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Regio- and stereodivergent antibiotic oxidative carbocyclizations catalysed by Rieske oxygenase-like enzymes


Oxidative cyclizations, exemplified by the biosynthetic assembly of the penicillin nucleus from a tripeptide precursor, are arguably the most synthetically powerful implementation of C–H activation reactions in nature. Here, we show that Rieske oxygenase-like enzymes mediate regio- and stereodivergent oxidative cyclizations to form 10- and 12-membered carbocyclic rings in the key steps of the biosynthesis of the antibiotics streptorubin B and metacycloprodigiosin, respectively. These reactions represent the first examples of oxidative carbocyclizations catalysed by non-haem iron-dependent oxidases and define a novel type of catalytic activity for Rieske enzymes. A better understanding of how these enzymes achieve such remarkable regio- and stereocontrol in the functionalization of unactivated hydrocarbon chains will greatly facilitate the development of selective man-made C–H activation catalysts.

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Figure 1: Key oxidative cyclization reactions in the biosynthesis of clinically used natural products.
Figure 2: Roles of Rieske non-haem iron-dependent oxygenases and oxidative cyclases, together with associated enzymes, in the biosynthesis of natural products and the degradation of organic compounds.
Figure 3: Data that elucidate the role of RedG and McpG in streptorubin B (9) and metacycloprodigiosin (7) biosynthesis, respectively.


  1. Konomi, T. et al. Cell-free conversion of δ-(L-alpha-aminoadipyl)-L-cysteinyl-D-valine into an antibiotic with the properties of isopenicillin N in Cephalosporium acremonium. Biochem. J. 184, 427–430 (1979).

    CAS  Article  Google Scholar 

  2. Elson, S. W. et al. Isolation of two novel intracellular β-lactams and a novel dioxygenase cyclizing enzyme from Streptomyces clavuligerus. J. Chem. Soc., Chem. Commun. 1736–1738 (1987).

  3. Seto, H. et al. Studies on the biosynthesis of fosfomycin. 2. Conversion of 2-hydroxypropyl-phosphonic acid to fosfomycin by blocked mutants of Streptomyces wedmorensis. J. Antibiot. 44, 1286–1288 (1991).

    CAS  Article  Google Scholar 

  4. Hammerschmidt, F. Biosynthesis of natural products with a P–C bond. Part 8: on the origin of the oxirane oxygen atom of fosfomycin in Streptomyces fradiae. J. Chem. Soc. Perkin Trans. 1 1993–1996 (1991).

  5. Zerbe, K. et al. An oxidative phenol coupling reaction catalyzed by OxyB, a cytochrome P450 from the vancomycin-producing microorganism. Angew. Chem. Int. Ed. 43, 6709–6713 (2004).

    CAS  Article  Google Scholar 

  6. Hollander, I. J., Shen, Y.-Q., Heim, J., Demain, A. L. & Wolfe, S. A pure enzyme catalyzing penicillin biosynthesis. Science 224, 610–612 (1984).

    CAS  Article  Google Scholar 

  7. Liu, P. et al. Protein purification and function assignment of the epoxidase catalyzing the formation of fosfomycin. J. Am. Chem. Soc. 123, 4619–4620 (2001).

    CAS  Article  Google Scholar 

  8. Roach, P. L. et al. Crystal structure of isopenicillin N synthase is the first from a new structural family of enzymes. Nature 375, 700–704 (1995).

    CAS  Article  Google Scholar 

  9. Zhang, Z. et al. Structural origins of the selectivity of the trifunctional oxygenase clavaminic acid synthase. Nature Struct. Biol. 7, 127–133 (2000).

    CAS  Article  Google Scholar 

  10. Higgins, L. J., Yan, F., Liu, P., Liu, H.-W. & Drennan, C. L. Structural insight into antibiotic fosfomycin biosynthesis by a mononuclear iron enzyme. Nature 437, 838–844 (2005).

    CAS  Article  Google Scholar 

  11. Zerbe, K. et al. Crystal structure of OxyB, a cytochrome P450 implicated in an oxidative phenol coupling reaction during vancomycin biosynthesis. J. Biol. Chem. 277, 47476–47485 (2002).

    CAS  Article  Google Scholar 

  12. Howard-Jones A. R. & Walsh, C. T. Staurosporine and rebeccamycin aglycones are assembled by the oxidative action of StaP, StaC and RebC on chromopyrrolic acid. J. Am. Chem. Soc. 128, 12289–12298 (2006).

    CAS  Article  Google Scholar 

  13. Winkler A. et al. A concerted mechanism for berberine bridge enzyme. Nature Chem. Biol. 4, 739–741 (2008).

    CAS  Article  Google Scholar 

  14. Roach, P. L. et al. Structure of isopenicillin N synthase complexed with substrate and the mechanism of penicillin formation. Nature 387, 827–830 (1997).

    CAS  Article  Google Scholar 

  15. Burzlaff, N. I. et al. The reaction cycle of isopenicillin N synthase observed by X-ray diffraction. Nature 401, 721–724 (1999).

    CAS  Article  Google Scholar 

  16. Price, J. C., Barr, E. W., Tirupati, B., Bollinger, J. M. Jr & Krebs, C. The first direct characterization of a high-valent iron intermediate in the reaction of an α-ketoglutarate-dependent dioxygenase: a high-spin FeIV complex in taurine/α-ketoglutarate dioxygenase (TauD) from Escherichia coli. Biochemistry 42, 7497–7508 (2003).

    CAS  Article  Google Scholar 

  17. Mirica, L. M., McCusker, K. P., Munos, J. W., Liu, H.-W. & Klinman, J. P. 18O kinetic isotope effects in non-heme iron enzymes: probing the nature of Fe/O2 intermediates J. Am. Chem. Soc. 130, 8122–8123 (2008).

    CAS  Article  Google Scholar 

  18. Wasserman, H. H., Shaw, C. K., Sykes, R. J. & Cushley, R. J. Biosynthesis of prodigiosin. III. Carbon-13 Fourier transform NMR. X. Biosynthesis of metacycloprodigiosin and undecylprodigiosin. Tetrahedron Lett. 2787–2790 (1974).

  19. Wasserman, H. H., Rodgers, G. C. & Keith, D. D. Metacycloprodigiosin, a tripyrrole pigment from Streptomyces longisporus ruber. J. Am. Chem. Soc. 91, 1263–1264 (1969).

    CAS  Article  Google Scholar 

  20. Wasserman, H. H., Rodgers, G. C. & Keith, D. D. Structure and synthesis of undecylprodigiosin. Prodigiosin analog from Streptomyces. Chem. Commun. 825–826 (1966).

  21. Laatsch, H., Kellner, M. & Weyland, H. Butyl-meta-cycloheptylprodiginine — a revision of the structure of the former ortho-isomer. J. Antibiot. 44, 187–191 (1991).

    CAS  Article  Google Scholar 

  22. Kawasaki, T., Sakurai, F. & Hayakawa, Y. A prodigiosin from the roseophilin producer Streptomyces griseoviridis. J. Nat. Prod. 71, 1265–1267 (2008).

    CAS  Article  Google Scholar 

  23. Kayakawa, Y., Kawakami, K., Seto, H. & Furihata, K. Structure of a new antibiotic, roseophilin. Tetrahedron Lett. 33, 2701–2704 (1992).

    CAS  Article  Google Scholar 

  24. Nguyen, M. et al. Small molecule obatoclax (GX15-070) antagonizes MCL-1 and overcomes MCL-1-mediated resistance to apoptosis. Proc. Natl Acad. Sci. USA 104, 19512–19517 (2007).

    CAS  Article  Google Scholar 

  25. Mo, S. J. et al. Elucidation of the Streptomyces coelicolor pathway to 2-undecylpyrrole, a key intermediate in undecylprodiginine and streptorubin B biosynthesis. Chem. Biol. 15, 137–148 (2008).

    CAS  Article  Google Scholar 

  26. Stanley, A. E., Walton, L. J., Kourdi-Zerikly, M., Corre, C. & Challis, G. L. Elucidation of the Streptomyces coelicolor pathway to 4-methoxy-2,2′-bipyrrole-5-carboxaldehyde, an intermediate in prodiginine biosynthesis. Chem. Commun. 3981–3983 (2006).

  27. Haynes, S. W., Sydor, P. K., Stanley, A. E., Song, L. & Challis, G. L. Role and substrate specificity of the Streptomyces coelicolor RedH enzyme in undecylprodiginine biosynthesis. Chem. Commun. 1865–1867 (2008).

  28. Cerdeno, A. M., Bibb M. J. & Challis, G. L. Analysis of the prodiginine biosynthesis gene cluster of Streptomyces coelicolor A3(2): new mechanisms for chain initiation and termination in modular multienzymes. Chem. Biol. 8, 817–829 (2001).

    CAS  Article  Google Scholar 

  29. Kauppi, B. et al. Structure of an aromatic-ring-hydroxylating dioxygenase-naphthalene 1,2-dioxygenase. Structure 6, 571–586 (1998).

    CAS  Article  Google Scholar 

  30. Gibson, D. T. & Parales R. E. Aromatic hydrocarbon dioxygenases in environmental biotechnology. Curr. Opin. Biotechnol. 11, 236–243 (2000).

    CAS  Article  Google Scholar 

  31. Lee, J., Simurdiak, M. & Zhao, H. Reconstitution and characterization of aminopyrrolnitrin oxygenase, a Rieske N-oxygenase that catalyzes unusual arylamine oxidation. J. Biol. Chem. 280, 36719–36727 (2005).

    CAS  Article  Google Scholar 

  32. Ferraro D. J., Gakhar L. & Ramaswamy S. Rieske business: structure–function of Rieske non-heme oxygenases. Biochem. Biophys. Res. Commun. 338, 175–190 (2005).

    CAS  Article  Google Scholar 

  33. Gust, B., Challis, G. L., Fowler, K., Kieser T., & Chater K. F. PCR-targeted Streptomyces gene replacement identifies a protein domain needed for biosynthesis of the sesquiterpene soil odor geosmin. Proc. Natl Acad. Sci. USA 100, 1541–1546 (2003).

    CAS  Article  Google Scholar 

  34. Hu, D. X., Clift, M. D., Lazarski, K. E. & Thomson R. J. Enantioselective total synthesis and confirmation of the absolute and relative stereochemistry of streptorubin B. J. Am. Chem. Soc. 133, 1799–1804 (2011).

    CAS  Article  Google Scholar 

  35. Haynes, S. W., Sydor, P. K., Corre, C., Song, L. & Challis G. L. Stereochemical elucidation of streptorubin B. J. Am. Chem. Soc. 133, 1793–1798 (2011).

    CAS  Article  Google Scholar 

  36. Kawasaki, T., Sakurai, F., Nagatsuka, S. & Hayakawa, Y. Prodigiosin biosynthesis gene cluster in the roseophilin producer Streptomyces griseoviridis. J. Antibiot. 62, 271–276 (2009).

    CAS  Article  Google Scholar 

  37. Bugg, T. D. H. & Ramaswamy, S. Non-heme iron-dependent dioxygenases: unraveling catalytic mechanisms for complex enzymatic oxidations. Curr. Opin. Chem. Biol. 12, 134–140 (2008).

    CAS  Article  Google Scholar 

  38. Chakrabarty, S., Austin, R. N., Deng, D., Groves, J. T. & Lipscomb, J. D. Radical intermediates in monooxygenase reactions of Rieske dioxygenases. J. Am. Chem. Soc. 129, 3514–3515 (2007).

    CAS  Article  Google Scholar 

  39. Chen, M. S. & White, M. C. A predictably selective aliphatic C–H oxidation reaction for complex molecule synthesis. Science 318, 783–787 (2007).

    CAS  Article  Google Scholar 

  40. Stang, E. M. & White, M. C. Total synthesis and study of 6-deoxyerythronolide B by late-stage C–H oxidation. Nature Chem. 1, 547–551 (2009).

    CAS  Article  Google Scholar 

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The authors acknowledge financial support from the University of Warwick, the National Institutes of Health (1R01GM77147-01A1), the Engineering and Physical Sciences Research Council and the European Union (contract no. 005224). The authors also thank R. Thomson for kindly providing the synthetic sample of the carbocyclic derivative of 2-undecylpyrrole. The assistance of D. Oves-Costales with the chemical conversion of desmethylundecylprodigiosin to undecylprodigiosin is gratefully acknowledged.

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P.K.S., S.M.B., O.M.O., F.B.G., S.W.H, C.C., L.S. and G.L.C. designed the research. P.K.S., S.M.B., O.M.O., F.B.G., S.W.H, C.C. and L.S. performed the research. P.K.S., S.M.B., O.M.O., F.B.G., S.W.H, C.C., L.S. and G.L.C. interpreted the data. G.L.C., P.K.S. and S.M.B. wrote the paper.

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Correspondence to Gregory L. Challis.

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Sydor, P., Barry, S., Odulate, O. et al. Regio- and stereodivergent antibiotic oxidative carbocyclizations catalysed by Rieske oxygenase-like enzymes. Nature Chem 3, 388–392 (2011).

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