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Structure of chalcone synthase and the molecular basis of plant polyketide biosynthesis

Nature Structural Biology volume 6, pages 775–784 (1999)Cite this article

Abstract

Chalcone synthase (CHS) is pivotal for the biosynthesis of flavonoid antimicrobial phytoalexins and anthocyanin pigments in plants. It produces chalcone by condensing one p-coumaroyl- and three malonyl-coenzyme A thioesters into a polyketide reaction intermediate that cyclizes. The crystal structures of CHS alone and complexed with substrate and product analogs reveal the active site architecture that defines the sequence and chemistry of multiple decarboxylation and condensation reactions and provides a molecular understanding of the cyclization reaction leading to chalcone synthesis. The structure of CHS complexed with resveratrol also suggests how stilbene synthase, a related enzyme, uses the same substrates and an alternate cyclization pathway to form resveratrol. By using the three-dimensional structure and the large database of CHS-like sequences, we can identify proteins likely to possess novel substrate and product specificity. The structure elucidates the chemical basis of plant polyketide biosynthesis and provides a framework for engineering CHS-like enzymes to produce new products.

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Figure 1: Products, product analogs and inhibitors.
Figure 2: a, Ribbon representation of the CHS homodimer.
Figure 3: Comparison of chalcone synthase and 3-ketoacyl-CoA thiolase.
Figure 4: Structures of CHS–Acyl-CoA complexes.
Figure 5: Structures of CHS–product analog complexes.
Figure 6: The proposed reaction mechanism of CHS.
Figure 7: Three-dimensional model of the elongation and cyclization reaction in CHS and STS.
Figure 8: Comparison of the active site volumes of CHS and GCHS2.

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References

  1. Bailey, J.A. & Mansfield, J.W. Phytoalexins. (John Wiley and Sons, New York; 1982).

    Google Scholar 

  2. Long, S.R. Rhizobium-legume nodulation. Cell 56, 203 –214 (1989).

    Article  CAS  Google Scholar 

  3. Dixon, R.A. & Paiva, N.L. Stress-induced phenylpropanoid metabolism. Plant Cell 7, 1085–1097 (1995).

    Article  CAS  Google Scholar 

  4. Schroeder, J. A family of plant-specific polyketide synthases: facts and predictions. Trends Plant Sci. 2, 373–378 (1997).

    Article  Google Scholar 

  5. Jang, M. et al. Cancer chemopreventive activity of resveratrol, a natural product derived from grapes. Science 275, 218– 220 (1997).

    Article  CAS  Google Scholar 

  6. Edwards, M.L., Stemerick, D.M. & Sunkara, P.S. Chalcones: a new class of antimitotic agents. J. Med. Chem. 33, 1948–1954 (1990).

    Article  CAS  Google Scholar 

  7. Gehm, B.D., McAndrews, J.M., Chien, P.-Y. & Jameson, J.L. Resveratrol, a polyphenolic compound found in grapes and wine, is an agonist for the estrogen receptor. Proc. Natl. Acad. Sci. USA 94, 14138–14143 (1997).

    Article  CAS  Google Scholar 

  8. Li, R. et al. In vitro antimalarial activity of chalcones and their derivatives. J. Med. Chem. 38, 5031– 5037 (1995).

    Article  CAS  Google Scholar 

  9. Zwaagstra, M.E. et al. Synthesis and structure–activity relationships of carboxylated chalcones. J. Med. Chem. 40, 1075– 1089 (1997).

    Article  CAS  Google Scholar 

  10. Frankel, E.N., Kanner, J., German, J.B., Parks, E. & Kinsella, J.E. Inhibition of oxidation of human LDL by phenolic substances in red wine. Lancet 341, 454– 457 (1993).

    Article  CAS  Google Scholar 

  11. Frankel, E.N., Waterhouse, A.L. & Kinsella, J.E. Inhibition of human LDL oxidation by resveratrol. Lancet 341, 1103–1104 (1993).

    Article  CAS  Google Scholar 

  12. Kreuzaler, F. & Hahlbrock, K. Enzymic synthesis of an aromatic ring from acetate units. Eur. J. Biochem. 56, 205–213 (1975).

    Article  CAS  Google Scholar 

  13. Wakil, S.J. Fatty acid synthase, a proficient multifunctional enzyme. Biochemistry 28, 4523–4530 ( 1989).

    Article  CAS  Google Scholar 

  14. Cane, D.E., Walsh, C.T. & Khosla, C. Harnessing the biosynthetic code. Science 282, 63–68 ( 1998).

    Article  CAS  Google Scholar 

  15. Tropf, S., Kaercher, B., Schroeder, J. & Schroeder, G. Reaction mechanisms of homodimeric plant polyketide synthase (stilbenes and chalcone synthase): a single active site for the condensing reaction is sufficient for synthesis of stilbenes, chalcones, and 6'-deoxychalcones. J. Biol. Chem. 270, 7922–7928 (1995).

    Article  CAS  Google Scholar 

  16. Preisig-Mueller, R., Gehlert, R., Melchior, F., Stietz, U. & Kindl, H. Plant polyketide synthases leading to stilbenoids have a domain catalyzing malonyl-CoA:CO2 exchange, malonyl-CoA decarboxylation, and covalent enzyme modification and a site for chain lengthening. Biochemistry 36, 8349 –8358 (1997).

    Article  CAS  Google Scholar 

  17. Schroeder, G., Brown, J.W.S. & Schroeder, J. Molecular analysis of resveratrol synthase: cDNA, genomic clones and relationship with chalcone synthase. Eur. J. Biochem. 172, 161–169 ( 1988).

    Article  CAS  Google Scholar 

  18. Preisig-Mueller, R., Gnau, P. & Kindl, H. The inducible 9,10-dihydrophenanthrene pathway: characterization and expression of bibenzyl synthase and S-adenosylhomocysteine hydrolase. Arch. Biochem. Biophys. 317, 201–207 (1995).

    Article  CAS  Google Scholar 

  19. Junghanns, K.T. et al. Molecular cloning and heterologous expression of acridone synthase from elicited Ruta graveolens cell suspension cultures. Plant Mol. Biol. 27, 681–692 (1995).

    Article  CAS  Google Scholar 

  20. Bednar, R.A. & Hadcock, J.R. Purification and characterization of chalcone isomerase from soybeans. J. Biol. Chem. 263, 9582–9588 (1988).

    CAS  PubMed  Google Scholar 

  21. Mathieu, M. et al. The 2.8 Å crystal structure of peroxisomal 3-ketoacyl-CoA thiolase of Saccharomyces cerevisiae. Structure 2, 797–808 (1994).

    Article  CAS  Google Scholar 

  22. Huang, W. et al. Crystal structure of β-ketoacyl-acyl carrier protein synthase II from E. coli reveals the molecular architecture of condensing enzymes. EMBO J. 17, 1183–1191 (1998).

    Article  CAS  Google Scholar 

  23. Schuez, R., Heller, W. & Hahlbrock, K. Substrate specificity of chalcone synthase from Petroselinum hortense. J. Biol. Chem. 258, 6730– 6734 (1983).

    CAS  Google Scholar 

  24. Siggaard-Andersen, M. Conserved residues in condensing enzyme domains of fatty acid synthases and related sequences. Prot. Seq. Data Anal. 5, 325–335 (1993).

    CAS  Google Scholar 

  25. Lanz, T., Tropf, S., Marner, F.J., Schroeder, J. & Schroeder, G. The role of cysteines in polyketide synthases: site-directed mutagenesis of resveratrol and chalcone synthases, two enzymes in different plant-specific pathways. J. Biol. Chem. 266, 9971–9976 (1991).

    CAS  PubMed  Google Scholar 

  26. Engel, C. & Wierenga, R.K. The diverse world of coenzyme A binding proteins Curr. Opin. Struct. Biol. 6, 790–797 (1996).

    Article  CAS  Google Scholar 

  27. Hrazdina, G., Kreuzaler, F., Hahlbrock, K. & Grisebach, H. Substrate specificity of flavanone synthase from cell suspension cultures of parsley and structure of release product in vitro. Arch. Biochem. Biophys. 175, 392–399 (1976).

    Article  CAS  Google Scholar 

  28. Kreuzaler, F., Light, R.J. & Hahlbrock, K. Flavanone synthase catalyzes CO2 exchange and decarboxylation of malonyl-CoA. FEBS Lett. 94, 175–178 (1978).

    Article  CAS  Google Scholar 

  29. Welle, R. & Grisebach, H. Isolation of a novel NADPH-dependent reductase which coacts with chalcone synthase in the biosynthesis of 6'-deoxychalcone. FEBS Lett. 236, 221–225 (1988).

    Article  CAS  Google Scholar 

  30. Schroeder, J. et al. Plant polyketide synthases: a chalcone synthase-type enzyme which performs a condensation reaction with methylmalonyl-CoA in the biosynthesis of C-methylated chalcones. Biochemistry 37, 8417–8425 (1998).

    Article  CAS  Google Scholar 

  31. Schoeppner, A. & Kindl, H. Purification and properties of a stilbene synthase from induced cell suspension cultures of peanut. J. Biol. Chem. 259, 6806– 6811 (1984).

    CAS  Google Scholar 

  32. Helariutta, Y. et al. Chalcone synthase-like genes active during corolla development are differentially expressed and encode enzymes with different catalytic properties in Gerbera hybrida. Plant Mol. Biol. 28, 47–60 (1995).

    Article  CAS  Google Scholar 

  33. Eckermann, S. et al. New pathway to polyketides in plants. Nature 396, 387–390 (1998).

    Article  CAS  Google Scholar 

  34. Junghans, H., Dalkin, K. & Dixon, R.A. Stress responses in alfalfa (Medicago sativa L.) 15: characterization and expression patterns of members of a subset of the chalcone synthase multigene family. Plant Mol. Biol. 22, 239–253 (1993).

    Article  CAS  Google Scholar 

  35. Otwinowski, Z. & Minor, W. Processing of x-ray diffraction data collected in oscillation mode. Methods Enzymol. 276, 307–326 ( 1997).

    Article  CAS  Google Scholar 

  36. Collaborative Computational Project, Number 4. CCP4 Suite: programs for protein crystallography. Acta Crystallogr. D 50, 760–763 ( 1994).

  37. McRee, D.E. A visual protein crystallographic software system for X11/Xview. J. Mol. Graph. 10, 44–46 (1992).

    Article  Google Scholar 

  38. Otwinowski, Z. ML–PHARE (CCP4, SERC Daresbury Laboratory, Warrington, UK) 1991.

    Google Scholar 

  39. 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  Google Scholar 

  40. Abrahams, J.P. & Leslie, A.G.W. Methods used in the structure determination of bovine mitochondrial F1 ATPase. Acta Crystallogr. D 52, 30–42 (1996).

    Article  CAS  Google Scholar 

  41. 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. D 49, 148–157 (1993).

    Google Scholar 

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

    Article  CAS  Google Scholar 

  43. Lamzin, V.S. & Wilson, K.S. Automated refinement of protein molecules. Acta Crystallogr. D 49, 129– 147 (1993).

    Article  CAS  Google Scholar 

  44. Sheldrick, G.M. & Schneider, T.R. SHELXL: High-resolution refinement. Methods Enzymol. 277, 319– 343 (1997).

    Article  CAS  Google Scholar 

  45. Laskowski, R.A., MacArthur, M.W., Moss, D.S. & Thornton, J.M. PROCHECK: a program to check the stereochemical quality of protein structures. J. Appl. Crystallogr. 26, 283– 291 (1993).

    Article  CAS  Google Scholar 

  46. 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 

  47. Amundsen, S. et al. X-POV-Team POV-Ray: persistence of vision ray-tracer. http://www.povray.org. (1997).

    Google Scholar 

  48. Kleywegt, G.J. & Jones, T.A. Biomolecular speleology. CCP4/ESF-EACBM Newsletter on Protein Crystallography 29, 26–28 (1993).

    Google Scholar 

  49. Sali, A., & Blundell, T.L. Comparative protein Modelling by satisfaction of spatial restraints. J. Mol. Biol. 234, 779–815 (1993).

    Article  CAS  Google Scholar 

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Acknowledgements

We thank C. Lamb, C.M. Starks, C. Zubieta and M.A. Verdecia for discussion and comments on the manuscript, and W. Kwiatkowski for help making figures. We also thank one of the reviewers for suggesting alternate mechanistic interpretations. J.M.J. received a Hoffman Foundation Fellowship. This work was supported by funds form the Salk Institute and the Samuel Roberts Noble Foundation (J.P.N.).

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Authors and Affiliations

  1. Structural Biology Laboratory, The Salk Institute for Biological Studies, 10010 N. Torrey Pines Rd., La Jolla, 92037, California, USA

    Jean-Luc Ferrer, Joseph M. Jez, Marianne E. Bowman & Joseph P. Noel

  2. IBS J.-P. Ebel CEA-CNRS/LCCP, 41 avenue des Martyrs, Grenoble, 38027 Cedex 1, France

    Jean-Luc Ferrer

  3. Plant Biology Division, Samuel Roberts Noble Foundation, P.O. Box 2180, Ardmore, 73402, Oklahoma, USA

    Richard A. Dixon

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Correspondence to Joseph P. Noel.

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Ferrer, JL., Jez, J., Bowman, M. et al. Structure of chalcone synthase and the molecular basis of plant polyketide biosynthesis. Nat Struct Mol Biol 6, 775–784 (1999). https://doi.org/10.1038/11553

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