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Structural basis for inhibition of the cyclin-dependent kinase Cdk6 by the tumour suppressor p16INK4a

Abstract

The cyclin-dependent kinases 4 and 6 (Cdk4/6) that control the G1 phase of the cell cycle and their inhibitor, the p16INK4a tumour suppressor, have a central role in cell proliferation and in tumorigenesis. The structures of Cdk6 bound to p16INK4a and to the related p19INK4d reveal that the INK4 inhibitors bind next to the ATP-binding site of the catalytic cleft, opposite where the activating cyclin subunit binds. They prevent cyclin binding indirectly by causing structural changes that propagate to the cyclin-binding site. The INK4 inhibitors also distort the kinase catalytic cleft and interfere with ATP binding, which explains how they can inhibit the preassembled Cdk4/6–cyclin D complexes as well. Tumour-derived mutations in INK4a and Cdk4 map to interface contacts, solidifying the role of CDK binding and inhibition in the tumour suppressor activity of p16INK4a.

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Figure 1: The INK4 inhibitors bind to one side of the catalytic cleft of Cdk6, and interact with both the N and C lobes.
Figure 2: p16 and p19 use conserved regions to make overall conserved contacts with Cdk6.
Figure 3: Conserved hydrogen-bond networks by the second and third ankyrin repeats of p16 and p19 have a central role in Cdk6 binding.
Figure 4: p16 locks the N and C lobes in a relative orientation not amenable to cyclin binding and activation.
Figure 5: p16 alters the ATP-binding site of Cdk6 and interferes with ATP binding.
Figure 6: The T loop has large displacements from the active conformation compared to Cdk2 structures.

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Acknowledgements

We thank S. Geromanos and H. Erdjument-Bromage of the Sloan-Kettering Microchemistry Facility for N-terminal sequence and mass spectroscopic analyses; H. Chou and E. D. Harlow for baculovirus vectors expressing Cdk6, GST–Cdk6 and cyclin D1; R. Marmorstein for the crystallographic coordinates of p18; C. Ogata of the National Synchrotron Light Source X4A beam line and the staff of the Cornell High Energy Synchrotron Source MacChess for help with data collection; and C. Murray for administrative help. Supported by the Howard Hughes Medical Institute, the NIH, the Pew Charitable Trusts, the Dewitt Wallace Foundation, and the Samuel and May Rudin Foundation.

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Correspondence to Nikola P. Pavletich.

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Russo, A., Tong, L., Lee, JO. et al. Structural basis for inhibition of the cyclin-dependent kinase Cdk6 by the tumour suppressor p16INK4a. Nature 395, 237–243 (1998). https://doi.org/10.1038/26155

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