CTK1/YKL139W Summary Help

Standard Name CTK1 1
Systematic Name YKL139W
Feature Type ORF, Verified
Description 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; similar to the Drosophila dCDK12 and human CDK12 and probably CDK13 (1, 2, 3, 4, 5 and see Summary Paragraph)
Name Description Carboxy-Terminal domain Kinase 1
Chromosomal Location
ChrXI:182958 to 184544 | ORF Map | GBrowse
Gene Ontology Annotations All CTK1 GO evidence and references
  View Computational GO annotations for CTK1
Molecular Function
Manually curated
Biological Process
Manually curated
Cellular Component
Manually curated
Regulators 2 genes
Classical genetics
Large-scale survey
511 total interaction(s) for 354 unique genes/features.
Physical Interactions
  • Affinity Capture-MS: 42
  • Affinity Capture-RNA: 4
  • Affinity Capture-Western: 19
  • Biochemical Activity: 6
  • Co-localization: 2
  • Co-purification: 2
  • Far Western: 1
  • PCA: 2
  • Reconstituted Complex: 21
  • Two-hybrid: 3

Genetic Interactions
  • Dosage Growth Defect: 21
  • Dosage Rescue: 1
  • Negative Genetic: 190
  • Phenotypic Enhancement: 14
  • Phenotypic Suppression: 3
  • Positive Genetic: 55
  • Synthetic Growth Defect: 61
  • Synthetic Lethality: 55
  • Synthetic Rescue: 9

Expression Summary
Length (a.a.) 528
Molecular Weight (Da) 60,501
Isoelectric Point (pI) 10.3
Phosphorylation PhosphoGRID | PhosphoPep Database
sequence information
ChrXI:182958 to 184544 | ORF Map | GBrowse
Last Update Coordinates: 2011-02-03 | Sequence: 1996-07-31
Subfeature details
Most Recent Updates
Coordinates Sequence
CDS 1..1587 182958..184544 2011-02-03 1996-07-31
Retrieve sequences
Analyze Sequence
S288C only
S288C vs. other species
S288C vs. other strains
External Links All Associated Seq | E.C. | Entrez Gene | Entrez RefSeq Protein | MIPS | Search all NCBI (Entrez) | UniProtKB
Primary SGDIDS000001622

The C-terminal domain kinase (CTDK-1), a three-subunit complex comprised of Ctk1p, Ctk2p, and Ctk3p, has key roles in regulation of transcription and translation, and in coordination of the two processes (reviewed in 6). The complex regulates the C-terminal repeat domain (CTD) of the largest subunit of RNA polymerase II, Rpo21p, via phosphorylation of the 2nd serine residue in the seven-amino acid repeat sequence that occurs multiple times within the domain (7). Variable phosphorylation of the Rpo21p CTD domain throughout the transcription cycle is mediated by several different kinases and phosphatases, and the differentially phosphorylated forms bind to other protein complexes important for transcription, chromatin remodeling, mRNA modification and processing, nuclear mRNA export, and other related processes (8, 9, 10, 11; reviewed in 6). The CTDK-1 complex may also have a role in regulation of RNA polymerase I transcription: the complex is partially located in the nucleolus and physically interacts with RNA Pol I, and mutations in the complex subunits cause a decrease in efficiency of formation of initiation complexes at rRNA gene promoters as well as abnormal nucleolar morphology (12). In addition to its roles in the nucleus and nucleolus, the CTDK-1 complex associates with polysomes and phosphorylates the small ribosomal subunit protein Rps2p to regulate translational efficiency and accuracy (3).

Ctk1p is the catalytic subunit of the CTDK-1 complex (1, 7). Ctk1p is itself phosphorylated by Cak1p, which also phosphorylates other cyclin-dependent kinases, and phosphorylation is important for full Ctk1p activity (13). Two other subunits, the cyclin C-related Ctk2p and Ctk3p, are also essential for function (7, 14). A screen for suppressors of human BRCA1-induced lethality in S. cerevisiae implicated CTDK-1 in a pathway for regulated RNA polymerase II degradation in response to DNA damage, which may have a role in the development of breast cancer (15).

Last updated: 2008-12-10 Contact SGD

References cited on this page View Complete Literature Guide for CTK1
1) Lee JM and Greenleaf AL  (1991) CTD kinase large subunit is encoded by CTK1, a gene required for normal growth of Saccharomyces cerevisiae. Gene Expr 1(2):149-67
2) Skaar DA and Greenleaf AL  (2002) The RNA polymerase II CTD kinase CTDK-I affects pre-mRNA 3' cleavage/polyadenylation through the processing component Pti1p. Mol Cell 10(6):1429-39
3) Rother S and Strasser K  (2007) The RNA polymerase II CTD kinase Ctk1 functions in translation elongation. Genes Dev 21(11):1409-21
4) Youdell ML, et al.  (2008) Roles for Ctk1 and Spt6 in regulating the different methylation states of histone H3 lysine 36. Mol Cell Biol 28(16):4915-26
5) Bartkowiak B, et al.  (2010) CDK12 is a transcription elongation-associated CTD kinase, the metazoan ortholog of yeast Ctk1. Genes Dev 24(20):2303-16
6) Hampsey M and Kinzy TG  (2007) Synchronicity: policing multiple aspects of gene expression by Ctk1. Genes Dev 21(11):1288-91
7) Sterner DE, et al.  (1995) The yeast carboxyl-terminal repeat domain kinase CTDK-I is a divergent cyclin-cyclin-dependent kinase complex. Mol Cell Biol 15(10):5716-24
8) Meinhart A, et al.  (2005) A structural perspective of CTD function. Genes Dev 19(12):1401-15
9) Fuchs SM, et al.  (2009) Protein modifications in transcription elongation. Biochim Biophys Acta 1789(1):26-36
10) Max T, et al.  (2007) Hyperphosphorylation of the C-terminal repeat domain of RNA polymerase II facilitates dissociation of its complex with mediator. J Biol Chem 282(19):14113-20
11) Xiao T, et al.  (2007) The RNA Polymerase II Kinase Ctk1 Regulates Positioning of a 5' Histone Methylation Boundary along Genes. Mol Cell Biol 27(2):721-31
12) Bouchoux C, et al.  (2004) CTD kinase I is involved in RNA polymerase I transcription. Nucleic Acids Res 32(19):5851-60
13) Ostapenko D and Solomon MJ  (2005) Phosphorylation by Cak1 regulates the C-terminal domain kinase Ctk1 in Saccharomyces cerevisiae. Mol Cell Biol 25(10):3906-13
14) Hautbergue G and Goguel V  (2001) Activation of the cyclin-dependent kinase CTDK-I requires the heterodimerization of two unstable subunits. J Biol Chem 276(11):8005-13
15) Bennett CB, et al.  (2008) Yeast Screens Identify the RNA Polymerase II CTD and SPT5 as Relevant Targets of BRCA1 Interaction. PLoS One 3(1):e1448