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:

Structural basis for the activation of PPARγ by oxidized fatty acids

Nature Structural & Molecular Biology volume 15, pages 924–931 (2008)Cite this article

Abstract

The nuclear receptor peroxisome proliferator–activated receptor-γ (PPARγ) has important roles in adipogenesis and immune response as well as roles in both lipid and carbohydrate metabolism. Although synthetic agonists for PPARγ are widely used as insulin sensitizers, the identity of the natural ligand(s) for PPARγ is still not clear. Suggested natural ligands include 15-deoxy-Δ12,14-prostaglandin J2 and oxidized fatty acids such as 9-HODE and 13-HODE. Crystal structures of PPARγ have revealed the mode of recognition for synthetic compounds. Here we report structures of PPARγ bound to oxidized fatty acids that are likely to be natural ligands for this receptor. These structures reveal that the receptor can (i) simultaneously bind two fatty acids and (ii) couple covalently with conjugated oxo fatty acids. Thermal stability and gene expression analyses suggest that such covalent ligands are particularly effective activators of PPARγ and thus may serve as potent and biologically relevant ligands.

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

Access options

Buy this article

  • Purchase on SpringerLink
  • Instant access to full article PDF
Buy now

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

Figure 1: PPARγ has a versatile fatty-acid binding pocket.
Figure 2: Recognition of 9-HODE and 13-HODE by PPARγ.
Figure 3: Binding of various oxidized fatty-acid ligands to PPARγ.
Figure 4: Thermal denaturation studies of the PPARγ LBD.
Figure 5: Activity of oxidized fatty acids in cell-based assays.
Figure 6: Cys285 is essential for the activity of covalent ligands.

Similar content being viewed by others

Accession codes

Primary accessions

Protein Data Bank

Referenced accessions

Protein Data Bank

References

  1. Tontonoz, P. & Spiegelman, B.M. Fat and beyond: the diverse biology of PPARγ. Annu. Rev. Biochem. 77, 289–312 (2008).

    Article  CAS  PubMed  Google Scholar 

  2. Lehmann, J.M. et al. An antidiabetic thiazolidinedione is a high affinity ligand for peroxisome proliferator-activated receptor γ (PPARγ). J. Biol. Chem. 270, 30221–30229 (1995).

    Article  PubMed  Google Scholar 

  3. Kliewer, S.A. et al. A prostaglandin J2 metabolite binds peroxisome proliferator-activated receptor gamma and promotes adipocyte differentiation. Cell 83, 813–819 (1995).

    Article  CAS  PubMed  Google Scholar 

  4. Forman, B.M. et al. 15-Deoxy-Δ12,14-prostaglandin J2 is a ligand for the adipocyte determination factor PPARγ. Cell 83, 803–812 (1995).

    Article  CAS  PubMed  Google Scholar 

  5. Powell, W.S. 15-Deoxy-Δ12,14–PGJ2: endogenous PPARγ ligand or minor eicosanoid degradation product? J. Clin. Invest. 112, 828–830 (2003).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Kliewer, S.A. et al. Fatty acids and eicosanoids regulate gene expression through direct interactions with peroxisome proliferator-activated receptors α and γ. Proc. Natl. Acad. Sci. USA 94, 4318–4323 (1997).

    Article  CAS  PubMed  Google Scholar 

  7. Krey, G., Braissant, O., L'Horset, F. & Kalkhoven, E. Fatty acids, eicosanoids, and hypolipidemic agents identified as ligands of peroxisome proliferator- activated receptors by coactivator-dependent receptor ligand assay. Mol. Endocrinol. 11, 779–791 (1997).

    Article  CAS  PubMed  Google Scholar 

  8. Nagy, L., Tontonoz, P., Alvarez, J.G., Chen, H. & Evans, R.M. Oxidized LDL regulates macrophage gene expression through ligand activation of PPARγ. Cell 93, 229–240 (1998).

    Article  CAS  PubMed  Google Scholar 

  9. Marx, N., Bourcier, T., Sukhova, G.K., Libby, P. & Plutzky, J. PPARγ activation in human endothelial cells increases plasminogen activator inhibitor type-1 expression: PPARγ as a potential mediator in vascular disease. Arterioscler. Thromb. Vasc. Biol. 19, 546–551 (1999).

    Article  CAS  PubMed  Google Scholar 

  10. Schild, R.L. et al. The activity of PPARγ in primary human trophoblasts is enhanced by oxidized lipids. J. Clin. Endocrinol. Metab. 87, 1105–1110 (2002).

    CAS  PubMed  Google Scholar 

  11. Renaud, J.P. & Moras, D. Structural studies on nuclear receptors. Cell. Mol. Life Sci. 57, 1748–1769 (2000).

    Article  CAS  PubMed  Google Scholar 

  12. Nagy, L. & Schwabe, J.W. Mechanism of the nuclear receptor molecular switch. Trends Biochem. Sci. 29, 317–324 (2004).

    Article  CAS  PubMed  Google Scholar 

  13. Khorasanizadeh, S. & Rastinejad, F. Nuclear-receptor interactions on DNA-response elements. Trends Biochem. Sci. 26, 384–390 (2001).

    Article  CAS  PubMed  Google Scholar 

  14. Johnson, B.A. et al. Ligand-induced stabilization of PPARγ monitored by NMR spectroscopy: implications for nuclear receptor activation. J. Mol. Biol. 298, 187–194 (2000).

    Article  CAS  PubMed  Google Scholar 

  15. Kallenberger, B.C., Love, J.D., Chatterjee, V.K. & Schwabe, J.W. A dynamic mechanism of nuclear receptor activation and its perturbation in a human disease. Nat. Struct. Biol. 10, 136–140 (2003).

    Article  CAS  PubMed  Google Scholar 

  16. Bruning, J.B. et al. Partial agonists activate PPARγ using a helix 12 independent mechanism. Structure 15, 1258–1271 (2007).

    Article  CAS  PubMed  Google Scholar 

  17. Cronet, P. et al. Structure of the PPARα and -γ ligand binding domain in complex with AZ 242; ligand selectivity and agonist activation in the PPAR family. Structure 9, 699–706 (2001).

    Article  CAS  PubMed  Google Scholar 

  18. Gampe, R.T., Jr et al. Asymmetry in the PPARγ/RXRα crystal structure reveals the molecular basis of heterodimerization among nuclear receptors. Mol. Cell 5, 545–555 (2000).

    Article  CAS  PubMed  Google Scholar 

  19. Nolte, R.T. et al. Ligand binding and co-activator assembly of the peroxisome proliferator-activated receptor-γ. Nature 395, 137–143 (1998).

    Article  CAS  PubMed  Google Scholar 

  20. Pochetti, G. et al. Insights into the mechanism of partial agonism: crystal structures of the peroxisome proliferator-activated receptor γ ligand-binding domain in the complex with two enantiomeric ligands. J. Biol. Chem. 282, 17314–17324 (2007).

    Article  CAS  PubMed  Google Scholar 

  21. Brunger, A.T. Version 1.2 of the Crystallography and NMR system. Nat. Protocols 2, 2728–2733 (2007).

    Article  CAS  PubMed  Google Scholar 

  22. Oakley, A.J. et al. The three-dimensional structure of the human Pi class glutathione transferase P1–1 in complex with the inhibitor ethacrynic acid and its glutathione conjugate. Biochemistry 36, 576–585 (1997).

    Article  CAS  PubMed  Google Scholar 

  23. Szatmari, I. et al. Activation of PPARγ specifies a dendritic cell subtype capable of enhanced induction of iNKT cell expansion. Immunity 21, 95–106 (2004).

    Article  CAS  PubMed  Google Scholar 

  24. Sarraf, P. et al. Loss-of-function mutations in PPARγ associated with human colon cancer. Mol. Cell 3, 799–804 (1999).

    Article  CAS  PubMed  Google Scholar 

  25. Shiraki, T. et al. α,β-unsaturated ketone is a core moiety of natural ligands for covalent binding to peroxisome proliferator-activated receptor γ. J. Biol. Chem. 280, 14145–14153 (2005).

    Article  CAS  PubMed  Google Scholar 

  26. Soares, A.F. et al. Covalent binding of 15-deoxy-Δ12,14-prostaglandin J2 to PPARγ. Biochem. Biophys. Res. Commun. 337, 521–525 (2005).

    Article  CAS  PubMed  Google Scholar 

  27. Schopfer, F.J. et al. Fatty acid transduction of nitric oxide signaling. Nitrolinoleic acid is a hydrophobically stabilized nitric oxide donor. J. Biol. Chem. 280, 19289–19297 (2005).

    Article  CAS  PubMed  Google Scholar 

  28. Baker, L.M. et al. Nitro-fatty acid reaction with glutathione and cysteine. Kinetic analysis of thiol alkylation by a Michael addition reaction. J. Biol. Chem. 282, 31085–31093 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. Erlemann, K.R., Rokach, J. & Powell, W.S. Oxidative stress stimulates the synthesis of the eosinophil chemoattractant 5-oxo-6,8,11,14-eicosatetraenoic acid by inflammatory cells. J. Biol. Chem. 279, 40376–40384 (2004).

    Article  CAS  PubMed  Google Scholar 

  30. Powell, W.S., Gravel, S. & Gravelle, F. Formation of a 5-oxo metabolite of 5,8,11,14,17-eicosapentaenoic acid and its effects on human neutrophils and eosinophils. J. Lipid Res. 36, 2590–2598 (1995).

    CAS  PubMed  Google Scholar 

  31. Ting-Beall, H.P., Needham, D. & Hochmuth, R.M. Volume and osmotic properties of human neutrophils. Blood 81, 2774–2780 (1993).

    CAS  PubMed  Google Scholar 

  32. Itoh, T., Murota, I., Yoshikai, K., Yamada, S. & Yamamoto, K. Synthesis of docosahexaenoic acid derivatives designed as novel PPARγ agonists and antidiabetic agents. Bioorg. Med. Chem. 14, 98–108 (2006).

    Article  CAS  PubMed  Google Scholar 

  33. Yamamoto, K. et al. Identification of putative metabolites of docosahexaenoic acid as potent PPARγ agonists and antidiabetic agents. Bioorg. Med. Chem. Lett. 15, 517–522 (2005).

    Article  CAS  PubMed  Google Scholar 

  34. Leslie, A.G. The integration of macromolecular diffraction data. Acta Crystallogr. D Biol. Crystallogr. 62, 48–57 (2006).

    Article  PubMed  Google Scholar 

  35. Collaborative Computational Project, Number 4. The CCP4 suite: programs for protein crystallography. Acta Crystallogr. D Biol. Crystallogr. 50, 760–763 (1994).

  36. Emsley, P. & Cowtan, K. Coot: model-building tools for molecular graphics. Acta Crystallogr. D Biol. Crystallogr. 60, 2126–2132 (2004).

    Article  PubMed  Google Scholar 

  37. Murshudov, G.N., Vagin, A.A. & Dodson, E.J. Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr. D Biol. Crystallogr. 53, 240–255 (1997).

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgements

MS was carried out by A.R. Bottrill and S. Ibrahim of the Protein and Nucleic Acid Chemistry Laboratories (PNACL) Proteomics Facility at the University of Leicester. The Schwabe laboratory is supported by the Wellcome Trust. The Nagy laboratory is supported by the Howard Hughes Medical Institute, the Wellcome Trust and the Hungarian Scientific Research Fund. We acknowledge the European Synchrotron Radiation Facility (ESRF) for provision of synchrotron radiation facilities and thank the staff on beamline ID14.3.

Author information

Authors and Affiliations

  1. Department of Biochemistry, Henry Wellcome Laboratories of Structural Biology, University of Leicester, Lancaster Road, Leicester, LE1 9HN, UK

    Toshimasa Itoh, Louise Fairall, Kush Amin & John W R Schwabe

  2. Laboratory of Drug Design and Medicinal Chemistry, Showa Pharmaceutical University, 3-3165 Higashi-tamagawagakuen, Machida, Tokyo, 194-8543, Japan

    Yuka Inaba & Keiko Yamamoto

  3. Department of Biochemistry and Molecular Biology, Apoptosis and Genomics Research Group of the Hungarian Academy of Sciences, Life Sciences Building, Medical and Health Science Center, University of Debrecen, Debrecen, H-4032, Egyetem ter 1., Hungary

    Attila Szanto, Balint L Balint & Laszlo Nagy

Authors
  1. Toshimasa Itoh
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Louise Fairall
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Kush Amin
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Yuka Inaba
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Attila Szanto
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Balint L Balint
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Laszlo Nagy
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Keiko Yamamoto
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. John W R Schwabe
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

T.I. and K.Y. designed and prepared the ligands (except 9-HODE and 13-HODE). T.I., L.F. and K.A. cloned, expressed and purified PPARγ and grew the crystals. T.I., L.F., K.A. and J.W.R.S. carried out the crystallographic structure determinations. T.I. prepared samples for MS. L.F. and K.A. performed the CD experiments. A.S., B.L.B. and L.N. designed and carried out the reporter gene and transcription assays shown in Figure 5 and in Supplementary Figures 1 and 2. Y.I. and K.Y. designed and carried out the reporter gene assays shown in Figure 6. J.W.R.S. supervised the project and prepared the manuscript with assistance from T.I. and L.F. and helpful comments from L.N. and K.Y.

Corresponding author

Correspondence to John W R Schwabe.

Ethics declarations

Competing interests

K.Y. has filed patent applications relating to the compounds 4-HDHA, 4-oxoDHA, 5-HEPA and 5-oxoEPA. These have been assigned to Pronova BioPharma. No other authors have competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1 and 2, and Supplementary Methods (PDF 380 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Itoh, T., Fairall, L., Amin, K. et al. Structural basis for the activation of PPARγ by oxidized fatty acids. Nat Struct Mol Biol 15, 924–931 (2008). https://doi.org/10.1038/nsmb.1474

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nsmb.1474

This article is cited by

Search

Advanced 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