SSN3 cyclin-dependent serine/threonine protein kinase SSN3 [Saccharomyces cerevisiae S288C] - Gene

Summary

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Official Symbol: SSN3
Official Full Name: cyclin-dependent serine/threonine protein kinase SSN3
Primary source: SGD:S000005963
Locus tag: YPL042C
See related: AllianceGenome:SGD:S000005963; FungiDB:YPL042C; VEuPathDB:YPL042C
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Saccharomyces cerevisiae S288C (strain: S288C)
Lineage: Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces
Also known as: CDK8; GIG2; NUT7; RYE5; SRB10; SSX7; UME5; URR1
Summary: Enables RNA polymerase II CTD heptapeptide repeat kinase activity and cyclin-dependent protein serine/threonine kinase activity. Involved in several processes, including nuclear-transcribed mRNA catabolic process, non-stop decay; protein destabilization; and regulation of transcription by RNA polymerase II. Part of mediator complex. Human ortholog(s) of this gene implicated in developmental and epileptic encephalopathy 87 and dilated cardiomyopathy. Orthologous to human CDK19 (cyclin dependent kinase 19) and CDK8 (cyclin dependent kinase 8). [provided by Alliance of Genome Resources, Jul 2025]
Orthologs: all
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Genomic context

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See SSN3 in Genome Data Viewer

Location:: chromosome: XVI

Exon count:: 1

Sequence:: Chromosome: XVI; NC_001148.4 (473040..474707, complement)

Chromosome XVI - NC_001148.4 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:: NC_001148.4

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

The Cdk8 kinase module regulates interaction of the mediator complex with RNA polymerase II.
Title: The Cdk8 kinase module regulates interaction of the mediator complex with RNA polymerase II.
CDK8 could overcome the transcriptional and posttranscriptional alterations of the fcp1 mutant by increasing Skn7 stability, protein levels, and likely the expression of target genes.
Title: Regulation of Skn7-dependent, oxidative stress-induced genes by the RNA polymerase II-CTD phosphatase, Fcp1, and Mediator kinase subunit, Cdk8, in yeast.
While active INO1 is associated with Cdk8(-) Mediator, during INO1 transcriptional memory, Cdk8(+) Mediator recruits poised RNAPII PIC lacking the Kin28 CTD kinase.
Title: Set1/COMPASS and Mediator are repurposed to promote epigenetic transcriptional memory.
with Srb10 clearing mostly inactive Gcn4 molecules at the promoter that are enriched for sumoylation of the activation domain, and Pho85 clearing molecules unbound to the UAS that include both fully functional and inactive Gcn4 species.
Title: Accumulation of a threonine biosynthetic intermediate attenuates general amino acid control by accelerating degradation of Gcn4 via Pho85 and Cdk8.
the detailed architecture of Cdk8 module, and suggest the Cdk8 module could positively regulate transcription by modulating Mediator conformation.
Title: Structural flexibility and functional interaction of Mediator Cdk8 module.
The function of the Mediator tail module component Med3, which is required for transcription activation, is suppressed by the kinase activity of the Cdk8 module.
Title: Suppression of Mediator is regulated by Cdk8-dependent Grr1 turnover of the Med3 coactivator.
discuss recent advances in our understanding of Cdk8 function and a possible role for Mediator as a hub for integrating transcription regulation with cell cycle progression
Title: Emerging roles of Cdk8 in cell cycle control.
It was shown that Phd1 is an unstable protein whose degradation is initiated through phosphorylation by Cdk8 of the RNA polymerase II mediator subcomplex.
Title: Cdk8 regulates stability of the transcription factor Phd1 to control pseudohyphal differentiation of Saccharomyces cerevisiae.
the Ccr4-Not complex has a critical role in the mechanism of activation of Skn7 that is dependent upon the Srb10 kinase
Title: The Ccr4-not complex regulates Skn7 through Srb10 kinase.
in Srb10p derivatives, the absence of CM-1 & CM-II motifs decreases the interaction of Srb10p with its cyclin partner Srb11p and with the component Tup1p of the general co-repressor complex Tup1p-Ssn6p.
Title: Functional motifs outside the kinase domain of yeast Srb10p. Their role in transcriptional regulation and protein-interactions with Tup1p and Srb11p.

Submit: New GeneRIF Correction See all GeneRIFs (12)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Homology

NCBI Orthologs

Orthologs from OrthoDB

Gene Ontology Provided by SGD

Function	Evidence Code	Pubs
enables ATP binding	IEA Inferred from Electronic Annotation more info
enables RNA polymerase II CTD heptapeptide repeat kinase activity	IDA Inferred from Direct Assay more info	PubMed
enables RNA polymerase II CTD heptapeptide repeat kinase activity	IEA Inferred from Electronic Annotation more info
enables RNA polymerase II CTD heptapeptide repeat kinase activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables cyclin-dependent protein serine/threonine kinase activity	IBA Inferred from Biological aspect of Ancestor more info
enables cyclin-dependent protein serine/threonine kinase activity	IDA Inferred from Direct Assay more info	PubMed
enables cyclin-dependent protein serine/threonine kinase activity	IEA Inferred from Electronic Annotation more info
enables cyclin-dependent protein serine/threonine kinase activity	ISS Inferred from Sequence or Structural Similarity more info	PubMed
enables kinase activity	IEA Inferred from Electronic Annotation more info
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables nucleotide binding	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein kinase activity	HDA more info	PubMed
enables protein kinase activity	IEA Inferred from Electronic Annotation more info
enables protein serine kinase activity	IEA Inferred from Electronic Annotation more info
enables protein serine/threonine kinase activity	IEA Inferred from Electronic Annotation more info
enables transferase activity	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in meiotic cell cycle	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of filamentous growth	IGI Inferred from Genetic Interaction more info	PubMed
involved_in negative regulation of filamentous growth	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of transcription by RNA polymerase II	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of transcription by RNA polymerase II	IPI Inferred from Physical Interaction more info	PubMed
involved_in nuclear-transcribed mRNA catabolic process, non-stop decay	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of biosynthetic process	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of transcription by RNA polymerase II	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in protein destabilization	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of cell cycle	IEA Inferred from Electronic Annotation more info
involved_in regulation of transcription by RNA polymerase II	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
part_of cyclin-dependent protein kinase holoenzyme complex	IBA Inferred from Biological aspect of Ancestor more info
part_of cyclin-dependent protein kinase holoenzyme complex	IEA Inferred from Electronic Annotation more info
part_of mediator complex	IBA Inferred from Biological aspect of Ancestor more info
part_of mediator complex	IDA Inferred from Direct Assay more info	PubMed
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: cyclin-dependent serine/threonine protein kinase SSN3

NP_015283.1

EC 2.7.11.22

EC 2.7.11.23

Component of the RNA polymerase II mediator complex; cyclin-dependent protein kinase involved in phosphorylation of the mediator component Pgd1p and suppression of transcription activation by RNA polymerase II; involved in glucose repression

NCBI Reference Sequences (RefSeq)

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Genome Annotation

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference assembly

Genomic

NC_001148.4 Reference assembly

Range

473040..474707 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001183856.1 → NP_015283.1 cyclin-dependent serine/threonine protein kinase SSN3

See identical proteins and their annotated locations for NP_015283.1

Status: REVIEWED

UniProtKB/Swiss-Prot

D6W3X1, P39073

UniProtKB/TrEMBL

B3LL23, C7GU11, C8ZIY7, N1NXB2

Conserved Domains (1) summary

cd07842
Location:74 → 463

STKc_CDK8_like; Catalytic domain of Cyclin-Dependent protein Kinase 8-like Serine/Threonine Kinases