CTK1 cyclin-dependent serine/threonine protein kinase CTK1 [Saccharomyces cerevisiae S288C] - Gene

Summary

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Official Symbol: CTK1
Official Full Name: cyclin-dependent serine/threonine protein kinase CTK1
Primary source: SGD:S000001622
Locus tag: YKL139W
See related: AllianceGenome:SGD:S000001622; FungiDB:YKL139W; VEuPathDB:YKL139W
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Saccharomyces cerevisiae S288C (strain: S288C)
Lineage: Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces
Summary: Enables cyclin-dependent protein serine/threonine kinase activity. Involved in gene expression and positive regulation of macromolecule biosynthetic process. Located in nucleolus and nucleoplasm. Part of CTDK-1 complex. Human ortholog(s) of this gene implicated in congenital heart defects, dysmorphic facial features, and intellectual developmental disorder; hepatocellular carcinoma; intellectual disability; and prostate carcinoma. Orthologous to several human genes including CDK13 (cyclin dependent kinase 13). [provided by Alliance of Genome Resources, Jan 2025]
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Genomic context

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See CTK1 in Genome Data Viewer

Location:: chromosome: XI

Exon count:: 1

Sequence:: Chromosome: XI; NC_001143.9 (182958..184544)

Chromosome XI - NC_001143.9 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:: NC_001143.9

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Structure and activation mechanism of the yeast RNA Pol II CTD kinase CTDK-1 complex.
Title: Structure and activation mechanism of the yeast RNA Pol II CTD kinase CTDK-1 complex.
Ctk1 stimulates 80S formation during translation initiation.
Title: Ctk1 function is necessary for full translation initiation activity in Saccharomyces cerevisiae.
Ctk1p and Ser2 CTD phosphorylation have a wide impact in termination of small non-coding RNAs but only affect a subset of mRNA coding genes.
Title: The role of Ctk1 kinase in termination of small non-coding RNAs.
A report on the mechanism involving Spt6 and Ctk1 in the regulation and maintenance of RNA polymerase II Ser2 C-terminal domain phosphorylation during transcription elongation.
Title: A feed forward circuit comprising Spt6, Ctk1 and PAF regulates Pol II CTD phosphorylation and transcription elongation.
Ctk1 is necessary for the release of RNA polymerase II from basal transcription factors.
Title: Ctk1 promotes dissociation of basal transcription factors from elongating RNA polymerase II.
The C-terminal region of Set2, in conjunction with the phosphorylated C-terminal domain of RNAPII, influences the KMTase activity to promote methylation of histone H3 at lysine 36 during transcription elongation.
Title: Roles for Ctk1 and Spt6 in regulating the different methylation states of histone H3 lysine 36.
Ctk1 phosphorylation on Thr-338 is carried out by Cak1 and is required for normal gene transcription during the transition into stationary phase
Title: Phosphorylation by Cak1 regulates the C-terminal domain kinase Ctk1 in Saccharomyces cerevisiae.
the interactions linking Cak1 with the PAF1 complex and with Ssu72 are not direct but mediated via Ctk1 and Bur1
Title: Kinase Cak1 functionally interacts with the PAF1 complex and phosphatase Ssu72 via kinases Ctk1 and Bur1.
Ctk1 controls the maintenance of suppressive chromatin in the coding regions of genes by promoting H3K36 methylation, which leads to histone deacetylation, and preventing the 3' spread of H3K4 trimethylation.
Title: The RNA polymerase II kinase Ctk1 regulates positioning of a 5' histone methylation boundary along genes.
mechanism by which H2B ubiquitylation acts as a barrier to Ctk1 association with active genes, while subsequent deubiquitylation by Ubp8 triggers Ctk1 recruitment at the appropriate point in activation
Title: H2B ubiquitylation acts as a barrier to Ctk1 nucleosomal recruitment prior to removal by Ubp8 within a SAGA-related complex.

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Pathways from PubChem

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Homology

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 S2 kinase activity	IEA Inferred from Electronic Annotation more info
enables RNA polymerase II CTD heptapeptide repeat S5 kinase activity	IEA Inferred from Electronic Annotation more info
enables RNA polymerase II CTD heptapeptide repeat S7 kinase activity	IEA Inferred from Electronic Annotation more info
enables RNA polymerase II CTD heptapeptide repeat T4 kinase activity	IEA Inferred from Electronic Annotation more info
enables RNA polymerase II CTD heptapeptide repeat Y1 kinase activity	IEA Inferred from Electronic Annotation more info
enables RNA polymerase II CTD heptapeptide repeat kinase activity	IBA Inferred from Biological aspect of Ancestor more info
enables RNA polymerase II CTD heptapeptide repeat kinase activity	IEA Inferred from Electronic Annotation more info
enables cyclin binding	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 protein kinase activity	HDA more info	PubMed
enables protein kinase activity	IEA Inferred from Electronic Annotation more info
enables protein serine/threonine kinase activity	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in DNA damage response	IEA Inferred from Electronic Annotation more info
involved_in mRNA 3'-end processing	IGI Inferred from Genetic Interaction more info	PubMed
involved_in mRNA 3'-end processing	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in mRNA processing	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of DNA-templated transcription, elongation	IDA Inferred from Direct Assay 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 I	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of transcription elongation by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive regulation of translational fidelity	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of DNA-templated transcription	IEA Inferred from Electronic Annotation more info
involved_in regulation of cell cycle	IEA Inferred from Electronic Annotation more info
involved_in translation	IEA Inferred from Electronic Annotation more info
involved_in translational initiation	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
part_of CTDK-1 complex	IDA Inferred from Direct Assay more info	PubMed
part_of cyclin/CDK positive transcription elongation factor complex	IBA Inferred from Biological aspect of Ancestor more info
located_in cytoplasm	IEA Inferred from Electronic Annotation more info
located_in nucleolus	IDA Inferred from Direct Assay more info	PubMed
located_in nucleolus	IEA Inferred from Electronic Annotation more info
located_in nucleoplasm	IDA Inferred from Direct Assay more info	PubMed
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
located_in nucleus	IEA Inferred from Electronic Annotation more info
part_of serine/threonine protein kinase complex	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: cyclin-dependent serine/threonine protein kinase CTK1

NP_012783.1

EC 2.7.11.23

Catalytic (alpha) subunit of C-terminal domain kinase I (CTDK-I); phosphorylates both RNA pol II subunit Rpo21p to affect transcription and pre-mRNA 3' end processing, and ribosomal protein Rps2p to increase translational fidelity; required for H3K36 trimethylation but not dimethylation by Set2p; suggested stimulatory role in 80S formation during translation initiation; similar to the Drosophila dCDK12 and human CDK12 and probably CDK13

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_001143.9 Reference assembly

Range

182958..184544

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001179705.1 → NP_012783.1 TPA: cyclin-dependent serine/threonine protein kinase CTK1 [Saccharomyces cerevisiae S288C]

See identical proteins and their annotated locations for NP_012783.1

Status: REVIEWED

UniProtKB/Swiss-Prot

D6VX57, Q03957

UniProtKB/TrEMBL

A6ZZI2, B3LQW1, N1P0Q5

Conserved Domains (1) summary

cd07840
Location:183 → 469

STKc_CDK9_like; Catalytic domain of Cyclin-Dependent protein Kinase 9-like Serine/Threonine Kinases