Q641Z4

PR
Gene name
Cdk9
Protein name
Cyclin-dependent kinase 9
Names
Cell division protein kinase 9
Species
Rattus norvegicus (Rat)
KEGG Pathway
rno:362110
EC number
2.7.11.22: Protein-serine/threonine kinases
Protein Class

Descriptions

The autoinhibited protein was predicted that may have potential autoinhibitory elements via cis-regPred.

Autoinhibitory domains (AIDs)

293-372 (Predicted disordered autoinhibitory region) PR

Target domain

Relief mechanism

Assay

cis-regPred

Accessory elements

166-193 (Activation loop from InterPro)

Target domain

19-315 (Protein kinase domain)

Relief mechanism

Assay

References

Autoinhibited structure

Activated structure

1 structures for Q641Z4

Entry ID Method Resolution Chain Position Source
AF-Q641Z4-F1 Predicted AlphaFoldDB

No variants for Q641Z4

Variant ID(s) Position Change Description Diseaes Association Provenance
No variants for Q641Z4

No associated diseases with Q641Z4

3 regional properties for Q641Z4

Type Name Position InterPro Accession
domain Protein kinase domain 19 - 315 IPR000719
active_site Serine/threonine-protein kinase, active site 145 - 157 IPR008271
binding_site Protein kinase, ATP binding site 25 - 48 IPR017441

Functions

Description
EC Number 2.7.11.22 Protein-serine/threonine kinases
Subcellular Localization
  • Nucleus
  • Cytoplasm
  • Nucleus, PML body
  • Accumulates on chromatin in response to replication stress
  • Complexed with CCNT1 in nuclear speckles, but uncomplexed form in the cytoplasm
  • The translocation from nucleus to cytoplasm is XPO1/CRM1-dependent
  • Associates with PML body when acetylated (By similarity)
PANTHER Family
PANTHER Subfamily
PANTHER Protein Class
PANTHER Pathway Category No pathway information available

7 GO annotations of cellular component

Name Definition
cyclin/CDK positive transcription elongation factor complex A transcription elongation factor complex that facilitates the transition from abortive to productive elongation by phosphorylating the CTD domain of the large subunit of DNA-directed RNA polymerase II, holoenzyme. Contains a cyclin and a cyclin-dependent protein kinase catalytic subunit.
cytoplasmic ribonucleoprotein granule A ribonucleoprotein granule located in the cytoplasm.
mediator complex A protein complex that interacts with the carboxy-terminal domain of the largest subunit of RNA polymerase II and plays an active role in transducing the signal from a transcription factor to the transcriptional machinery. The mediator complex is required for activation of transcription of most protein-coding genes, but can also act as a transcriptional corepressor. The Saccharomyces complex contains several identifiable subcomplexes: a head domain comprising Srb2, -4, and -5, Med6, -8, and -11, and Rox3 proteins; a middle domain comprising Med1, -4, and -7, Nut1 and -2, Cse2, Rgr1, Soh1, and Srb7 proteins; a tail consisting of Gal11p, Med2p, Pgd1p, and Sin4p; and a regulatory subcomplex comprising Ssn2, -3, and -8, and Srb8 proteins. Metazoan mediator complexes have similar modular structures and include homologs of yeast Srb and Med proteins.
nucleus A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
P-TEFb complex A dimeric positive transcription elongation factor complex b that comprises a cyclin-dependent kinase containing the catalytic subunit, Cdk9, and a regulatory subunit, cyclin T.
PML body A class of nuclear body; they react against SP100 auto-antibodies (PML, promyelocytic leukemia); cells typically contain 10-30 PML bodies per nucleus; alterations in the localization of PML bodies occurs after viral infection.
transcription elongation factor complex Any protein complex that interacts with RNA polymerase II to increase (positive transcription elongation factor) or reduce (negative transcription elongation factor) the rate of transcription elongation.

13 GO annotations of molecular function

Name Definition
7SK snRNA binding Binding to a 7SK small nuclear RNA (7SK snRNA).
ATP binding Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
chromatin binding Binding to chromatin, the network of fibers of DNA, protein, and sometimes RNA, that make up the chromosomes of the eukaryotic nucleus during interphase.
cyclin-dependent protein serine/threonine kinase activity Cyclin-dependent catalysis of the reactions: ATP + protein serine = ADP + protein serine phosphate, and ATP + protein threonine = ADP + protein threonine phosphate.
DNA binding Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
protein kinase binding Binding to a protein kinase, any enzyme that catalyzes the transfer of a phosphate group, usually from ATP, to a protein substrate.
protein serine kinase activity Catalysis of the reactions: ATP + protein serine = ADP + protein serine phosphate.
protein serine/threonine kinase activity Catalysis of the reactions: ATP + protein serine = ADP + protein serine phosphate, and ATP + protein threonine = ADP + protein threonine phosphate.
RNA polymerase II cis-regulatory region sequence-specific DNA binding Binding to a specific upstream regulatory DNA sequence (transcription factor recognition sequence or binding site) located in cis relative to the transcription start site (i.e., on the same strand of DNA) of a gene transcribed by RNA polymerase II.
RNA polymerase II CTD heptapeptide repeat kinase activity Catalysis of the reaction: ATP + RNA polymerase II large subunit CTD heptapeptide repeat (YSPTSPS) = ADP + H+ + phosphorylated RNA polymerase II.
snRNA binding Binding to a small nuclear RNA (snRNA).
transcription cis-regulatory region binding Binding to a specific sequence of DNA that is part of a regulatory region that controls transcription of that section of the DNA. The transcribed region might be described as a gene, cistron, or operon.
transcription coactivator binding Binding to a transcription coactivator, a protein involved in positive regulation of transcription via protein-protein interactions with transcription factors and other proteins that positively regulate transcription. Transcription coactivators do not bind DNA directly, but rather mediate protein-protein interactions between activating transcription factors and the basal transcription machinery.

22 GO annotations of biological process

Name Definition
cellular response to cytokine stimulus Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a cytokine stimulus.
DNA repair The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.
negative regulation of mRNA polyadenylation Any process that stops, prevents or reduces the frequency, rate or extent of mRNA polyadenylation.
phosphorylation of RNA polymerase II C-terminal domain The process of introducing a phosphate group on to an amino acid residue in the C-terminal domain of RNA polymerase II. Typically, this occurs during the transcription cycle and results in production of an RNA polymerase II enzyme where the carboxy-terminal domain (CTD) of the largest subunit is extensively phosphorylated, often referred to as hyperphosphorylated or the II(0) form. Specific types of phosphorylation within the CTD are usually associated with specific regions of genes, though there are exceptions. The phosphorylation state regulates the association of specific complexes such as the capping enzyme or 3'-RNA processing machinery to the elongating RNA polymerase complex.
phosphorylation of RNA polymerase II C-terminal domain serine 2 residues involved in positive regulation of transcription elongation from RNA polymerase II promoter Any phosphorylation of RNA polymerase II C-terminal domain serine 2 residues that is involved in positive regulation of transcription elongation from RNA polymerase II promoter.
phosphorylation of RNA polymerase II C-terminal domain serine 5 residues involved in positive regulation of transcription elongation from RNA polymerase II promoter Any phosphorylation of RNA polymerase II C-terminal domain serine 5 residues that is involved in positive regulation of transcription elongation from RNA polymerase II promoter.
positive regulation by host of viral transcription Any process in which a host organism activates or increases the frequency, rate or extent of viral transcription, the synthesis of either RNA on a template of DNA or DNA on a template of RNA.
positive regulation of cardiac muscle hypertrophy Any process that increases the rate, frequency or extent of the enlargement or overgrowth of all or part of the heart due to an increase in size (not length) of individual cardiac muscle fibers, without cell division.
positive regulation of histone H2B ubiquitination Any process that activates or increases the frequency, rate or extent of histone H2B ubiquitination.
positive regulation of mRNA 3'-UTR binding Any process that activates or increases the frequency, rate or extent of mRNA 3'-UTR binding.
positive regulation of protein localization to chromatin Any process that activates or increases the frequency, rate or extent of protein localization to chromatin.
positive regulation of transcription by RNA polymerase II Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
positive regulation of transcription elongation by RNA polymerase II Any process that activates or increases the frequency, rate or extent of transcription elongation, the extension of an RNA molecule after transcription initiation and promoter clearance by the addition of ribonucleotides, catalyzed by RNA polymerase II.
protein phosphorylation The process of introducing a phosphate group on to a protein.
regulation of cell cycle Any process that modulates the rate or extent of progression through the cell cycle.
regulation of DNA repair Any process that modulates the frequency, rate or extent of DNA repair.
regulation of histone modification Any process that modulates the frequency, rate or extent of the covalent alteration of a histone.
regulation of mRNA 3'-end processing Any process that modulates the frequency, rate or extent of mRNA 3'-end processing, any process involved in forming the mature 3' end of an mRNA molecule.
regulation of muscle cell differentiation Any process that modulates the frequency, rate or extent of muscle cell differentiation.
replication fork processing The process in which a DNA replication fork that has stalled is restored to a functional state and replication is restarted. The stalling may be due to DNA damage, DNA secondary structure, bound proteins, dNTP shortage, or other causes.
response to xenobiotic stimulus Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus from a xenobiotic, a compound foreign to the organim exposed to it. It may be synthesized by another organism (like ampicilin) or it can be a synthetic chemical.
transcription by RNA polymerase II The synthesis of RNA from a DNA template by RNA polymerase II (RNAP II), originating at an RNA polymerase II promoter. Includes transcription of messenger RNA (mRNA) and certain small nuclear RNAs (snRNAs).

13 homologous proteins in AiPD

UniProt AC Gene Name Protein Name Species Evidence Code
Q5EAB2 CDK9 Cyclin-dependent kinase 9 Bos taurus (Bovine) PR
Q5ZKN1 CDK9 Cyclin-dependent kinase 9 Gallus gallus (Chicken) PR
P50750 CDK9 Cyclin-dependent kinase 9 Homo sapiens (Human) PR
Q99J95 Cdk9 Cyclin-dependent kinase 9 Mus musculus (Mouse) PR
Q4KM47 Cdk10 Cyclin-dependent kinase 10 Rattus norvegicus (Rat) PR
Q66HE7 Cdkl1 Cyclin-dependent kinase-like 1 Rattus norvegicus (Rat) PR
Q5XIT0 Cdkl2 Cyclin-dependent kinase-like 2 Rattus norvegicus (Rat) PR
Q4KM34 Cdk20 Cyclin-dependent kinase 20 Rattus norvegicus (Rat) PR
O35831 Cdk17 Cyclin-dependent kinase 17 Rattus norvegicus (Rat) PR
Q9JM01 Cdkl3 Cyclin-dependent kinase-like 3 Rattus norvegicus (Rat) PR
F4I114 At1g09600 Probable serine/threonine-protein kinase At1g09600 Arabidopsis thaliana (Mouse-ear cress) PR
Q9ZVM9 At1g54610 Probable serine/threonine-protein kinase At1g54610 Arabidopsis thaliana (Mouse-ear cress) PR
Q6GLD8 cdk9 Cyclin-dependent kinase 9 Xenopus tropicalis (Western clawed frog) (Silurana tropicalis) PR
10 20 30 40 50 60
MAKQYDSVEC PFCDEVTKYE KLAKIGQGTF GEVFKAKHRQ TGQKVALKKV LMENEKEGFP
70 80 90 100 110 120
ITALREIKIL QLLKHENVVN LIEICRTKAS PYNRCKGSIY LVFDFCEHDL AGLLSNVLVK
130 140 150 160 170 180
FTLSEIKRVM QMLLNGLYYI HRNKILHRDM KAANVLITRD GVLKLADFGL ARAFSLAKNS
190 200 210 220 230 240
QPNRYTNRVV TLWYRPPELL LGERDYGPPI DLWGAGCIMA EMWTRSPIMQ GNTEQHQLAL
250 260 270 280 290 300
ISQLCGSITP EVWPNVDKYE LFEKLELVKG QKRKVKDRLK AYVRDPYALD LIDKLLVLDP
310 320 330 340 350 360
AQRIDSDDAL NHDFFWSDPM PSDLKGMLST HLTSMFEYLA PPRRKGSQIT QQSTNQSRNP
370
ATTNQTEFER VF