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Cited by 51Microbial Natural Products and BiosynthesisChemical Synthesis and AnalysisBiochemical and Structural Characterization

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Biosynthesis of Macrocyclic Peptides with C‑Terminal β‑Amino-α-keto Acid Groups by Three Different Metalloenzymes

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Nguyen, Dinh T., Zhu, Lingyang, Gray, Danielle L., Woods, Toby J., Padhi, Chandrashekhar, Flatt, Kristen M., Mitchell, Douglas A., van der Donk, Wilfred A.·2024·ACS Central Science
DOI 10.1021/acscentsci.4c00088PMC PMC11117315

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Abstract

Advances in genome sequencing and bioinformatics methods have identified a myriad of biosynthetic gene clusters (BGCs) encoding uncharacterized molecules. By mining genomes for BGCs containing a prevalent peptide-binding domain used for the biosynthesis of ribosomally synthesized and post-translationally modified peptides (RiPPs), we uncovered a new compound class involving modifications installed by a cytochrome P450, a multinuclear iron-dependent non-heme oxidative enzyme (MNIO, formerly DUF692), a cobalamin- and radical S-adenosyl-l-methionine-dependent enzyme (B12-rSAM), and a methyltransferase. All enzymes were functionally expressed in Burkholderia sp. FERM BP-3421. Structural characterization demonstrated that the P450 enzyme catalyzed the formation of a biaryl C–C cross-link between two Tyr residues with the B12-rSAM generating β-methyltyrosine. The MNIO transformed a C-terminal Asp residue into aminopyruvic acid, while the methyltransferase acted on the β-carbon of this α-keto acid. Exciton-coupled circular dichroism spectroscopy and microcrystal electron diffraction (MicroED) were used to elucidate the stereochemical configuration of the atropisomer formed upon biaryl cross-linking. To the best of our knowledge, the MNIO featured in this pathway is the first to modify a residue other than Cys. This study underscores the utility of genome mining to isolate new macrocyclic RiPPs biosynthesized via previously undiscovered enzyme chemistry.

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Metadata

Authors
Nguyen, D. T., Zhu, L., Gray, D. L., Woods, T. J., Padhi, C., Flatt, K. M., Mitchell, D. A., & van der Donk, W. A.
Affiliations
University of Illinois Urbana-Champaign (US)
Corresponding author
  • Mitchell, Douglas A.
  • van der Donk, Wilfred A.
ORCID
Venue
ACS Central Science
Publisher
American Chemical Society (ACS)
Published
2024-04-11
Volume
10
Issue
5
Pages
1022-1032
ISSN
  • 2374-7943 (ISSN-L)
  • 2374-7951
DOI
10.1021/acscentsci.4c00088
PMC
PMC11117315
OpenAlex
W4394727767
Cited by
51
References
2
Citations by year
2026: 21 · 2025: 19 · 2024: 11
FWCI
14.41
Type
journal article
Language
en
Open access
Licence
Locations
  • ACS Central Science (publishedVersion, cc-by)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • PubMed Central (submittedVersion, cc-by)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
Funders
  • , National Institute of General Medical Sciences (R37)
  • Division of Microbiology and Infectious Diseases (AI144967)
Topics
  • Life Sciences › Immunology and Microbiology › Applied Microbiology and Biotechnology › Microbial Natural Products and Biosynthesis
  • Physical Sciences › Chemistry › Organic Chemistry › Chemical Synthesis and Analysis
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Biochemical and Structural Characterization
Keywords
macrocyclic peptides, ribosomally synthesized and post-translationally modified peptides, biosynthetic gene clusters, genome mining, cytochrome P450, cobalamin-dependent enzymes, methyltransferase, atropisomerism, stereochemistry

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