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Nature chemical biology
Mar, 2024;20 (3): 382-391.

Structural and mechanistic basis for RiPP epimerization by a radical SAM enzyme.

Xavier Kubiak, Ivan Polsinelli, Leonard M G Chavas, Cameron D Fyfe, Alain Guillot, Laura Fradale, Clémence Brewee, Stéphane Grimaldi, Guillaume Gerbaud, Aurélien Thureau, Pierre Legrand, Olivier Berteau, Alhosna Benjdia
Author Information
  1. Xavier Kubiak: Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, ChemSyBio, Jouy-en-Josas, France.
  2. Ivan Polsinelli: Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, ChemSyBio, Jouy-en-Josas, France.
  3. Leonard M G Chavas: Nagoya University, Nagoya, Japan.
  4. Cameron D Fyfe: Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, ChemSyBio, Jouy-en-Josas, France.
  5. Alain Guillot: Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, ChemSyBio, Jouy-en-Josas, France.
  6. Laura Fradale: Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, ChemSyBio, Jouy-en-Josas, France.
  7. Clémence Brewee: Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, ChemSyBio, Jouy-en-Josas, France.
  8. Stéphane Grimaldi: Aix-Marseille Université, CNRS, BIP, IMM, IM2B, Marseille, France. ORCID
  9. Guillaume Gerbaud: Aix-Marseille Université, CNRS, BIP, IMM, IM2B, Marseille, France. ORCID
  10. Aurélien Thureau: Synchrotron SOLEIL, HelioBio Group, L'Orme des Merisiers, Saint-Aubin, France. ORCID
  11. Pierre Legrand: Synchrotron SOLEIL, HelioBio Group, L'Orme des Merisiers, Saint-Aubin, France. ORCID
  12. Olivier Berteau: Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, ChemSyBio, Jouy-en-Josas, France. olivier.berteau@inrae.fr. ORCID
  13. Alhosna Benjdia: Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, ChemSyBio, Jouy-en-Josas, France. alhosna.benjdia@inrae.fr. ORCID
PMID: 38158457 DOI: 10.1038/s41589-023-01493-1

Abstract

D-Amino acid residues, found in countless peptides and natural products including ribosomally synthesized and post-translationally modified peptides (RiPPs), are critical for the bioactivity of several antibiotics and toxins. Recently, radical S-adenosyl-L-methionine (SAM) enzymes have emerged as the only biocatalysts capable of installing direct and irreversible epimerization in RiPPs. However, the mechanism underpinning this biochemical process is ill-understood and the structural basis for this post-translational modification remains unknown. Here we report an atomic-resolution crystal structure of a RiPP-modifying radical SAM enzyme in complex with its substrate properly positioned in the active site. Crystallographic snapshots, size-exclusion chromatography-small-angle x-ray scattering, electron paramagnetic resonance spectroscopy and biochemical analyses reveal how epimerizations are installed in RiPPs and support an unprecedented enzyme mechanism for peptide epimerization. Collectively, our study brings unique perspectives on how radical SAM enzymes interact with RiPPs and catalyze post-translational modifications in natural products.

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Grants

  1. ANR-17-CE11-0014/Agence Nationale de la Recherche (French National Research Agency)
  2. ANR-20-CE44-0005/Agence Nationale de la Recherche (French National Research Agency)

MeSH Term

S-Adenosylmethionine
Amino Acids
Anti-Bacterial Agents
Biological Products
Peptides

Chemicals

S-Adenosylmethionine
Amino Acids
Anti-Bacterial Agents
Biological Products
Peptides
Journal Article
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Word Cloud

Created with Highcharts 10.0.0RiPPsradicalSAMepimerizationenzymepeptidesnaturalproductsenzymesmechanismbiochemicalbasispost-translationalD-Aminoacidresiduesfoundcountlessincludingribosomallysynthesizedpost-translationallymodifiedcriticalbioactivityseveralantibioticstoxinsRecentlyS-adenosyl-L-methionineemergedbiocatalystscapableinstallingdirectirreversibleHoweverunderpinningprocessill-understoodstructuralmodificationremainsunknownreportatomic-resolutioncrystalstructureRiPP-modifyingcomplexsubstrateproperlypositionedactivesiteCrystallographicsnapshotssize-exclusionchromatography-small-anglex-rayscatteringelectronparamagneticresonancespectroscopyanalysesrevealepimerizationsinstalledsupportunprecedentedpeptideCollectivelystudybringsuniqueperspectivesinteractcatalyzemodificationsStructuralmechanisticRiPP

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