Structural basis of the cyclin Y/14-3-3 protein-mediated activation of CDK16

Cyclin-dependent protein kinase 16 (CDK16) regulates both physiological and pathological processes, including autophagy, spermatogenesis and cancer. Unlike other CDKs, CDK16 is regulated by an unclear mechanism involving phosphorylated cyclin Y (CCNY) in complex with 14-3-3 proteins rather than CCNY alone. The present study aims at elucidating this mechanism by structurally characterizing CDK16 in complex with CCNY and 14-3-3 using several biophysical techniques. As shown by cryo-EM analysis and hydrogen/deuterium exchange coupled to mass spectrometry, 14-3-3 binding modulates the conformation of a key moiety of the CDK binding surface of CCNY, thereby enabling CDK16 activation. CDK16 interacts with the cyclin box of CCNY, while 14-3-3 provides additional contacts, including with the activation segment of CDK16. CDK16 activation also requires interactions of CCNY with the N-terminal extension of CDK16. These findings not only clarify the role of CCNY and 14-3-3 in CDK16 activation but also highlight the potential of targeting CDK16 protein-protein interactions for cancer therapy.