Different Mechanisms of CDK5 and CDK2 Activation as Revealed by CDK5/p25 and CDK2/Cyclin A Dynamics

Iveta Bártová,Michal Otyepka,Zdeněk Kříž,Jaroslav Koča

doi:10.1074/jbc.m509699200

Iveta Bártová, Michal Otyepka + Show 2 more

Open Access

https://doi.org/10.1074/jbc.m509699200

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Abstract

A detailed analysis is presented of the dynamics of human CDK5 in complexes with the protein activator p25 and the purine-like inhibitor roscovitine. These and other findings related to the activation of CDK5 are critically reviewed from a molecular perspective. In addition, the results obtained on the behavior of CDK5 are compared with data on CDK2 to assess the differences and similarities between the two kinases in terms of (i) roscovitine binding, (ii) regulatory subunit association, (iii) conformational changes in the T-loop following CDK/regulatory subunit complex formation, and (iv) specificity in CDK/regulatory subunit recognition. An energy decomposition analysis, used for these purposes, revealed why the binding of p25 alone is sufficient to stabilize the extended active T-loop conformation of CDK5, whereas the equivalent conformational change in CDK2 requires both the binding of cyclin A and phosphorylation of the Thr(160) residue. The interaction energy of the CDK5 T-loop with p25 is about 26 kcal.mol(-1) greater than that of the CDK2 T-loop with cyclin A. The binding pattern between CDK5 and p25 was compared with that of CDK2/cyclin A to find specific regions involved in CDK/regulatory subunit recognition. The analyses performed revealed that the alphaNT-helix of cyclin A interacts with the alpha6-alpha7 loop and the alpha7 helix of CDK2, but these regions do not interact in the CDK5/p25 complex. Further differences between the CDK5/p25 and CDK2/cyclin A systems studied are discussed with respect to their specific functionality.

Highlights

The overall protein fold was stable throughout the simulations, except for the glycine-rich loop (G-loop), which relaxed in both the CDK5/p25 and CDK5/ p25/roscovitine complexes at an early stage of the simulations
CDK5/CDK2-Roscovitine Interactions—Roscovitine belongs to the class of very effective, selective, and therapeutically potent purine-like inhibitors of Cyclin-dependent kinases (CDKs) [25, 27, 28] and competes with ATP for occupation of the CDK active site
The mean CDK5/roscovitine and CDK2/roscovitine interaction energies are equal to Ϫ54.4 Ϯ 0.1 and Ϫ50.3 Ϯ 0.1 kcal1⁄7molϪ1, respectively

Summary

Introduction

Several CDKs (CDK1– 4 and CDK6) show a dual mechanism of activation based on the binding of the cyclin box fold (CBF) region of the regulatory subunit to the kinase and phosphorylation of the activation loop ( known as the T-loop) of the kinase [1]. This mode of activation is not observed in CDK5, despite sequence identities of almost 60% for CDK2-CDK5 pairs in different species (Scheme 1). There are some noteworthy structural and regulatory differences between the two complexes One such difference is that even in the absence of a phosphate group on Ser159, the CDK5 activation loop adopts the correct. CDKs belong to class of the CMGC group of protein kinases [4]; the complete human kinome has been published previously [36]

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Conclusion