PXD058613-1

PXD058613 is an original dataset announced via ProteomeXchange.

Title	Broad substrate scope C-C oxidation in cyclodipeptides catalysed by a flavin-dependent filament
Description	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 catalyzed 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 demonstrate 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 suggest that a step linked to FMN regeneration controls 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.
HostingRepository	PRIDE
AnnounceDate	2025-01-06
AnnouncementXML	Submission_2025-01-06_05:56:57.303.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Sally Shirran
SpeciesList	scientific name: Nocardiopsis dassonvillei; NCBI TaxID: 2014;
ModificationList	iodoacetic acid derivatized residue
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2024-12-05 08:34:00	ID requested
⏵ 1	2025-01-06 05:56:57	announced

Dataset with its publication pending

submitter keyword: Diketopiperazine, flavin, oxidation, cyclodipeptide, filament

Clarissa Melo Czekster
contact affiliation	School of Biology, University of St Andrews, Biomedical Sciences Research Complex, St Andrews, Fife KY16 9ST, U.K.
contact email	cmc27@st-andrews.ac.uk
lab head
Sally Shirran
contact affiliation	University of St Andrews
contact email	ss101@st-andrews.ac.uk
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD058613
     1. Label: PRIDE project
     2. Name: Broad substrate scope C-C oxidation in cyclodipeptides catalysed by a flavin-dependent filament