The structural basis of CDK recognition and activation by the CDK-activating kinase
Cyclin-dependent kinases (CDKs) are the prototypical regulators of the cell cycle. Due to the importance of accurate control of the cell cycle, the activity of CDKs is subject to intricate regulation by cyclin binding, post-translational modifications, and other mechanisms. One of the pivotal regulatory events during CDK activation is the phosphorylation of the regulatory T-loop of the CDK by the CDK-activating kinase.
Despite the critical importance of this step, the mechanisms by which the CDK-activating kinase recognises and activates its CDK-type substrates remained poorly understood. We therefore set out to study this process by determining structures of the CDK-activating kinase bound to its substrates. Our mechanistic insights into this process have been published recently in Science.
Despite the critical importance of this step, the mechanisms by which the CDK-activating kinase recognises and activates its CDK-type substrates remained poorly understood. We therefore set out to study this process by determining structures of the CDK-activating kinase bound to its substrates. Our mechanistic insights into this process have been published recently in Science.
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(A-D) Cryo-EM maps and atomic models of CAK-CDK2-cyclin A and CAK-CDK2 complexes.
(E) CDK7 and its substrate, CDK2, form a pseudo-symmetric assembly. (F) Cryo-EM structure of CAK-CDK1-cyclin B. (G) Cryo-EM structure CAK-CDK11. Cushing VI, McGeoch AJS, Williams SL, Roumeliotis TI, Feng J, Dan LM, Choudhary JS, Davey NE, Greber BJ (2025). Structural basis of T-loop-independent recognition and activation of CDKs by the CDK-activating kinase. Science, adw0053, epub 16 October 2025. Link |
We found that CAK binds to one of its substrates, CDK2, by formation of interactions of the N- and C-terminal lobes of both CDK7 and CDK2. This leads to the formation of a pseudo-symmetric kinase-kinase dimer. It is worth noting that the T-loop, which is the segment that receives the phosphorylation, does not participate in these interactions. This explains why the sequence of the T-loop itself was found not to play a role in substrate specificity in this system in earlier studies.
Based on AlphaFold3 structure predictions of complexes between CAK and all its currently known CDK-type substrates as well as cryo-EM structures of CAK-CDK1-cyclin B and CAK-CDK11, we propose that this overall architecture applies generally to CAK-CDK complexes, hinting at a generalised mechanism of substrate recognition by the CAK. However, additional substrate-specific variations of this common theme are likely to exist, given that, for example, the order of cyclin binding and T-loop phosphorylation differs between CDK1 and CDK2. The mechanistic basis of these CDK-specific unique features during CDK activation will be the subject of future studies.
Based on AlphaFold3 structure predictions of complexes between CAK and all its currently known CDK-type substrates as well as cryo-EM structures of CAK-CDK1-cyclin B and CAK-CDK11, we propose that this overall architecture applies generally to CAK-CDK complexes, hinting at a generalised mechanism of substrate recognition by the CAK. However, additional substrate-specific variations of this common theme are likely to exist, given that, for example, the order of cyclin binding and T-loop phosphorylation differs between CDK1 and CDK2. The mechanistic basis of these CDK-specific unique features during CDK activation will be the subject of future studies.
