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Protein

CTD kinase subunit alpha

Gene

CTK1

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed-Annotation score: 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 – 2121ATPPROSITE-ProRule annotation
Active sitei306 – 3061Proton acceptorPROSITE-ProRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi189 – 1979ATPPROSITE-ProRule annotation

GO - Molecular functioni

GO - Biological processi

  • cellular response to DNA damage stimulus Source: UniProtKB-KW
  • mRNA 3'-end processing Source: SGD
  • peptidyl-serine phosphorylation Source: SGD
  • phosphorylation of RNA polymerase II C-terminal domain Source: SGD
  • positive regulation of DNA-templated transcription, elongation Source: SGD
  • positive regulation of transcription from RNA polymerase I promoter Source: SGD
  • positive regulation of translational fidelity Source: SGD
  • protein phosphorylation Source: SGD
  • transcription, DNA-templated Source: UniProtKB-KW
  • translational initiation Source: SGD
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.
2.7.11.23. 984.
ReactomeiR-SCE-674695. RNA Polymerase II Pre-transcription Events.
R-SCE-6796648. TP53 Regulates Transcription of DNA Repair Genes.

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
Proteomesi
  • UP000002311 Componenti: Chromosome XI

Organism-specific databases

EuPathDBiFungiDB:YKL139W.
SGDiS000001622. CTK1.

Subcellular locationi

GO - Cellular componenti

  • CTDK-1 complex Source: SGD
  • cytoplasm Source: UniProtKB-SubCell
  • nucleolus Source: SGD
  • nucleoplasm Source: SGD
  • nucleus 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 alphaPRO_0000085906Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei14 – 141Phosphoserine; by autocatalysisBy 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.1 Publication

Keywords - PTMi

Phosphoprotein

Proteomic databases

MaxQBiQ03957.

PTM databases

iPTMnetiQ03957.

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. 356 interactions.
DIPiDIP-6631N.
IntActiQ03957. 26 interactions.
MINTiMINT-636105.

Structurei

3D structure databases

ProteinModelPortaliQ03957.
SMRiQ03957. Positions 189-471.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini183 – 469287Protein kinasePROSITE-ProRule annotationAdd
BLAST

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi37 – 448Nuclear localization signalSequence analysis

Compositional bias

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

Sequence similaritiesi

Contains 1 protein kinase domain.PROSITE-ProRule annotation

Phylogenomic databases

GeneTreeiENSGT00830000128304.
HOGENOMiHOG000233024.
InParanoidiQ03957.
KOiK00916.
OMAiYADNDLS.
OrthoDBiEOG092C2FL8.

Family and domain databases

InterProiIPR011009. Kinase-like_dom.
IPR000719. Prot_kinase_dom.
IPR017441. Protein_kinase_ATP_BS.
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

        10         20         30         40         50
MSYNNGNTYS KSYSRNNKRP LFGKRSPNPQ SLARPPPPKR IRTDSGYQSN
60 70 80 90 100
MDNISSHRVN SNDQPGHTKS RGNNNLSRYN DTSFQTSSRY QGSRYNNNNT
110 120 130 140 150
SYENRPKSIK RDETKAEFLS HLPKGPKSVE KSRYNNSSNT SNDIKNGYHA
160 170 180 190 200
SKYYNHKGQE GRSVIAKKVP VSVLTQQRST SVYLRIMQVG EGTYGKVYKA
210 220 230 240 250
KNTNTEKLVA LKKLRLQGER EGFPITSIRE IKLLQSFDHP NVSTIKEIMV
260 270 280 290 300
ESQKTVYMIF EYADNDLSGL LLNKEVQISH SQCKHLFKQL LLGMEYLHDN
310 320 330 340 350
KILHRDVKGS NILIDNQGNL KITDFGLARK MNSRADYTNR VITLWYRPPE
360 370 380 390 400
LLLGTTNYGT EVDMWGCGCL LVELFNKTAI FQGSNELEQI ESIFKIMGTP
410 420 430 440 450
TINSWPTLYD MPWFFMIMPQ QTTKYVNNFS EKFKSVLPSS KCLQLAINLL
460 470 480 490 500
CYDQTKRFSA TEALQSDYFK EEPKPEPLVL DGLVSCHEYE VKLARKQKRP
510 520
NILSTNTNNK GNGNSNNNNN NNNDDDDK
Length:528
Mass (Da):60,501
Last modified:October 1, 1993 - v1
Checksum:i9862EB10FD476F6B
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
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:
EMBLi
GenBanki
DDBJi
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.

3D structure databases

ProteinModelPortaliQ03957.
SMRiQ03957. Positions 189-471.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi33997. 356 interactions.
DIPiDIP-6631N.
IntActiQ03957. 26 interactions.
MINTiMINT-636105.

PTM databases

iPTMnetiQ03957.

Proteomic databases

MaxQBiQ03957.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

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

Organism-specific databases

EuPathDBiFungiDB:YKL139W.
SGDiS000001622. CTK1.

Phylogenomic databases

GeneTreeiENSGT00830000128304.
HOGENOMiHOG000233024.
InParanoidiQ03957.
KOiK00916.
OMAiYADNDLS.
OrthoDBiEOG092C2FL8.

Enzyme and pathway databases

BioCyciYEAST:G3O-31916-MONOMER.
BRENDAi2.7.11.22. 984.
2.7.11.23. 984.
ReactomeiR-SCE-674695. RNA Polymerase II Pre-transcription Events.
R-SCE-6796648. TP53 Regulates Transcription of DNA Repair Genes.

Miscellaneous databases

PROiQ03957.

Family and domain databases

InterProiIPR011009. Kinase-like_dom.
IPR000719. Prot_kinase_dom.
IPR017441. Protein_kinase_ATP_BS.
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]
ProtoNetiSearch...

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: September 7, 2016
This is version 162 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.1 Publication

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

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.