Eukaryotic cell cycle progression is controlled by the ordered action of cyclin-dependent kinases, activation of which occurs through the binding of the cyclin to the Cdk followed by phosphorylation of a conserved threonine in the T-loop of the Cdk by Cdk-activating kinase (CAK). Despite our understanding of the structural changes, which occur upon Cdk/cyclin formation and activation, little is known about the dynamics of the molecular events involved. We have characterized the mechanism of Cdk2/cyclin A complex formation and activation at the molecular and dynamic level by rapid kinetics and demonstrate here that it is a two-step process. The first step involves the rapid association between the PSTAIRE helix of Cdk2 and helices 3 and 5 of the cyclin to yield an intermediate complex in which the threonine in the T-loop is not accessible for phosphorylation. Additional contacts between the C-lobe of the Cdk and the N-terminal helix of the cyclin then induce the isomerization of the Cdk into a fully mature form by promoting the exposure of the T-loop for phosphorylation by CAK and the formation of the substrate binding site. This conformational change is selective for the cyclin partner.Eukaryotic cell cycle progression is governed by members of the cyclin-dependent kinase family (Cdks), 1 heterodimeric complexes consisting of a catalytic Ser/Thr protein kinase subunit, Cdk, and of a regulatory cyclin subunit. The activation of monomeric Cdk subunits involves the binding of a cyclin partner, which confers basal kinase activity to the Cdk/cyclin complex and enables subsequent phosphorylation of the Cdk on a conserved threonine in the activation loop (Thr 160 in Cdk2), thereby finally converting the complex into a fully active form (1, 2). The determination of the structure of unphosphorylated and phosphorylated Cdk2/cyclin A complexes has revealed that cyclin binding induces conformational changes within Cdk2 that are critical for its activation (3-6). The most significant feature is the reconfiguration of the ATP binding site into a conformation that favors its nucleophilic attack by the substrate and brings Glu 51 together with Lys 33 and Asp 145 for catalysis. In addition, cyclin binding induces a positional switch of the T-loop by 20 Å, which opens the catalytic cleft, affects the orientation of the putative substrate binding site of Cdk2, and leads to appropriate exposure of Thr 160 . Subsequent phosphorylation of Thr 160 by Cdk7/cyclin H (CAK) induces further conformational changes in the T-loop and in the Cterminal lobe of Cdk2 and stabilizes the substrate binding site (5, 6). More recently, the determination of the crystal structures of Cdk6/cyclin K (7), Cdk2/cyclin M (8), and Cdk2/Kap (9) suggest that interactions involving the C-lobe of Cdks play an important role in activation and regulation of the latter.Although the structural changes involved in Cdk/cyclin formation and activation have been identified, the mechanism and dynamics of the molecular events underlying this process are still poorly unders...