Structural basis of ribosomal peptide macrocyclization in plants

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Abstract

Constrained, cyclic peptides encoded by plant genes represent a new generation of drug leads. Evolution has repeatedly recruited the Cys-protease asparaginyl endopeptidase (AEP) to perform their head-to-tail ligation. These macrocyclization reactions use the substrates amino terminus instead of water to deacylate, so a peptide bond is formed. How solvent-exposed plant AEPs macrocyclize is poorly understood. Here we present the crystal structure of an active plant AEP from the common sunflower, Helianthus annuus. The active site contained electron density for a tetrahedral intermediate with partial occupancy that predicted a binding mode for peptide macrocyclization. By substituting catalytic residues we could alter the ratio of cyclic to acyclic products. Moreover, we showed AEPs from other species lacking cyclic peptides can perform macrocyclization under favorable pH conditions. This structural characterization of AEP presents a logical framework for engineering superior enzymes that generate macrocyclic peptide drug leads.

Data availability

The following data sets were generated

1. Bond CS
(2017) Asparaginyl endopeptidase 1 bound to AAN peptide, a tetrahedral intermediate
Available at Protein Data Bank under accession code number 6AZT.

http://www.rcsb.org/pdb/search/structidSearch.do?structureId=6AZT

Article and author information

Author details

Joel Haywood

School of Molecular Sciences, The University of Western Australia, Perth, Australia

Competing interests
The authors declare that no competing interests exist.
Jason W Schmidberger

School of Molecular Sciences, The University of Western Australia, Perth, Australia

Competing interests
The authors declare that no competing interests exist.
Amy M James

School of Molecular Sciences, The University of Western Australia, Perth, Australia

Competing interests
The authors declare that no competing interests exist.
Samuel G Nonis

School of Molecular Sciences, The University of Western Australia, Perth, Australia

Competing interests
The authors declare that no competing interests exist.
Kirill V Sukhoverkov

School of Molecular Sciences, The University of Western Australia, Perth, Australia

Competing interests
The authors declare that no competing interests exist.
Mikael Elias

Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, St Paul, United States

Competing interests
The authors declare that no competing interests exist.
Charles S Bond

School of Molecular Sciences, The University of Western Australia, Perth, Australia

Competing interests
The authors declare that no competing interests exist.
Joshua S Mylne

School of Molecular Sciences, The University of Western Australia, Perth, Australia

For correspondence
joshua.mylne@uwa.edu.au

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0003-4957-6388

Funding

Australian Research Council (FT120100013)

Joshua S Mylne

Australian Research Council (DP160100107)

Joshua S Mylne

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Copyright

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.