Figure 1. A preliminary stage in transcription. Cdk7, along with regulatory subunits cyclin H and Mat1, are integral components of TFIIH. This factor assembles into the preinitiation complex (PIC) at Pol II promoters.
CDK7 is a small protein consisting of only 346 amino acid residues. CDK7 is made up of both alpha helices and beta strands. The CDK7 has a kinase fold, consisting of two lobes: an composed mostly of beta strands and the NRTALRE helix (Ξ±C) and the composed of mostly alpha helices, where ATP binds between the lobes. CDK7 is phosphorylated on a conserved threonine, , along with the presence of ATP in the activation loop indicating an active state (Fisher et al.). Additionally, CDK7 can be phosphorylated at a second phosphorylation site in the activation segment at . Phosphorylation at this site enhances cyclin binding and protein activity. CDK7 operates in complex with cyclin H and MAT1, with cyclin H as the activator cyclin and MAT1 as a key regulatory subunit in facilitating its assembly. When cyclin H, MAT1 and ATP are present in the protein complex, CDK7 is in its active state and ready to phosphorylate other substrates.
CDK7 is phosphorylated on a conserved threonine, , along with the presence of ATP in the activation loop indicating an active state (Fisher et al.). Additionally, CDK7 can be phosphorylated at a second phosphorylation site in the activation segment at . Phosphorylation at this site enhances cyclin binding and protein activity. CDK7 operates in complex with cyclin H and MAT1, with cyclin H as the activator cyclin and MAT1 as a key regulatory subunit in facilitating its assembly. When cyclin H, MAT1 and ATP are present in the protein complex, CDK7 is in its active state and ready to phosphorylate other substrates.
CDK7's activation segment located on residues Gly163 to His171 contains the sequence for the contacts between the phosphorylated Thr170, that is necessary for the protein's phosphorylated state, and the glycine loop of Gln22. The activation segment is phosphorylated on Thr170. While phosphorylation at Ser164 is not necessary, phosphorylation at this site does enhance the proteins activity and cyclin binding. CDK7s activation loop, also known as the T-loop, has the conserved sequence helix located in the N-terminal from . Where the phosphorylated Threonine170 lives, this sequence and amino acid Thr170 is a key spot in the activation of CDK7. Two of the gamma phosphate oxygens bind to the main chains of and at the π1/π2 turn making a nicely fit association with the glycine loop. The third oxygen on the gamma phosphate of ATP binds to .
CDK7s activation loop, also known as the T-loop, has the conserved sequence helix located in the N-terminal from . Where the phosphorylated Threonine170 lives, this sequence and amino acid Thr170 is a key spot in the activation of CDK7.
Two of the gamma phosphate oxygens bind to the main chains of and at the π1/π2 turn making a nicely fit association with the glycine loop. The third oxygen on the gamma phosphate of ATP binds to .
CDK7 shares a 44% amino acid identity sequence with CDK2. Interestingly both have a t-loop in their differed conserved sequence for their activation loop: NRTALRE corresponds to PSTAIRE in CDK2, both utilizing the central threonine as their site of phosphorylation. However, there are large differences in the proteins, like the C-terminal domains. CDK7 has a proline-rich C-terminal region that makes more intimate contacts with the rest of the protein than CDK2. The C-terminal region threads between the β loop to allow for more favorable contacts and interactions than CDK2 . Another major difference is the βdeletionβ of a residue in CDK7 in the recognition site of binding kinase-associated phosphatase (KAP). In the phosphorylated CDK2 complex, Lys237 makes an ion pair with Glu191 of KAP (Figure 2B). In CDK7, the correspondent is Val247 which cannont interact with Glu191 (Figure 2C) . This suggests that KAP would not be as easily recognized to phosphorylated CDK7 as it is to recognize CDK2.
CDK7 has a proline-rich C-terminal region that makes more intimate contacts with the rest of the protein than CDK2. The C-terminal region threads between the β loop to allow for more favorable contacts and interactions than CDK2 .
Another major difference is the βdeletionβ of a residue in CDK7 in the recognition site of binding kinase-associated phosphatase (KAP). In the phosphorylated CDK2 complex, Lys237 makes an ion pair with Glu191 of KAP (Figure 2B). In CDK7, the correspondent is Val247 which cannont interact with Glu191 (Figure 2C) . This suggests that KAP would not be as easily recognized to phosphorylated CDK7 as it is to recognize CDK2.
Figure 2. (a) CDK7 in brown, CDK2 in blue. Binding to KAP. (b) Phosphorylated CDK2/KAP binding. KAP in magenta. Specifically showing the ionic interaction between LYS237 and Glu191. (c) Val 247 can not interact like Lys237 to interact favorably with Glu191, like CDK2 does.
CDK7 has been a target for cancer therapy because of its role in regulating the cell cycle and transcription by phosphorylating key substrates - like the RNA polymerase II C terminal domain. Researchers have investigated CDK7 inhibitors, like BS-181 (Bo-Yong Wang et al.) to selectively block CDK7's activity and disrupt cancer cell proliferation. The downregulation or upregulation of anti-apoptotic or proapoptotic genes may contribute to the favorability of programmed cell death (Figure 3). Inhibition of CDK7 has shown promising results in pre clinical trials where cells were induced to cell cycle arrest, apoptosis, and inhibit tumor growth (Bo-Yong Wang et al.).
Figure 3. Regulation of the super-enhancers is a common therapeutic strategy to cancer cells. The super-enhancer region in normal cells (a) becomes dysregulated in cancer cells (b), which leads to altered gene expression. CDK7 inhibitors diminish the gene expression influenced by super-enhancers in cancer cells when compared to their impact on normal cells. (CDK7i = CDK7 inhibitor).
Bo-Yong Wang, Quan-Yan Liu, Jun Cao, Ji-Wei Chen & Zhi-Su Liu. Selective CDK7 inhibition with BS-181 suppresses cell proliferation and induces cell cycle arrest and apoptosis in gastric cancer. Drug Design, Development and Therapy. 2016 Mar; 10:, 1181-1189, DOI: 10.2147/DDDT.S86317
Cao K, Shilatifard A. Inhibit globally, act locally: CDK7 inhibitors in cancer therapy. Cancer Cell. 2014 Aug 11;26(2):158-9. doi: 10.1016/j.ccr.2014.07.020. PMID: 25117707.
Fisher RP. Cdk7: a kinase at the core of transcription and in the crosshairs of cancer drug discovery. Transcription. 2019 Apr;10(2):47-56. doi: 10.1080/21541264.2018.1553483. Epub 2018 Dec 6. PMID: 30488763; PMCID: PMC6602562.
Lolli G, Lowe ED, Brown NR, Johnson LN. The crystal structure of human CDK7 and its protein recognition properties.Structure 2004 Nov;12(11):2067-79. doi: 10.1016/j.str.2004.08.013. PMID: 15530371.
Sava GP, Fan H, Coombes RC, Buluwela L, Ali S. CDK7 inhibitors as anticancer drugs. Cancer Metastasis Rev. 2020 Sep;39(3):805-823. doi: 10.1007/s10555-020-09885-8. PMID: 32385714; PMCID: PMC7497306.
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