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Enzymatic catalysis of anti-Baldwin ring closure in polyether biosynthesis

Nature volume 483, pages 355–358 (2012)Cite this article

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Abstract

Polycyclic polyether natural products have fascinated chemists and biologists alike owing to their useful biological activity, highly complex structure and intriguing biosynthetic mechanisms. Following the original proposal for the polyepoxide origin of lasalocid and isolasalocid1 and the experimental determination of the origins of the oxygen and carbon atoms of both lasalocid and monensin, a unified stereochemical model for the biosynthesis of polyether ionophore antibiotics was proposed2. The model was based on a cascade of nucleophilic ring closures of postulated polyepoxide substrates generated by stereospecific oxidation of all-trans polyene polyketide intermediates2. Shortly thereafter, a related model was proposed for the biogenesis of marine ladder toxins, involving a series of nominally disfavoured anti-Baldwin, endo-tet epoxide-ring-opening reactions3,4,5. Recently, we identified Lsd19 from the Streptomyces lasaliensis gene cluster as the epoxide hydrolase responsible for the epoxide-opening cyclization of bisepoxyprelasalocid A6 to form lasalocid A7,8. Here we report the X-ray crystal structure of Lsd19 in complex with its substrate and product analogue9 to provide the first atomic structure—to our knowledge—of a natural enzyme capable of catalysing the disfavoured epoxide-opening cyclic ether formation. On the basis of our structural and computational studies, we propose a general mechanism for the enzymatic catalysis of polyether natural product biosynthesis.

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Figure 1: Polyether natural products and proposed steps in the cyclic ether formation.
Figure 2: Crystal structure of Lsd19.
Figure 3: Computational studies of the Lsd19-catalysed epoxide-opening cyclization reactions.

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Protein Data Bank

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The coordinates and structure factors have been deposited with the Protein Data Bank under accession number 3RGA. Reprints and permissions information is available at www.nature.com/reprints.

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Acknowledgements

This work was supported by the Royal Commission for the Exhibition of 1851 and Fulbright-AstraZeneca Research Fellowship (R.S.P.), the Japan Society for the Promotion of Science (No. LS103) (K.W.), the National Institutes of Health grant GM075962 (K.N.H.), the MEXT research grant on innovative area 22108002 (H.O.), and the National University of Singapore Life Sciences Institute Young Investigator Award (C.-Y.K.). Data collection was performed at the Stanford Synchrotron Radiation Lightsource. We thank D. W. Christianson, D. Hilvert and C. Khosla for critical reading and discussion of the manuscript.

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Author notes

  1. Kinya Hotta and Xi Chen: These authors contributed equally to this work.

Authors and Affiliations

  1. Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, 117543 Singapore,

    Kinya Hotta, Xi Chen, Hao Li, Kunchithapadam Swaminathan & Chu-Young Kim

  2. Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK,

    Robert S. Paton

  3. Division of Chemistry, Hokkaido University, Graduate School of Science, North 10 West 8, Sapporo 060-0810, Japan,

    Atsushi Minami & Hideaki Oikawa

  4. Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, 2575 Sand Hill Road MS 99, Menlo Park, California 95124, USA,

    Irimpan I. Mathews

  5. Division of Pharmaceutical Sciences, University of Shizuoka, Graduate School of Pharmaceutical Sciences, 52-1 Yada, Suruga-ku, Shizuoka City, Shizuoka 422-8526, Japan,

    Kenji Watanabe

  6. Department of Chemistry and Biochemistry, University of California Los Angeles, 607 Charles E. Young Drive East, Box 951569, Los Angeles, California 90095-1569, USA,

    Kendall N. Houk

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  1. Kinya Hotta
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Contributions

A.M. and H.O. prepared the substrate analogue. K.W. cloned and purified Lsd19. X.C. and H.L. purified and crystallized Lsd19. X.C. and I.I.M. collected diffraction data and determined the structure. K.H., X.C. and I.I.M. refined the structure. K.S. provided assistance for crystallography. K.N.H. prepared and analysed models of Lsd19 homologues. R.S.P. and K.N.H. performed the computational study. C.-Y.K. conceived and supervised the project. C.-Y.K. prepared the manuscript with contributions from all co-authors.

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Correspondence to Chu-Young Kim.

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The authors declare no competing financial interests.

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Hotta, K., Chen, X., Paton, R. et al. Enzymatic catalysis of anti-Baldwin ring closure in polyether biosynthesis. Nature 483, 355–358 (2012). https://doi.org/10.1038/nature10865

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