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Q03957 (CTK1_YEAST) Reviewed, UniProtKB/Swiss-Prot

Last modified June 11, 2014. Version 141. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (3) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
CTD kinase subunit alpha

Short name=CTDK-I subunit alpha
EC=2.7.11.23
Alternative name(s):
CTD kinase 58 kDa subunit
CTD kinase subunit 1
Gene names
Name:CTK1
Ordered Locus Names:YKL139W
OrganismSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) [Reference proteome]
Taxonomic identifier559292 [NCBI]
Taxonomic lineageEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces

Protein attributes

Sequence length528 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Catalytic subunit of the CTDK-I complex, which hyperphosphorylates the C-terminal heptapeptide repeat domain (CTD) of the largest RNA polymerase II subunit. CTDK-I phosphorylates 'Ser-5' if the CTD substrate is not phosphorylated at 'Ser-5', but will phosphorylate 'Ser-2' of a CTD substrate if 'Ser-5' is already phosphorylated. CTDK-I is also more reactive toward substrates that are prephosphorylated at 'Ser-2' or 'Ser-5' compared with an unphosphorylated CTD substrate, therefore efficiently creating doubly phosphorylated CTD repeats. Involved in RNA polymerase II transcriptional elongation, and through PTI1, pre-mRNA 3'-end processing. Participates in both positive and negative regulation of CTD phosphorylation. Required for DNA damage induced transcription, including the expression of the RNR genes, and reprogramming of gene expression upon amino acid starvation. Required for SET2 mediated H3K36 methylation. Also regulates H3K4 methylation. Controls the maintenance of suppressive chromatin in the coding regions of genes by both promoting H3K36 methylation, which leads to histone deacetylation, and catalyzing phosphorylation of the CTD required to localize H3K4 chromatin modification specifically to the 5' ends of genes, thereby creating a boundary for H3K4 methylation that prevents a mark associated with transcriptional initiation from spreading into the bodies of genes. Involved in RNA polymerase I transcription. Involved in telomere maintenance. Acts together with SNF1 to induce GSY2 transcription in response to glucose limitation. Involved in the adaptation to alternative carbon sources, including galactose, glycerol and ethanol, but not raffinose. Required for the integrity of the rDNA locus. Functions in translation elongation by enhancing decoding fidelity. Needed for translational accuracy by phosphorylating RPS2. Ref.5 Ref.6 Ref.9 Ref.10 Ref.11 Ref.14 Ref.15 Ref.16 Ref.17 Ref.19 Ref.20 Ref.21

Catalytic activity

ATP + [DNA-directed RNA polymerase] = ADP + [DNA-directed RNA polymerase] phosphate.

Subunit structure

CTDK-I consists of three subunits, CTK1, CTK2 and CTK3 (also called alpha, beta and gamma). Interacts directly with the CTK2 and CTK3 subunits, this interaction is required for kinase activity. Interacts with RNA polymerase I. Interacts with SNF1, but only at low glucose concentrations. Interacts with translating ribosomes. Ref.4 Ref.8 Ref.15 Ref.17 Ref.20

Subcellular location

Nucleusnucleolus. Cytoplasm Ref.12 Ref.15.

Post-translational modification

Phosphorylated on Thr-338 by CAK1. Phosphorylation is essential for the elevated CTD Ser-2 phosphorylation and required to activate transcription of stationary-phase genes during the diauxic shift. Ref.14 Ref.18

Disruption phenotype

Null mutants are viable, but grow more slowly than wild-type cells at 30 degrees Celsius. They are cold-sensitive, failing to grow at 12 degrees Celsius. They display flocculent growth in liquid media and they show abnormal cell morphologies, for example, a significant fraction of the cells are greatly enlarged. Deletion mutant has increased phosphorylation of 'Ser-5' of the CTD repeat during logarithmic growth. Deletion eliminates transient increase in CTD 'Ser-2' phosphorylation observed during diauxic shift. Deletion mutant is synthetically lethal when combined with deletion of DST1 or ELP genes. Deletion mutants are modestly sensitive to the uracil analog 6-azauracil (6AU), which inhibits elongation by depleting nucleotide pools. Deletion mutant is sensitive to the DNA synthesis inhibitor hydroxyurea (HU) and UV irradiation. 'Ser-2' phosphorylation within the CTD repeats is not increased in deletion mutants upon treatment with DNA-damaging agents. Ref.4 Ref.6 Ref.7 Ref.10

Miscellaneous

Present with 125 molecules/cell in log phase SD medium.

Sequence similarities

Belongs to the protein kinase superfamily. CMGC Ser/Thr protein kinase family. CDC2/CDKX subfamily.

Contains 1 protein kinase domain.

Ontologies

Keywords
   Biological processDNA damage
mRNA processing
Protein biosynthesis
Stress response
Transcription
   Cellular componentCytoplasm
Nucleus
   LigandATP-binding
Nucleotide-binding
   Molecular functionKinase
Serine/threonine-protein kinase
Transferase
   PTMPhosphoprotein
   Technical termComplete proteome
Reference proteome
Gene Ontology (GO)
   Biological_processcellular response to DNA damage stimulus

Inferred from electronic annotation. Source: UniProtKB-KW

mRNA 3'-end processing

Inferred from mutant phenotype Ref.9. Source: SGD

peptidyl-serine phosphorylation

Inferred from direct assay Ref.20. Source: SGD

phosphorylation of RNA polymerase II C-terminal domain

Inferred from mutant phenotype PubMed 19328068. Source: SGD

positive regulation of DNA-templated transcription, elongation

Inferred from direct assay Ref.5. Source: SGD

positive regulation of transcription from RNA polymerase I promoter

Inferred from mutant phenotype Ref.15. Source: SGD

positive regulation of translational fidelity

Inferred from mutant phenotype Ref.20. Source: SGD

protein phosphorylation

Inferred from mutant phenotype Ref.1. Source: SGD

transcription, DNA-templated

Inferred from electronic annotation. Source: UniProtKB-KW

translation

Inferred from electronic annotation. Source: UniProtKB-KW

   Cellular_componentcytoplasm

Inferred from electronic annotation. Source: UniProtKB-SubCell

nucleolus

Inferred from direct assay Ref.15. Source: SGD

nucleoplasm

Inferred from direct assay Ref.15. Source: SGD

nucleus

Inferred from direct assay Ref.5. Source: SGD

trimeric positive transcription elongation factor complex b

Inferred from direct assay Ref.4. Source: SGD

   Molecular_functionATP binding

Inferred from electronic annotation. Source: UniProtKB-KW

RNA polymerase II carboxy-terminal domain kinase activity

Inferred from electronic annotation. Source: UniProtKB-EC

cyclin-dependent protein serine/threonine kinase activity

Inferred from direct assay Ref.4. Source: SGD

protein binding

Inferred from physical interaction Ref.8PubMed 11805826PubMed 16429126PubMed 20489023. Source: IntAct

Complete GO annotation...

Binary interactions

With

Entry

#Exp.

IntAct

Notes

CTK2P4696210EBI-5230,EBI-5236
CTK3P469638EBI-5230,EBI-5241

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 528528CTD kinase subunit alpha
PRO_0000085906

Regions

Domain183 – 469287Protein kinase
Nucleotide binding189 – 1979ATP By similarity
Motif37 – 448Nuclear localization signal Potential
Compositional bias506 – 52823Asn/Asp-rich

Sites

Active site3061Proton acceptor By similarity
Binding site2121ATP By similarity

Amino acid modifications

Modified residue141Phosphoserine; by autocatalysis By similarity
Modified residue3381Phosphothreonine Ref.18

Experimental info

Mutagenesis3241D → N: Cold-sensitive. Sensitive to hydroxyurea and UV irradiation. Interferes with ATP-binding. Ref.10 Ref.18
Mutagenesis3381T → A: Cold-sensitive. Abolishes kinase activity. Delayed growth at early stationary phase. Shows no increase in CTD Ser-2 phosphorylation in the transition from rapid growth to stationary phase. Has compromised transcriptional activation of two stationary-phase genes CTT1 and SPI1. Ref.18

Sequences

Sequence LengthMass (Da)Tools
Q03957 [UniParc].

Last modified October 1, 1993. Version 1.
Checksum: 9862EB10FD476F6B

FASTA52860,501
        10         20         30         40         50         60 
MSYNNGNTYS KSYSRNNKRP LFGKRSPNPQ SLARPPPPKR IRTDSGYQSN MDNISSHRVN 

        70         80         90        100        110        120 
SNDQPGHTKS RGNNNLSRYN DTSFQTSSRY QGSRYNNNNT SYENRPKSIK RDETKAEFLS 

       130        140        150        160        170        180 
HLPKGPKSVE KSRYNNSSNT SNDIKNGYHA SKYYNHKGQE GRSVIAKKVP VSVLTQQRST 

       190        200        210        220        230        240 
SVYLRIMQVG EGTYGKVYKA KNTNTEKLVA LKKLRLQGER EGFPITSIRE IKLLQSFDHP 

       250        260        270        280        290        300 
NVSTIKEIMV ESQKTVYMIF EYADNDLSGL LLNKEVQISH SQCKHLFKQL LLGMEYLHDN 

       310        320        330        340        350        360 
KILHRDVKGS NILIDNQGNL KITDFGLARK MNSRADYTNR VITLWYRPPE LLLGTTNYGT 

       370        380        390        400        410        420 
EVDMWGCGCL LVELFNKTAI FQGSNELEQI ESIFKIMGTP TINSWPTLYD MPWFFMIMPQ 

       430        440        450        460        470        480 
QTTKYVNNFS EKFKSVLPSS KCLQLAINLL CYDQTKRFSA TEALQSDYFK EEPKPEPLVL 

       490        500        510        520 
DGLVSCHEYE VKLARKQKRP NILSTNTNNK GNGNSNNNNN NNNDDDDK 

« Hide

References

« Hide 'large scale' references
[1]"CTD kinase large subunit is encoded by CTK1, a gene required for normal growth of Saccharomyces cerevisiae."
Lee J.M., Greenleaf A.L.
Gene Expr. 1:149-167(1991) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]"Complete DNA sequence of yeast chromosome XI."
Dujon B., Alexandraki D., Andre B., Ansorge W., Baladron V., Ballesta J.P.G., Banrevi A., Bolle P.-A., Bolotin-Fukuhara M., Bossier P., Bou G., Boyer J., Buitrago M.J., Cheret G., Colleaux L., Daignan-Fornier B., del Rey F., Dion C. expand/collapse author list , Domdey H., Duesterhoeft A., Duesterhus S., Entian K.-D., Erfle H., Esteban P.F., Feldmann H., Fernandes L., Fobo G.M., Fritz C., Fukuhara H., Gabel C., Gaillon L., Garcia-Cantalejo J.M., Garcia-Ramirez J.J., Gent M.E., Ghazvini M., Goffeau A., Gonzalez A., Grothues D., Guerreiro P., Hegemann J.H., Hewitt N., Hilger F., Hollenberg C.P., Horaitis O., Indge K.J., Jacquier A., James C.M., Jauniaux J.-C., Jimenez A., Keuchel H., Kirchrath L., Kleine K., Koetter P., Legrain P., Liebl S., Louis E.J., Maia e Silva A., Marck C., Monnier A.-L., Moestl D., Mueller S., Obermaier B., Oliver S.G., Pallier C., Pascolo S., Pfeiffer F., Philippsen P., Planta R.J., Pohl F.M., Pohl T.M., Poehlmann R., Portetelle D., Purnelle B., Puzos V., Ramezani Rad M., Rasmussen S.W., Remacha M.A., Revuelta J.L., Richard G.-F., Rieger M., Rodrigues-Pousada C., Rose M., Rupp T., Santos M.A., Schwager C., Sensen C., Skala J., Soares H., Sor F., Stegemann J., Tettelin H., Thierry A., Tzermia M., Urrestarazu L.A., van Dyck L., van Vliet-Reedijk J.C., Valens M., Vandenbol M., Vilela C., Vissers S., von Wettstein D., Voss H., Wiemann S., Xu G., Zimmermann J., Haasemann M., Becker I., Mewes H.-W.
Nature 369:371-378(1994) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: ATCC 204508 / S288c.
[3]"The reference genome sequence of Saccharomyces cerevisiae: Then and now."
Engel S.R., Dietrich F.S., Fisk D.G., Binkley G., Balakrishnan R., Costanzo M.C., Dwight S.S., Hitz B.C., Karra K., Nash R.S., Weng S., Wong E.D., Lloyd P., Skrzypek M.S., Miyasato S.R., Simison M., Cherry J.M.
G3 (Bethesda) 4:389-398(2014) [PubMed] [Europe PMC] [Abstract]
Cited for: GENOME REANNOTATION.
Strain: ATCC 204508 / S288c.
[4]"The yeast carboxyl-terminal repeat domain kinase CTDK-I is a divergent cyclin-cyclin-dependent kinase complex."
Sterner D.E., Lee J.M., Hardin S.E., Greenleaf A.L.
Mol. Cell. Biol. 15:5716-5724(1995) [PubMed] [Europe PMC] [Abstract]
Cited for: CTD KINASE ACTIVITY, SUBUNIT, DISRUPTION PHENOTYPE.
[5]"Modulation of RNA polymerase II elongation efficiency by C-terminal heptapeptide repeat domain kinase I."
Lee J.M., Greenleaf A.L.
J. Biol. Chem. 272:10990-10993(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION IN RNA POLYMERASE II TRANSCRIPTION.
[6]"Yeast carboxyl-terminal domain kinase I positively and negatively regulates RNA polymerase II carboxyl-terminal domain phosphorylation."
Patturajan M., Conrad N.K., Bregman D.B., Corden J.L.
J. Biol. Chem. 274:27823-27828(1999) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION IN PHOSPHORYLATION REGULATION, DISRUPTION PHENOTYPE.
[7]"Involvement of yeast carboxy-terminal domain kinase I (CTDK-I) in transcription elongation in vivo."
Jona G., Wittschieben B.O., Svejstrup J.Q., Gileadi O.
Gene 267:31-36(2001) [PubMed] [Europe PMC] [Abstract]
Cited for: DISRUPTION PHENOTYPE.
[8]"Activation of the cyclin-dependent kinase CTDK-I requires the heterodimerization of two unstable subunits."
Hautbergue G., Goguel V.
J. Biol. Chem. 276:8005-8013(2001) [PubMed] [Europe PMC] [Abstract]
Cited for: ACTIVATION, INTERACTION WITH CTK2 AND CTK3.
[9]"The RNA polymerase II CTD kinase CTDK-I affects pre-mRNA 3' cleavage/polyadenylation through the processing component Pti1p."
Skaar D.A., Greenleaf A.L.
Mol. Cell 10:1429-1439(2002) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION IN PRE-MRNA END PROCESSING.
[10]"Budding yeast CTDK-I is required for DNA damage-induced transcription."
Ostapenko D., Solomon M.J.
Eukaryot. Cell 2:274-283(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION, MUTAGENESIS OF ASP-324, DISRUPTION PHENOTYPE.
[11]"Phosphorylation of RNA polymerase II CTD regulates H3 methylation in yeast."
Xiao T., Hall H., Kizer K.O., Shibata Y., Hall M.C., Borchers C.H., Strahl B.D.
Genes Dev. 17:654-663(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION IN H3K36 METHYLATION.
[12]"Global analysis of protein localization in budding yeast."
Huh W.-K., Falvo J.V., Gerke L.C., Carroll A.S., Howson R.W., Weissman J.S., O'Shea E.K.
Nature 425:686-691(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
[13]"Global analysis of protein expression in yeast."
Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N., O'Shea E.K., Weissman J.S.
Nature 425:737-741(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
[14]"C-terminal repeat domain kinase I phosphorylates Ser2 and Ser5 of RNA polymerase II C-terminal domain repeats."
Jones J.C., Phatnani H.P., Haystead T.A., MacDonald J.A., Alam S.M., Greenleaf A.L.
J. Biol. Chem. 279:24957-24964(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION OF THE CTDK-I COMPLEX IN PHOSPHORYLATION.
[15]"CTD kinase I is involved in RNA polymerase I transcription."
Bouchoux C., Hautbergue G., Grenetier S., Carles C., Riva M., Goguel V.
Nucleic Acids Res. 32:5851-5860(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION IN RNA POLYMERASE I TRANSCRIPTION, INTERACTION WITH RNA POLYMERASE I, SUBCELLULAR LOCATION.
[16]"A genome-wide screen for Saccharomyces cerevisiae deletion mutants that affect telomere length."
Askree S.H., Yehuda T., Smolikov S., Gurevich R., Hawk J., Coker C., Krauskopf A., Kupiec M., McEachern M.J.
Proc. Natl. Acad. Sci. U.S.A. 101:8658-8663(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION IN TELOMERE MAINTENANCE.
[17]"Glucose deprivation mediates interaction between CTDK-I and Snf1 in Saccharomyces cerevisiae."
Van Driessche B., Coddens S., Van Mullem V., Vandenhaute J.
FEBS Lett. 579:5318-5324(2005) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION IN RESPONSE TO GLUCOSE LIMITATION, INTERACTION WITH SNF1.
[18]"Phosphorylation by Cak1 regulates the C-terminal domain kinase Ctk1 in Saccharomyces cerevisiae."
Ostapenko D., Solomon M.J.
Mol. Cell. Biol. 25:3906-3913(2005) [PubMed] [Europe PMC] [Abstract]
Cited for: PHOSPHORYLATION AT THR-338 BY CAK1, MUTAGENESIS OF ASP-324 AND THR-338.
[19]"CTD kinase I is required for the integrity of the rDNA tandem array."
Grenetier S., Bouchoux C., Goguel V.
Nucleic Acids Res. 34:4996-5006(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION.
[20]"The RNA polymerase II CTD kinase Ctk1 functions in translation elongation."
Roether S., Straesser K.
Genes Dev. 21:1409-1421(2007) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION IN TRANSLATION, INTERACTION WITH RIBOSOMES.
[21]"The RNA polymerase II kinase Ctk1 regulates positioning of a 5' histone methylation boundary along genes."
Xiao T., Shibata Y., Rao B., Laribee R.N., O'Rourke R., Buck M.J., Greenblatt J.F., Krogan N.J., Lieb J.D., Strahl B.D.
Mol. Cell. Biol. 27:721-731(2007) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION IN H3K4 METHYLATION.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
M69024 Genomic DNA. Translation: AAC41642.1.
Z28139 Genomic DNA. Translation: CAA81980.1.
BK006944 Genomic DNA. Translation: DAA09023.1.
PIRS32593.
RefSeqNP_012783.1. NM_001179705.1.

3D structure databases

ProteinModelPortalQ03957.
SMRQ03957. Positions 183-492.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid33997. 354 interactions.
DIPDIP-6631N.
IntActQ03957. 26 interactions.
MINTMINT-636105.
STRING4932.YKL139W.

Proteomic databases

MaxQBQ03957.
PaxDbQ03957.
PeptideAtlasQ03957.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblFungiYKL139W; YKL139W; YKL139W.
GeneID853718.
KEGGsce:YKL139W.

Organism-specific databases

CYGDYKL139w.
SGDS000001622. CTK1.

Phylogenomic databases

eggNOGCOG0515.
GeneTreeENSGT00740000114964.
HOGENOMHOG000233024.
KOK00916.
OMAYADNDLS.
OrthoDBEOG7K3TWD.

Enzyme and pathway databases

BioCycYEAST:G3O-31916-MONOMER.
BRENDA2.7.11.22. 984.

Gene expression databases

GenevestigatorQ03957.

Family and domain databases

InterProIPR011009. Kinase-like_dom.
IPR000719. Prot_kinase_dom.
IPR017441. Protein_kinase_ATP_BS.
IPR002290. Ser/Thr_dual-sp_kinase_dom.
IPR008271. Ser/Thr_kinase_AS.
[Graphical view]
PfamPF00069. Pkinase. 1 hit.
[Graphical view]
SMARTSM00220. S_TKc. 1 hit.
[Graphical view]
SUPFAMSSF56112. SSF56112. 1 hit.
PROSITEPS00107. PROTEIN_KINASE_ATP. 1 hit.
PS50011. PROTEIN_KINASE_DOM. 1 hit.
PS00108. PROTEIN_KINASE_ST. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

NextBio974737.
PROQ03957.

Entry information

Entry nameCTK1_YEAST
AccessionPrimary (citable) accession number: Q03957
Secondary accession number(s): D6VX57
Entry history
Integrated into UniProtKB/Swiss-Prot: October 1, 1993
Last sequence update: October 1, 1993
Last modified: June 11, 2014
This is version 141 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Relevant documents

Yeast chromosome XI

Yeast (Saccharomyces cerevisiae) chromosome XI: entries and gene names

Yeast

Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD

SIMILARITY comments

Index of protein domains and families