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CDK-activating kinase (CAK) activates the cyclin-CDK complex by phosphorylating threonine residue 160 in the CDK activation loop. CAK itself is a member of the Cdk family and functions as a positive regulator of Cdk1, Cdk2, Cdk4, and Cdk6. [1]
Cdk activation requires two steps. First, cyclin must bind to the Cdk. In the second step, CAK must phosphorylate the cyclin-Cdk complex on the threonine residue 160, which is located in the Cdk activation segment. Since Cdks need to be free of Cdk inhibitor proteins (CKIs) and associated with cyclins in order to be activated, CAK activity is considered to be indirectly regulated by cyclins.[ by whom? ]
Phosphorylation is generally considered a reversible modification used to change enzyme activity in different conditions. However, activating phosphorylation of Cdk by CAK appears to be an exception to this trend. In fact, CAK activity remains high throughout the cell cycle and is not regulated by any known cell-cycle control mechanism. However compared to normal cells, CAK activity is reduced in quiescent G0 cells and slightly elevated in tumor cells. [1]
In mammals, activating phosphorylation by CAK can only occur once cyclin is bound. In budding yeast, activating phosphorylation by CAK can take place before cyclin binding. In both humans and yeast, cyclin binding is the rate limiting step in the activation of Cdk. Therefore, phosphorylation of Cdk by CAK is considered a post-translational modification that is necessary for enzyme activity. Although activating phosphorylation by CAK is not exploited for cell-cycle regulation purposes, it is a highly conserved process because CAK also regulates transcription.
CAK varies dramatically in different species. In vertebrates and Drosophila, CAK is a trimeric protein complex consisting of Cdk7 (a Cdk-related protein kinase), cyclin H, and Mat1. [2] The Cdk7 subunit is responsible for Cdk activation while the Mat1 subunit is responsible for transcription. The CAK trimer can be phosphorylated on the activation segment of Cdk7 subunit. However, unlike other Cdks, this phosphorylation is might not be essential for CAK activity. In the presence of Mat1, activation of CAK does not require phosphorylation of the activation segment. However, in the absence of Mat1, phosphorylation of the activation segment is required for CAK activity. [1]
In vertebrates, CAK localizes to the nucleus. This suggests that CAK is not only involved in cell-cycle regulation but is also involved in transcription. In fact, the Cdk7 subunit of vertebrate CAK phosphorylates several components of the transcriptional machinery.
In budding yeast, CAK is a monomeric protein kinase and is referred to as Cak1. [2] Cak1 is distantly homologous to Cdks. Cak1 localizes to the cytoplasm and is responsible for Cdk activation. Budding yeast Cdk7 homolog, Kin28, does not have CAK activity.
Fission yeasts have two CAKs with both overlapping and specialized functions. The first CAK is a complex of Msc6 and Msc2. The Msc6 and Msc2 complex is related to the vertebrate Cdk7-cyclinH complex. Msc6 and Msc2 complex not only activates cell cycle Cdks but also regulates gene expression because it is part of the transcription factor TFIIH. The second fission yeast CAK, Csk1, is an ortholog of budding yeast Cak1. Csk1 can activate Cdks but is not essential for Cdk activity. [2]
Table of Cdk-activating Kinases
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Credit to: Oxford University Press "Morgan: The Cell Cycle"
Cdkactivation
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Credit to: Oxford University Press "Morgan: The Cell Cycle"
The conformation of the Cdk2 active site changes dramatically upon cyclin binding and CAK phosphorylation. The active site of Cdk2 lies in a cleft between the two lobes of the kinase. ATP binds deep within the cleft and its phosphate is oriented outwards. Protein substrates bind to the entrance of the active site cleft.
In its inactive form, Cdk2 cannot bind substrate because the entrance of its active site is blocked by the T-loop. Inactive Cdk2 also has a misoriented ATP binding site. When Cdk2 is inactive, the small L12 helix pushes the large PSTAIRE helix outwards. The PSTAIRE helix contains a residue, glutamate 51, that is important for positioning the ATP phosphates. [2]
When cyclinA binds, several conformational changes take place. The T-loop moves out of active site entrance and no longer blocks the substrate binding site. The PSTAIRE helix moves in. The L12 helix becomes a beta strand. This allows glutamate 51 to interact with lysine 33. Aspartate 145 also changes position. Together these structural changes allow ATP phosphates to bind correctly. [2]
When CAK phosphorylates Cdk's threonine residue160, the T-loop flattens and interacts more closely with cyclin A. Phosphorylation also allows the Cdk to interact more effectively with substrates that contain the SPXK sequence. Phosphorylation also increases the activity of cyclinA-Cdk2 complex. Different cyclins produce different conformation changes in Cdk.
Image Link - Structural Basis of Cdk Activation
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Credit to: Oxford University Press "Morgan: The Cell Cycle"
In addition to activating Cdks, CAK also regulates transcription. Two forms of CAK have been identified: free CAK and TFIIH-associated CAK. Free CAK is more abundant than TFIIH-associated CAK. [1] Free CAK phosphorylates Cdks and is involved in cell cycle regulation. Associated CAK is part of the general transcription factor TFIIH. CAK associated with TFIIH phosphorylates proteins involved in transcription including RNA polymerase II. More specifically, associated CAK is involved in promoter clearance and progression of transcription from the preinitiation to the initiation stage.
In vertebrates, the trimeric CAK complex is responsible for transcription regulation. In budding yeast, the Cdk7 homolog, Kin28, regulates transcription. In fission yeast, the Msc6 Msc2 complex controls basal gene transcription. [2]
In addition to regulating transcription, CAK also enhances transcription by phosphorylating retinoic acid and estrogen receptors. Phosphorylation of these receptors leads to increased expression of target genes. In leukemic cells, where DNA is damaged, CAK’s ability to phosphorylate retinoic acid and estrogen receptors is decreased. Decreased CAK activity creates a feedback loop, which turns off TFIIH activity.
CAK also plays a role in DNA damage response. [1] The activity of CAK associated with TFIIH decreases when DNA is damaged by UV irradiation. Inhibition of CAK prevents cell cycle from progressing. This mechanism ensures the fidelity of chromosome transmission. [1]
The cell cycle, or cell-division cycle, is the sequential series of events that take place in a cell that causes it to divide into two daughter cells. These events include the growth of the cell, duplication of its DNA and some of its organelles, and subsequently the partitioning of its cytoplasm, chromosomes and other components into two daughter cells in a process called cell division.
Anaphase-promoting complex is an E3 ubiquitin ligase that marks target cell cycle proteins for degradation by the 26S proteasome. The APC/C is a large complex of 11–13 subunit proteins, including a cullin (Apc2) and RING (Apc11) subunit much like SCF. Other parts of the APC/C have unknown functions but are highly conserved.
Cyclin-dependent kinases (CDKs) are a predominant group of serine/threonine protein kinases involved in the regulation of the cell cycle and its progression, ensuring the integrity and functionality of cellular machinery. These regulatory enzymes play a crucial role in the regulation of eukaryotic cell cycle and transcription, as well as DNA repair, metabolism, and epigenetic regulation, in response to several extracellular and intracellular signals. They are present in all known eukaryotes, and their regulatory function in the cell cycle has been evolutionarily conserved. The catalytic activities of CDKs are regulated by interactions with CDK inhibitors (CKIs) and regulatory subunits known as cyclins. Cyclins have no enzymatic activity themselves, but they become active once they bind to CDKs. Without cyclin, CDK is less active than in the cyclin-CDK heterodimer complex. CDKs phosphorylate proteins on serine (S) or threonine (T) residues. The specificity of CDKs for their substrates is defined by the S/T-P-X-K/R sequence, where S/T is the phosphorylation site, P is proline, X is any amino acid, and the sequence ends with lysine (K) or arginine (R). This motif ensures CDKs accurately target and modify proteins, crucial for regulating cell cycle and other functions. Deregulation of the CDK activity is linked to various pathologies, including cancer, neurodegenerative diseases, and stroke.
A cyclin-dependent kinase complex is a protein complex formed by the association of an inactive catalytic subunit of a protein kinase, cyclin-dependent kinase (CDK), with a regulatory subunit, cyclin. Once cyclin-dependent kinases bind to cyclin, the formed complex is in an activated state. Substrate specificity of the activated complex is mainly established by the associated cyclin within the complex. Activity of CDKCs is controlled by phosphorylation of target proteins, as well as binding of inhibitory proteins.
The restriction point (R), also known as the Start or G1/S checkpoint, is a cell cycle checkpoint in the G1 phase of the animal cell cycle at which the cell becomes "committed" to the cell cycle, and after which extracellular signals are no longer required to stimulate proliferation. The defining biochemical feature of the restriction point is the activation of G1/S- and S-phase cyclin-CDK complexes, which in turn phosphorylate proteins that initiate DNA replication, centrosome duplication, and other early cell cycle events. It is one of three main cell cycle checkpoints, the other two being the G2-M DNA damage checkpoint and the spindle checkpoint.
Cell cycle checkpoints are control mechanisms in the eukaryotic cell cycle which ensure its proper progression. Each checkpoint serves as a potential termination point along the cell cycle, during which the conditions of the cell are assessed, with progression through the various phases of the cell cycle occurring only when favorable conditions are met. There are many checkpoints in the cell cycle, but the three major ones are: the G1 checkpoint, also known as the Start or restriction checkpoint or Major Checkpoint; the G2/M checkpoint; and the metaphase-to-anaphase transition, also known as the spindle checkpoint. Progression through these checkpoints is largely determined by the activation of cyclin-dependent kinases by regulatory protein subunits called cyclins, different forms of which are produced at each stage of the cell cycle to control the specific events that occur therein.
Cyclin A is a member of the cyclin family, a group of proteins that function in regulating progression through the cell cycle. The stages that a cell passes through that culminate in its division and replication are collectively known as the cell cycle Since the successful division and replication of a cell is essential for its survival, the cell cycle is tightly regulated by several components to ensure the efficient and error-free progression through the cell cycle. One such regulatory component is cyclin A which plays a role in the regulation of two different cell cycle stages.
Cyclin D is a member of the cyclin protein family that is involved in regulating cell cycle progression. The synthesis of cyclin D is initiated during G1 and drives the G1/S phase transition. Cyclin D protein is anywhere from 155 to 477 amino acids in length.
Transcription factor II H (TFIIH) is an important protein complex, having roles in transcription of various protein-coding genes and DNA nucleotide excision repair (NER) pathways. TFIIH first came to light in 1989 when general transcription factor-δ or basic transcription factor 2 was characterized as an indispensable transcription factor in vitro. This factor was also isolated from yeast and finally named TFIIH in 1992.
CDK7 is a cyclin-dependent kinase shown to be not easily classified. CDK7 is both a CDK-activating kinase (CAK) and a component of the general transcription factor TFIIH.
A cyclin-dependent kinase inhibitor protein(also known as CKIs, CDIs, or CDKIs) is a protein that inhibits the enzyme cyclin-dependent kinase (CDK) and Cyclin activity by stopping the cell cycle if there are unfavorable conditions, therefore, acting as tumor suppressors. Cell cycle progression is stopped by Cyclin-dependent kinase inhibitor protein at the G1 phase. CKIs are vital proteins within the control system that point out whether the processes of DNA synthesis, mitosis, and cytokines control one another. When a malfunction hinders the successful completion of DNA synthesis in the G1 phase, it triggers a signal that delays or halts the progression to the S phase. Cyclin-dependent kinase inhibitor proteins are essential in the regulation of the cell cycle. If cell mutations surpass the cell cycle checkpoints during cell cycle regulation, it can result in various types of cancer.
Cyclin-dependent kinase 1 also known as CDK1 or cell division cycle protein 2 homolog is a highly conserved protein that functions as a serine/threonine protein kinase, and is a key player in cell cycle regulation. It has been highly studied in the budding yeast S. cerevisiae, and the fission yeast S. pombe, where it is encoded by genes cdc28 and cdc2, respectively. With its cyclin partners, Cdk1 forms complexes that phosphorylate a variety of target substrates ; phosphorylation of these proteins leads to cell cycle progression.
Cyclin-dependent kinase 7, or cell division protein kinase 7, is an enzyme that in humans is encoded by the CDK7 gene.
CDK-activating kinase assembly factor MAT1 is an enzyme that in humans is encoded by the MNAT1 gene.
Cyclin-H is a protein that in humans is encoded by the CCNH gene.
General transcription factor IIH subunit 1 is a protein that in humans is encoded by the GTF2H1 gene.
RNA polymerase II holoenzyme is a form of eukaryotic RNA polymerase II that is recruited to the promoters of protein-coding genes in living cells. It consists of RNA polymerase II, a subset of general transcription factors, and regulatory proteins known as SRB proteins.
Pho4 is a protein with a basic helix-loop-helix (bHLH) transcription factor. It is found in S. cerevisiae and other yeasts. It functions as a transcription factor to regulate phosphate responsive genes located in yeast cells. The Pho4 protein homodimer is able to do this by binding to DNA sequences containing the bHLH binding site 5'-CACGTG-3'. This sequence is found in the promoters of genes up-regulated in response to phosphate availability such as the PHO5 gene.
In cell biology, eukaryotes possess a regulatory system that ensures that DNA replication occurs only once per cell cycle.
The Cyclin E/Cdk2 complex is a structure composed of two proteins, cyclin E and cyclin-dependent kinase 2 (Cdk2). Similar to other cyclin/Cdk complexes, the cyclin E/Cdk2 dimer plays a crucial role in regulating the cell cycle, with this specific complex peaking in activity during the G1/S transition. Once the cyclin and Cdk subunits join together, the complex gets activated, allowing it to phosphorylate and bind to downstream proteins to ultimately promote cell cycle progression. Although cyclin E can bind to other Cdk proteins, its primary binding partner is Cdk2, and the majority of cyclin E activity occurs when it exists as the cyclin E/Cdk2 complex.
