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Structural basis for precursor protein–directed ribosomal peptide macrocyclization


Macrocyclization is a common feature of natural product biosynthetic pathways including the diverse family of ribosomal peptides. Microviridins are architecturally complex cyanobacterial ribosomal peptides that target proteases with potent reversible inhibition. The product structure is constructed via three macrocyclizations catalyzed sequentially by two members of the ATP-grasp family, a unique strategy for ribosomal peptide macrocyclization. Here we describe in detail the structural basis for the enzyme-catalyzed macrocyclizations in the microviridin J pathway of Microcystis aeruginosa. The macrocyclases MdnC and MdnB interact with a conserved α-helix of the precursor peptide using a novel precursor-peptide recognition mechanism. The results provide insight into the unique protein–protein interactions that are key to the chemistry, suggest an origin for the natural combinatorial synthesis of microviridin peptides, and provide a framework for future engineering efforts to generate designed compounds.

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Figure 1: Biosynthesis of microviridin J.
Figure 2: Binding and cyclization activity of macrocyclases toward MdnA variants.
Figure 3: Overall structures of MdnC and MdnB.
Figure 4: MdnC uses ATP to catalyze the macrocyclization of the precursor peptide MdnA.
Figure 5: Leader-peptide-directed peptide macrocyclization in the microviridin J biosynthetic pathway.

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We thank the staff at the 21-ID-G and 22-ID beamlines at Argonne National Laboratory Advanced Photon Source for help with data acquisition and processing. We thank T. Montavon and S. Lagishetty for providing experimental contributions supporting this work. We also are grateful to N. Polfer and A. Patrick for assistance with peptide synthesis. This work was supported by US National Institutes of Health grant GM086570 and funds from the University of Florida (S.D.B.).

Author information




K.L., H.L.C. and S.D.B. conceived the project and designed the experiments. K.L. and H.L.C. performed cloning, expression screening, protein purification, crystallization and X-ray diffraction data collection, structure solution and refinement. H.L.C. carried out kinetic analysis. K.L. and G.L. prepared and analyzed mutant proteins. K.L., H.L.C., Y.D. and S.D.B. interpreted the data and wrote the manuscript.

Corresponding author

Correspondence to Steven D Bruner.

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The authors declare no competing financial interests.

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Supplementary Results, Supplementary Tables 1–5 and Supplementary Figures 1–13. (PDF 1195 kb)

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Li, K., Condurso, H., Li, G. et al. Structural basis for precursor protein–directed ribosomal peptide macrocyclization. Nat Chem Biol 12, 973–979 (2016).

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