Abstract

Polyketide natural products constitute a broad class of compounds with diverse structural features and biological activities. Their biosynthetic machinery, represented by type I polyketide synthases (PKSs), has an architecture in which successive modules catalyse two-carbon linear extensions and keto-group processing reactions on intermediates covalently tethered to carrier domains. Here we used electron cryo-microscopy to determine sub-nanometre-resolution three-dimensional reconstructions of a full-length PKS module from the bacterium Streptomyces venezuelae that revealed an unexpectedly different architecture compared to the homologous dimeric mammalian fatty acid synthase. A single reaction chamber provides access to all catalytic sites for the intramodule carrier domain. In contrast, the carrier from the preceding module uses a separate entrance outside the reaction chamber to deliver the upstream polyketide intermediate for subsequent extension and modification. This study reveals for the first time, to our knowledge, the structural basis for both intramodule and intermodule substrate transfer in polyketide synthases, and establishes a new model for molecular dissection of these multifunctional enzyme systems.

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Data deposits

Cryo-EM maps have been deposited in the Electron Microscopy Data Bank under accession numbers EMD-5647 (holo-PikAIII conformation I), EMD-5648 (holo-PikAIII conformation II), EMD-5649 (PikAIII(ΔACP5)), EMD-5651 (pentaketide–ACP4–PikAIII(C209A/ΔACP5)), EMD-5653 (MM–PikAIII) and EMD-5662 (holo-ACP4–PikAIII(C209A/ΔACP5)).

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Acknowledgements

We thank R. Henderson for sharing the phase-randomization program and for valuable advice on the implementation of the tilt-pair validation, and Y. Cheng and X. Li for sharing the image sub-frame alignment program. This work was supported by the Pew Scholar Program in Biomedical Sciences (G.S.), the University of Michigan Biological Sciences Scholars Program (G.S.), Rackham Merit and American Foundation for Pharmaceutical Education predoctoral fellowships (D.A.H.), a National Research Service Award postdoctoral fellowship (J.A.C.), the Life Sciences Research Foundation (A.R.H.N.), National Institutes of Health grants 1R21CA138331-01A1 (K.H.), GM076477 (D.H.S. and J.L.S.), DK042303 (J.L.S.) and DK090165 (G.S.), and the Hans W. Vahlteich Professorship (to D.H.S.).

Author information

Author notes

    • Somnath Dutta
    •  & Jonathan R. Whicher

    These authors contributed equally to this work.

Affiliations

  1. Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, USA

    • Somnath Dutta
    • , Jonathan R. Whicher
    • , Douglas A. Hansen
    • , Joseph A. Chemler
    • , Grady R. Congdon
    • , Alison R. H. Narayan
    • , David H. Sherman
    • , Janet L. Smith
    •  & Georgios Skiniotis
  2. Chemical Biology Graduate Program, University of Michigan, Ann Arbor, Michigan 48109, USA

    • Jonathan R. Whicher
  3. Department of Medicinal Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA

    • Douglas A. Hansen
    •  & David H. Sherman
  4. Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA

    • Wendi A. Hale
    • , Kristina Håkansson
    •  & David H. Sherman
  5. Department of Microbiology & Immunology, University of Michigan, Ann Arbor, Michigan 48109, USA

    • David H. Sherman
  6. Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA

    • Janet L. Smith
    •  & Georgios Skiniotis

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Contributions

S.D. carried out cryo-EM data collection and processing. J.R.W. produced PikAIII variants and conducted enzyme assays. G.R.C. assisted with cryo-EM image processing. W.A.H., A.R.H.N. and K.H. carried out mass-spectrometry analysis. D.A.H. synthesized the thiophenol-activated pentaketide and pentaketide–CoA substrates. J.A.C. produced initial PikAIII samples and prepared Fig. 1. S.D., J.R.W., J.L.S. and G.S. analysed the data and interpreted results. K.H., D.H.S., J.L.S. and G.S. designed research. S.D., J.R.W., D.H.S., J.L.S. and G.S. wrote the manuscript.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Georgios Skiniotis.

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https://doi.org/10.1038/nature13423

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