CAK1 (also CIV1) encodes the CDK-activating kinase of Saccharomyces cerevisiae, an essential 368-residue serine/threonine protein kinase that phosphorylates the activation-loop (T-loop) threonine of cyclin-dependent kinases. Unlike the metazoan and fission-yeast CAK (CDK7-cyclin H-MAT1; Mcs6-Mcs2), Cak1 is only distantly related to CDKs, lacks the canonical glycine-rich ATP-binding loop, is active as a monomer without a cyclin or activating phosphorylation, has full activity when expressed in bacteria and is not a subunit of TFIIH; it represents a fungal-specific solution to CDK activation. Its principal substrate is Cdc28 (Cdk1), which it phosphorylates on Thr169, preferentially as monomeric CDK before cyclin binding; this modification is required for Cdc28 kinase activity, so loss of Cak1 lowers Cdc28 activity and delays cells in G2 (with a substantial G1 fraction), and CAK1 is essential unless CDC28 carries T-loop-bypassing hyperactive substitutions. Cak1 also activates the transcriptional CDKs by the same mechanism: Kin28 (Thr162, the TFIIH kinase that phosphorylates the RNA polymerase II CTD on Ser5), Bur1 (Thr240) and Ctk1 (Thr338, CTD Ser2 kinase), and through Ctk1 it feeds the Set2/Rpd3C(S) pathway that suppresses cryptic intragenic transcription initiation. It additionally has Cdc28-independent, catalysis-dependent roles in sporulation, being required for timely premeiotic DNA replication and sporulation-gene expression and for activation of the Smk1 MAP kinase that drives spore wall assembly, although its direct meiotic targets are not identified. Cak1 abundance and activity are constant through the mitotic cell cycle, decline in stationary phase and oscillate during meiosis; the protein is dispersed throughout the cell with the largest pool in the cytoplasm.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0000086 G2/M transition of mitotic cell cycle | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT node PTN008391902 (a small clade that includes Cak1 itself, SGD:S000001865) inherits G2/M transition of the mitotic cell cycle. Cak1 is the sole CDK-activating kinase of budding yeast: it phosphorylates Cdc28 Thr169, and cak1-ts cells show a G2 delay with low Cdc28 kinase activity (PMID:8752210) and conditional loss of Cdc28 phosphorylation and activity (PMID:8752211). Reason: The IBD is grounded in Cak1's own IMP evidence (PMID:8752210, PMID:8752211); the target appearing in its own WITH/FROM is expected and marks experimental grounding on the target itself. Activating T-loop phosphorylation of the mitotic CDK is a step of the G2/M transition as GO defines it (the transition begins when M-cyclin/CDK activity reaches threshold), and the CAK step is the budding-yeast variant in the G2/M module (modules/g2_m_transition.yaml). Core function. Supporting Evidence: PMID:8752210 A temperature-sensitive mutation in CAK1 confers a G2 delay accompanied by low Cdc28p protein kinase activity and shows genetic interactions with altered expression of the gene for the major mitotic cyclin, CLB2. PMID:8752211 The CIV1 gene is essential for yeast cell viability, and Cdc28 phosphorylation and activity are conditionally inhibited in a civ1-4 temperature-sensitive mutant. |
| GO:0000086 G2/M transition of mitotic cell cycle | IMP PMID:8752210 The Cdk-activating kinase (CAK) from budding yeast. | ACCEPT | Summary: Kaldis, Sutton and Solomon purified and cloned the budding-yeast CAK, showed Cak1 is an active monomer that is not part of TFIIH, and found that a temperature-sensitive cak1 allele confers a G2 delay with low Cdc28 kinase activity and genetic interactions with CLB2 expression. Reason: Direct mutant-phenotype evidence (G2 delay, low Cdc28 activity, CLB2 interaction) that Cak1 activity is required for mitotic entry; Cak1 does the work by phosphorylating Cdc28 Thr169. Core function. Supporting Evidence: PMID:8752210 A temperature-sensitive mutation in CAK1 confers a G2 delay accompanied by low Cdc28p protein kinase activity and shows genetic interactions with altered expression of the gene for the major mitotic cyclin, CLB2. PMID:8752210 Unlike CAKs from other organisms, Cak1p is active as a monomer, has full activity when expressed in E. coli, and is not a component of the basal transcription factor, TFIIH. |
| GO:0000086 G2/M transition of mitotic cell cycle | IMP PMID:8752211 Civ1 (CAK in vivo), a novel Cdk-activating kinase. | ACCEPT | Summary: Thuret et al. identified Civ1 (= Cak1) as the in vivo CAK: CIV1 is essential, Civ1 binds and phosphorylates Cdc28, and Cdc28 phosphorylation and kinase activity are conditionally lost in a civ1-4 temperature-sensitive mutant. The cached record is abstract-only; the G2/M-arrest phenotype of civ1-4 was read by the SGD curator from the full text. Reason: The abstract establishes conditional loss of Cdc28 phosphorylation and activity in civ1-4 cells, which is the mechanistic basis of the G2/M requirement, and the independent cak1-ts study (PMID:8752210) documents the G2 delay directly. Deferring to the curator on the full-text phenotype is appropriate; the function is clearly correct for the gene. Supporting Evidence: PMID:8752211 The CIV1 gene is essential for yeast cell viability, and Cdc28 phosphorylation and activity are conditionally inhibited in a civ1-4 temperature-sensitive mutant. PMID:8752211 Civ1 binds tightly to and phosphorylates Cdc28, thereby allowing its subsequent activation by the binding of a cyclin. |
| GO:0004672 protein kinase activity | IEA GO_REF:0000120 | ACCEPT | Summary: Combined automated annotation (ARBA rule + InterPro IPR008271 Ser/Thr kinase active-site signature) to the generic protein kinase activity term. Cak1 is a demonstrated protein kinase with activity when expressed in E. coli (PMID:8752210). Reason: Correct though general; it is the parent of the experimentally supported protein serine/threonine kinase activity. Harmless electronic annotation. Supporting Evidence: PMID:8752210 Unlike CAKs from other organisms, Cak1p is active as a monomer, has full activity when expressed in E. coli, and is not a component of the basal transcription factor, TFIIH. |
| GO:0004674 protein serine/threonine kinase activity | IBA GO_REF:0000033 | ACCEPT | Summary: Deep PAINT node PTN000623091 (the CDK/CMGC clade, seeded by dozens of experimentally characterised CDKs across eukaryotes) propagates protein serine/threonine kinase activity. Cak1 phosphorylates threonine residues in the activation loops of Cdc28 (Thr169), Kin28 (Thr162), Bur1 (Thr240) and Ctk1 (Thr338), and is active as a monomer with full activity when expressed in E. coli. Reason: The core molecular function of Cak1. Direct evidence: purified/recombinant Cak1 phosphorylates Cdc28 and Kin28 in vitro (PMID:8752210, PMID:8752211, PMID:10373527), and the atypical, cyclin-independent monomeric kinase is nevertheless a bona fide Ser/Thr kinase. The node placement at the CMGC/CDK clade is sound for a divergent CDK-like kinase. Supporting Evidence: PMID:8752210 Unlike CAKs from other organisms, Cak1p is active as a monomer, has full activity when expressed in E. coli, and is not a component of the basal transcription factor, TFIIH. PMID:10373527 Finally, we show that Kin28p is no longer phosphorylated on Thr-162 following inactivation of Cak1p in vivo, that Cak1p can phosphorylate Kin28p on Thr-162 in vitro, and that this phosphorylation stimulates the CTD kinase activity of Kin28p. file:yeast/CAK1/CAK1-deep-research-falcon.md Recombinant Cak1 stimulates Bur1βBur2-associated CTD kinase activity. file:yeast/CAK1/CAK1-deep-research-falcon.md In contrast, Pho85 and Srb10 activities were not detectably dependent on Cak1, demonstrating selectivity among yeast CDKs. |
| GO:0004693 cyclin-dependent protein serine/threonine kinase activity | IEA GO_REF:0000003 | MODIFY | Summary: Electronic transfer from the UniProt EC number 2.7.11.22 (cyclin-dependent kinase). The EC assignment is itself a loose fit: GO:0004693 is defined as cyclin-dependent catalysis, whereas Cak1 is a monomeric, cyclin-independent kinase (PMID:8752210, PMID:8752211, PMID:9819350) that activates cyclin-dependent kinases rather than being one. Reason: The term's defining property (cyclin dependence) is directly contradicted by the discovery papers: Cak1 is active as a monomer and has full activity in E. coli. The essence (Ser/Thr kinase activity of a CDK-like fold) is right, so the row should be recorded as protein serine/threonine kinase activity (GO:0004674); the CDK-activating role is a process, best captured by GO:0045737 positive regulation of cyclin-dependent protein serine/threonine kinase activity, since the dedicated CAK activity term GO:0019912 was obsoleted in 2025. Proposed replacements: protein serine/threonine kinase activity Supporting Evidence: PMID:8752210 Unlike CAKs from other organisms, Cak1p is active as a monomer, has full activity when expressed in E. coli, and is not a component of the basal transcription factor, TFIIH. PMID:8752211 Civ1 is most similar in sequence to the Cdks, but unlike them is active as a monomer and may thus be the founding member of a novel family of kinases. |
| GO:0005515 protein binding | IPI PMID:10688190 A comprehensive analysis of protein-protein interactions in ... | REMOVE | Summary: Bare protein-binding record of the Cak1-Cdc28 interaction from the Uetz et al. genome-wide two-hybrid screen. Cdc28 is the principal substrate of Cak1, which phosphorylates its Thr169. Reason: GO:0005515 carries no functional information. The Cak1-Cdc28 interaction is genuine and is an enzyme-substrate relationship (Civ1 binds tightly to and phosphorylates Cdc28, PMID:8752211); it belongs on the kinase-activity annotation as an input (has_input Cdc28), not as a stand-alone binding term. Removal does not question the interaction itself; the high-throughput screen does not by itself support a more informative molecular-function term. Supporting Evidence: PMID:10688190 These approaches resulted in the detection of 957 putative interactions involving 1,004 S. cerevisiae proteins. PMID:8752211 Civ1 binds tightly to and phosphorylates Cdc28, thereby allowing its subsequent activation by the binding of a cyclin. |
| GO:0005515 protein binding | IPI PMID:14690591 Assigning function to yeast proteins by integration of techn... | REMOVE | Summary: Bare protein-binding record of the Cak1-Cdc28 interaction from the Hazbun et al. multi-technology (affinity purification/MS, two-hybrid) survey of essential yeast ORFs. Cdc28 is the principal substrate of Cak1. Reason: GO:0005515 carries no functional information. The Cak1-Cdc28 interaction is genuine and is an enzyme-substrate relationship (Civ1 binds tightly to and phosphorylates Cdc28, PMID:8752211); it belongs on the kinase-activity annotation as an input (has_input Cdc28), not as a stand-alone binding term. Removal does not question the interaction itself; the high-throughput screen does not by itself support a more informative molecular-function term. Supporting Evidence: PMID:14690591 These proteins were subjected to affinity purification and mass spectrometry analysis to identify copurifying proteins, two-hybrid analysis to identify interacting proteins, fluorescence microscopy to localize the proteins, and structure prediction methodology to predict structural domains or identify remote homologies. PMID:8752211 Civ1 binds tightly to and phosphorylates Cdc28, thereby allowing its subsequent activation by the binding of a cyclin. |
| GO:0005515 protein binding | IPI PMID:20489023 A global protein kinase and phosphatase interaction network ... | REMOVE | Summary: Bare protein-binding record of the Cak1-Cdc28 interaction from the Breitkreutz et al. kinase/phosphatase affinity-purification mass-spectrometry network. Cdc28 is the principal substrate of Cak1. Reason: GO:0005515 carries no functional information. The Cak1-Cdc28 interaction is genuine and is an enzyme-substrate relationship (Civ1 binds tightly to and phosphorylates Cdc28, PMID:8752211); it belongs on the kinase-activity annotation as an input (has_input Cdc28), not as a stand-alone binding term. Removal does not question the interaction itself; the high-throughput screen does not by itself support a more informative molecular-function term. Supporting Evidence: PMID:20489023 We identified a kinase and phosphatase interaction (KPI) network of 1844 interactions in budding yeast by mass spectrometric analysis of protein complexes. PMID:8752211 Civ1 binds tightly to and phosphorylates Cdc28, thereby allowing its subsequent activation by the binding of a cyclin. |
| GO:0005524 ATP binding | IEA GO_REF:0000002 | ACCEPT | Summary: InterPro protein-kinase-domain (IPR000719) mapping to ATP binding. Cak1 is an ATP-dependent protein kinase, although it lacks the canonical glycine-rich GxGxxG loop and is only distantly related to CDKs (PMID:8781234). Reason: Correct: kinase activity requires ATP binding, demonstrated by phosphotransfer from ATP in vitro. Standard, uncontroversial domain-based annotation. Supporting Evidence: PMID:8781234 CAK from the budding yeast Saccharomyces cerevisiae was identified as an unusual 44-kilodalton protein kinase, Cak1, that is only distantly related to CDKs. |
| GO:0005634 nucleus | IBA GO_REF:0000033 | ACCEPT | Summary: Deep PAINT node PTN000623091 (CDK clade) propagates nucleus as the site of activity. Immunofluorescence shows Cak1 dispersed throughout the cell, with most of the protein in the cytoplasm by fractionation (PMID:9819350); its physiological substrates include the nuclear transcriptional CDKs Kin28 (TFIIH), Bur1 and Ctk1 (PMID:10373527, PMID:19269370). Reason: The inherited nuclear location is consistent with target-specific evidence: Cak1 is present throughout the cell and activates nuclear kinases (Kin28 Thr162 phosphorylation is lost when Cak1 is inactivated in vivo). There is no evidence of nuclear exclusion that would argue against the node placement. The cytoplasm is nevertheless the predominant pool. Supporting Evidence: PMID:9819350 We have found that Cak1p is dispersed throughout the cell as shown by immunofluorescence; biochemical subcellular fractionation confirmed that most of the Cak1p is found in the cytoplasm. PMID:10373527 Finally, we show that Kin28p is no longer phosphorylated on Thr-162 following inactivation of Cak1p in vivo, that Cak1p can phosphorylate Kin28p on Thr-162 in vitro, and that this phosphorylation stimulates the CTD kinase activity of Kin28p. |
| GO:0005737 cytoplasm | IDA PMID:9819350 Localization and regulation of the cdk-activating kinase (Ca... | ACCEPT | Summary: Kaldis et al. localised Cak1 by immunofluorescence (dispersed throughout the cell) and by biochemical subcellular fractionation, which placed most of the protein in the cytoplasm; Cak1 is a monomeric, stable, unmodified enzyme whose levels fall in stationary phase and oscillate in meiosis. Reason: Direct localisation evidence for the predominant Cak1 pool; fits its preference for monomeric (pre-cyclin) Cdc28 as substrate. Core location. Supporting Evidence: PMID:9819350 We have found that Cak1p is dispersed throughout the cell as shown by immunofluorescence; biochemical subcellular fractionation confirmed that most of the Cak1p is found in the cytoplasm. |
| GO:0051321 meiotic cell cycle | IMP PMID:11739722 CAK1 promotes meiosis and spore formation in Saccharomyces c... | KEEP AS NON CORE | Summary: Schaber et al. showed, using a CAK1-independent hyperactive CDC28 allele (CDC28-43244) to bypass the mitotic requirement, that cak1-null diploids are blocked early in meiosis (delayed premeiotic DNA synthesis, poor induction of IME1 and early/middle sporulation genes, few cells completing MI/MII) and that Cak1 catalytic activity is required to activate the Smk1 MAP kinase for spore wall assembly; both roles are Cdc28-independent and Cak1 does not phosphorylate Smk1 or Ime2 directly in vitro. Reason: Real, catalytically dependent function in meiotic development (the kinase-dead cak1-D169R allele phenocopies the null), so the annotation is sound and Cak1 is doing work by phosphorylating (unidentified) kinase targets. It is, however, a developmental extension of the CDK-activating kinase rather than its core function, and the direct meiotic substrate is unknown; the post-meiotic spore-wall (Smk1) role is arguably better captured by ascospore formation (GO:0030437), which is left for the curator to consider rather than proposed as NEW. Supporting Evidence: PMID:11739722 We also found that mutants lacking CAK1 are blocked early in meiotic development, as they show substantial delays in premeiotic DNA synthesis and defects in the expression of sporulation-specific genes, including IME1. PMID:11739722 Here we show that Smk1p, like other MAP kinases, is phosphorylated in its activation loop and that Smk1p is not activated in a cak1 missense mutant. PMID:11739722 These results indicate that the catalytic activity of Cak1p is required for its functions in meiosis and spore formation. |
| GO:0060633 negative regulation of transcription initiation by RNA polymerase II | IGI PMID:19269370 Functional organization of the S. cerevisiae phosphorylation... | KEEP AS NON CORE | Summary: Fiedler et al. (signalling E-MAP) found positive genetic interactions between CAK1 and SET2 (SGD:S000003704) and EAF3 that were confirmed by tetrad analysis, and showed that cak1-DAmP and cak1-ts alleles derepress cryptic transcription initiation from an internal TATA in FLO8, placing Cak1 (via its substrate Ctk1) in the Set2/Rpd3C(S) pathway that suppresses spurious initiation. Reason: The phenotype is real and mechanistically explained: Cak1 activates Ctk1 (Thr338) and Bur1 (Thr240) by T-loop phosphorylation, and Ctk1-dependent CTD Ser2 phosphorylation recruits Set2 to methylate H3K36, which in turn recruits Rpd3C(S) via Eaf3 to deacetylate coding-region chromatin and suppress cryptic intragenic initiation. Cak1 therefore does the work of activating the upstream kinase of this pathway, which justifies a regulation-of-transcription-initiation term. It is a downstream consequence of CDK activation rather than a core function, and the evidence (positive genetic interaction plus a FLO8 cryptic-initiation reporter in cak1 hypomorphs) is genetic. Supporting Evidence: PMID:19269370 The positive genetic interactions of CAK1 with SET2 and EAF3 were confirmed by tetrad analysis and spot testing, which showed that eaf3Ξ and set2Ξ suppressed the slow growth phenotype observed in a cak1-DAmP background (Figure 6b). PMID:19269370 Finally, the cak1-DAmP strain, as well as other previously characterized CAK1 mutants (cak1-22, cak1-23, cak1-95) (Espinoza et al., 1998), showed a significant increase of transcription initiation from a cryptic internal TATA site within FLO8 (Figure 6c). PMID:19269370 In agreement with these data, Ostapenko and Solomon reported that Cak1 phosphorylates Ctk1 in vivo (Ostapenko and Solomon, 2005), and we found that deletion of CTK1 (or CTK2 and CTK3) also results in a cryptic initiation defect (Figure 6e) file:yeast/CAK1/CAK1-deep-research-falcon.md Wild-type Ctk1 efficiently phosphorylates an RNA-polymerase-II CTD peptide, whereas Ctk1-T338A has near-background activity comparable to a catalytic mutant. |
| GO:0060633 negative regulation of transcription initiation by RNA polymerase II | IGI PMID:19269370 Functional organization of the S. cerevisiae phosphorylation... | KEEP AS NON CORE | Summary: Same E-MAP study; the partner here is EAF3 (SGD:S000006227), the Rpd3C(S) subunit that reads Set2-deposited H3K36 methylation. eaf3 deletion suppressed the slow growth of cak1-DAmP cells, and cak1 mutants show the same FLO8 cryptic-initiation defect as set2 and ctk1 mutants. Reason: The phenotype is real and mechanistically explained: Cak1 activates Ctk1 (Thr338) and Bur1 (Thr240) by T-loop phosphorylation, and Ctk1-dependent CTD Ser2 phosphorylation recruits Set2 to methylate H3K36, which in turn recruits Rpd3C(S) via Eaf3 to deacetylate coding-region chromatin and suppress cryptic intragenic initiation. Cak1 therefore does the work of activating the upstream kinase of this pathway, which justifies a regulation-of-transcription-initiation term. It is a downstream consequence of CDK activation rather than a core function, and the evidence (positive genetic interaction plus a FLO8 cryptic-initiation reporter in cak1 hypomorphs) is genetic. Supporting Evidence: PMID:19269370 The positive genetic interactions of CAK1 with SET2 and EAF3 were confirmed by tetrad analysis and spot testing, which showed that eaf3Ξ and set2Ξ suppressed the slow growth phenotype observed in a cak1-DAmP background (Figure 6b). PMID:19269370 Finally, the cak1-DAmP strain, as well as other previously characterized CAK1 mutants (cak1-22, cak1-23, cak1-95) (Espinoza et al., 1998), showed a significant increase of transcription initiation from a cryptic internal TATA site within FLO8 (Figure 6c). PMID:19269370 Overall these data demonstrate that Cak1 acts as a key regulator controlling two kinases cascades involved in regulating intergenic chromatin integrity (Figure 6d). |
| GO:0097472 cyclin-dependent protein kinase activity | IDA PMID:10373527 Activating phosphorylation of the Kin28p subunit of yeast TF... | MODIFY | Summary: Kimmelman et al. showed that Cak1 phosphorylates Kin28 (the TFIIH kinase, itself a CDK) on Thr162 in vitro, that Kin28 Thr162 phosphorylation is lost in vivo when Cak1 is inactivated, and that this phosphorylation stimulates Kin28 CTD kinase activity: Kin28 joins Cdc28 as a physiological Cak1 substrate. (Direct biochemical evidence row.) Reason: GO:0097472 is defined as cyclin-dependent catalysis of protein phosphorylation, i.e. the activity of a CDK holoenzyme. Cak1 is the opposite case: a monomeric kinase that is active without a cyclin, has full activity when expressed in E. coli, is not a TFIIH subunit, and whose function is to activate CDKs by T-loop phosphorylation. SGD evidently used this term as the nearest available home for CDK-activating kinase activity (the dedicated term GO:0019912 was obsoleted in 2025 with GO:0097472 and GO:0004672 listed only as terms to consider). The evidence is sound but the term asserts cyclin dependence that the same papers rule out, so the row should be recorded as protein serine/threonine kinase activity (GO:0004674), with the CAK role captured at the process level by GO:0045737 positive regulation of cyclin-dependent protein serine/threonine kinase activity. Proposed replacements: protein serine/threonine kinase activity Supporting Evidence: PMID:10373527 Finally, we show that Kin28p is no longer phosphorylated on Thr-162 following inactivation of Cak1p in vivo, that Cak1p can phosphorylate Kin28p on Thr-162 in vitro, and that this phosphorylation stimulates the CTD kinase activity of Kin28p. PMID:10373527 Thus, Kin28p joins Cdc28p, the major cell cycle Cdk in budding yeast, as a physiological Cak1p substrate. |
| GO:0097472 cyclin-dependent protein kinase activity | IDA PMID:8752210 The Cdk-activating kinase (CAK) from budding yeast. | MODIFY | Summary: Kaldis, Sutton and Solomon purified the budding-yeast CDK-activating kinase, cloned CAK1, and showed that Cak1 is active as a monomer with full activity when expressed in E. coli and is not a TFIIH component; a cak1-ts allele lowers Cdc28 kinase activity. (Direct biochemical evidence row.) Reason: GO:0097472 is defined as cyclin-dependent catalysis of protein phosphorylation, i.e. the activity of a CDK holoenzyme. Cak1 is the opposite case: a monomeric kinase that is active without a cyclin, has full activity when expressed in E. coli, is not a TFIIH subunit, and whose function is to activate CDKs by T-loop phosphorylation. SGD evidently used this term as the nearest available home for CDK-activating kinase activity (the dedicated term GO:0019912 was obsoleted in 2025 with GO:0097472 and GO:0004672 listed only as terms to consider). The evidence is sound but the term asserts cyclin dependence that the same papers rule out, so the row should be recorded as protein serine/threonine kinase activity (GO:0004674), with the CAK role captured at the process level by GO:0045737 positive regulation of cyclin-dependent protein serine/threonine kinase activity. Proposed replacements: protein serine/threonine kinase activity Supporting Evidence: PMID:8752210 Unlike CAKs from other organisms, Cak1p is active as a monomer, has full activity when expressed in E. coli, and is not a component of the basal transcription factor, TFIIH. |
| GO:0097472 cyclin-dependent protein kinase activity | IDA PMID:8752211 Civ1 (CAK in vivo), a novel Cdk-activating kinase. | MODIFY | Summary: Thuret et al. identified Civ1 (Cak1) as a novel CAK that is most similar to CDKs but active as a monomer; Civ1 binds tightly to and phosphorylates Cdc28, permitting its activation by cyclin, and Cdc28 phosphorylation and activity are lost in civ1-4 cells. (Direct biochemical evidence row.) Reason: GO:0097472 is defined as cyclin-dependent catalysis of protein phosphorylation, i.e. the activity of a CDK holoenzyme. Cak1 is the opposite case: a monomeric kinase that is active without a cyclin, has full activity when expressed in E. coli, is not a TFIIH subunit, and whose function is to activate CDKs by T-loop phosphorylation. SGD evidently used this term as the nearest available home for CDK-activating kinase activity (the dedicated term GO:0019912 was obsoleted in 2025 with GO:0097472 and GO:0004672 listed only as terms to consider). The evidence is sound but the term asserts cyclin dependence that the same papers rule out, so the row should be recorded as protein serine/threonine kinase activity (GO:0004674), with the CAK role captured at the process level by GO:0045737 positive regulation of cyclin-dependent protein serine/threonine kinase activity. Proposed replacements: protein serine/threonine kinase activity Supporting Evidence: PMID:8752211 Civ1 is most similar in sequence to the Cdks, but unlike them is active as a monomer and may thus be the founding member of a novel family of kinases. PMID:8752211 Civ1 binds tightly to and phosphorylates Cdc28, thereby allowing its subsequent activation by the binding of a cyclin. |
| GO:0097472 cyclin-dependent protein kinase activity | IDA PMID:8781234 A cyclin-dependent kinase-activating kinase (CAK) in budding... | MODIFY | Summary: Espinoza et al. purified yeast CAK as an unusual 44 kDa kinase, Cak1, only distantly related to CDKs, that accounts for most CAK activity in lysates, is constant through the cell cycle and is essential; it is unrelated to the vertebrate CDK7-cyclin H-MAT1 CAK. (Direct biochemical evidence row.) Reason: GO:0097472 is defined as cyclin-dependent catalysis of protein phosphorylation, i.e. the activity of a CDK holoenzyme. Cak1 is the opposite case: a monomeric kinase that is active without a cyclin, has full activity when expressed in E. coli, is not a TFIIH subunit, and whose function is to activate CDKs by T-loop phosphorylation. SGD evidently used this term as the nearest available home for CDK-activating kinase activity (the dedicated term GO:0019912 was obsoleted in 2025 with GO:0097472 and GO:0004672 listed only as terms to consider). The evidence is sound but the term asserts cyclin dependence that the same papers rule out, so the row should be recorded as protein serine/threonine kinase activity (GO:0004674), with the CAK role captured at the process level by GO:0045737 positive regulation of cyclin-dependent protein serine/threonine kinase activity. Proposed replacements: protein serine/threonine kinase activity Supporting Evidence: PMID:8781234 CAK from the budding yeast Saccharomyces cerevisiae was identified as an unusual 44-kilodalton protein kinase, Cak1, that is only distantly related to CDKs. PMID:8781234 Cak1 accounted for most CAK activity in yeast cell lysates, and its activity was constant throughout the cell cycle. The CAK1 gene was essential for cell viability. |
| GO:0097472 cyclin-dependent protein kinase activity | IMP PMID:10373527 Activating phosphorylation of the Kin28p subunit of yeast TF... | MODIFY | Summary: Kimmelman et al. showed that Cak1 phosphorylates Kin28 (the TFIIH kinase, itself a CDK) on Thr162 in vitro, that Kin28 Thr162 phosphorylation is lost in vivo when Cak1 is inactivated, and that this phosphorylation stimulates Kin28 CTD kinase activity: Kin28 joins Cdc28 as a physiological Cak1 substrate. (Mutant-phenotype evidence row.) Reason: GO:0097472 is defined as cyclin-dependent catalysis of protein phosphorylation, i.e. the activity of a CDK holoenzyme. Cak1 is the opposite case: a monomeric kinase that is active without a cyclin, has full activity when expressed in E. coli, is not a TFIIH subunit, and whose function is to activate CDKs by T-loop phosphorylation. SGD evidently used this term as the nearest available home for CDK-activating kinase activity (the dedicated term GO:0019912 was obsoleted in 2025 with GO:0097472 and GO:0004672 listed only as terms to consider). The evidence is sound but the term asserts cyclin dependence that the same papers rule out, so the row should be recorded as protein serine/threonine kinase activity (GO:0004674), with the CAK role captured at the process level by GO:0045737 positive regulation of cyclin-dependent protein serine/threonine kinase activity. Proposed replacements: protein serine/threonine kinase activity Supporting Evidence: PMID:10373527 Finally, we show that Kin28p is no longer phosphorylated on Thr-162 following inactivation of Cak1p in vivo, that Cak1p can phosphorylate Kin28p on Thr-162 in vitro, and that this phosphorylation stimulates the CTD kinase activity of Kin28p. PMID:10373527 Thus, Kin28p joins Cdc28p, the major cell cycle Cdk in budding yeast, as a physiological Cak1p substrate. |
| GO:0097472 cyclin-dependent protein kinase activity | IMP PMID:8752210 The Cdk-activating kinase (CAK) from budding yeast. | MODIFY | Summary: Kaldis, Sutton and Solomon purified the budding-yeast CDK-activating kinase, cloned CAK1, and showed that Cak1 is active as a monomer with full activity when expressed in E. coli and is not a TFIIH component; a cak1-ts allele lowers Cdc28 kinase activity. (Mutant-phenotype evidence row.) Reason: GO:0097472 is defined as cyclin-dependent catalysis of protein phosphorylation, i.e. the activity of a CDK holoenzyme. Cak1 is the opposite case: a monomeric kinase that is active without a cyclin, has full activity when expressed in E. coli, is not a TFIIH subunit, and whose function is to activate CDKs by T-loop phosphorylation. SGD evidently used this term as the nearest available home for CDK-activating kinase activity (the dedicated term GO:0019912 was obsoleted in 2025 with GO:0097472 and GO:0004672 listed only as terms to consider). The evidence is sound but the term asserts cyclin dependence that the same papers rule out, so the row should be recorded as protein serine/threonine kinase activity (GO:0004674), with the CAK role captured at the process level by GO:0045737 positive regulation of cyclin-dependent protein serine/threonine kinase activity. Proposed replacements: protein serine/threonine kinase activity Supporting Evidence: PMID:8752210 Unlike CAKs from other organisms, Cak1p is active as a monomer, has full activity when expressed in E. coli, and is not a component of the basal transcription factor, TFIIH. |
| GO:0097472 cyclin-dependent protein kinase activity | IMP PMID:8752211 Civ1 (CAK in vivo), a novel Cdk-activating kinase. | MODIFY | Summary: Thuret et al. identified Civ1 (Cak1) as a novel CAK that is most similar to CDKs but active as a monomer; Civ1 binds tightly to and phosphorylates Cdc28, permitting its activation by cyclin, and Cdc28 phosphorylation and activity are lost in civ1-4 cells. (Mutant-phenotype evidence row.) Reason: GO:0097472 is defined as cyclin-dependent catalysis of protein phosphorylation, i.e. the activity of a CDK holoenzyme. Cak1 is the opposite case: a monomeric kinase that is active without a cyclin, has full activity when expressed in E. coli, is not a TFIIH subunit, and whose function is to activate CDKs by T-loop phosphorylation. SGD evidently used this term as the nearest available home for CDK-activating kinase activity (the dedicated term GO:0019912 was obsoleted in 2025 with GO:0097472 and GO:0004672 listed only as terms to consider). The evidence is sound but the term asserts cyclin dependence that the same papers rule out, so the row should be recorded as protein serine/threonine kinase activity (GO:0004674), with the CAK role captured at the process level by GO:0045737 positive regulation of cyclin-dependent protein serine/threonine kinase activity. Proposed replacements: protein serine/threonine kinase activity Supporting Evidence: PMID:8752211 Civ1 is most similar in sequence to the Cdks, but unlike them is active as a monomer and may thus be the founding member of a novel family of kinases. PMID:8752211 Civ1 binds tightly to and phosphorylates Cdc28, thereby allowing its subsequent activation by the binding of a cyclin. |
| GO:0097472 cyclin-dependent protein kinase activity | IMP PMID:8781234 A cyclin-dependent kinase-activating kinase (CAK) in budding... | MODIFY | Summary: Espinoza et al. purified yeast CAK as an unusual 44 kDa kinase, Cak1, only distantly related to CDKs, that accounts for most CAK activity in lysates, is constant through the cell cycle and is essential; it is unrelated to the vertebrate CDK7-cyclin H-MAT1 CAK. (Mutant-phenotype evidence row.) Reason: GO:0097472 is defined as cyclin-dependent catalysis of protein phosphorylation, i.e. the activity of a CDK holoenzyme. Cak1 is the opposite case: a monomeric kinase that is active without a cyclin, has full activity when expressed in E. coli, is not a TFIIH subunit, and whose function is to activate CDKs by T-loop phosphorylation. SGD evidently used this term as the nearest available home for CDK-activating kinase activity (the dedicated term GO:0019912 was obsoleted in 2025 with GO:0097472 and GO:0004672 listed only as terms to consider). The evidence is sound but the term asserts cyclin dependence that the same papers rule out, so the row should be recorded as protein serine/threonine kinase activity (GO:0004674), with the CAK role captured at the process level by GO:0045737 positive regulation of cyclin-dependent protein serine/threonine kinase activity. Proposed replacements: protein serine/threonine kinase activity Supporting Evidence: PMID:8781234 CAK from the budding yeast Saccharomyces cerevisiae was identified as an unusual 44-kilodalton protein kinase, Cak1, that is only distantly related to CDKs. PMID:8781234 Cak1 accounted for most CAK activity in yeast cell lysates, and its activity was constant throughout the cell cycle. The CAK1 gene was essential for cell viability. |
| GO:0106310 protein serine kinase activity | IEA GO_REF:0000116 | MODIFY | Summary: Rhea mapping (RHEA:17989, generic protein-serine phosphorylation) attached to the EC 2.7.11.22 assignment. Every characterised Cak1 phosphorylation site is a threonine in a kinase activation loop (Cdc28 Thr169, Kin28 Thr162, Bur1 Thr240, Ctk1 Thr338); no serine substrate has been reported. Reason: The serine-specific claim is an artefact of the generic EC-to-Rhea mapping, not of any evidence; GO has no protein threonine kinase term, so the accurate and supported term is the parent, protein serine/threonine kinase activity (GO:0004674). Proposed replacements: protein serine/threonine kinase activity Supporting Evidence: PMID:9819350 Thr-169 is phosphorylated by the cdk-activating kinase (CAK), Cak1p, which was recently identified as the physiological CAK in budding yeast. PMID:10373527 Finally, we show that Kin28p is no longer phosphorylated on Thr-162 following inactivation of Cak1p in vivo, that Cak1p can phosphorylate Kin28p on Thr-162 in vitro, and that this phosphorylation stimulates the CTD kinase activity of Kin28p. |
| GO:1902749 regulation of cell cycle G2/M phase transition | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT node PTN008391902 (seeded by human CDK10, UniProtKB:Q15131) propagates regulation of the cell cycle G2/M phase transition. GO defines this term as a signalling process that modulates a cell-cycle CDK to modulate the G2-to-M switch, which is literally what Cak1 does: it phosphorylates Cdc28 Thr169, and cak1-ts cells show a G2 delay with low Cdc28 activity. Reason: Consistent with Cak1's own IMP evidence (PMID:8752210). Two caveats for the record: Cak1 activity is constant through the cell cycle (PMID:8781234), so it is a constitutive priming step rather than a timed switch, and the more direct term GO:0000086 is already carried; the regulation term is acceptable but adds little. Supporting Evidence: PMID:8752210 A temperature-sensitive mutation in CAK1 confers a G2 delay accompanied by low Cdc28p protein kinase activity and shows genetic interactions with altered expression of the gene for the major mitotic cyclin, CLB2. PMID:8781234 Cak1 accounted for most CAK activity in yeast cell lysates, and its activity was constant throughout the cell cycle. The CAK1 gene was essential for cell viability. |
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Download this section (compressed HTML)Q: Which kinase(s) does Cak1 phosphorylate to promote premeiotic DNA replication and to activate Smk1 in sporulating cells, given that it does not phosphorylate Smk1 or Ime2 directly in vitro?
Q: Should the GO:0097472 (cyclin-dependent protein kinase activity) rows be re-homed now that the dedicated CAK activity term GO:0019912 is obsolete: is protein serine/threonine kinase activity with has_input Cdc28, plus GO:0045737 at the process level, the intended representation of a cyclin-independent CDK-activating kinase?
Q: How does the predominantly cytoplasmic Cak1 pool reach and activate the nuclear transcriptional CDKs (Kin28, Bur1, Ctk1): by phosphorylating them before nuclear import, or via a shuttling nuclear pool?
Experiment: Perform phosphoproteomics on sporulating cak1-D169R CDC28-43244 versus CAK1 CDC28-43244 diploids, focusing on activation-loop threonines of sporulation-expressed kinases, and test candidates (e.g. Ime2, Sps1 alternatives) by in vitro Cak1 phosphorylation and T-loop mutant rescue.
Hypothesis: Cak1 activates an intermediary kinase upstream of Smk1 during sporulation, rather than Smk1 itself.
Type: phosphoproteomics + genetics
Experiment: Combine an analogue-sensitive cak1 allele with acute inhibition, subcellular fractionation and phospho-Thr169 immunoblotting of cyclin-bound versus free Cdc28 to determine where and in which state Cdc28 receives the activating phosphate.
Hypothesis: Cak1 phosphorylates Cdc28 predominantly on the monomeric CDK in the cytoplasm before cyclin binding and nuclear import.
Type: chemical genetics + fractionation
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Download this section (compressed HTML)Cyclin-dependent kinase-activating kinase; required for passage through the cell cycle; phosphorylates and activates Cdc28p; nucleotide-binding pocket differs significantly from those of most other protein kinases; required for premeiotic DNA synthesis, expression of early and middle sporulation specific genes and direct phosphorylation of the Smk1p MAPK to regulate spore morphogenesis
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