Information on EC 2.7.11.23 - [RNA-polymerase]-subunit kinase

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The enzyme appears in viruses and cellular organisms

EC NUMBER
COMMENTARY hide
2.7.11.23
-
RECOMMENDED NAME
GeneOntology No.
[RNA-polymerase]-subunit kinase
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
ATP + [DNA-directed RNA polymerase] = ADP + phospho-[DNA-directed RNA polymerase]
show the reaction diagram
-
-
-
-
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
phospho group transfer
-
-
-
-
SYSTEMATIC NAME
IUBMB Comments
ATP:[DNA-directed RNA polymerase] phosphotransferase
The enzyme appears to be distinct from other protein kinases. It brings about multiple phosphorylations of the unique C-terminal repeat domain of the largest subunit of eukaryotic DNA-directed RNA polymerase (EC 2.7.7.6). The enzyme does not phosphorylate casein, phosvitin or histone.
CAS REGISTRY NUMBER
COMMENTARY hide
122097-00-1
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ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
-
-
-
Manually annotated by BRENDA team
var. genotype A2
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-
Manually annotated by BRENDA team
wild-type BY4741 strain
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-
Manually annotated by BRENDA team
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-
-
Manually annotated by BRENDA team
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-
-
Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
evolution
malfunction
metabolism
physiological function
additional information
structure and function of the CTDK-I complex, overview. Prediction of a possible CTD-binding domain (CID) in the N-terminal region of Ctk3 and of a three-helix bundle in the C-terminal region of Ctk3
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
ATP + C-terminal domain of RNA polymerase II
ADP + phosphorylated C-terminal domain of RNA polymerase II
show the reaction diagram
the recombinant GST-tagged CTD substrate is hyperphosphorylated by Kin28
-
-
?
ATP + casein
ADP + phosphocasein
show the reaction diagram
ATP + chicken myosin regulatory light-chain
ADP + chicken myosin regulatory light-chain phosphate
show the reaction diagram
-
-
-
-
?
ATP + CTD-containing fusion proteins
ADP + ?
show the reaction diagram
ATP + DYRKtide
ADP + phospho-DYRKtide
show the reaction diagram
-
-
-
-
?
ATP + GST-tagged yCTD fusion protein
?
show the reaction diagram
hCDK13 purified from nuclear extracts displays CTD kinase activity in vitro with recombinant GST-tagged yeast CTD fusion proteins as substrate, hyperphosphorylation of the CTD by hCDK13 kinase
-
-
?
ATP + histone H1
ADP + phosphohistone H1
show the reaction diagram
ATP + histone H3
?
show the reaction diagram
ATP + HIV Tat
ADP + phosphorylated HIV-Tat
show the reaction diagram
ATP + holo-RNA polymerase II
?
show the reaction diagram
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C-terminal domain phosphorylation by the serine 5-specific TFIIH complex, its kinase module TFIIK or by the C-terminal domain serine 2-specific kinase CTDK1
-
-
?
ATP + numatrin
ADP + phosphonumatrin
show the reaction diagram
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and other nuclear proteins
-
-
?
ATP + RNA polymerase II
?
show the reaction diagram
ATP + RNA polymerase II C-terminal domain
ADP + phosphoylated RNA polymerase II C-terminal domain
show the reaction diagram
ATP + RNA polymerase II C-terminal domain
ADP + phosphoylated RNA polymerase II C-terminal subunit
show the reaction diagram
ATP + RNA polymerase II C-terminal repeat domain
ADP + phosphoylated RNA polymerase II C-terminal repeat domain
show the reaction diagram
ATP + RNA polymerase II C-terminal subunit
ADP + phosphoylated RNA polymerase II C-terminal subunit
show the reaction diagram
ATP + RNA polymerase II carboxy terminal domain
ADP + phosphorylated RNA polymerase II carboxy terminal domain
show the reaction diagram
ATP + Rps2
?
show the reaction diagram
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phosphorylates on Ser 238, phosphorylation of Rps2 is needed for translational accuracy
-
-
?
ATP + Rps2
ADP + phosphorylated Rps2
show the reaction diagram
ATP + synthetic peptides
ADP + ?
show the reaction diagram
ATP + [DNA-directed eukaryotic RNA polymerase II subunit IIa]
ADP + phospho-[DNA-directed RNA polymerase II subunit IIa]
show the reaction diagram
ATP + [DNA-directed RNA polymerase II]
ADP + phospho-[DNA-directed RNA polymerase II]
show the reaction diagram
ATP + [DNA-directed RNA polymerase]
ADP + phospho-[DNA-directed RNA polymerase]
show the reaction diagram
dATP + [DNA-directed eukaryotic RNA polymerase II subunit IIa]
dADP + ?
show the reaction diagram
-
-
-
-
?
GTP + [DNA-directed eukaryotic RNA polymerase II subunit IIa]
GDP + ?
show the reaction diagram
additional information
?
-
NATURAL SUBSTRATES
NATURAL PRODUCTS
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
ATP + HIV Tat
ADP + phosphorylated HIV-Tat
show the reaction diagram
-
-
-
-
?
ATP + RNA polymerase II C-terminal domain
ADP + phosphoylated RNA polymerase II C-terminal domain
show the reaction diagram
Q03957
the SRI domain of Set2 interacts with the phosphorylated CTD of elongating RNAPII leading to methylation of the chromatin during transcription
-
-
?
ATP + RNA polymerase II C-terminal domain
ADP + phosphoylated RNA polymerase II C-terminal subunit
show the reaction diagram
ATP + RNA polymerase II C-terminal repeat domain
ADP + phosphoylated RNA polymerase II C-terminal repeat domain
show the reaction diagram
-
hyperphosphorylation, the Mediator complex associates with RNA polymerase II, RNAPII, at least partly via the RNAPII C-terminal repeat domain, CTD, whose phosphorylation is involved in triggering promoter clearance
-
-
?
ATP + RNA polymerase II C-terminal subunit
ADP + phosphoylated RNA polymerase II C-terminal subunit
show the reaction diagram
ATP + RNA polymerase II carboxy terminal domain
ADP + phosphorylated RNA polymerase II carboxy terminal domain
show the reaction diagram
-
the phosphorylated RNAPII CTD, interacts with BRCA1 for induction of DEF1-dependent cleavage and accumulation of a RNAPII fragment containing the P-CTD, overview
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-
?
ATP + Rps2
ADP + phosphorylated Rps2
show the reaction diagram
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a protein of the small ribosomal subunit, Ctk1 interacts with the transcription and mRNA export, TREX, complex, which couples transcription to mRNA export, and Ctk1 enhances efficient and accurate translation of the mRNA, Ctk1 is a prerequisite for correct decoding in vivo overview
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-
?
ATP + [DNA-directed eukaryotic RNA polymerase II subunit IIa]
ADP + phospho-[DNA-directed RNA polymerase II subunit IIa]
show the reaction diagram
ATP + [DNA-directed RNA polymerase II]
ADP + phospho-[DNA-directed RNA polymerase II]
show the reaction diagram
ATP + [DNA-directed RNA polymerase]
ADP + phospho-[DNA-directed RNA polymerase]
show the reaction diagram
additional information
?
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COFACTOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
additional information
-
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
additional information
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
(S)-2-(4-(4-chlorophenyl)-2,3,9-trimethyl-6H-thieno[3,2-f][1,2,4]triazolo[4,3-a][1,4]diazepin-6-yl)acetamide
i.e. CPI203, phosphorylation of the CTD Ser2 is inhibited in vivo by a BRD4 inhibitor that blocks its binding to chromatin
(S)-tert-butyl 2-(4-(4-chlorophenyl)-2,3,9-trimethyl-6H-thieno[3,2-f][1,2,4]triazolo[4,3-a][1,4]diazepin-6-yl)acetate
i.e. JQ1
1-(5-isoquinolinesulfonyl)-2-methylpiperazine
1-NA-PP1
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potent inhibitor of Kin28as allele kinase activity, Kin28as inhibition reduces transcript capping, overview, but inhibition of Kin28 does not inhibit transcription
5,6-dichloro-1-beta-D-ribofuranosylbenzimidazole
8-(methylthio)-4,5-dihydrothieno[3',4':5,6]benzoisoxazole-6-carboamide
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KM05283, CTD kinase inhibitor
anisomycin
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inhibits translation elongation of wild-type
Bovine serum albumin conjugated to heptapeptide
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with RNA-polymerase II subunit as substrate
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cycloheximide
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inhibits translation elongation of wild-type
flavopiridol
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causes a reduction in Ser2 phosphorylation and a defect in the transcription elongation of heat shock genes
geneticin
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inhibits translation elongation of wild-type
GST-CTD
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overexpression of this fragment inhibits tyrosine phosphorylation of RNAP II in vivo
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harmine
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High salt concentrations
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above 250 mM
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hygromycin B
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inhibits translation elongation of wild-type
roscovitine
spermidine
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3 mM
Synthetic peptide
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multimers of consensus heptapeptide repeat Pro-Thr-Ser-Pro-Ser-Tyr-Ser, with RNA-polymerase II subunit as substrate
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additional information
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ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
cyclin H
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required by Cdk7
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cyclin T1
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CYCLINT protein
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endogenous from Medicago sativa and from Medicago trunculata, the enzyme is organized in the CDKC-1/CYCLINT-1 kinase complex, CYCLINT protein is a specific interactor of the enzyme forming the active kinase complex which localizes to the nucleus
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DNA
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activation
Mediator
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stimulates the CTD kinase activity of TFIIH manyfold, immobilized holo-RNAPII can be separated into RNAPII and Mediator
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Rsp5
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stimulates CTD kinase activity
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Rsp5 protein
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the unrelated CTD-binding protein, Rsp5, is capable of stimulating this CTD kinase activity
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additional information
-
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.212 - 0.243
Arg-hepta peptide
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0.01 - 0.06
ATP
0.00022
CTD-containing fusion protein
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room temperature, pH 7.8
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0.18
GTP
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30°C, pH 7.9
0.189 - 0.2
hepta-six peptide
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0.15
Synthetic peptide
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27°C, pH 7.5
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0.000085
[DNA-directed RNA polymerase]
recombinant enzyme, pH 6.0-7.5, temperature not specified in the publication
additional information
additional information
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kinetics
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IC50 VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.03 - 0.099
(S)-2-(4-(4-chlorophenyl)-2,3,9-trimethyl-6H-thieno[3,2-f][1,2,4]triazolo[4,3-a][1,4]diazepin-6-yl)acetamide
Mus musculus
Q9ESU6
pH 6.0-7.5, temperature not specified in the publication
0.022 - 0.081
(S)-tert-butyl 2-(4-(4-chlorophenyl)-2,3,9-trimethyl-6H-thieno[3,2-f][1,2,4]triazolo[4,3-a][1,4]diazepin-6-yl)acetate
Mus musculus
Q9ESU6
pH 6.0-7.5, temperature not specified in the publication
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
1.238
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after second phenyl-superose chromatography
65040
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after purification with Mono S column
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
6 - 7.5
high activity
6.5
assay at; assay at; assay at
7 - 8.2
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7.5 - 8
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pH RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
6 - 9
active at
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
27 - 28
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-
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
SOURCE
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foreskin fibroblasts
Manually annotated by BRENDA team
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fibrosarcoma cell line
Manually annotated by BRENDA team
additional information
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY hide
GeneOntology No.
LITERATURE
SOURCE
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; Ctk1 is associated with polysomes
Manually annotated by BRENDA team
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is associated with translating ribosomes in vivo
Manually annotated by BRENDA team
additional information
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
32000
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tentatively alphabetagamma, 1 * 58000 + 1 * 38000 + 1 * 32000, SDS-PAGE
38000
-
tentatively alphabetagamma, 1 * 58000 + 1 * 38000 + 1 * 32000, SDS-PAGE
58000
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tentatively alphabetagamma, 1 * 58000 + 1 * 38000 + 1 * 32000, SDS-PAGE
67000
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1 * 67000 + 1 * 83000, component B, SDS-PAGE
83000
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1 * 67000 + 1 * 83000, component B, SDS-PAGE
120000
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glycerol density gradient centrifugation
180000
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gel filtration, enzyme component B
200000
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gel filtration
340000
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gel filtration, enzyme component A
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
dimer
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1 * 67000 + 1 * 83000, component B, SDS-PAGE
trimer
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tentatively alphabetagamma, 1 * 58000 + 1 * 38000 + 1 * 32000, SDS-PAGE
additional information
POSTTRANSLATIONAL MODIFICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
phosphoprotein
recombinant BRD4, purified from insect SF9 cells, autophosphorylates, and recombinant BRD4 purified from Escherichia coli also autophosphorylates
Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
N-terminal domain of the Ctk3 homologue, hanging drop vapor diffusion method, mixing of 14.5 mg/ml protein in 50 mM HEPES pH 8.0, 50 mM NaCl, 1 mM DTT, with reservoir solution containing 26% PEG 6000, 100 mM citric acid, pH 4.0, 0.8 M lithium chloride, and 5 mM Tris(2-carboxyethyl)phosphin, 4°C, X-ray diffraction structure determination and analysis at 2.0 A resolution
GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
purified mouse enzymes are rather unstable with a half-life of several days, bovine serum albumin does not stabilize
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STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
-70°C, glycerol, 20% v/v
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Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
native Ctk1 complex
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native hCDK13 from nuclear extracts of HeLa cells by Ion exchange chromatography and affinity chromatography, recombinant His-tagged chimeric mutant Ctk1/13 kinase from Saccharomyces cerevisiae strain FY23 by cation exchange chromatography and nickel affinity chromatography; recombinant His-tagged chimeric mutant Ctk1/12 kinase from Saccharomyces cerevisiae strain FY23 by cation exchange chromatographyand nickel affinity chromatography
native TFIIK, and native CTD kinase 1 by a tandem affinity purification method; TFIIK, CTDK1 by tandem affinity purification
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partial
partial; two kinases: CDTK1 and CDTK2
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purification of either recombinant Myc-tagged Ctk1 and recombinant HA-tagged Ctk1 in complex with RNA polymerase I by several chromatographic steps
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recombinant BRD4 from Escherichia coli and from Spodoptera frugiperda Sf9 insect cells
recombinant C-terminally His6-tagged wildtype and selenomethionine-labeled Ctk3 and the Ctk3 N-terminal domain from Escherichia coli strain BL21(DE3)RIL or strain B834 by nickel affinity chromatography, dialysis, tag removal by thrombin cleavage, followed by anion exchange chromatography and gel filtration
recombinant His-tagged CDKC-1 from Escherichia coli by nickel affinity chromatography, native CDKC-1 partially from cell suspension cultured cells by immunoprecipitation, immobilization of the enzyme on protein A agarose
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recombinant His-tagged chimeric mutant Ctk1/12 kinase from Saccharomyces cerevisiae strain FY23 by cation exchange chromatography and nickel affinity chromatography
two components: A and B
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two kinases: cdc2/p58 and cdc2/p62
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Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
analysis of genetic interaction between ESS1 and CTD kinase genes, overexpression of wild-type and mutant CTD kinases Ctk1, Bur1, Kin28, and Srb10 in wild-type or mutant yeast strains, the latter being deficient in enzyme activity or in Ess1, overview
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cDNA copy of cdk9HA placed into a lentiviral vector where its transcription is driven by an EF1alpha promoter, overexpression in HFF cells; overexpression of HA-tagged cdk9 in 293FT cells
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dCDK12, recombinant expression of the His-tagged chimeric mutant Ctk1/12 kinase in Saccharomyces cerevisiae strain FY23
DG75 cells transfected with pcDNA3-K41M, pFLAG-CMV2-D173A or pFLAG-CMV2-D167N
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expression in saos-2 cells
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expression of HA-tagged Ctk1 and of Myc-tagged Ctk1 in strain HIS5
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expression of plasmid-encoded Ctk1 in enzyme-deficient ctk1DELTA mutant strain
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expression of the substrate as GST-CTD fusion protein in Escherichia coli
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gene CRK9, quantitative real-time reverse transcription-PCR expression analysis
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hCDK12, recombinant expression of the His-tagged chimeric mutant Ctk1/12 kinase in Saccharomyces cerevisiae strain FY23; hCDK13, recombinant expression of the His-tagged chimeric mutant Ctk1/13 kinase in Saccharomyces cerevisiae strain FY23
in vitro transcription of CDKC-1, transient co-expression of Myc-tagged CDKC-1 and HA-tagged CYCLINT in Arabidopsis thaliana protoplasts for transcription analysis, expression of CDKC-1 as His-tagged and as GST-tagge protein in Escherichia coli strain BL21(DE3)
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recombinant expression of BRD4 in Escherichia coli and in Spodoptera frugiperda Sf9 insect cells, in vitro transcription was done using HeLa nuclear extract and the MHC I gene promoter in the presence of ATP
recombinant expression of C-terminally His6-tagged Ctk3 (residues 1-218) and the Ctk3 N-terminal domain (residues 1-140) in Escherichia coli strain BL21(DE3)RIL or in strain B834 for the selenomethionine-labeled variants
ENGINEERING
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
D167N
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dominant-negative mutant of CDK9, inhibits transcriptional activation by EBNA 2
D173A
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CDK8 mutant, shows no effect on basal or EBNA 2-activated transcription
K41M
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CDK7 mutant, both EBNA 2-activated and basal transcription from Cp reporter construct are not particularly dependent on CDK7 kinase activity with only small effects observed in the presence of high levels of mutant K41M
T162A
the kin28-T162A allele, which does not display a slow growth phenotype, has reduced activity in vitro, but does not detectably affect CTD phosphorylation and capping enzymes recruitment in vivo
T17D
the mutant has decreased CTD kinase activity, a defect in capping enzyme recruitment, and is slow growing at 25°C and 37°C
T338A
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amino acid substitution that does not affect catalytic function
D324N
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with catalytically dead allele of CTK1
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T338A
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amino acid substitution that does not affect catalytic function
-
additional information
APPLICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
medicine
additional information
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