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Q03957

- CTK1_YEAST

UniProt

Q03957 - CTK1_YEAST

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Protein
CTD kinase subunit alpha
Gene
CTK1, YKL139W
Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed - Annotation score: 5 out of 5 - Experimental evidence at protein leveli

Functioni

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 RPS2.12 Publications

Catalytic activityi

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

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei212 – 2121ATP By similarity
Active sitei306 – 3061Proton acceptor By similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi189 – 1979ATP By similarity

GO - Molecular functioni

  1. ATP binding Source: UniProtKB-KW
  2. RNA polymerase II carboxy-terminal domain kinase activity Source: UniProtKB-EC
  3. cyclin-dependent protein serine/threonine kinase activity Source: SGD
  4. protein binding Source: IntAct

GO - Biological processi

  1. cellular response to DNA damage stimulus Source: UniProtKB-KW
  2. mRNA 3'-end processing Source: SGD
  3. peptidyl-serine phosphorylation Source: SGD
  4. phosphorylation of RNA polymerase II C-terminal domain Source: SGD
  5. positive regulation of DNA-templated transcription, elongation Source: SGD
  6. positive regulation of transcription from RNA polymerase I promoter Source: SGD
  7. positive regulation of translational fidelity Source: SGD
  8. protein phosphorylation Source: SGD
  9. transcription, DNA-templated Source: UniProtKB-KW
  10. translation Source: UniProtKB-KW
Complete GO annotation...

Keywords - Molecular functioni

Kinase, Serine/threonine-protein kinase, Transferase

Keywords - Biological processi

DNA damage, mRNA processing, Protein biosynthesis, Stress response, Transcription

Keywords - Ligandi

ATP-binding, Nucleotide-binding

Enzyme and pathway databases

BioCyciYEAST:G3O-31916-MONOMER.
BRENDAi2.7.11.22. 984.

Names & Taxonomyi

Protein namesi
Recommended name:
CTD kinase subunit alpha (EC:2.7.11.23)
Short name:
CTDK-I subunit alpha
Alternative name(s):
CTD kinase 58 kDa subunit
CTD kinase subunit 1
Gene namesi
Name:CTK1
Ordered Locus Names:YKL139W
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
ProteomesiUP000002311: Chromosome XI

Organism-specific databases

CYGDiYKL139w.
SGDiS000001622. CTK1.

Subcellular locationi

Nucleusnucleolus. Cytoplasm 2 Publications

GO - Cellular componenti

  1. cytoplasm Source: UniProtKB-SubCell
  2. nucleolus Source: SGD
  3. nucleoplasm Source: SGD
  4. nucleus Source: SGD
  5. trimeric positive transcription elongation factor complex b Source: SGD
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Nucleus

Pathology & Biotechi

Disruption phenotypei

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.4 Publications

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi324 – 3241D → N: Cold-sensitive. Sensitive to hydroxyurea and UV irradiation. Interferes with ATP-binding. 2 Publications
Mutagenesisi338 – 3381T → 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. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 528528CTD kinase subunit alpha
PRO_0000085906Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei14 – 141Phosphoserine; by autocatalysis By similarity
Modified residuei338 – 3381Phosphothreonine1 Publication

Post-translational modificationi

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.2 Publications

Keywords - PTMi

Phosphoprotein

Proteomic databases

MaxQBiQ03957.
PaxDbiQ03957.
PeptideAtlasiQ03957.

Expressioni

Gene expression databases

GenevestigatoriQ03957.

Interactioni

Subunit structurei

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.5 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
CTK2P4696210EBI-5230,EBI-5236
CTK3P469638EBI-5230,EBI-5241

Protein-protein interaction databases

BioGridi33997. 354 interactions.
DIPiDIP-6631N.
IntActiQ03957. 26 interactions.
MINTiMINT-636105.
STRINGi4932.YKL139W.

Structurei

3D structure databases

ProteinModelPortaliQ03957.
SMRiQ03957. Positions 183-492.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini183 – 469287Protein kinase
Add
BLAST

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi37 – 448Nuclear localization signal Reviewed prediction

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi506 – 52823Asn/Asp-rich
Add
BLAST

Sequence similaritiesi

Phylogenomic databases

eggNOGiCOG0515.
GeneTreeiENSGT00740000114964.
HOGENOMiHOG000233024.
KOiK00916.
OMAiYADNDLS.
OrthoDBiEOG7K3TWD.

Family and domain databases

InterProiIPR011009. 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]
PfamiPF00069. Pkinase. 1 hit.
[Graphical view]
SMARTiSM00220. S_TKc. 1 hit.
[Graphical view]
SUPFAMiSSF56112. SSF56112. 1 hit.
PROSITEiPS00107. PROTEIN_KINASE_ATP. 1 hit.
PS50011. PROTEIN_KINASE_DOM. 1 hit.
PS00108. PROTEIN_KINASE_ST. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q03957-1 [UniParc]FASTAAdd to Basket

« Hide

MSYNNGNTYS KSYSRNNKRP LFGKRSPNPQ SLARPPPPKR IRTDSGYQSN    50
MDNISSHRVN SNDQPGHTKS RGNNNLSRYN DTSFQTSSRY QGSRYNNNNT 100
SYENRPKSIK RDETKAEFLS HLPKGPKSVE KSRYNNSSNT SNDIKNGYHA 150
SKYYNHKGQE GRSVIAKKVP VSVLTQQRST SVYLRIMQVG EGTYGKVYKA 200
KNTNTEKLVA LKKLRLQGER EGFPITSIRE IKLLQSFDHP NVSTIKEIMV 250
ESQKTVYMIF EYADNDLSGL LLNKEVQISH SQCKHLFKQL LLGMEYLHDN 300
KILHRDVKGS NILIDNQGNL KITDFGLARK MNSRADYTNR VITLWYRPPE 350
LLLGTTNYGT EVDMWGCGCL LVELFNKTAI FQGSNELEQI ESIFKIMGTP 400
TINSWPTLYD MPWFFMIMPQ QTTKYVNNFS EKFKSVLPSS KCLQLAINLL 450
CYDQTKRFSA TEALQSDYFK EEPKPEPLVL DGLVSCHEYE VKLARKQKRP 500
NILSTNTNNK GNGNSNNNNN NNNDDDDK 528
Length:528
Mass (Da):60,501
Last modified:October 1, 1993 - v1
Checksum:i9862EB10FD476F6B
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
M69024 Genomic DNA. Translation: AAC41642.1.
Z28139 Genomic DNA. Translation: CAA81980.1.
BK006944 Genomic DNA. Translation: DAA09023.1.
PIRiS32593.
RefSeqiNP_012783.1. NM_001179705.1.

Genome annotation databases

EnsemblFungiiYKL139W; YKL139W; YKL139W.
GeneIDi853718.
KEGGisce:YKL139W.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
M69024 Genomic DNA. Translation: AAC41642.1 .
Z28139 Genomic DNA. Translation: CAA81980.1 .
BK006944 Genomic DNA. Translation: DAA09023.1 .
PIRi S32593.
RefSeqi NP_012783.1. NM_001179705.1.

3D structure databases

ProteinModelPortali Q03957.
SMRi Q03957. Positions 183-492.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

BioGridi 33997. 354 interactions.
DIPi DIP-6631N.
IntActi Q03957. 26 interactions.
MINTi MINT-636105.
STRINGi 4932.YKL139W.

Proteomic databases

MaxQBi Q03957.
PaxDbi Q03957.
PeptideAtlasi Q03957.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblFungii YKL139W ; YKL139W ; YKL139W .
GeneIDi 853718.
KEGGi sce:YKL139W.

Organism-specific databases

CYGDi YKL139w.
SGDi S000001622. CTK1.

Phylogenomic databases

eggNOGi COG0515.
GeneTreei ENSGT00740000114964.
HOGENOMi HOG000233024.
KOi K00916.
OMAi YADNDLS.
OrthoDBi EOG7K3TWD.

Enzyme and pathway databases

BioCyci YEAST:G3O-31916-MONOMER.
BRENDAi 2.7.11.22. 984.

Miscellaneous databases

NextBioi 974737.
PROi Q03957.

Gene expression databases

Genevestigatori Q03957.

Family and domain databases

InterProi IPR011009. 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 ]
Pfami PF00069. Pkinase. 1 hit.
[Graphical view ]
SMARTi SM00220. S_TKc. 1 hit.
[Graphical view ]
SUPFAMi SSF56112. SSF56112. 1 hit.
PROSITEi PS00107. PROTEIN_KINASE_ATP. 1 hit.
PS50011. PROTEIN_KINASE_DOM. 1 hit.
PS00108. PROTEIN_KINASE_ST. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  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.
    , 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. 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. Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
  13. 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. 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.

Entry informationi

Entry nameiCTK1_YEAST
AccessioniPrimary (citable) accession number: Q03957
Secondary accession number(s): D6VX57
Entry historyi
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 statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Miscellaneous

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

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families
  2. Yeast
    Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
  3. Yeast chromosome XI
    Yeast (Saccharomyces cerevisiae) chromosome XI: entries and gene names

External Data

Dasty 3

Similar proteinsi