PXD041104

PXD041104 is an original dataset announced via ProteomeXchange.

Title	Mass spectrometric analyses for the C281-dimedone adduct and the sulfinylated peptide fragments of Orf1
Description	Oxidized cysteine residues are highly reactive and can form functional covalent conjugates, of which the allosteric redox switch formed by the lysine-cysteine NOS bridge is an example. Here, we report a non-canonical FAD-dependent enzyme Orf1 that adds a glycine-derived N-formimidoyl group to glycinothricin to form the antibiotic BD-12. X-ray crystallography was used to investigate this complex enzymatic process, which showed Orf1 has two substrate-binding sites that sit 13.5 Å apart unlike canonical FAD-dependent oxidoreductases. One site could accommodate glycine and the other glycinothricin or glycylthricin. Moreover, an intermediate-enzyme adduct with a NOS-covalent linkage was observed in the later site, where it acts as a two-scissile-bond linkage facilitating nucleophilic addition and cofactor-free decarboxylation. The chain length of nucleophilic acceptors vies with bond cleavage sites at either N–O or O–S accounting for N-formimidoylation or N-iminoacetylation. The resultant product is no longer sensitive to aminoglycoside-modifying enzymes, a strategy that antibiotic-producing species employ to counter drug resistance in competing species.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_08:47:34.906.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD041104
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Yung-Lin Wang
SpeciesList	scientific name: Escherichia coli; NCBI TaxID: 562;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Synapt MS

Revision	Datetime	Status	ChangeLog Entry
0	2023-03-24 20:11:52	ID requested
1	2023-05-10 14:42:05	announced
⏵ 2	2023-11-14 08:47:38	announced	2023-11-14: Updated project metadata.

Wang YL, Chang CY, Hsu NS, Lo IW, Lin KH, Chen CL, Chang CF, Wang ZC, Ogasawara Y, Dairi T, Maruyama C, Hamano Y, Li TL, N-Formimidoylation/-iminoacetylation modification in aminoglycosides requires FAD-dependent and ligand-protein NOS bridge dual chemistry. Nat Commun, 14(1):2528(2023) [pubmed]

10.6019/PXD041104;

submitter keyword: N-formimmidolation and iminoacetylation enzyme

Tsung-Lin Li
contact affiliation	Genomics Research Center, Academia Sinica, Taipei, 11529 Taiwan
contact email	tlli@gate.sinica.edu.tw
lab head
Yung-Lin Wang
contact affiliation	Genomics Research Center, Academia Sinica
contact email	hcvns3@gate.sinica.edu.tw
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD041104
     1. Label: PRIDE project
     2. Name: Mass spectrometric analyses for the C281-dimedone adduct and the sulfinylated peptide fragments of Orf1