Cyclin-dependent kinase 7, or cell division protein kinase 7, is an enzyme that in humans is encoded by the CDK7 gene.
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 Saccharomyces cerevisiae cdc28, and Schizosaccharomyces pombe cdc2, and are known to be important regulators of cell cycle progression.
This protein forms a trimeric complex with cyclin H and MAT1, which functions as a CDK-activating kinase (CAK). It is an essential component of Transcription factor II H, which is involved in transcription initiation and DNA repair. This protein is thought to serve as a direct link between the regulation of transcription and the cell cycle.
Background An intricate network of cyclin-dependent kinases (CDKs) is organized in a pathway to ensure that each cell accurately replicates its DNA and segregates it equally between the two daughter cells.Morgan DO. (2007). The Cell Cycle: Principles of Control. New Science Press Ltd: London, UK One CDKthe CDK7 complexcannot be so easily classified. CDK7 is both a CDK-activating kinase (CAK), which phosphorylates cell-cycle CDKs within the activation segment (T-loop), and a component of the general Transcription factor II H, which phosphorylates the C-terminal domain (CTD) of the largest subunit of Pol II.Harper, J. W., Elledge, S. J., Keyomarski, K., Dynlacht, B., Tsai, L.-H., Zhang, P., Dobrowolski, S., Bai, C., Connell-Crowley, L., Swindell, E. et al. (1995). Inhibition of cyclin-dependent kinases by p21. Mol. Biol. Cell 6, 387-400 A proposed mode of CDK7 inhibition is the phosphorylation of cyclin H by CDK7 itselfLolli, G., Lowe, E. D., Brown, N. R. and Johnson, L. N. (2004). The crystal structure of human CDK7 and its protein recognition properties. Structure 12, 2067-2079 or by another kinase.Akoulitchev, S. and Reinberg, D. (1998). The molecular mechanism of mitotic inhibition of TFIIH is mediated by phosphorylation of CDK7. Genes Dev. 12, 3541-3550
CDK7 has been observed as a prerequisite to S phase entry and mitosis. CDK7 is activated by the binding of cyclin H and its substrate specificity is altered by the binding of MAT1.Patel, Shetal A., and M. Celeste Simon. "Functional analysis of the CDK7· cyclin H· Mat1 complex in mouse embryonic stem cells and embryos." Journal of Biological Chemistry 285.20 (2010): 15587-15598. The free form of the complex formed, CDK7-cycH-MAT1, operates as CDK-activating kinase (CAK). In vivo, CDK7 forms a stable complex with cyclin H and MAT1 only when its T-loop is phosphorylated on either Ser164 or Thr170 residues.Larochelle, S et al. “T-loop phosphorylation stabilizes the CDK7-cyclin H-MAT1 complex in vivo and regulates its CTD kinase activity.” The EMBO Journal vol. 20,14 (2001): 3749-59. doi:10.1093/emboj/20.14.3749
The T-loop To be active, most CDKs require not only a cyclin partner but also phosphorylation at one particular site, which corresponds to Thr161 in human CDK1, and which is located within the so-called T-loop (or activation loop) of kinase subdomain VIII.Morgan DO: Principles of CDK regulation. Nature 1995, 374:131-134Solomon MJ: The function(s) of CAK, the p34cdc2 activating kinase. Trends Biochem Sci 1994,19:496-500 CDKl, CDK2 and CDK4 all require T-loop phosphorylation for maximum activity.Connell-Cowley L, Solomon MJ, Wei N, Harper JW: Phosphorylation independent activation of human cyclindependent kinase 2 by cyclin A in vitro. Mol Biol Cell 1993, 4:79-92Matsuoka M, Kate JY, Fisher RP, Mor of cyclin-dependent kinase 4 (cdk4 by B mouse M015-an associated klnase. Mol Cell Biol 1994, 14:7265-7275.
The free form of CDK7-cycH-MAT1 phosphorylates the T-loops of CDK1, CDK2, CDK4 and CDK6.Fisher, Robert P. "Secrets of a double agent: CDK7 in cell-cycle control and transcription." Journal of cell science 118.22 (2005): 5171-5180. For all CDK substrates of CDK7, phosphorylation by CDK7 occurs following the binding of the substrate kinase to its associated cyclin.Lolli, Graziano, and Louise N. Johnson. "CAK—cyclin-dependent activating kinase: a key kinase in cell cycle control and a target for drugs?" Cell cycle 4.4 (2005): 565-570. This two-step process has been observed in CDK2, where the association of CDK2 with cyclin A results in a conformational change that primes the catalytic site for binding of its ATP substrate and phosphorylation by CDK7 of Thr160 in its activation segment improves the substrate protein's ability to bind. It has been further observed that CDK1 is not phosphorylated by CDK7 in its monomeric form and that monomeric CDK2 and CDK6 are poorly phosphorylated by CDK7, since the activation segment threonine is inaccessible to CDK7 in monomeric CDKs.
While CDK7 is indeed responsible for the phosphorylation of CDK1, CDK2, CDK4 and CDK6 in vivo, it has been observed that they have varying levels of dependence on CDK7. CDK1 and CDK2 require phosphorylation by CDK7 in order to reach their active states, while CDK4 and CDK6 have been found to require consistent CDK7 activity in order to maintain their phosphorylation states. This discrepancy is likely because the phosphorylated T-loops on CDK2 and CDK1 are protected when they are bound to cyclin while the phosphorylated T-loops on CDK4 and CDK6 remain exposed and therefore are vulnerable to phosphatases. It is therefore proposed that phosphatases work to counter the phosphorylation of CDK4 and CDK6 by CDK7, creating a competition between CDK7 and phosphatases.Schachter, Miriam Merzel, et al. "A Cdk7-Cdk4 T-loop phosphorylation cascade promotes G1 progression." Molecular cell 50.2 (2013): 250-260.
Dual activity An entirely new perspective on CDK7 function was opened when CDK7 was identified as a subunit of Transcription factor II H (TFIIH) and shown to phosphorylate the carboxy-terminal domain (CTD) of RNA polymerase II (RNAPII).Roy R, Adamczewski JP, Seroz T, Vermeulen W, Tassan JP, Schaeffer L, Nigg EA, Hoejimakers JHJ, Egly JM: The MO15 cell cycle kinase is associated with the TFIIH transcription-DNA repair factor. Cell 1994, 79:1093-1101 TFIIH is a multiprotein complex required not only for class II transcription but also for nucleotide-excision repair.Seroz T, Hwang JR, Moncollin V, Egly JM: TFIIH: a link between transcription, DNA repair and cell cycle regulation. Gun Opin Gener Dev 1995, 5:217-221 Its associated CTD-kinase activity is considered important for the promoter-clearance step of transcription, but the precise structural consequences of the phosphorylation of the CTD remain the subject of debate.Dahmus ME: The role of multisite phosphorylatlon in the regulation of RNA polymerase II activity. Prog Nucleic Acid Res Mol Biol 1994, 48: 143-179 Cyclin H and MAT1 are also present in TFIIH,Shiekhattar R, Mermelstein F, Fisher R, Drapkin R, Dynlacht B, Wessling HC, Morgan DO, Reinberg D: Cdk-activating kinase complex is a component of human transcription factor TFIIH. Nature 1995, 374:203-287 and it is not known what, if anything, distinguishes the TFIIH-associated form of CDK7 from the quantitatively predominant free form. Whether CDK7 really displays dual-substrate specificity remains to be further explored, but there is no question that the CDK7-cyclin H-MAT1 complex is able to phosphorylate both the T-loop of CDKs and the YSPTSPS (single-letter code for amino acids) repeats of the RNAPII CTD in vitro.
CDK7-cycH-MAT1 binds to TFIIH, which alters the substrate preference of CDK7. CDK7-cycH-MAT1 then preferentially phosphorylates the large subunit C-terminal domain of polymerase II instead of CDK2 when compared to the free-form complex.Yankulov, Krassimir Y., and David L. Bentley. "Regulation of CDK7 substrate specificity by MAT1 and TFIIH." The EMBO Journal 16.7 (1997): 1638-1646. In addition, phosphorylation of the Thr170 residue on the T-loop of CDK7 has been found to greatly increase activity of the CDK7– cyclin H–MAT1 complex in favor of CTD phosphorylation. Phosphorylation of Thr170, then, is a proposed mechanism for regulating CTD phosphorylation when CDK7 is associated with TFIIH.
The role of CDK7 in transcription was confirmed in vivo in Caenorhabditis elegans embryos. Mutants with cdk-7(ax224) were both unable to synthesize most mRNAs and had greatly reduced CTD phosphorylation as well, indicating that CDK7 is required for both transcription and CTD phosphorylation.Wallenfang, Matthew R., and Geraldine Seydoux. "cdk-7 is required for mRNA transcription and cell cycle progression in Caenorhabditis elegans embryos." Proceedings of the National Academy of Sciences 99.8 (2002): 5527-5532. In addition, similar results have been found in human cells. An "analog sensitive" CDK7 mutant (CDK7as) was devised which operates normally but is inhibited by an ATP analog competitive inhibitor. Inhibition of CDK7as was correlated with a reduction in CTD phosphorylation, where high inhibition led to very little instances of phosphorylated CTD-Ser5 (the phosphorylation target of CDK7 on CTD).Ebmeier, Christopher C., et al. "Human TFIIH kinase CDK7 regulates transcription-associated chromatin modifications." Cell reports 20.5 (2017): 1173-1186.
Stem Cells The CDK7-cycH-MAT1 complex has been found to play a role in the differentiation of embryonic stem cells. It has been observed that the depletion of Cyclin H leads to differentiation of embryonic stem cells. In addition, Spt5, which leads to the differentiation of stem cells upon down-regulation, is a phosphorylation target of CDK7 in vitro, suggesting a possible mechanism by which Cyclin H depletion leads to differentiation.
Clinical significance Cancer Given that CDK7 is involved in two important regulation roles, it's expected that CDK7 regulation may play a role in cancerous cells. Cells from breast cancer tumors were found to have elevated levels of CDK7 and Cyclin H when compared to normal breast cells. It was also found that the higher levels were generally found in ER-positive breast cancer. Together, these findings indicate that CDK7 therapy might make sense for some breast cancer patients. Further confirming these findings, recent research indicates that inhibition of CDK7 may be an effective therapy for HER2-positive breast cancers, even overcoming therapeutic resistance. THZ1 was tested on HER2-positive breast cancer cells and exhibited high potency for the cells regardless of their sensitivity to HER2 inhibitors. This finding was demonstrated in vivo, where inhibition of HER2 and CDK7 resulted in tumor regression in therapeutically resistant HER2+ xenograft models.
Inhibition of HER2 and CDK7 resulted in tumor regression in therapeutically resistant HER2+ xenograft models.Sun, Bowen, et al. "Inhibition of the transcriptional kinase CDK7 overcomes therapeutic resistance in HER2-positive breast cancers." Oncogene (2019): 1-14.
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