Structural basis of ribosomal peptide macrocyclization in plants

Joel Haywood, Jason W Schmidberger, Amy M James, Samuel G Nonis, Kirill V Sukhoverkov, Mikael Elias, Charles S Bond, Joshua S Mylne

Research output: Contribution to journalArticle

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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.

LanguageEnglish
Article numbere32955
JournaleLife
Volume7
DOIs
StatePublished - 31 Jan 2018

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asparaginylendopeptidase
Cyclic Peptides
Helianthus
Peptides
Plant Structures
Plant Genes
Pharmaceutical Preparations
Carrier concentration
Ligation
Catalytic Domain
Peptide Hydrolases
Genes
Crystal structure
Electrons
Water
Substrates
Enzymes

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Haywood, Joel ; Schmidberger, Jason W ; James, Amy M ; Nonis, Samuel G ; Sukhoverkov, Kirill V ; Elias, Mikael ; Bond, Charles S ; Mylne, Joshua S. / Structural basis of ribosomal peptide macrocyclization in plants. In: eLife. 2018 ; Vol. 7.
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Structural basis of ribosomal peptide macrocyclization in plants. / Haywood, Joel; Schmidberger, Jason W; James, Amy M; Nonis, Samuel G; Sukhoverkov, Kirill V; Elias, Mikael; Bond, Charles S; Mylne, Joshua S.

In: eLife, Vol. 7, e32955, 31.01.2018.

Research output: Contribution to journalArticle

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AU - Haywood,Joel

AU - Schmidberger,Jason W

AU - James,Amy M

AU - Nonis,Samuel G

AU - Sukhoverkov,Kirill V

AU - Elias,Mikael

AU - Bond,Charles S

AU - Mylne,Joshua S

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AB - 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.

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Haywood J, Schmidberger JW, James AM, Nonis SG, Sukhoverkov KV, Elias M et al. Structural basis of ribosomal peptide macrocyclization in plants. eLife. 2018 Jan 31;7. e32955. Available from, DOI: 10.7554/eLife.32955