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Cited by 2Microbial Natural Products and BiosynthesisEnzyme Structure and FunctionMetal-Catalyzed Oxygenation Mechanisms

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Broad substrate scope C-C oxidation in cyclodipeptides catalysed by a flavin-dependent filament

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Sutherland, Emmajay, Harding, Christopher J., du Monceau de Bergendal, Tancrède, Florence, Gordon J., Ackermann, Katrin, Bode, Bela E., Synowsky, Silvia, Sundaramoorthy, Ramasubramanian, Czekster, Clarissa Melo·2025·Nature Communications
DOI 10.1038/s41467-025-56127-yPMC PMC11760959

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Abstract

Cyclic dipeptides are produced by organisms across all domains of life, with many exhibiting anticancer and antimicrobial properties. Oxidations are often key to their biological activities, particularly C-C bond oxidation catalysed by tailoring enzymes including cyclodipeptide oxidases. These flavin-dependent enzymes are underexplored due to their intricate three-dimensional arrangement involving multiple copies of two distinct small subunits, and mechanistic details underlying substrate selection and catalysis are lacking. Here, we determined the structure and mechanism of the cyclodipeptide oxidase from the halophile Nocardiopsis dassonvillei (NdasCDO), a component of the biosynthetic pathway for nocazine natural products. We demonstrated that NdasCDO forms filaments in solution, with a covalently bound flavin mononucleotide (FMN) cofactor at the interface between three distinct subunits. The enzyme exhibits promiscuity, processing various cyclic dipeptides as substrates in a distributive manner. The reaction is optimal at high pH and involves the formation of a radical intermediate. Pre-steady-state kinetics, a significant solvent kinetic isotope effect, and the absence of viscosity effects suggested that a step linked to FMN regeneration controlled the reaction rate. Our work elucidates the complex mechanistic and structural characteristics of this dehydrogenation reaction, positioning NdasCDO as a promising biocatalyst and expanding the FMN-dependent oxidase family to include enzyme filaments.

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Metadata

Authors
Sutherland, E., Harding, C. J., du Monceau de Bergendal, T., Florence, G. J., Ackermann, K., Bode, B. E., Synowsky, S., Sundaramoorthy, R., & Czekster, C. M.
Affiliations
  • University of St Andrews (GB)
  • University of Dundee (GB)
Corresponding author
  • Sundaramoorthy, Ramasubramanian
  • Czekster, Clarissa Melo
ORCID
Venue
Nature Communications
Publisher
Springer Science and Business Media LLC
Published
2025-01-24
Volume
16
Issue
1
Pages
995-995
ISSN
2041-1723 (ISSN-L)
DOI
10.1038/s41467-025-56127-y
PMC
PMC11760959
OpenAlex
W4406795620
Cited by
2
References
1
Citations by year
2026: 2
FWCI
1.13
Type
journal article
Language
en
Open access
Licence
Locations
  • Nature Communications (publishedVersion, cc-by)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • Discovery Research Portal (University of Dundee) (publishedVersion, cc-by)
  • St Andrews Research Repository (St Andrews Research Repository) (submittedVersion, cc-by)
  • RePEc: Research Papers in Economics (submittedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
Funders
  • University of Dundee
  • Wellcome Trust (210486/Z/18/Z, 204821/Z/16/Z, 223816/Z/21/Z)
  • Diamond Light Source
  • University of St Andrews (204821/Z/16/Z)
  • Medical Research Council
  • Biotechnology and Biological Sciences Research Council (BB/R013780/, BB/R013780/1)
Topics
  • Life Sciences › Immunology and Microbiology › Applied Microbiology and Biotechnology › Microbial Natural Products and Biosynthesis
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › Enzyme Structure and Function
  • Physical Sciences › Chemistry › Inorganic Chemistry › Metal-Catalyzed Oxygenation Mechanisms
Keywords
Nocardiopsis dassonvillei, flavin mononucleotide, C=C bond oxidation, dehydrogenation, substrate promiscuity, radical intermediates, solvent kinetic isotope effect, enzyme mechanism, halophilic bacteria, biocatalysis
MeSH terms
Bacterial Proteins, Catalysis, Dipeptides, Flavins, Flavin Mononucleotide, Hydrogen-Ion Concentration, Kinetics, Models, Molecular, Oxidation-Reduction, Oxidoreductases, Peptides, Cyclic, Substrate Specificity, Crystallography, X-Ray, Actinobacteria, Biocatalysis

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