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Information on EC 2.7.11.23 - [RNA-polymerase]-subunit kinase and Organism(s) Schizosaccharomyces pombe and UniProt Accession Q96WV9
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2.7.11.23 [RNA-polymerase]-subunit kinaseIUBMB Comments
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.
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Word Map
- 2.7.11.23
- cyclin
- strand
- chromatin
- histone
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non-homologous
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cyclin-dependent
-
end-joining
-
radiosensitivity
-
transactivation
- helicase
-
checkpoint
-
radiation-induced
- pigmentosum
- xeroderma
- ataxia
- telangiectasia
- h2ax
-
dna-damaging
- tfiie
- wortmannin
-
preinitiation
- ataxia-telangiectasia
-
rejoin
- cak
-
cockayne
- brd4
-
pausing
-
snrnp
- tbp
- rad3-related
-
cdk-activating
-
bromodomains
- xrcc4
-
pikks
-
promoter-proximal
- rad51
-
paused
-
ir-induced
-
end-binding
- drb
- flavopiridol
-
artemis
-
unrepaired
-
gammah2ax
-
transcription-coupled
-
t-loop
-
atm-dependent
-
dsb-induced
- rpb1
-
atm-deficient
- medicine
The taxonomic range for the selected organisms is: Schizosaccharomyces pombe
The expected taxonomic range for this enzyme is: Eukaryota, Archaea, Bacteria
The expected taxonomic range for this enzyme is: Eukaryota, Archaea, Bacteria
Reaction Schemes
Synonyms
dna-pk, tfiih, p-tefb, dna-dependent protein kinase, positive transcription elongation factor b, kin28, ctd kinase, srb10, ctdk-i, tfiih kinase, 
more
topSYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
C-terminal repeat domain kinase
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CTD kinase
kinase, ribonucleate nucleotidyltransferase II C-terminal domain (phosphorylating)
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kinase, ribonucleate nucleotidyltransferase isozyme II IIa subunit (phosphorylating)
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RNA polymerase II CTD kinase
CTD kinase
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RNA polymerase II CTD kinase
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REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
phospho group transfer
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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
122097-00-1
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SUBSTRATE
PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
ATP + [DNA-directed RNA polymerase II]
ADP + phospho-[DNA-directed RNA polymerase II]
only Rpb1, the largest subunit of RNAPII evolved a unique, highly repetitive carboxy-terminal domain, termed CTD. Dynamic phosphorylation patterns of serine residues in the CTD during gene transcription. Phosphorylation of Ser2, Ser5, Thr4, and Tyr1 in the CTD. CTD is composed of multiple tandem heptapeptides with the evolutionary conserved consensus motif Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7
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-
?
ATP + [DNA-directed RNA polymerase II]
ADP + phospho-[DNA-directed RNA polymerase II]
kinases Cdk9 and Lsk1 phosphorylate Ser2. Thr4 is also phosphorylated by a kinase
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-
?
ATP + [DNA-directed RNA polymerase II]
ADP + phospho-[DNA-directed RNA polymerase II]
only Rpb1, the largest subunit of RNAPII evolved a unique, highly repetitive carboxy-terminal domain, termed CTD. Dynamic phosphorylation patterns of serine residues in the CTD during gene transcription. Phosphorylation of Ser2, Ser5, Thr4, and Tyr1 in the CTD. CTD is composed of multiple tandem heptapeptides with the evolutionary conserved consensus motif Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7
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-
?
ATP + [DNA-directed RNA polymerase II]
ADP + phospho-[DNA-directed RNA polymerase II]
kinases Cdk9 and Lsk1 phosphorylate Ser2. Thr4 is also phosphorylated by a kinase
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-
?
ATP + [DNA-directed RNA polymerase II]
ADP + phospho-[DNA-directed RNA polymerase II]
the cyclin-dependent kinase subunit Mcs6 of TFIIH phosphorylates Ser5 and Ser7 of the CTD early in the transcription cycle in a Mediator-dependent manner, which leads to the dissociation of Mediator. Thr4 is also phosphorylated by a kinase
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-
?
ATP + [DNA-directed RNA polymerase]
ADP + phospho-[DNA-directed RNA polymerase]
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-
-
?
ATP + [DNA-directed RNA polymerase]
ADP + phospho-[DNA-directed RNA polymerase]
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CTD phosphorylation facilitates pre-mRNA processing, CTD phosphorylation and transcription cycle overview
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?
ATP + [DNA-directed RNA polymerase]
ADP + phospho-[DNA-directed RNA polymerase]
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the enzyme phosphorylates the C-terminal CTD domain of the RNA polymerase II large subunit, the CTD phosphorylation pattern is precisely modified as RNA polymerase II progresses along the genes and is involved in sequential recruitment of RNA processing factors, multiple phosphorylation sites and epitopes, overview
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?
additional information
?
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dynamic changes in the CTD phosphorylation pattern due to a complex interplay of various kinases and phosphatases subsequently orchestrate the binding of CTD interacting proteins, cf. CTD code
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-
?
additional information
?
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dynamic changes in the CTD phosphorylation pattern due to a complex interplay of various kinases and phosphatases subsequently orchestrate the binding of CTD interacting proteins, cf. CTD code
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-
?
additional information
?
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dynamic changes in the CTD phosphorylation pattern due to a complex interplay of various kinases and phosphatases subsequently orchestrate the binding of CTD interacting proteins, cf. CTD code
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?
additional information
?
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Ctdk-1 interacts with RNA polymerase I forming a complex
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?
additional information
?
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dynamic changes in the CTD phosphorylation pattern due to a complex interplay of various kinases and phosphatases subsequently orchestrate the binding of CTD interacting proteins, cf. CTD code
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-
?
additional information
?
-
dynamic changes in the CTD phosphorylation pattern due to a complex interplay of various kinases and phosphatases subsequently orchestrate the binding of CTD interacting proteins, cf. CTD code
-
-
?
additional information
?
-
dynamic changes in the CTD phosphorylation pattern due to a complex interplay of various kinases and phosphatases subsequently orchestrate the binding of CTD interacting proteins, cf. CTD code
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?
additional information
?
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Ctk3 shows no binding to CTD peptides
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?
additional information
?
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Ctk3 shows no binding to CTD peptides
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?
NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
ATP + [DNA-directed RNA polymerase II]
ADP + phospho-[DNA-directed RNA polymerase II]
only Rpb1, the largest subunit of RNAPII evolved a unique, highly repetitive carboxy-terminal domain, termed CTD. Dynamic phosphorylation patterns of serine residues in the CTD during gene transcription. Phosphorylation of Ser2, Ser5, Thr4, and Tyr1 in the CTD. CTD is composed of multiple tandem heptapeptides with the evolutionary conserved consensus motif Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7
-
-
?
ATP + [DNA-directed RNA polymerase II]
ADP + phospho-[DNA-directed RNA polymerase II]
only Rpb1, the largest subunit of RNAPII evolved a unique, highly repetitive carboxy-terminal domain, termed CTD. Dynamic phosphorylation patterns of serine residues in the CTD during gene transcription. Phosphorylation of Ser2, Ser5, Thr4, and Tyr1 in the CTD. CTD is composed of multiple tandem heptapeptides with the evolutionary conserved consensus motif Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7
-
-
?
ATP + [DNA-directed RNA polymerase]
ADP + phospho-[DNA-directed RNA polymerase]
-
-
-
?
ATP + [DNA-directed RNA polymerase]
ADP + phospho-[DNA-directed RNA polymerase]
-
CTD phosphorylation facilitates pre-mRNA processing, CTD phosphorylation and transcription cycle overview
-
-
?
additional information
?
-
dynamic changes in the CTD phosphorylation pattern due to a complex interplay of various kinases and phosphatases subsequently orchestrate the binding of CTD interacting proteins, cf. CTD code
-
-
?
additional information
?
-
dynamic changes in the CTD phosphorylation pattern due to a complex interplay of various kinases and phosphatases subsequently orchestrate the binding of CTD interacting proteins, cf. CTD code
-
-
?
additional information
?
-
dynamic changes in the CTD phosphorylation pattern due to a complex interplay of various kinases and phosphatases subsequently orchestrate the binding of CTD interacting proteins, cf. CTD code
-
-
?
additional information
?
-
dynamic changes in the CTD phosphorylation pattern due to a complex interplay of various kinases and phosphatases subsequently orchestrate the binding of CTD interacting proteins, cf. CTD code
-
-
?
additional information
?
-
dynamic changes in the CTD phosphorylation pattern due to a complex interplay of various kinases and phosphatases subsequently orchestrate the binding of CTD interacting proteins, cf. CTD code
-
-
?
additional information
?
-
dynamic changes in the CTD phosphorylation pattern due to a complex interplay of various kinases and phosphatases subsequently orchestrate the binding of CTD interacting proteins, cf. CTD code
-
-
?
COFACTOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Mg2+
ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY
GeneOntology No.
LITERATURE
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
malfunction
mutation of Thr4 in substrate RNAPII CTD is not lethal to fission yeast cells
physiological function
two enzymes share the job to phosphorylate Ser2: Bur1 orthologue Cdk9, which is directed to the transcription machinery by the Ser5-P dependent capping enzyme, and Lsk1, which is responsible for the majority of Ser2-P
malfunction
physiological function
additional information
malfunction
mutation of Thr4 in substrate RNAPII CTD is not lethal to fission yeast cells
malfunction
the lethality caused by the substitution of Ser5 to alanine in CTD can be circumvented by covalent tethering of mRNA capping enzymes to the CTD in fission yeast. Mutation of Thr4 in substrate RNAPII CTD is not lethal to fission yeast cells
physiological function
CTDK-I is a yeast kinase complex that phosphorylates the C-terminal repeat domain (CTD) of RNA polymerase II (Pol II) to promote transcription elongation. CTDK-I contains the cyclin-dependent kinase Ctk1 (homologous to human CDK9/CDK12), the cyclin Ctk2 (human cyclin K), and the yeast-specific subunit Ctk3, which is required for CTDK-I stability and activity
physiological function
the placement of the 7-methyl-guanosine cap on the 5' end of newly synthesized transcripts is phospho-CTD-dependent. Recruitment of the capping machinery is a main function of Ser5-P. Other protein interactions require the Ser5-P as well
physiological function
two enzymes share the job to phosphorylate Ser2: Bur1 orthologue Cdk9, which is directed to the transcription machinery by the Ser5-P dependent capping enzyme, and Lsk1,which is responsible for the majority of Ser2-P
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
additional information
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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
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
additional information
additional information
the enzyme Ctk3 consists of a N-terminal CTD-interacting domain (CID) and a C-terminal three helix bundle domain. The structure reveals eight helices arranged into a right-handed superhelical fold. Ctk3 shows no binding to CTD peptides. Structure and function of the CTDK-I complex, overview. Ctk1 (Lsk1) associates with its cyclin partner Ctk2 (Lsc1) and a third subunit, Ctk3 (Lsg1), to form the CTD kinase I (CTDK-I) complex. This trimeric structure is unique amongst CDK complexes. The Ctk3 N-terminal domain has a noncanonical surface
additional information
-
the enzyme Ctk3 consists of a N-terminal CTD-interacting domain (CID) and a C-terminal three helix bundle domain. The structure reveals eight helices arranged into a right-handed superhelical fold. Ctk3 shows no binding to CTD peptides. Structure and function of the CTDK-I complex, overview. Ctk1 (Lsk1) associates with its cyclin partner Ctk2 (Lsc1) and a third subunit, Ctk3 (Lsg1), to form the CTD kinase I (CTDK-I) complex. This trimeric structure is unique amongst CDK complexes. The Ctk3 N-terminal domain has a noncanonical surface
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
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
additional information
-
construction of ctk-disruption mutant strains displaying defects in nucleolar structure, the RNA polymerase I functions less effective in the mutant cells, the in vitro transcription is impaired
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
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 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
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
expression of HA-tagged Ctk1 and of Myc-tagged Ctk1 in strain HIS5
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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
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Palancade, B.; Bensaude, O.
Investigating RNA polymerase II carboxyl-terminal domain (CTD) phosphorylation
Eur. J. Biochem.
270
3859-3870
2003
Saccharomyces cerevisiae, Drosophila melanogaster, Homo sapiens, Schizosaccharomyces pombe
Bouchoux, C.; Hautbergue, G.; Grenetier, S.; Carles, C.; Riva, M.; Goguel, V.
CTD kinase I is involved in RNA polymerase I transcription
Nucleic Acids Res.
32
5851-5860
2004
Schizosaccharomyces pombe
Heidemann, M.; Hintermair, C.; Vo, K.; Eick, D.
Dynamic phosphorylation patterns of RNA polymerase II CTD during transcription
Biochim. Biophys. Acta
1829
55-62
2013
Schizosaccharomyces pombe (O14098), Schizosaccharomyces pombe (Q12126), Schizosaccharomyces pombe (Q96WV9), Saccharomyces cerevisiae (P06242), Saccharomyces cerevisiae (P23293), Saccharomyces cerevisiae (P39073), Saccharomyces cerevisiae (Q03957), Homo sapiens (P49336), Homo sapiens (P50613), Homo sapiens (P50750), Homo sapiens (Q9H4B4), Drosophila melanogaster (Q24216), Drosophila melanogaster (Q9VT57), Schizosaccharomyces pombe ATCC 24843 (O14098), Schizosaccharomyces pombe ATCC 24843 (Q12126), Schizosaccharomyces pombe ATCC 24843 (Q96WV9)
Muehlbacher, W.; Mayer, A.; Sun, M.; Remmert, M.; Cheung, A.C.; Niesser, J.; Soeding, J.; Cramer, P.
Structure of Ctk3, a subunit of the RNA polymerase II CTD kinase complex, reveals a noncanonical CTD-interacting domain fold
Proteins
83
1849-1858
2015
Schizosaccharomyces pombe (Q9USJ8), Schizosaccharomyces pombe
EXTERNAL LINKS (specific for EC-Number 2.7.11.23)
Transporter Classification Database (TCDB): 1.I.1.1.3
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