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Structural insights into phosphoinositide 3-kinase catalysis and signalling

Nature volume 402, pages 313–320 (1999)Cite this article

Abstract

Phosphoinositide 3-kinases (PI3Ks) are ubiquitous lipid kinases that function both as signal transducers downstream of cell-surface receptors and in constitutive intracellular membrane and protein trafficking pathways. All PI3Ks are dual-specificity enzymes with a lipid kinase activity which phosphorylates phosphoinositides at the 3-hydroxyl, and a protein kinase activity. The products of PI3K-catalysed reactions, phosphatidylinositol 3,4,5-trisphosphate (PtdIns(3,4,5)P3), PtdIns(3,4)P2 and PtdIns(3)P, are second messengers in a variety of signal transduction pathways, including those essential to cell proliferation, adhesion, survival, cytoskeletal rearrangement and vesicle trafficking1,2. Here we report the 2.2 Å X-ray crystallographic structure of the catalytic subunit of PI3Kγ, the class I enzyme that is activated by heterotrimeric G-protein βγ subunits and Ras. PI3Kγ has a modular organization centred around a helical-domain spine, with C2 and catalytic domains positioned to interact with phospholipid membranes, and a Ras-binding domain placed against the catalytic domain where it could drive allosteric activation of the enzyme.

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Figure 1: Overall structure of PI3Kγ.
Figure 2: The catalytic domain of PI3Kγ.
Figure 3: Secondary structure of the PI3Kγ p110 subunit and sequence alignments with other PI3K family members.
Figure 4: Model of phospholipid headgroup interactions with PI3Kγ.
Figure 5: Model of the Ras–PI3Kγ interaction based on the structure of the RalGDS–Ras complex.
Figure 6: Ribbon diagram of the PI3Kγ C2 domain, and the interactions it makes with the rest of the enzyme.
Figure 7: The helical domain (for colours see Fig. 1).

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References

  1. Toker,A. & Cantley,L. C. Signalling through the lipid products of phosphoinositide-3-OH kinase. Nature 387, 673–676 (1997).

    Article  ADS  CAS  PubMed  Google Scholar 

  2. Domin,J. & Waterfield,M. D. Using structure to define the function of phosphoinositide 3-kinase family members. FEBS Lett. 410, 91–95 (1997).

    Article  CAS  PubMed  Google Scholar 

  3. Stoyanov,B. et al. Cloning and characterisation of a G protein-activated human phosphoinositide-3 kinase. Science 269, 690–693 (1995).

    Article  ADS  CAS  PubMed  Google Scholar 

  4. Stephens,L. R. et al. The Gβγ sensitivity of a PI3K is dependent upon a tightly associated adaptor, p101. Cell 89, 105–114 (1997).

    Article  CAS  PubMed  Google Scholar 

  5. Krugmann,S., Hawkins,P. T., Pryer,N. & Braselmann,S. Characterizing the interactions between the two subunits of the p101/p110γ phosphoinositide 3-kinase and their role in the activation of this enzyme by Gβγ subunits. J. Biol. Chem. 274, 17152–17158 (1999).

    Article  CAS  PubMed  Google Scholar 

  6. Taylor,S. S. et al. Catalytic subunit of cyclic AMP-dependent protein kinase: structure and dynamics of the active site cleft. Pharmacol. Ther. 82, 133–141 (1999).

    Article  CAS  PubMed  Google Scholar 

  7. Dhand,R. et al. PI3-kinase is a dual specificity enzyme—autoregulation by an intrinsic protein serine kinase activity. EMBO J. 13, 522–533 (1994).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Stack,J. H. & Emr,S. D. Vps34p required for yeast vacuolar protein sorting is a multiple specificity kinase that exhibits both protein kinase and phosphatidylinositol-specific PI-3-kinase activities. J. Biol. Chem. 269, 31552–31562 (1994).

    Article  CAS  PubMed  Google Scholar 

  9. Wymann,M. P. et al. Wortmannin inactivates phosphoinositide 3-kinase by covalent modification of Lys-802, a residue involved in the phosphate transfer reaction. Mol. Cell. Biol. 16, 1722–1733 (1996).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Bondeva,T. et al. Bifurcation of lipid and protein kinase signals of PI3Kγ to the protein kinases PKB and MAPK. Science 282, 293–296 (1998).

    Article  ADS  CAS  PubMed  Google Scholar 

  11. Vanhaesebroeck,B. et al. Autophosphorylation of p110δ phosphoinositide 3-kinase: a new paradigm for the regulation of lipid kinases in vitro and in vivo. EMBO J. 18, 1292–1302 (1999).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Kim,K. & Cole,P. A. Measurement of a Brønsted nucleophile coefficient and insights into the transition state for a protein tyrosine kinase. J. Am. Chem. Soc. 119, 11096–11097 (1997).

    Article  CAS  Google Scholar 

  13. Marshall,C. J. Ras effectors. Curr. Opin. Cell Biol. 8, 197–204 (1996).

    Article  CAS  PubMed  Google Scholar 

  14. Moodie,S. A. et al. Different structural requirements within the switch II region of the Ras protein for interactions with specific downstream targets. Oncogene 11, 447–454 (1995).

    CAS  PubMed  Google Scholar 

  15. Rodriguez-Viciana,P. et al. Role of phosphoinositide 3-OH kinase in cell transformation and control of the actin cytoskeleton by Ras. Cell 89, 457–467 (1997).

    Article  CAS  PubMed  Google Scholar 

  16. Nassar,M. et al. the 2.2 Å crystal structure of the Ras-binding domain of the serine/threonine kinase c-Raf1 in complex with Rap1A and a GTP analogue. Nature 375, 554–560 (1995).

    Article  ADS  CAS  PubMed  Google Scholar 

  17. Huang,L., Hofer,F., Martin,G. S. & Kim,S.-H. Structural basis for the interaction of Ras with RalGDS. Nature Struct. Biol. 5, 422–426 (1998).

    Article  CAS  PubMed  Google Scholar 

  18. Essen,L.-O., Perisic,O., Lynch,D. E., Katan,M. & Williams,R. L. A ternary metal binding site in the C2 domain of phosphoinositide-specific phospholipase C-δ1. Biochemistry 36, 2753-2762 (1997).

    Article  PubMed  Google Scholar 

  19. Rao,V. D., Misra,S., Boronenkov,I. V., Anderson,R. A. & Hurley,J. H. Structure of type IIβ phosphatidylinositol phosphate kinase: a protein kinase fold flattened for interfacial phosphorylation. Cell 94, 829–839 (1998).

    Article  CAS  PubMed  Google Scholar 

  20. Groves,M. R., Hanlon,N., Turowski,P., Hemmings,B. A. & Barford,D. The structure of the protein phosphatase 2A PR65/A subunit reveals the conformation of its 15 tandemly repeated HEAT motifs. Cell 96, 99–110 (1999).

    Article  CAS  PubMed  Google Scholar 

  21. Vetter,I. R., Arndt,A., Kutay,U., Görlich,D. & Wittinghofer,A. Structural view of the Ran-importin β interaction at 2.3 Å resolution. Cell 97, 635–646 (1999).

    Article  CAS  PubMed  Google Scholar 

  22. Dennis,P. B., Fumagalli,S. & Thomas,G. Target of rapamycin (TOR): balancing the opposing forces of protein synthesis and degradation. Curr. Opin. Genet. Dev. 9, 49–54 (1999).

    Article  CAS  PubMed  Google Scholar 

  23. Leslie,A. G. W. Recent changes to the MOSFLM package for film and image plate data, in Joint CCP4 and ESF-EACMB Newsletter on Protein Crystallography Vol. 26 (Daresbury Laboratory, Warrington, UK, 1992).

    Google Scholar 

  24. CCP4. Collaborative Computing Project 4: A suite of programs for protein crystallography. Acta Crystallogr. D 50, 760–763 (1994).

    Article  Google Scholar 

  25. Terwilliger,T. C. & Berendzen,J. Automated structure solution for MIR and MAD. Acta Crystallogr. D 55, 849–861 (1999).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. de La Fortelle,E. & Bricogne,G. Maximum-likelihood heavy-atom parameter refinement for multiple isomorphous replacement and multiwavelength anomalous diffraction methods. Methods Enzymol. 276, 472–494 (1997).

    Article  CAS  PubMed  Google Scholar 

  27. Jones,T. A., Zou,J.-Y., Cowan,S. W. & Kjeldgaard,M. Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr. A 47, 110–119 (1991).

    Article  PubMed  Google Scholar 

  28. Brünger,A. T. et al. Crystallography & NMR system: a new software suite for macromolecular structure determination. Acta Crystallogr. D 54, 905–921 (1998).

    Article  PubMed  Google Scholar 

  29. Nicholls,A., Sharp,K. A. & Honig,B. Protein folding and association: insights from the interfacial and thermodynamic properties of hydrocarbons. Proteins Struct. Funct. Genet. 11, 281–296 (1991).

    Article  CAS  PubMed  Google Scholar 

  30. Yamaguchi,H. & Hendrickson,W. A. Structural basis for the activation of human lymphocyte kinase Lck tyrosine phosphorylation. Nature 384, 484–489 (1996).

    Article  ADS  CAS  PubMed  Google Scholar 

  31. 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 

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Acknowledgements

We thank D. Lynch for technical assistance, S. Krugmann for PI3K assays, the staff of synchrotron beamlines ID2b, ID14-3 and ID14-4 at ESRF, IMCA-CAT at APS, X11 at EMBL Hamburg, Station 9.6 at Daresbury SRS, and Elettra, Italy, for help in synchrotron data collection. We thank P. Roversi and G. Bricogne for their assistance with BUSTER, R. Rubin and C. Humblet for access to the IMCA-CAT beamline, and P. Hawkins and A. Murzin for helpful discussions. C.R. was supported by the Deutsche Forschungsgemeinschaft. We are grateful for support from the BBSRC (via a senior fellowship to P. Hawkins), the British Heart Foundation, Parke-Davis and Onyx Pharmaceuticals (R.L.W.).

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  1. MRC Laboratory of Molecular Biology, MRC Centre, Hills Road, Cambridge, CB2 2QH, UK

    Edward H. Walker, Olga Perisic, Christian Ried & Roger L. Williams

  2. The Babraham Institute, Babraham, Cambridge, CB2 4AT, UK

    Len Stephens

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Correspondence to Roger L. Williams.

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Walker, E., Perisic, O., Ried, C. et al. Structural insights into phosphoinositide 3-kinase catalysis and signalling. Nature 402, 313–320 (1999). https://doi.org/10.1038/46319

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