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Structural basis for selectivity in a highly reducing type II polyketide synthase

Nature Chemical Biology volume 16, pages 776–782 (2020)Cite this article

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Abstract

In type II polyketide synthases (PKSs), the ketosynthase–chain length factor (KS–CLF) complex catalyzes polyketide chain elongation with the acyl carrier protein (ACP). Highly reducing type II PKSs, represented by IgaPKS, produce polyene structures instead of the well-known aromatic skeletons. Here, we report the crystal structures of the Iga11–Iga12 (KS–CLF) heterodimer and the covalently cross-linked Iga10=Iga11–Iga12 (ACP=KS–CLF) tripartite complex. The latter structure revealed the molecular basis of the interaction between Iga10 and Iga11–Iga12, which differs from that between the ACP and KS of Escherichia coli fatty acid synthase. Furthermore, the reaction pocket structure and site-directed mutagenesis revealed that the negative charge of Asp 113 of Iga11 prevents further condensation using a β-ketoacyl product as a substrate, which distinguishes IgaPKS from typical type II PKSs. This work will facilitate the future rational design of PKSs.

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Fig. 1: The reaction catalyzed by IgaPKS and overall structures of Iga11–Iga12 in three different states.
Fig. 2: Interaction between Iga11–Iga12 and Iga10.
Fig. 3: The reaction pocket structure of C8Cl-Iga10=Iga11–Iga12.
Fig. 4: The proposed mechanism of the reaction catalyzed by Iga11–Iga12.

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Data availability

Structures have been deposited at the Protein Data Bank under accession codes 6KXD (Iga11–Iga12), 6KXE (C6=Iga11–Iga12) and 6KXF (C8Cl-Iga10=Iga11–Iga12).

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Acknowledgements

We thank A. Harada and M. Senda, and the staff of the Photon Factory and Swiss Light Source (proposal number 2017G165) for the X-ray data collection. The research is supported by Grants-in-Aid for Scientific Research on Innovative Areas from the Ministry of Education, Culture, Sports, Science and Technology of Japan (JP18H02144 and JP19H04645 to Y.K.), a Research Fellow Grant-in-Aid from the Japan Society for the Promotion of Science (JSPS; JP17J09439, to D.D.), JSPS A3 Foresight Program grant (to Y.O.), NIH R01 grant GM095970 to M.D.B. and NIH K12 GM068524 grant, to T.D.D. (San Diego IRACDA Postdoctoral Fellow).

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Authors and Affiliations

  1. Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan

    Danyao Du, Yohei Katsuyama, Masanobu Horiuchi, Shinya Fushinobu & Yasuo Ohnishi

  2. Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo, Japan

    Yohei Katsuyama, Shinya Fushinobu & Yasuo Ohnishi

  3. Department of Chemistry and Biochemistry, University of California, San Diego, San Diego, CA, USA

    Aochiu Chen, Tony D. Davis & Michael D. Burkart

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Contributions

Y.K., M.D.B. and D.D. designed the research. T.D.D. synthesized the chemical probes. The crystallization of the proteins was done by D.D. The X-ray diffraction experiment was carried out by Y.K. and D.D. The experimental phasing was done by Y.K. Refinement and validation of the structure was done by D.D., Y.K. and S.F. Site-directed mutagenesis and analysis of mutants were done by D.D. and M.H. The cross-linked complex was prepared by D.D. and A.C. D.D. and Y.K. wrote the draft manuscript. A.C., T.D.D., M.D.B., S.F. and Y.O. commented on the draft. Y.K. and Y.O. finalized the manuscript and all authors approved it. Y.K., M.D.B. and Y.O. directed the research.

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Correspondence to Yohei Katsuyama or Michael D. Burkart.

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Du, D., Katsuyama, Y., Horiuchi, M. et al. Structural basis for selectivity in a highly reducing type II polyketide synthase. Nat Chem Biol 16, 776–782 (2020). https://doi.org/10.1038/s41589-020-0530-0

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