMBO reports 281 11256614
2002 TFDP1, CUL4A, and CDC16 identified as targets for amplification at 13q34 in hepatocellular carcinomas. Hepatology (Baltimore, Md.) 161 12029633
1993 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? The EMBO journal 145 8334988
1998 Byr4 and Cdc16 form a two-component GTPase-activating protein for the Spg1 GTPase that controls septation in fission yeast. Current biology : CB 143 9742395
2006 Screening for target Rabs of TBC (Tre-2/Bub2/Cdc16) domain-containing proteins based on their Rab-binding activity. Genes to cells : devoted to molecular & cellular mechanisms 134 16923123
1994 Bypassing anaphase by fission yeast cut9 mutation: requirement of cut9+ to initiate anaphase. The Journal of cell biology 96 7798319
2003 The NOMEGA gene required for female gametophyte development encodes the putative APC6/CDC16 component of the Anaphase Promoting Complex in Arabidopsis. The Plant journal : for cell and molecular biology 83 14675450
1996 The yeast CDC16 and CDC27 genes restrict DNA replication to once per cell cycle. Cell 80 8620535
1997 The serine/threonine phosphatase PP5 interacts with CDC16 and CDC27, two tetratricopeptide repeat-containing subunits of the anaphase-promoting complex. The Journal of biological chemistry 67 9405394
2015 The Evolutionarily Conserved Tre2/Bub2/Cdc16 (TBC), Lysin Motif (LysM), Domain Catalytic (TLDc) Domain Is Neuroprotective against Oxidative Stress. The Journal of biological chemistry 65 26668325
2004 The TBC (Tre-2/Bub2/Cdc16) domain protein TRE17 regulates plasma membrane-endosomal trafficking through activation of Arf6. Molecular and cellular biology 64 15509780
2010 The APC/C subunit Cdc16/Cut9 is a contiguous tetratricopeptide repeat superhelix with a homo-dimer interface similar to Cdc27. The EMBO journal 63 20924356
1995 Molecular cloning of a cDNA with a novel domain present in the tre-2 oncogene and the yeast cell cycle regulators BUB2 and cdc16. Oncogene 63 7566974
2004 Swm1/Apc13 is an evolutionarily conserved subunit of the anaphase-promoting complex stabilizing the association of Cdc16 and Cdc27. Molecular and cellular biology 62 15060174
2008 Identification and characterization of a novel Tre-2/Bub2/Cdc16 (TBC) protein that possesses Rab3A-GAP activity. Genes to cells : devoted to molecular & cellular mechanisms 46 19077034
2009 Insights into anaphase promoting complex TPR subdomain assembly from a CDC26-APC6 structure. Nature structural & molecular biology 45 19668213
1987 Metal-binding, nucleic acid-binding finger sequences in the CDC16 gene of Saccharomyces cerevisiae. Nucleic acids research 33 2823230
2016 Structural Basis of the Interaction between Tuberous Sclerosis Complex 1 (TSC1) and Tre2-Bub2-Cdc16 Domain Family Member 7 (TBC1D7). The Journal of biological chemistry 31 26893383
2010 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. The Journal of biological chemistry 29 20937822
1999 Regions of Byr4, a regulator of septation in fission yeast, that bind Spg1 or Cdc16 and form a two-component GTPase-activating protein with Cdc16. The Journal of biological chemistry 27 10196225
1998 CDC16 controls initiation at chromosome replication origins. Molecular cell 27 9660930
2022 DEPDC1B Promotes Melanoma Angiogenesis and Metastasis through Sequestration of Ubiquitin Ligase CDC16 to Stabilize Secreted SCUBE3. Advanced science (Weinheim, Baden-Wurttemberg, Germany) 19 35088579
1998 Byr4, a dosage-dependent regulator of cytokinesis in S. pombe, interacts with a possible small GTPase pathway including Spg1 and Cdc16. Molecules and cells 19 9638658
2001 Down-regulation of the human CDC16 gene after exposure to ionizing radiation: a possible role in the radioadaptive response. Radiation research 14 11121214
2004 A screen for Schizosaccharomyces pombe mutants defective in rereplication identifies new alleles of rad4+, cut9+ and psf2+. Genetics 13 15466421
2000 The gene encoding TBC1D1 with homology to the tre-2/USP6 oncogene, BUB2, and cdc16 maps to mouse chromosome 5 and human chromosome 4. Cytogenetics and cell genetics 7 10965142
2019 YDJC Induces Epithelial-Mesenchymal Transition via Escaping from Interaction with CDC16 through Ubiquitination of PP2A. Journal of oncology 6 31485224
2018 YdjC chitooligosaccharide deacetylase homolog induces keratin reorganization in lung cancer cells: involvement of interaction between YDJC and CDC16. Oncotarget 4 29796162
2025 c-Jun promotes neuroblastoma cell differentiation by inhibiting APC formation via CDC16 and reduces neuroblastoma malignancy. Biology direct 1 40149013