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CDK9 cyclin dependent kinase 9 [ Homo sapiens (human) ]

Gene ID: 1025, updated on 8-Jul-2018
Official Symbol
CDK9provided by HGNC
Official Full Name
cyclin dependent kinase 9provided by HGNC
Primary source
HGNC:HGNC:1780
See related
Ensembl:ENSG00000136807 MIM:603251; Vega:OTTHUMG00000020715
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
TAK; C-2k; CTK1; CDC2L4; PITALRE
Summary
The protein encoded by this gene is a member of the cyclin-dependent protein kinase (CDK) family. CDK family members are highly similar to the gene products of S. cerevisiae cdc28, and S. pombe cdc2, and known as important cell cycle regulators. This kinase was found to be a component of the multiprotein complex TAK/P-TEFb, which is an elongation factor for RNA polymerase II-directed transcription and functions by phosphorylating the C-terminal domain of the largest subunit of RNA polymerase II. This protein forms a complex with and is regulated by its regulatory subunit cyclin T or cyclin K. HIV-1 Tat protein was found to interact with this protein and cyclin T, which suggested a possible involvement of this protein in AIDS. [provided by RefSeq, Jul 2008]
Expression
Ubiquitous expression in ovary (RPKM 32.0), spleen (RPKM 23.0) and 25 other tissues See more
Orthologs
See CDK9 in Genome Data Viewer
Location:
9q34.11
Exon count:
7
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 9 NC_000009.12 (127785538..127790782)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (130548305..130553052)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene tetratricopeptide repeat domain 16 Neighboring gene torsin family 2 member A Neighboring gene SH2 domain containing 3C Neighboring gene uncharacterized LOC107987132 Neighboring gene microRNA 3960 Neighboring gene microRNA 2861 Neighboring gene uncharacterized LOC102723566 Neighboring gene folylpolyglutamate synthase Neighboring gene endoglin

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Jun 15 11:32:44 2016

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Replication interactions

Interaction Pubs
HIV transcription is restricted by the dissociation of a functional P-TEFb complex (CCNT1-CDK9) caused by PPP1R10 (PNUTS) PubMed
HIV-1 NL4-3 replication requires CDK9 as replication is inhibited when CDK9 is deleted through CRISPR/Cas9 genome editing PubMed

Protein interactions

Protein Gene Interaction Pubs
Nef nef HIV-1 Nef induces cyclin K interaction with CDK9, which contributes to the inhibition of CDK9 nuclear translocation PubMed
nef CDK9 mRNA and kinase activity are upregulated in HIV-1 Nef-expressing human T cell lines PubMed
nef HIV-1 Nef interacts with Hsp40, leading to increased Hsp40 translocation to the nucleus of infected cells and facilitation of viral gene expression by complex formation of Hsp40 with the cdk9-associated transcription complex PubMed
Tat tat HIV-1 Tat binds to CDK9 and CCNT1 (CycT1) in an additive manner as shown through Fluoppi (fluorescent-based technology detecting protein-protein interactions) PubMed
tat The N-terminus (amino acids 1-48, including activation domain) of HIV-1 Tat binds to P-TEFb through a direct interaction with the N-terminus (amino acids 1-290) of cyclin T1 during Tat-mediated transactivation of the HIV-1 LTR promoter PubMed
tat Binding of HIV-1 Tat to CDK9 stabilizes hydrogen bonds between ATP and residues Lys48, Asp104, and Cys106 and facilitates the salt bridge network pertaining to the phosphorylated Thr186 at the activation loop PubMed
tat HIV-1 Tat competes with HEXIM1 for binding to 7SK RNA and inhibits the formation of the P-TEFb-HEXIM1-7SK complex. Tat binds to nucleotides 10-48 of 7SK RNA PubMed
tat A La-related protein, LARP7, is associated with P-TEFb, HEXIM1/2, MEPCE, and 7SK RNA in a large stable complex form. Knockdown of LARP7 decreases the steady-state level of 7SK, but increases free P-TEFb and enhances Tat-mediated transcription PubMed
tat HIV-1 Tat forms at least two distinct P-TEFb-containing complexes. Tatcom1 is composed of P-TEFb, AF9, ENL, ELL, AFF1, AFF4, and PAF1, presenting strong CTD-kinase activity, while Tatcom2 consists of 7SK, LARP7, and MEPCE with two molecules of Tat/P-TEFb PubMed
tat HIV-1 Tat recruits P-TEFb to the HIV-1 Transcription Activation Response (TAR) RNA during Tat-mediated transactivation of the HIV-1 LTR promoter PubMed
tat P-TEFb interacts with HIV-1 Tat as part of both the HIV-1 transcription preinitiation and elongation complexes PubMed
tat Cyclin-dependent kinase 9 (CDK9, CDC2-related kinase) is identified to interact with HIV-1 Tat mutant Nullbasic in HeLa cells by LC MS/MS PubMed
tat A homogeneous assay in AlphaLISA indicates that the affinity between HIV-1 Tat and pTEFb is determined to be approximately 20pM, and only 7% of purified Tat is found to be active in forming tertiary complex with pTEFb PubMed
tat AFF1 enhances the affinity of HIV-1 Tat for CycT1, which competitively dissociates HEXIM1 and is responsible for AFF1's promotion of Tat's extraction of CDK9/CycT1 from 7SK snRNP PubMed
tat HIV-1 Tat increases the amount of ELL2 bound to P-TEFb without affecting the AFF4-P-TEFb binding. CDK9 is required for the Tat-induced ELL2 accumulation and Tat interaction with ELL2 PubMed
tat The interaction of HIV-1 Tat with HIV-1 Transcription Activation Response (TAR) RNA is enhanced by the interaction of Tat with P-TEFb, and TAR RNA also enhances the interaction between Tat and cyclin T1 PubMed
tat P-TEFb is required for HIV-1 Tat-mediated transcriptional activation PubMed
tat During HIV-1 Tat mediated transactivation of the HIV-1 LTR promoter, Tat stimulates the phosphorylation of the C-terminal domain (CTD) of RNA polymerase II by P-TEFb, leading to transcription elongation PubMed
tat ZASC1, a cellular transcription factor, interacts with HIV-1 Tat and cellular proteins CDK9/Cyclin T1 (P-TEFb) in a TAR-independent manner, suggesting that the Tat/P-TEFb complex in the transcriptional elongation site is promoted by ZASC1 PubMed
tat Small molecule ligands disrupt the CDK9/Cyclin T1/Tat complex and dissociate CDK9 away from the HIV-1 transcription complex PubMed
tat The Tat-AFF4-P-TEFb complex containing HIV-1 Tat (residues 1-48), human Cyclin T1 (residues 1-266), human Cdk9 (residues 7-332), and human AFF4 (residues 27-69) is determined by the crystal structure analysis PubMed
tat HIV-1 Tat recruits PPM1G phosphatase protein to dephosphorylate the T loop of CDK9 and release P-TEFb from the 7SK snRNP complex PubMed
tat Binding of isolated AFF1(1-308) CBS to CDK9/CycT1 prevents HIV-1 Tat from activating HIV transcription and assembling complete SECs (AFF1, AFF4, ELL2, and ENL). The AFF1(1-308) M60A/L61A mutant shows no suppression of Tat transactivation PubMed
tat The interaction of HIV-1 Tat with cellular transcription factors CDK9 and Sp1 is required for Tat activation of MAP2K3-, MAP2K6-, and IRF7-mediated luciferase transcription PubMed
tat The interaction of Tip110 with HIV-1 Tat and the RNAPII C-terminal domain leads to the recruitment of increased CDK9/CycT1 to the transcription complex PubMed
tat CDK9-CycT1-AFF1 is stimulated by HIV-1 Tat and transferred as a single complex unit to BRD4 upon stress-induced disruption of AFF1-containing 7SK snRNP (HEXIM1, MEPCE, LARP7, 7SK RNA, CDK9, CycT1, and AFF1) PubMed
tat Phosphorylation of CDK9 at position Ser175 regulates the competition between HIV-1 Tat and BRD4 for P-TEFb binding PubMed
tat JQ1, a small molecule inhibitor of Brd4, increases CDK9 T-loop phosphorylation in Tat-dependent manner and partially dissociates P-TEFb from 7SK snRNP in Jurkat cells PubMed
tat Brd4 inhibits HIV-1 Tat-human super elongation complex (components AFF4, ELL2, CycT1, and CDK9) by competing with HIV-1 Tat for binding to P-TEFb on HIV-1 promoter PubMed
tat CDK2 regulates HIV-1 Tat-mediated transcription by phosphorylation of CDK9 at position Ser90 and decreases 7SK RNA levels PubMed
tat HIV-1 Tat mutations at positions Y26 and K28 show the most defect in the Tat:TAR:P-TEFb complex formation, but Tat:P-TEFb assembly is not abolished PubMed
tat HIV-1 Tat mutations at positions P3, P6, W11, K12, T20, T23, V36, I39, T40, and Y47 show decreased Tat activity and P-TEFb assembly/Cdk9 activation, with three residues P3, P6, and W11 possibly involved in Cdk9 interactions PubMed
tat Coexpression of RNA-binding domain deficient Tat (T-RS) and two fusion proteins CycT1N-Rev and Cdk9-Rev synergistically stimulates transcription when P-TEFb is tethered to RNA through Rev, and thus T-RS is no longer as an inhibitor PubMed
tat An RNA-binding domain deficient Tat excludes wild-type Tat from the promoter by preferentially assembling with P-TEFb through the Tat activation domain, but can not facilitate transfer of P-TEFb to TAR, thus blocking transition to elongation PubMed
tat HIV-1 Tat-mediated release of P-TEFb from the 7SK sn RNP results in a conformational change in 7SK RNA and release of HEXIM1 from the complex PubMed
tat TAR binds Tat and P-TEFb as it emerges on the nascent transcript, competitively displacing the inhibitory 7SK snRNP (HEXIM1 and LARP7) and activating the P-TEFb kinase PubMed
tat HIV-1 Tat stimulates the phosphorylation of SPT5 by P-TEFb during transactivation of the HIV-1 LTR promoter PubMed
tat HIV-1 Tat-mediated stimulation of RNA polymerase II C-terminal domain phosphorylation by P-TEFb leads to stimulation of co-transcriptional capping of HIV-1 mRNA PubMed
tat Inhibition of Ca(2+) signaling leads to dephosphorylation of Thr186 on CDK9, which results in the decreased transactivation of the HIV-1 LTR by HIV-1 Tat PubMed
tat ATP analogs are effective inhibitors of HIV-1 Tat-mediated activated transcription with a decreased loading of CDK9 onto the HIV-1 DNA PubMed
tat HIV-1 Q35L mutant fails to efficiently bind either CDK9 or CycT1 resulting in the defective gene expression. However, the I39Q mutation rescues the Q35L mutant's loss of function PubMed
tat SKIP is required for Tat transactivation in vivo and stimulates HIV-1 transcription elongation by associating with CycT1:CDK9 (P-TEFb) and Tat:P-TEFb complexes both in nuclear extracts and in recombinant Tat:P-TEFb:TAR RNA complexes in vitro PubMed
tat HIV-1 Tat and P-TEFb undergo constant association and dissociation cycles with TAR and the elongating polymerase in living cells PubMed
tat Tat-C/EBPbeta association is mediated through cdk9, which phosphorylates C/EBPbeta. C/EBPbeta-cyclin T1 association requires the presence of cdk9 PubMed
tat HIV-1 infection leads to activation of P-TEFb due to HIV-1 Tat-mediated release of P-TEFb from the large form PubMed
tat The P-TEFb binding region (amino acids 1209-1362) of BRD4 is required for HIV-1 Tat-mediated release of P-TEFb from the 7SK snRNP PubMed
tat CDK11 depletion reduces protein expression of CDK9 and HEXIM1 and Tat transactivation of HIV-1 provirus PubMed
tat Acetylation of HIV-1 Tat by cellular histone acetyltransferases regulates the binding of Tat to P-TEFb PubMed
tat Mutant CycT1 protein containing triple T-to-A mutations in the N-terminal region (amino acids T143, T149, and T155) associates with CDK9 and HIV-1 Tat as a kinase-negative complex and blocks HIV transactivation PubMed
tat The human I-mfa domain-containing protein (HIC) interacts with both P-TEFb and HIV-1 Tat, and modulates Tat transactivation of the HIV-1 LTR promoter PubMed
tat Cyclin T1 is capable of recruiting CDK9 and HIV-1 Tat to splicing factor-rich nuclear speckle regions, suggesting nuclear speckles are a site of P-TEFb and Tat function PubMed
tat The up and downregulation of expression of CDK9 and cyclin T1 or sequestration of cyclin T1 in infected cells may regulate HIV-1 latency by up or downregulating HIV-1 Tat transcriptional activation PubMed
tat Amino acids 260-263 of cyclin T1 are critical for HIV-1 Tat-mediated transcriptional activation, and mediate the species specificity of cyclin T1 and P-TEFb binding to Tat PubMed
tat P-TEFb regulates HIV-1 Tat-mediated activation of transcription through two built-in auto inhibitory mechanisms, autophosphorylation of CDK9 and cyclin T1 binding to the transcription elongation factor Tat-SF1 PubMed
tat Undetectable CycT1 protein and un-phosphorylation of CDK9 in undifferentiated monocytes result in the lack of Tat transactivation of the LTR promoter in early viral life cycle PubMed
tat Interaction of P-TEFb with histone H1 results in its phosphorylation at position Ser-183 in a Tat-dependent manner, which is necessary for transcription from the HIV-1 LTR PubMed
tat CDK9 is involved in Tat-induced MCP-1/CCL2 gene expression in human astrocytes PubMed
tat PARP1 negatively regulates HIV-1 transcription by directly competing with Tat-P-TEFb complex for binding to TAR RNA PubMed
tat HIV-1 Tat-induced kinase activity of P-TEFb is highly sensitive to flavopiridol, a CDK inhibitor. P-TEFb-mediated phosphorylation of RNAP II CTD, SPT5, and Tat-SF1 during HIV-1 transcription elongation is also highly sensitive to flavopiridol PubMed
tat The p160 nuclear receptor co-activator GRIP1 binds to the N-terminal region of HIV-1 Tat, bridging HIV-1 LTR promoter-bound factors to the Tat-P-TEFb complex and enhancing the transactivating activity of Tat PubMed
tat Cdk9, the catalytic subunit of P-TEFb, is ubiquitinated by Skp1/Cul1/F-box protein E3 ubiquitin ligase Skp2, which facilitates the formation of the RNA-protein complex between P-TEFb, Tat, and TAR, thereby enhancing Tat transactivation PubMed
tat The growth factor granulin and the promyelocytic leukemia (PML) protein regulate HIV-1 Tat-mediated transcriptional activation by competing with the Tat interaction with cyclin T1/P-TEFb PubMed
tat TFIIH inhibits the phosphorylation of CDK9 in the HIV-1 transcription preinitiation complex, while HIV-1 Tat stimulates CDK9 autophosphorylation to activate transcription elongation PubMed
tat Overexpression of CDK9 or CDK9 mutants inhibits HIV-1 Tat transcriptional activation PubMed
tat Tat-SF1 is a required cofactor for HIV-1 Tat activity that complexes with P-TEFb and Tat, and stimulates Tat-mediated activation of the HIV-1 LTR promoter PubMed
tat P-TEFb, Puralpha and HIV-1 Tat cooperate to activate the TNFalpha promoter PubMed
tat Hsp70 and Hsp90/Cdc37 stabilize CDK9 as well as the assembly of an active P-TEFb complex which is stimulated by HIV-1 Tat during HIV-1 transcriptional activation PubMed
tat HIV-1 Tat competes with CIITA for the binding to P-TEFb, leading to the downregulation of MHC class II gene expression PubMed
tat MAQ1 and 7SK RNA interact with P-TEFb and compete with the binding of HIV-1 Tat to cyclin T1, suggesting the TAR RNA/Tat lentivirus system evolved to subvert the cellular 7SK RNA/MAQ1 system PubMed
Vif vif HIV-1 Vif interacts with CDK9 to regulate Vif-mediated G1-to-S transition and siRNA against CDK9 counteracts the transition PubMed
Vpr vpr HIV-1 Vpr interacts with CDK9 through binding to HIV-1 Tat and cyclin T1 in a ternary complex, Tat-Vpr-Cyclin T1-CDK9, and enhances Tat transactivation of the viral LTR promoter PubMed

Go to the HIV-1, Human Interaction Database

Products Interactant Other Gene Complex Source Pubs Description

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
7SK snRNA binding IDA
Inferred from Direct Assay
more info
PubMed 
ATP binding IEA
Inferred from Electronic Annotation
more info
 
DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
RNA polymerase II carboxy-terminal domain kinase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
RNA polymerase II carboxy-terminal domain kinase activity IDA
Inferred from Direct Assay
more info
PubMed 
RNA polymerase II proximal promoter sequence-specific DNA binding IEA
Inferred from Electronic Annotation
more info
 
chromatin binding ISS
Inferred from Sequence or Structural Similarity
more info
 
cyclin binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cyclin-dependent protein serine/threonine kinase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cyclin-dependent protein serine/threonine kinase activity IDA
Inferred from Direct Assay
more info
PubMed 
kinase activity TAS
Traceable Author Statement
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein kinase activity TAS
Traceable Author Statement
more info
PubMed 
protein kinase binding IEA
Inferred from Electronic Annotation
more info
 
protein serine/threonine kinase activity TAS
Traceable Author Statement
more info
 
transcription coactivator binding IPI
Inferred from Physical Interaction
more info
PubMed 
transcription factor binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
transcription regulatory region DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Process Evidence Code Pubs
DNA repair IEA
Inferred from Electronic Annotation
more info
 
cell proliferation TAS
Traceable Author Statement
more info
PubMed 
cellular response to cytokine stimulus IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of cell cycle arrest IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of mRNA polyadenylation IMP
Inferred from Mutant Phenotype
more info
PubMed 
phosphorylation of RNA polymerase II C-terminal domain IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
positive regulation of cardiac muscle hypertrophy IEA
Inferred from Electronic Annotation
more info
 
positive regulation of histone H2B ubiquitination IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of histone phosphorylation IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of mRNA 3'-UTR binding IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
positive regulation of transcription by RNA polymerase II IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of transcription by RNA polymerase II TAS
Traceable Author Statement
more info
 
positive regulation of transcription elongation from RNA polymerase II promoter IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
positive regulation of viral transcription TAS
Traceable Author Statement
more info
 
protein phosphorylation IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
protein phosphorylation IDA
Inferred from Direct Assay
more info
PubMed 
regulation of DNA repair IDA
Inferred from Direct Assay
more info
PubMed 
regulation of histone modification IDA
Inferred from Direct Assay
more info
PubMed 
NOT regulation of mitotic cell cycle IMP
Inferred from Mutant Phenotype
more info
PubMed 
regulation of muscle cell differentiation IMP
Inferred from Mutant Phenotype
more info
PubMed 
replication fork processing IDA
Inferred from Direct Assay
more info
PubMed 
response to drug IEA
Inferred from Electronic Annotation
more info
 
snRNA transcription by RNA polymerase II TAS
Traceable Author Statement
more info
 
transcription by RNA polymerase II TAS
Traceable Author Statement
more info
 
transcription elongation from RNA polymerase II promoter IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
transcription elongation from RNA polymerase II promoter TAS
Traceable Author Statement
more info
 
transcription initiation from RNA polymerase II promoter TAS
Traceable Author Statement
more info
PubMed 
Component Evidence Code Pubs
PML body IDA
Inferred from Direct Assay
more info
PubMed 
chromosome IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cyclin-dependent protein kinase holoenzyme complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cyclin/CDK positive transcription elongation factor complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cyclin/CDK positive transcription elongation factor complex IDA
Inferred from Direct Assay
more info
PubMed 
cytoplasmic ribonucleoprotein granule IDA
Inferred from Direct Assay
more info
 
membrane HDA PubMed 
nuclear chromatin IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nucleoplasm IDA
Inferred from Direct Assay
more info
 
nucleoplasm TAS
Traceable Author Statement
more info
 
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
transcription elongation factor complex IDA
Inferred from Direct Assay
more info
PubMed 
Preferred Names
cyclin-dependent kinase 9
Names
CDC2-related kinase
cell division cycle 2-like protein kinase 4
cell division protein kinase 9
serine/threonine protein kinase PITALRE
tat-associated kinase complex catalytic subunit
NP_001252.1

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_033942.1 RefSeqGene

    Range
    5001..9748
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001261.3NP_001252.1  cyclin-dependent kinase 9

    See identical proteins and their annotated locations for NP_001252.1

    Status: REVIEWED

    Source sequence(s)
    BC001968, BE549667, BX091973, DB120461
    Consensus CDS
    CCDS6879.1
    UniProtKB/Swiss-Prot
    P50750
    UniProtKB/TrEMBL
    A0A024R880
    Related
    ENSP00000362361.4, OTTHUMP00000022198, ENST00000373264.4, OTTHUMT00000054235
    Conserved Domains (1) summary
    cd07865
    Location:6315
    STKc_CDK9; Catalytic domain of the Serine/Threonine Kinase, Cyclin-Dependent protein Kinase 9

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000009.12 Reference GRCh38.p12 Primary Assembly

    Range
    127785538..127790782
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RNA

  1. XR_002956743.1 RNA Sequence

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