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

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. Access through your institution Buy or subscribe This is a preview of subscription content, access via your institution ACCESS OPTIONS Access

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support SIMILAR CONTENT BEING VIEWED BY OTHERS C–N BOND FORMATION BY A POLYKETIDE SYNTHASE Article Open access 10 March 2023 STRUCTURE AND MECHANISM OF A DEHYDRATASE/DECARBOXYLASE ENZYME

COUPLE INVOLVED IN POLYKETIDE Β-METHYL BRANCH INCORPORATION Article Open access 18 September 2020 A POLYKETOACYL-COA THIOLASE-DEPENDENT PATHWAY FOR THE SYNTHESIS OF POLYKETIDE BACKBONES

Article 22 June 2020 DATA AVAILABILITY Structures have been deposited at the Protein Data Bank under accession codes 6KXD (Iga11–Iga12), 6KXE (C6=Iga11–Iga12) and 6KXF

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references 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). AUTHOR INFORMATION AUTHORS AND AFFILIATIONS * 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 * Collaborative Research Institute

for Innovative Microbiology, The University of Tokyo, Tokyo, Japan Yohei Katsuyama, Shinya Fushinobu & Yasuo Ohnishi * Department of Chemistry and Biochemistry, University of California,

San Diego, San Diego, CA, USA Aochiu Chen, Tony D. Davis & Michael D. Burkart Authors * Danyao Du View author publications You can also search for this author inPubMed Google Scholar *

Yohei Katsuyama View author publications You can also search for this author inPubMed Google Scholar * Masanobu Horiuchi View author publications You can also search for this author inPubMed

 Google Scholar * Shinya Fushinobu View author publications You can also search for this author inPubMed Google Scholar * Aochiu Chen View author publications You can also search for this

author inPubMed Google Scholar * Tony D. Davis View author publications You can also search for this author inPubMed Google Scholar * Michael D. Burkart View author publications You can also

search for this author inPubMed Google Scholar * Yasuo Ohnishi View author publications You can also search for this author inPubMed Google Scholar 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. CORRESPONDING AUTHORS Correspondence to Yohei Katsuyama or Michael D. Burkart. ETHICS DECLARATIONS

COMPETING INTERESTS The authors declare no competing interests. ADDITIONAL INFORMATION PUBLISHER’S NOTE Springer Nature remains neutral with regard to jurisdictional claims in published maps

and institutional affiliations. SUPPLEMENTARY INFORMATION SUPPLEMENTAL INFORMATION Supplementary Figs. 1–14 and Tables 1–4. REPORTING SUMMARY RIGHTS AND PERMISSIONS Reprints and permissions

ABOUT THIS ARTICLE CITE THIS ARTICLE 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 Download citation * Received: 02 October 2019 * Accepted: 27 March 2020 * Published: 04 May 2020 * Issue Date: July 2020 * DOI:

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