Conformational rearrangements enable iterative backbone N-methylation in RiPP biosynthesis

• Published in: Nature communications Vol. 12; no. 1; p. 5355
• Main Authors: Miller, Fredarla S., Crone, Kathryn K., Jensen, Matthew R., Shaw, Sudipta, Harcombe, William R., Elias, Mikael H., Freeman, Michael F.
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 09.09.2021; Nature Publishing Group; Nature Portfolio
• Subjects: 45/70; 631/45/611; 631/535/1266; 631/92/349; 639/638/60; 82/58; 82/80; 82/83; Algorithms; Backbone; Bacterial Proteins - chemistry; Bacterial Proteins - genetics; Bacterial Proteins - metabolism; Binding Sites - genetics; Biological membranes; Biological Products - metabolism; Biosynthesis; Crystallography, X-Ray; Humanities and Social Sciences; Kinetics; Membrane permeability; Methylation; Methyltransferase; Methyltransferases - chemistry; Methyltransferases - genetics; Methyltransferases - metabolism; multidisciplinary; Mutation; N-Methyltransferase; Natural products; Peptides; Peptides - chemistry; Peptides - genetics; Peptides - metabolism; Physicochemical properties; Precursors; Protein Conformation; Protein Multimerization; Protein Processing, Post-Translational; Ribosomes - genetics; Ribosomes - metabolism; Science; Science (multidisciplinary); Shewanella - enzymology; Shewanella - genetics; Substrate Specificity; Substrates
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-021-25575-7

Peptide backbone α- N -methylations change the physicochemical properties of amide bonds to provide structural constraints and other favorable characteristics including biological membrane permeability to peptides. Borosin natural product pathways are the only known ribosomally encoded and posttranslationally modified peptides (RiPPs) pathways to incorporate backbone α- N -methylations on translated peptides. Here we report the discovery of type IV borosin natural product pathways (termed ‘split borosins’), featuring an iteratively acting α- N -methyltransferase and separate precursor peptide substrate from the metal-respiring bacterium Shewanella oneidensis . A series of enzyme-precursor complexes reveal multiple conformational states for both α- N -methyltransferase and substrate. Along with mutational and kinetic analyses, our results give rare context into potential strategies for iterative maturation of RiPPs. Borosins are ribosomally encoded and posttranslationally modified peptide (RiPP) natural products featuring amide-backbone α- N -methylation. Here, the authors report the discovery and characterization of type IV borosin ‘split’ pathways encoding distinct, separate α- N -methyltransferases and precursor peptide substrates.