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Structure of the cyclin-dependent kinase inhibitor p19Ink4d

Abstract

In cancer, the biochemical pathways that are dominated by the two tumour-suppressor proteins, p53 and Rb, are the most frequently disrupted. Cyclin D-dependent kinases phosphorylate Rb to control its activity and they are, in turn, specifically inhibited by the Ink4 family of cyclin-dependent kinase inhibitors (CDKIs) which cause arrest at the G1 phase of the cell cycle. Mutations in Rb, cyclin D1, its catalytic subunit Cdk4, and the CDKI p16Ink4a, which alter the protein or its level of expression, are all strongly implicated in cancer. This suggests that the Rb ‘pathway’ is of particular importance1. Here we report the structure of the p19Ink4d protein, determined by NMR spectroscopy2,3,4. The structure indicates that most mutations to the p16Ink4a gene, which result in loss of function, are due to incorrectly folded and/or insoluble protein5. We propose a model for the interaction of Ink4 proteins with D-type cyclin-Cdk4/6 complexes that might provide a basis for the design of therapeutics against cancer.

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Figure 1: Amino-acid sequence of the mouse p19Ink4d protein showing the homology between different ankyrin repeats (defined as i.
Figure 2: a, Stereoviews of the backbone (N, Cα and C′) of residues 8–163 from the 20 lowest-energy structures of p19Ink4d (out of 33 that converged from the 54 computed).
Figure 3: a, Comparison of the structure of p19Ink4d closest to the mean with that of 53BP2.

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References

  1. Sherr, C. J. Cancer cell cycles. Science 274, 1672–1677 (1996).

    Article  ADS  CAS  Google Scholar 

  2. Chan, F. K. M., Zhang, J., Cheng, L., Shapiro, D. N. & Winoto, D. A. Identification of human and mouse p19, a novel CDK4 and CDK6 inhibitor with homology to p16INK4. Mol. Cell. Biol. 15, 2682–2688 (1995).

    Article  CAS  Google Scholar 

  3. Guan, K. et al. Isolation and characterization of p19INK4d, a p16 related inhibitor specific to CDK6 and CDK4. Mol. Biol. Cell 7, 57–70 (1996).

    Article  CAS  Google Scholar 

  4. Hirai, H., Roussel, M. F., Kato, H.-Y., Ashmun, R. A. & Sherr, C. J. Novel INK4 proteins, p19 and p18, are specific inhibitors of the cyclin D-dependent kinases CDK4 and CDK6. Mol. Cell. Biol. 15, 2672–2681 (1995).

    Article  CAS  Google Scholar 

  5. Zhang, B. & Peng, Z.-y. Defective folding of mutant p16INK4a proteins encoded by tumor-derived alleles. J. Biol. Chem. 271, 28734–28737 (1996).

    Article  CAS  Google Scholar 

  6. Serrano, M., Hannon, G. J. & Beach, D. Anew regulatory motif in cell-cycle control causing specific inhibition of cyclin D/Cdk4. Nature 366, 704–707 (1993).

    Article  ADS  CAS  Google Scholar 

  7. Bork, P. Hundreds of ankyrin-like repeats in functionally diverse proteins: mobile modules that cross phyla horizontally. Prot. Struct. Funct. Genet. 17, 363–374 (1993).

    Article  CAS  Google Scholar 

  8. Hannon, G. J. & Beach, D. p15INK4B is a potential effector of TGF-β-induced cell-cycle arrest. Nature 371, 257–261 (1994).

    Article  ADS  CAS  Google Scholar 

  9. Foulkes, W. D., Flanders, T. Y., Pollock, P. M. & Hayward, N. K. The CDKN2A (p16) gene and human cancer. Mol. Med. 3, 5–20 (1997).

    Article  CAS  Google Scholar 

  10. Serrano, M. et al. Role of the INK4a locus in tumor suppression and cell mortality. Cell 85, 27–37 (1996).

    Article  CAS  Google Scholar 

  11. Merlo, A. et al. 5′ CPG island methylation is associated with transcriptional silencing of the tumor-suppressor p16CDKN2/MTS1 in human cancers. Nature Med. 1, 686–692 (1995).

    Article  CAS  Google Scholar 

  12. Yasukawa, T. et al. Increase of solubility of foreign proteins in Escherichia coli by co-production of the bacterial thioredoxin. J. Biol. Chem. 270, 25328–25331 (1995).

    Article  CAS  Google Scholar 

  13. Wick, S. T., Dubay, M. M., Imanil, I. & Brizuela, L. Biochemical and mutagenic analysis of the melanoma tumor-suppressor gene-product p16. Oncogene 11, 2013–2019 (1995).

    PubMed  Google Scholar 

  14. Wölfel, T. et al. Ap16INK4A-insensitive CDK4 mutant targeted by cytolytic T-lymphocytes in a human melanoma. Science 269, 1281–1284 (1995).

    Article  ADS  Google Scholar 

  15. Kalus, W. et al. NMR structural characterization of the CDK inhibitor p19INK4d. FEBS Lett. 401, 127–132 (1997).

    Article  CAS  Google Scholar 

  16. Gorina, S. & Pavletich, N. P. Structure of the p53 tumor suppressor bound to the ankyrin and SH3 domains of 53BP2. Science 274, 1001–1005 (1996).

    Article  ADS  CAS  Google Scholar 

  17. Tevelev, A. et al. Tumor suppressor p16INK4A: Structural characterization of wild-type and mutant proteins by NMR and circular dichroism. Biochemistry 35, 9475–9487 (1996).

    Article  CAS  Google Scholar 

  18. Yang, R., Gombart, A. F., Serrano, M. & Koeffler, H. P. Mutational effects on the p16INK4a tumor suppressor protein. Cancer Res. 55, 2503–2506 (1995).

    CAS  PubMed  Google Scholar 

  19. Ranade, K. et al. Mutations associated with familial melanoma impair p16INK4 function. Nature Genet. 10, 114–116 (1995).

    Article  CAS  Google Scholar 

  20. Koh, J., Enders, G. H., Dynlacht, B. D. & Harlow, E. Tumour-derived p16 alleles encoding proteins defective in cell-cycle inhibition. Nature 375, 506–510 (1995).

    Article  ADS  CAS  Google Scholar 

  21. Parry, D. & Peters, G. Temperature-sensitive mutants of p16CDKN2 associated with familial melanoma. Mol. Cell. Biol. 16, 3844–3852 (1996).

    Article  CAS  Google Scholar 

  22. Fåhraeus, R., Paramio, J. M., Ball, K. L., Lain, S. & Lane, D. P. Inhibition of pRB phosphorylation and cell-cycle progression by a 20-residue peptide derived from p16CDKN2/INK4A. Curr. Biol. 6, 84–91 (1996).

    Article  Google Scholar 

  23. Smith, B. O. et al. An approach to global fold determination using limited NMR data from larger proteins selectively protonated at specific residue types. J. Biomol. NMR 8, 360–368 (1996).

    Article  CAS  Google Scholar 

  24. Clowes, R. T., Crawford, A., Raine, A. R. C., Smith, B. O. & Laue, E. D. Structural studies of proteins using NMR spectroscopy. Curr. Opin. Biotechnol. 6, 81–88 (1995).

    Article  CAS  Google Scholar 

  25. Brünger, A. T. X-PLOR, Version 3.1: A System for X-ray Crystallography and NMR (Yale Univ. Press, New Haven and London, (1992)).

    Google Scholar 

  26. Clore, G. M. & Gronenborn, A. M. Structures of larger proteins in solution—3-dimensional and 4-dimensional heteronuclear NMR spectroscopy. Science 252, 1390–1399 (1991).

    Article  ADS  CAS  Google Scholar 

  27. Vuister, G. W. & Bax, A. Quantitative J correlation: A new approach for measuring homonuclear three-bond J(HNHα) coupling constants in 15N-enriched proteins. J. Am. Chem. Soc. 115, 7772–7777 (1993).

    Article  CAS  Google Scholar 

  28. Nilges, M., Marcias, M. J., O'Donoghue, S. I. & Oschkinat, H. Automated NOESY interpretation with ambiguous distance restraints: the refined NMR solution structure of the pleckstrin homology domain from β-spectrin. J. Mol. Biol. 269, 408–422 (1997).

    Article  CAS  Google Scholar 

  29. Kraulis, P. J. MOLSCRIPT: A program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallogr. 24, 946–950 (1991).

    Article  Google Scholar 

  30. Gilson, M. K., Sharp, K. A. & Honig, B. Calculation of the total electrostatic energy of a macromolecular system—solvation energies, binding energies and conformational analysis. J. Comput. Chem. 9, 327–335 (1988).

    Article  CAS  Google Scholar 

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Acknowledgements

We thank C. J. Sherr for the plasmid expressing GST-p19Ink4d; S. Ishii for plasmids expressing GroEL and GroES; W. Boucher for computer programming; M. Nilges for protocols for the structure calculations; J. Krywko for the model of Cdk4; M. Serrano and D. Beach for assaying p19Ink4d and for communicating unpublished results; N. Pavletich for the coordinates of 53BP2; and A. Murzin for helpful discussion. This work was supported by a grant from the BBSRC. The Cambridge Centre for Molecular Recognition is supported by the BBSRC and the Wellcome Trust.

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Correspondence to Ernest D. Laue.

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Luh, F., Archer, S., Domaille, P. et al. Structure of the cyclin-dependent kinase inhibitor p19Ink4d. Nature 389, 999–1003 (1997). https://doi.org/10.1038/40202

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