Broad substrate scope C-C oxidation in cyclodipeptides catalysed by a flavin-dependent filament
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. Th...
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Nature Portfolio
2025-01-01
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| Online Access: | https://doi.org/10.1038/s41467-025-56127-y |
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| author | Emmajay Sutherland Christopher J. Harding Tancrède du Monceau de Bergendal Gordon J. Florence Katrin Ackermann Bela E. Bode Silvia Synowsky Ramasubramanian Sundaramoorthy Clarissa Melo Czekster |
| author_facet | Emmajay Sutherland Christopher J. Harding Tancrède du Monceau de Bergendal Gordon J. Florence Katrin Ackermann Bela E. Bode Silvia Synowsky Ramasubramanian Sundaramoorthy Clarissa Melo Czekster |
| author_sort | Emmajay Sutherland |
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| description | 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. |
| format | Article |
| id | doaj-art-eb04d6c7c74445baa692a96fda3041bc |
| institution | Kabale University |
| issn | 2041-1723 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Nature Communications |
| spelling | doaj-art-eb04d6c7c74445baa692a96fda3041bc2025-01-26T12:40:16ZengNature PortfolioNature Communications2041-17232025-01-0116111410.1038/s41467-025-56127-yBroad substrate scope C-C oxidation in cyclodipeptides catalysed by a flavin-dependent filamentEmmajay Sutherland0Christopher J. Harding1Tancrède du Monceau de Bergendal2Gordon J. Florence3Katrin Ackermann4Bela E. Bode5Silvia Synowsky6Ramasubramanian Sundaramoorthy7Clarissa Melo Czekster8University of St Andrews, School of Biology, North Haugh, Biomolecular Sciences BuildingUniversity of St Andrews, School of Biology, North Haugh, Biomolecular Sciences BuildingUniversity of St Andrews, School of Biology, North Haugh, Biomolecular Sciences BuildingUniversity of St Andrews, EaStCHEM School of Chemistry, North Haugh, Purdie BuildingUniversity of St Andrews, EaStCHEM School of Chemistry, North Haugh, Purdie BuildingUniversity of St Andrews, EaStCHEM School of Chemistry, North Haugh, Purdie BuildingUniversity of St Andrews, BSRC Mass Spectrometry and Proteomics Facility, North Haugh, Biomolecular Sciences BuildingLaboratory of Chromatin Structure and Function, MCDB, School of Life Sciences, University of DundeeUniversity of St Andrews, School of Biology, North Haugh, Biomolecular Sciences BuildingAbstract 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.https://doi.org/10.1038/s41467-025-56127-y |
| spellingShingle | Emmajay Sutherland Christopher J. Harding Tancrède du Monceau de Bergendal Gordon J. Florence Katrin Ackermann Bela E. Bode Silvia Synowsky Ramasubramanian Sundaramoorthy Clarissa Melo Czekster Broad substrate scope C-C oxidation in cyclodipeptides catalysed by a flavin-dependent filament Nature Communications |
| title | Broad substrate scope C-C oxidation in cyclodipeptides catalysed by a flavin-dependent filament |
| title_full | Broad substrate scope C-C oxidation in cyclodipeptides catalysed by a flavin-dependent filament |
| title_fullStr | Broad substrate scope C-C oxidation in cyclodipeptides catalysed by a flavin-dependent filament |
| title_full_unstemmed | Broad substrate scope C-C oxidation in cyclodipeptides catalysed by a flavin-dependent filament |
| title_short | Broad substrate scope C-C oxidation in cyclodipeptides catalysed by a flavin-dependent filament |
| title_sort | broad substrate scope c c oxidation in cyclodipeptides catalysed by a flavin dependent filament |
| url | https://doi.org/10.1038/s41467-025-56127-y |
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