7U58

YcaO-mediated ATP-dependent peptidase activity in ribosomal peptide biosynthesis

Summary for 7U58

• Entry DOI: 10.2210/pdb7u58/pdb
• EMDB information: 26344
• Descriptor: MusD, ZINC ION, MAGNESIUM ION (3 entities in total)
• Functional Keywords: ripps, ycao domain, musd, cyanobactin, hydrolase
• Biological source: Desmonostoc sp. PCC 7906
• Total number of polymer chains: 2
• Total formula weight: 177917.65

Authors

Zheng, Y.,Nair, S.K. (deposition date: 2022-03-01, release date: 2022-11-02, Last modification date: 2024-06-12)

Primary citation

Zheng, Y.,Nair, S.K.
YcaO-mediated ATP-dependent peptidase activity in ribosomal peptide biosynthesis.
Nat.Chem.Biol., 19:111-119, 2023

PubMed Abstract: YcaO enzymes catalyze ATP-dependent post-translation modifications on peptides, including the installation of (ox/thi)azoline, thioamide and/or amidine moieties. Here we demonstrate that, in the biosynthesis of the bis-methyloxazolic alkaloid muscoride A, the YcaO enzyme MusD carries out both ATP-dependent cyclodehydration and peptide bond cleavage, which is a mechanism unprecedented for such a reaction. YcaO-catalyzed modifications are proposed to occur through a backbone O-phosphorylated intermediate, but this mechanism remains speculative. We report, to our knowedge, the first characterization of an acyl-phosphate species consistent with the proposed mechanism for backbone amide activation. The 3.1-Å-resolution cryogenic electron microscopy structure of MusD along with biochemical analysis allow identification of residues that enable peptide cleavage reaction. Bioinformatics analysis identifies other cyanobactin pathways that may deploy bifunctional YcaO enzymes. Our structural, mutational and mechanistic studies expand the scope of modifications catalyzed by YcaO proteins to include peptide hydrolysis and provide evidence for a unifying mechanism for the catalytically diverse outcomes.

PubMed: 36280794
DOI: 10.1038/s41589-022-01141-0

Experimental method

ELECTRON MICROSCOPY (3.1 Å)