Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Article
  • Published:

Crystal structure of the PI 3-kinase p85 amino-terminal SH2 domain and its phosphopeptide complexes

Abstract

Crystal structures of the amino-terminal SH2 domain of the p85α subunit of phosphatidylinositol (PI) 3-kinase, alone and in complex with phosphopeptides bearing pTyr-Met/Val-Xaa-Met motifs, show that phosphopeptides bind in the two-pronged manner seen in high-affinity Lck and Src SH2 complexes, with conserved interactions between the domain and the peptide segment from phosphotyrosine to Met+3. Peptide binding requires the rearrangement of a tyrosyl side chain in the BG loop to create the hydrophobic Met+3 binding pocket. The structures suggest a mechanism for the biological specificity exhibited by PI 3-kinase in its interactions with phosphoprotein partners.

This is a preview of subscription content, access via your institution

Access options

Buy this article

Prices may be subject to local taxes which are calculated during checkout

Similar content being viewed by others

References

  1. Kapeller, R. & Cantley, L.C. Phosphatidylinositol 3-kinase. Bioessays 16, 565–576 (1994).

    Article  CAS  Google Scholar 

  2. Yao, R. & Cooper, G.M. Requirement for phosphatidyinositol-3 kinase in the prevention of apotosis by nerve growth factor. Science 267, 2003–2005 (1995).

    Article  CAS  Google Scholar 

  3. Skolnik, E.Y. et al. Cloning of PI3 kinase-associated p85 utilizing a novel method for expression/cloning of target proteins for receptor tyrosine kinases. Cell 65, 83–90 (1991).

    Article  CAS  Google Scholar 

  4. Otsu, M. et al. Characterization of two 85 kD proteins that associate with receptor tyrosine kinases, middle-T/pp60c-src complexes and PI3-kinase. Cell 65, 91–104 (1991).

    Article  CAS  Google Scholar 

  5. Escobedo, J.A. et al. cDNA cloning of a novel 85 kD protein that has SH2 domains and regulates binding of PI3-kinase to the PDGF b-receptor. Cell 65, 75–82 (1991).

    Article  CAS  Google Scholar 

  6. Klippel, A., Escobedo, J.A., Hu, Q. & Williams, L.T. A region of the 85-kda subunit of phosphatidylinositol 3-kinase binds the 110-kda catalytic subunit in vivo. Mol. Cell. Biol. 13, 5560–5566 (1994).

    Article  Google Scholar 

  7. Dhand, R. et al. PI 3-kinase - structural and functional analysis of intersubunit interactions. Embo J. 13, 511–521 (1994).

    Article  CAS  Google Scholar 

  8. Hu, P., Mondino, A., Skolnik, E.Y. & J., S. Cloning of a novel ubiquitously expressed human phosphatidylinositol 3-kinase and identification of its binding site on p85. Mol. Cell. Biol. 13, 7677–7688 (1993).

    Article  CAS  Google Scholar 

  9. Soltoff, S.P., Carraway, K.L., Prigent, S.A., Gullick, W.G. & Cantley, L.C. ErbB3 is involved in activation of phosphatidyinositol 3-kinase by epidermal growth factor. Mol. Cell. Biol. 14, 3550–3558 (1994).

    Article  CAS  Google Scholar 

  10. Lev, S., Givol, D. & Yarden, Y. Interkinase domain of kit contains the binding site for phosphatidylinositol 3' kinase. Proc Natl. Acad. Sci. USA 89, 678–682 (1992).

    Article  CAS  Google Scholar 

  11. Reedijk, M. et al. Tyr721 regulates specific binding of the CSF-1 receptor kinase insert to PI 3'-kinase SH2 domains: a model for SH2-mediated receptor-target interactions. Embo J. 11, 1365–1372 (1992).

    Article  CAS  Google Scholar 

  12. Sun, X.J. et al. The structure of the insulin receptor substrate IRS-1 defines a unique signal transduction protein. Nature 352, 73–77 (1991).

    Article  CAS  Google Scholar 

  13. Prasad, K.V.S. et al. T-cell antigen CD28 interacts with the lipid kinase phosphatidylinositol 3-kinase by a cytoplasmic pTyr-Met-Xxx-Met motif. Proc. Natl. Acad. Sci. USA 91, 2834–2838 (1994).

    Article  CAS  Google Scholar 

  14. Auger, K.R., Carpenter, C.L., Shoelson, S.E., Piwnica-Worms, H. & Cantley, L.C. Polyoma virus middle T antigen/pp60c-src complex associates with purified phosphatidylinositol 3-kinase in vitro:dependence on protein-tyrosine kinase activity. J Biol. Chem. 267, 5408–5415 (1992).

    CAS  PubMed  Google Scholar 

  15. Cantley, L.C. et al. Oncogenes and signal transduction. Cell 64, 281–302 (1991).

    Article  CAS  Google Scholar 

  16. Songyang, Z. et al. SH2 domains recognize specific phosphopeptide sequences. Cell 72, 767–778 (1993).

    Article  CAS  Google Scholar 

  17. Piccione, E. et al. PI 3-kinase p85 SH2 domains specificity defined by direct phosphopeptide/SH2 domain binding. Biochemistry 32, 3197–3202 (1993).

    Article  CAS  Google Scholar 

  18. Songyang, Z. et al. Specific motifs recognized by the SH2 domains of Csk 3BP2, fps/fes, Grb-2, HCP, SHC, Syk and Vav. Mol. Cell. Biol. 14, 2777–2785 (1994).

    Article  CAS  Google Scholar 

  19. Booker, G.W. et al. Structure of SH2 domain of the p85α subunit of phosphatidylinositol-3-OH kinase. Nature 358, 684–687 (1992).

    Article  CAS  Google Scholar 

  20. Eck, M.J., Shoelson, S.E. & Harrison, S.C. Recognition of a high-affinity phosphotyrosyl peptide by the Src homology-2 domain of p56lck. Nature 362, 87–91 (1993).

    Article  CAS  Google Scholar 

  21. Hatada, M.H. et al. Molecular basis for the interaction of the protein tyrosine kinase ZAP-70 with the T-cell receptor. Nature 377, 32–38 (1995).

    Article  CAS  Google Scholar 

  22. Lee, C.H. et al. Crystal structures of peptide complexes of the N-terminal SH2 domain of the Syp tyrosine phosphatase. Structure 2, 423–438 (1994).

    Article  CAS  Google Scholar 

  23. Pascal, S.M. et al. Nuclear magnetic resonance structure of an SH2 domain of PLC complexed with a high affinity binding peptide. Cell 77, 461–472 (1994).

    Article  CAS  Google Scholar 

  24. Overduin, M., Rios, C.B., Mayer, B.J., Baltimore, D. & Cowburn, D. Three-Dimensional Solution Structure of the src Homology 2 Domain of c-abl. Cell 70, 697–704 (1992).

    Article  CAS  Google Scholar 

  25. Waksman, G. et al. Crystal structure of the phosphotyrosine recognition domain SH2 of v-src complexed with tyrosine phosphorylated peptides. Nature 356, 646–653 (1992).

    Article  Google Scholar 

  26. Waksman, G., Shoelson, S.E., Pant, N., Cowburn, D. & Kuriyan, J. Binding of a high affinity phosphotyrosyl peptide to the Src SH2 domain: Crystal structures of the complexed and peptide-free forms. Cell 72, 779–790 (1993).

    Article  CAS  Google Scholar 

  27. Zhou, M.M. et al. Solution structure of the She SH2 domain complexed with a tyrosine-phosphorylated peptide from the T-cell receptor. Proc. Natl. Acad. Sci. USA 92, 7784–7788 (1995).

    Article  CAS  Google Scholar 

  28. Eck, M.J., Atwell, S.K., Shoelson, S.E. & Harrison, S.C. Crystal structure of the regulatory domains of the Src-family tyrosine kinase p56lck. Nature 368, 764–769 (1994).

    Article  CAS  Google Scholar 

  29. Panayotou, G. et al. Interaction of the p85 subunit of PI 3-kinase and its N-terminal SH2 domain with a PDGF receptor phosphorylation site: structural features and analysis of conformational changes. Embo J. 11, 4261–4272 (1992).

    Article  CAS  Google Scholar 

  30. Shoelson, S.E. et al. Specific phosphopeptide binding regulates a conformational change in the PI 3-kinase SH2 domain associated with enzyme activation. Embo J. 12, 795–802 (1993).

    Article  CAS  Google Scholar 

  31. Williams, K.P. & Shoelson, S.E. A photoaffinity scan maps regions of the p85 SH2 domain involved in phosphoprotein binding. J. Biol. Chem. 268, 5362–5364 (1993).

    Google Scholar 

  32. Hensmann, M. et al. Phosphopeptide binding to the N-terminal SH2 domain of of the p85a subunit of PI 3-kinase: A heteronuclear NMR study. Prot. Sci. 3, 1020–1028 (1994).

    Article  CAS  Google Scholar 

  33. Waksman, G. et al. Crystal structrue of the phosphotyrosine recognition domain SH2 of v-src complexed with tyrosine-phosphorylated peptides. Nature 358, 646–653 (1992).

    Article  CAS  Google Scholar 

  34. Eck, M.J., Pluskey, S., Trub, T., Harrison, S.C. & Shoelson, S.E. Spatial constraints on the recognition of phosphoproteins by the tandem SH2 domains of the phosphatase SH-PTP2. Nature 349, 277–280 (1996).

    Article  Google Scholar 

  35. Songyang, Z., Gish, G., Mbamalu, G., Pawson, T. & Cantley, L.C. A single point mutation switches the specificity of group III Src homology (SH) 2 domains to that of group I SH2 domains. J. Biol. Chem. 270, 26029–26032 (1995).

    Article  CAS  Google Scholar 

  36. Mahadevan, D. et al. Comparison of calcium-dependent co nformational changes in the N-terminal SH2 domains of p85 and GAP defines distinct properties for SH2 domains. Biochemistry 33, 746–754 (1994).

    Article  CAS  Google Scholar 

  37. Backer, J.M. et al. Phosphatidylinositol 3′-kinase is activated by association with IRS-1 during insulin stimulation. Embo J. 11, 3469–3479 (1992).

    Article  CAS  Google Scholar 

  38. Carpenter, C.L. et al. Phosphoinositide 3-kinase is activated by phosphopeptides that bind to the SH2 domains of the 85 kDa subunit. J. Biol. Chem. 268, 9478–9483 (1993).

    CAS  PubMed  Google Scholar 

  39. Herbst, J.J. et al. Potent activation of phospahatidylinositol 3-kinase by simple phosphotyrosine peptides derived from insulin receptor substrate 1 containing two YMXM motifs for binding SH2 domains. Biochemistry 33, 9376–9381 (1994).

    Article  CAS  Google Scholar 

  40. Marengere, L.E.M. et al. SH2 domain specificity and activity modified by a single residue. Nature 369, 502–505 (1994).

    Article  CAS  Google Scholar 

  41. Sambrook, J., Fritsch, E. & Maniatis, T. Molecular Cloning: A laboratory manual (Cold Spring Harbor Laboratory Press, 1989).

    Google Scholar 

  42. Hendrickson, W.A., Horton, J.R. & LeMaster, D.M. Selenomethionyl proteins produced for analysis by multiwavelength anonomalous diffraction (MAD): a vehicle for direct determination of three-dimensional structure. EMBO J. 9, 1665–1672 (1990).

    Article  CAS  Google Scholar 

  43. Kabsch, W. Evaluation of single crystal diffraction data from a position sensitive detector. J. Appl. Crystallogr. 21, 916–924 (1988).

    Article  CAS  Google Scholar 

  44. CollaborativeComputationalProjectNumber4. The CCP4 suite: Programs for protein crystallography. Acta Crystallogr. D50, 760–776 (1994).

  45. Otwinowski, Z. Maximun likelihood refinement of heavy atom parameters (1991).

  46. Cowtan, K. “DM”: an automated procedure for phase improvement by density modification. Joint CCP4 and ESF-EACBM Newsletter on Protein Crystallography 31, 34–38 (1994).

    Google Scholar 

  47. Jones, T.A., Zou, J.Y., Cowan, S. & Kjeldgaard, M. Improved methods for building protein models in electron density maps and the location of errors in these models. Acta. Crystallogr. A47, 110–119 (1991).

    Article  CAS  Google Scholar 

  48. Brünger, A. X-PLOR Version 3.0: A System for Crystallography and NMR (Yale University Press, New Haven, 1992).

    Google Scholar 

  49. Navaza, J. . in Molecular Replacement: Proceedings of the CCP4 Study Weekend (eds. Dodson, E.J., Gover, S. & Wolf, W.) 87–90 (SERC, Daresbury, UK, 1992).

    Google Scholar 

  50. 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 

  51. 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  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Rights and permissions

Reprints and permissions

About this article

Cite this article

Nolte, R., Eck, M., Schlessinger, J. et al. Crystal structure of the PI 3-kinase p85 amino-terminal SH2 domain and its phosphopeptide complexes. Nat Struct Mol Biol 3, 364–374 (1996). https://doi.org/10.1038/nsb0496-364

Download citation

  • Received:

  • Accepted:

  • Issue date:

  • DOI: https://doi.org/10.1038/nsb0496-364

This article is cited by

Search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing