CDC4 (P07834/YFL009W) in *Saccharomyces cerevisiae*: Functional-Annotation Report Falcon Edison Scientific Literature 44 citations 1 artifacts 2026-09-25T04:19:00.148104

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CDC4 (P07834/YFL009W) in Saccharomyces cerevisiae: Functional-Annotation Report

Executive summary

The requested identity is internally consistent: CDC4/YFL009W encodes the budding-yeast Cell Division Control protein 4, an essential, predominantly nuclear F-box/WD40 protein. This report concerns S. cerevisiae strain S288c and does not substitute evidence from human FBXW7, fission-yeast Pop1/Pop2, or unrelated yeast genes such as CDC40 and CDC46.

Cdc4 is best annotated as the phosphorylation-dependent substrate receptor of the SCF^Cdc4 E3 ubiquitin-ligase complex. It is not itself an enzyme that catalyzes a free-standing small-molecule reaction. Its F-box connects it to Skp1 and the Cdc53–Rbx1 SCF core, whereas its WD40 β-propeller binds phosphorylated degradation motifs—Cdc4 phosphodegrons—in regulatory proteins. The recruited Cdc34 E2 transfers ubiquitin, usually creating a proteasomal degradation signal. This mechanism converts kinase activity into irreversible changes in protein abundance and controls G1/S entry, replication licensing, mating recovery, transcriptional programs, chromatin responses, and kinetochore assembly (patton1998cdc53isa pages 1-2, tang2007suprafacialorientationof pages 1-2).

1. Identity verification and ambiguity control

The target specified by the user is:

The literature phenotype and architecture agree with this assignment. Budding-yeast CDC4 was originally identified through mutants unable to initiate DNA replication at the G1/S transition, and species-specific studies consistently describe Cdc4 as an essential nuclear F-box/WD40 protein associated with SCF-mediated proteolysis (jonkers2009lessonsfromfungal pages 3-4, au2020skpcullinfbox pages 3-5). Its reported F-box, WD40 substrate-binding region, and D dimerization domain align with the supplied InterPro annotations IPR001810, IPR036047, IPR015943, IPR020472, and IPR031740 (tang2007suprafacialorientationof pages 1-2, jonkers2009lessonsfromfungal pages 2-3).

The symbol is nevertheless hazardous across species. Human literature commonly calls the ortholog FBXW7, sometimes CDC4, while fission yeast uses distinct Pop proteins. Those records were excluded from functional claims about P07834.

2. Molecular function and domain architecture

2.1 Role in the SCF ubiquitin ligase

SCF^Cdc4 consists of the Cdc53/Cul1 scaffold, Skp1, Cdc4, and the RING protein Rbx1/Hrt1. Cdc53 connects the Skp1–Cdc4 substrate-receptor arm to Rbx1, which recruits ubiquitin-charged Cdc34 E2. Thus, Cdc4 selects substrates and orients them for ubiquitination; Cdc34 performs ubiquitin transfer. The usual net outcome is polyubiquitylation followed by 26S-proteasome degradation (patton1998cdc53isa pages 1-2, tang2007suprafacialorientationof pages 1-2).

This distinction is important for annotation: Cdc4 is appropriately described as an E3-complex substrate adaptor/receptor, not as a catalytic ubiquitin-transfer enzyme in isolation.

2.2 Domains

Structural modeling placed the two substrate-binding and two E2 sites on the same face of the dimer, with reported separations of approximately 64 Å within and 102 Å between monomers. This “suprafacial” organization can accommodate different substrate lysine positions and helps explain why dimerization improves ubiquitination without necessarily increasing degron affinity. Tang et al., published June 2007, DOI: https://doi.org/10.1016/j.cell.2007.04.042 (tang2007suprafacialorientationof pages 1-2).

2.3 Substrate specificity

The defining input is normally a phosphorylated degron, often produced through sequential or multisite kinase action. Recognition is therefore conditional: a protein may be abundant and stable until phosphorylation creates a competent Cdc4-binding surface. Affinity can arise from one optimized phosphodegron, multiple weaker sites, or cooperative multisite phosphorylation.

Sic1 is the classical example. Efficient recognition requires phosphorylation of at least six of its nine CDK sites, yielding a threshold-like response to rising CDK activity. This provides a biochemical mechanism for switch-like G1/S progression rather than degradation in response to a single stochastic phosphorylation event (tang2007suprafacialorientationof pages 1-2).

Cdc4 is not restricted to one invariant peptide sequence. Physiological specificity additionally depends on kinase choice, degron accessibility, substrate localization, multivalent binding, and assembly state. Ame1 illustrates masking of a degron by a binding partner, while Cse4 recognition involves cooperation with another F-box protein rather than a simple isolated Cdc4–phosphodegron interaction (au2020skpcullinfbox pages 19-21, bohm2021cdc4phosphodegronsallow pages 1-2).

3. Cellular localization

Cdc4 is principally a nuclear protein, consistent with most firmly established substrates being nuclear cell-cycle, transcriptional, chromatin, or kinetochore regulators (au2020skpcullinfbox pages 3-5).

Localization is mechanistically instructive rather than merely descriptive. SCF^Cdc4 ubiquitylates Far1 in the nucleus, causing nuclear Far1 degradation while allowing cytoplasmic Far1 to participate in polarized growth during mating. Thus, compartmentalization helps determine which pool of a substrate is degraded. Blondel et al., published November 2000, DOI: https://doi.org/10.1093/emboj/19.22.6085 (jonkers2009lessonsfromfungal pages 4-5, blondel2001nuclear‐specificdegradationof pages 1-3).

Cdc4 has also historically been associated with the nuclear skeleton, but the most defensible modern annotation is nuclear SCF substrate receptor, with action on soluble nuclear and chromatin-associated targets rather than a constitutive structural component of one organelle.

4. Principal substrates and pathways

The following table summarizes the strongest species-specific evidence.

Feature/substrate Mechanistic role or degron input Biological consequence Localization/context Evidence strength and key publication
F-box–Skp1 interface Cdc4’s F-box binds Skp1, coupling the substrate receptor to the SCF core. Enables assembly of functional SCF^Cdc4 and turnover of cell-cycle regulators. Predominantly nuclear SCF complex. High: biochemical/genetic evidence; 1998, DOI: 10.1101/gad.12.5.692 (patton1998cdc53isa pages 1-2)
WD40 substrate-binding domain C-terminal WD40 β-propeller recognizes phosphorylated Cdc4 phosphodegrons; it provides substrate specificity rather than catalytic activity. Converts kinase signals into selective substrate ubiquitylation. Substrate-facing portion of nuclear SCF^Cdc4. High: biochemical and structural evidence; 2003, DOI: 10.1016/S0092-8674(03)00034-5; supporting review evidence (tang2007suprafacialorientationof pages 1-2, jonkers2009lessonsfromfungal pages 2-3)
45-aa D dimerization domain Conserved D domain immediately N-terminal to the F-box mediates Cdc4 homodimerization. Disruption has little effect on Sic1 affinity but substantially impairs ubiquitin conjugation. Dimerization accommodates different substrate geometries and improves productive polyubiquitylation. SCF^Cdc4 dimer has coplanar substrate- and E2-binding sites; modeled separations are approximately 64 Å within and 102 Å between monomers. High: structure, mutagenesis, SAXS and ubiquitylation assays; 2007, DOI: 10.1016/j.cell.2007.04.042 (tang2007suprafacialorientationof pages 1-2)
SCF^Cdc4 catalytic assembly Cdc53/Cul1 scaffolds Skp1–Cdc4 and Rbx1/Hrt1; Rbx1 recruits the Cdc34 E2, which transfers ubiquitin. Cdc4 is the substrate receptor, not the ubiquitin-transfer enzyme. Builds polyubiquitin signals that generally direct bound substrates to the 26S proteasome. Predominantly nuclear; spatial restriction contributes to substrate selectivity. High: reconstitution, interaction and genetic evidence; 1998, DOI: 10.1101/gad.12.5.692; 2007, DOI: 10.1016/j.cell.2007.04.042 (patton1998cdc53isa pages 1-2, tang2007suprafacialorientationof pages 1-2)
Sic1 Multisite Cdk phosphorylation creates cooperative Cdc4-binding input; efficient recognition requires phosphorylation of at least six of nine Cdk sites. Sic1 destruction releases S-phase Clb–Cdk activity, promoting the G1/S transition and DNA-replication initiation. Nuclear G1/S control. High: genetics, binding and in-vitro ubiquitylation; 1998, DOI: 10.1101/gad.12.5.692; 2007, DOI: 10.1016/j.cell.2007.04.042 (patton1998cdc53isa pages 1-2, tang2007suprafacialorientationof pages 1-2)
Far1 Phosphorylated Far1 is recognized and ubiquitylated by SCF^Cdc4 specifically in the nucleus. Removes the mating-pathway Cdk inhibitor, enabling cell-cycle re-entry while permitting cytoplasmic Far1 functions in polarized growth. Explicitly nuclear-specific degradation governed by Cdc4 localization. High: localization, mutant and degradation evidence; 2000, DOI: 10.1093/emboj/19.22.6085 (jonkers2009lessonsfromfungal pages 4-5, blondel2001nuclear‐specificdegradationof pages 1-3)
Cdc6 Cdk1 priming and Mck1/GSK-3 phosphorylation generate a Cdc4-binding phosphodegron; the C-terminal T368–S372 region is critical. Cdc6 destruction after origin firing and during mitosis blocks pre-replicative-complex reassembly and DNA rereplication; degradation increases after MMS damage. Nuclear replication-licensing and genome-integrity control. High: phosphosite mutagenesis, kinase and stability assays; 2015, DOI: 10.1091/mbc.E14-07-1213 (alzain2015cdc6degradationrequires pages 11-11, alzain2015cdc6degradationrequires pages 1-2)
Gcn4 Pho85–Pcl5-dependent phosphorylation promotes SCF^Cdc4 recognition of the transcription factor. Couples amino-acid and nutrient conditions to rapid attenuation of Gcn4-dependent transcription, particularly after transfer to nutrient-rich conditions. Nuclear transcriptional regulation. High-to-moderate: genetic and degradation evidence; 2000, DOI: 10.1091/mbc.11.3.915 (jonkers2009lessonsfromfungal pages 4-5, au2020skpcullinfbox pages 31-32)
Tec1 Fus3 MAPK-dependent multisite phosphorylation creates the recognition input for Cdc4 and subsequent proteasomal destruction. Suppresses inappropriate Tec1-driven filamentation transcription during mating signaling and helps maintain pathway specificity. Nuclear MAPK/transcriptional-signaling context. High: phosphosite, binding and in-vivo destruction evidence; 2010, DOI: 10.1128/EC.00250-09 (jonkers2009lessonsfromfungal pages 2-3, jonkers2009lessonsfromfungal pages 4-5)
Hst3 Cdk1 phosphorylation of T380 and T384 creates a diphosphodegron required for SCF^Cdc4-mediated polyubiquitylation; T384 lies within a weak degron sequence. Times removal of the H3K56 deacetylase, coordinating genome-wide H3K56 acetylation with cell-cycle progression and replication-stress responses; degron mutation causes a fitness defect exacerbated by MMS. Nuclear chromatin and DNA-damage-response context; turnover occurs from G2/anaphase through the following cell-cycle interval. High: phosphosite mapping, mutagenesis and ubiquitylation assays; 2014, DOI: 10.1074/jbc.M113.523530 and DOI: 10.1073/pnas.1315325111 (edenberg2014hst3isturned pages 6-6, delgoshaie2014regulationofthe pages 1-2)
Ame1/CENP-U Cdk1-dependent phosphodegrons become progressively activated toward M phase. Mtw1-complex binding masks the proximal degron on assembled Ame1. Preferentially clears excess or unassembled CCAN material while protecting kinetochore-bound Ame1, supporting centromere-restricted kinetochore assembly. Nuclear kinetochore quality control during mitosis. High: phosphoproteomics, biochemistry, degron engineering and genetic tests; 2021, DOI: 10.7554/eLife.67390 (bohm2021differentiallyaccessiblecdc4 pages 1-4, bohm2021cdc4phosphodegronsallow pages 1-2)
Cse4/CENP-A Cdc4 cooperates with the F-box protein Met30; Met30 is required for efficient Cse4 recognition, making this distinct from canonical isolated Cdc4-phosphodegron recognition. Limits endogenous Cse4 abundance and prevents stable deposition at non-centromeric chromatin, thereby reducing chromosome instability. Nuclear chromatin/centromere proteostasis across G1, S and M phases. High for cooperative regulation: interaction, conditional-mutant, turnover and localization evidence; 2020, DOI: 10.1371/journal.pgen.1008597 (au2020skpcullinfbox pages 19-21, au2020skpcullinfbox pages 3-5)
2024 yeast DDR ubiquitinome — contextual only Quantitative MMS-response proteomics identified 5,397 ubiquitylated peptides from 1,853 proteins; 473 proteins increased more than twofold, with 519 potentially regulated sites in 435 proteins. Expands the discovery framework for DNA-damage-regulated ubiquitylation but does not establish new direct SCF^Cdc4 substrates. Proteome-wide S. cerevisiae DNA-replication-stress context. Contextual, not direct CDC4 evidence: 2024, DOI: 10.1016/j.mcpro.2023.100695 (blaszczak2024dissectingubiquitylationand pages 1-3)

Table: A compact, species-restricted summary of the domain architecture, SCF mechanism, localization, and experimentally supported substrates of S. cerevisiae Cdc4/P07834. Evidence strength distinguishes direct mechanistic studies from the contextual 2024 ubiquitinome.

4.1 G1/S transition: Sic1

Sic1 inhibits S-phase cyclin–Cdk complexes. Its multisite CDK phosphorylation permits Cdc4 binding, SCF-dependent polyubiquitylation, and proteasomal destruction. Loss of Cdc4, Cdc34, Cdc53, or Skp1 prevents normal Sic1 removal and produces G1 arrest. Cdc4 therefore does not directly initiate DNA synthesis; it removes an inhibitor that otherwise blocks S-phase CDK activity (patton1998cdc53isa pages 1-2, tang2007suprafacialorientationof pages 1-2).

4.2 Mating-pathway recovery: Far1

Far1 is a CDK inhibitor and polarity regulator. Phosphorylation-dependent, nuclear SCF^Cdc4 degradation removes its cell-cycle inhibitory pool, permitting re-entry into proliferation, while spatial restriction protects cytoplasmic functions. This is among the clearest demonstrations that Cdc4 specificity depends jointly on degron state and localization (jonkers2009lessonsfromfungal pages 4-5, blondel2001nuclear‐specificdegradationof pages 1-3).

4.3 Replication licensing: Cdc6

Cdc6 loads the Mcm2–7 helicase during pre-replicative-complex assembly. After origin firing, its abundance and binding state must be controlled to prevent relicensing and rereplication. Sequential phosphorylation by Cdk1 and the yeast GSK-3 homolog Mck1 creates an SCF^Cdc4-binding input. Mutational analysis identified the C-terminal T368–S372 region as crucial: substitutions at T368, P369, S372, or P373 stabilized Cdc6, and combined regulatory mutations produced mitotic defects. Mck1-dependent Cdc6 destruction occurs during mitosis and is enhanced by methyl methanesulfonate-induced DNA damage. Al-Zain et al., published July 2015, DOI: https://doi.org/10.1091/mbc.E14-07-1213 (alzain2015cdc6degradationrequires pages 1-2).

The pathway-level consequence is prevention of pre-RC reassembly and DNA rereplication, thereby preserving genome integrity. Later work has added phosphatase-dependent reversal and cyclin-binding controls, but these refine rather than overturn the Cdk/Mck1–SCF^Cdc4 model.

4.4 Nutrient-responsive transcription: Gcn4

Gcn4 is a transcriptional activator of amino-acid biosynthetic genes. Pho85–Pcl5-dependent phosphorylation promotes its Cdc4-mediated destruction, especially when cells move from poor to rich nutrient conditions. SCF^Cdc4 therefore helps terminate a costly starvation transcriptional program when nutrients become available (jonkers2009lessonsfromfungal pages 4-5, au2020skpcullinfbox pages 31-32).

4.5 MAPK pathway insulation: Tec1

Tec1 promotes filamentous-growth gene expression. During mating signaling, Fus3-dependent multisite phosphorylation makes Tec1 recognizable by Cdc4, leading to destruction. This prevents inappropriate activation of a filamentation program by shared MAPK-network components and is an example of proteolysis enforcing signaling specificity (jonkers2009lessonsfromfungal pages 2-3, jonkers2009lessonsfromfungal pages 4-5).

4.6 Chromatin and replication stress: Hst3

Hst3 is a sirtuin that removes H3K56 acetylation after S phase. Cdk1 phosphorylation at T380 and T384 creates a diphosphodegron required for efficient SCF^Cdc4 polyubiquitylation. Degron mutation does not completely stabilize Hst3, indicating additional turnover inputs, but it produces a significant fitness defect that becomes particularly severe after methyl methanesulfonate treatment. Hst3 can be degraded between G2 and anaphase, coordinating its period of chromatin deacetylation with subsequent removal. Delgoshaie et al., published May 9, 2014, DOI: https://doi.org/10.1074/jbc.M113.523530 (delgoshaie2014regulationofthe pages 1-2).

A complementary 2014 study characterized this as a replication-stress-responsive SCF^Cdc4 phosphodegron. DOI: https://doi.org/10.1073/pnas.1315325111 (edenberg2014hst3isturned pages 6-6). Together, these data connect Cdc4 to genome-wide H3K56-acetylation dynamics and replication-stress adaptation rather than implying that Cdc4 directly modifies histones.

4.7 Kinetochore assembly quality control: Ame1

Ame1/CENP-U is an essential inner-kinetochore subunit. Cdk1 progressively activates Ame1 phosphodegrons toward M phase, permitting SCF^Cdc4 degradation of excess material. When Ame1 is incorporated into a kinetochore complex, Mtw1 binding shields a proximal degron. This creates an assembly-state checkpoint: unassembled Ame1 is vulnerable, whereas properly assembled kinetochore material is protected. Strengthening the degron partially suppressed a temperature-sensitive cdc4 phenotype, and Ame1–Okp1 overexpression was toxic in SCF mutants. Böhm et al., published July 26, 2021, DOI: https://doi.org/10.7554/eLife.67390 (bohm2021cdc4phosphodegronsallow pages 1-2).

The study reports that budding-yeast kinetochore assembly after centromere replication is completed within approximately 10–15 minutes and involves more than 40 proteins, emphasizing the need for rapid stoichiometric quality control (bohm2021differentiallyaccessiblecdc4 pages 1-4, bohm2021cdc4phosphodegronsallow pages 1-2).

4.8 CENP-A/Cse4 proteostasis

Cse4 is the budding-yeast CENP-A histone variant. Cdc4 and Met30 cooperatively regulate endogenous Cse4 proteolysis, preventing stable accumulation at non-centromeric chromatin and protecting chromosome segregation. Cse4 stabilization occurred in cdc4-1 and met30-6 backgrounds across G1, S, and M arrests, arguing against a simple secondary consequence of one cell-cycle block (au2020skpcullinfbox pages 19-21).

A genome-wide synthetic-dosage-lethality screen tested 786 conditional mutants representing 560 essential genes, plus 186 nonessential deletions. Across three replicates, 160 alleles in 140 genes showed significant growth inhibition with Cse4 overexpression; SCF and proteasome categories were enriched. Follow-up genetics implicated CDC53, MET30, and CDC4. Importantly, Met30 facilitates Cse4 recognition, so Cse4 should be annotated as a cooperatively regulated substrate, not assumed to use the same simple recognition mechanism as Sic1. Au et al., published February 7, 2020, DOI: https://doi.org/10.1371/journal.pgen.1008597 (au2020skpcullinfbox pages 3-5).

5. Biological interpretation

Cdc4’s unifying role is signal-gated proteolysis. Kinases write phosphodegrons; Cdc4 reads them; the SCF–Cdc34 machinery converts recognition into ubiquitin chains; and the proteasome removes the target. This arrangement provides several regulatory advantages:

  1. Directionality: degradation makes kinase decisions effectively irreversible over short timescales.
  2. Thresholding: multisite substrates such as Sic1 respond only after sufficient kinase activity accumulates.
  3. Spatial control: nuclear localization restricts Far1 destruction to the relevant compartment.
  4. Assembly surveillance: degron masking protects complex-incorporated Ame1 while exposing excess subunits.
  5. Pathway insulation: Tec1 degradation prevents mating MAPK signals from triggering filamentation.
  6. Genome protection: Cdc6, Hst3, Ame1, and Cse4 turnover constrain rereplication, chromatin-state errors, and ectopic kinetochore formation.

The broad phenotypes of cdc4 mutants are therefore pleiotropic because one receptor coordinates several short-lived regulatory proteins. The primary molecular function, however, remains precise: binding selected phosphorylated proteins and presenting them to SCF for ubiquitination.

6. Recent developments, 2023–2024

No retrieved 2023–2024 study materially revised the core Cdc4 mechanism. Recent work instead reflects a shift toward proteome-scale discovery. A 2024 quantitative study of the budding-yeast DNA-damage ubiquitin landscape identified 5,397 ubiquitylated peptides from 1,853 proteins. Following methyl methanesulfonate treatment, 473 proteins appeared more than twofold increased in the enriched ubiquitin fraction, with 519 potentially regulated sites in 435 proteins. Published in Molecular & Cellular Proteomics, January 2024, DOI: https://doi.org/10.1016/j.mcpro.2023.100695 (blaszczak2024dissectingubiquitylationand pages 1-3).

That dataset reinforces the scale of ubiquitin-mediated DNA-damage regulation and provides a resource for discovering candidate pathways around established Cdc4 targets such as Hst3. It does not, by itself, prove that newly observed sites are direct SCF^Cdc4 substrates; direct assignment still requires dependence on Cdc4, physical recognition, degron mutagenesis, and preferably reconstituted ubiquitination.

This relative scarcity of new 2023–2024 Cdc4-specific mechanistic papers reflects maturity of the core field rather than uncertainty about the annotation. Current research is extending the established framework into proteome-wide substrate identification, degron accessibility, complex assembly, and damage-responsive proteostasis.

7. Applications and real-world implementation

Yeast Cdc4 currently has no established direct clinical use. Its principal applications are experimental and technological:

8. Confidence and remaining uncertainties

High-confidence annotation: nuclear F-box/WD40 substrate receptor of SCF^Cdc4; phosphodegron-dependent recognition; essential role in Sic1 degradation and G1/S progression; D-domain-mediated dimerization; established roles in Far1, Cdc6, Gcn4, Tec1, Hst3, and Ame1 regulation.

Mechanistically qualified annotation: Cse4 is controlled cooperatively with Met30, so its recognition should not be generalized as an ordinary isolated Cdc4 phosphodegron interaction.

Remaining uncertainties: the complete physiological substrate set, quantitative contributions of dimerization for each substrate, and the extent to which proteome-wide stress-regulated ubiquitination events are directly attributable to SCF^Cdc4 remain incompletely resolved.

Conclusion

For functional annotation, S. cerevisiae CDC4 should be described as an essential, predominantly nuclear F-box/WD40 phosphoprotein receptor within the SCF^Cdc4 ubiquitin ligase. Its F-box assembles the receptor with Skp1, its WD40 propeller recognizes phosphorylated degrons, and its D domain promotes productive dimeric ubiquitination geometry. By directing selected regulators to proteasomal degradation, Cdc4 links kinase signaling to G1/S entry, replication licensing, mating recovery, transcriptional adaptation, chromatin homeostasis, and centromere-restricted kinetochore assembly. The domain architecture and substrate evidence strongly support this annotation, with no need to infer function from a different organism’s similarly named protein.

References

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Artifacts

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