Structure-based discovery and definition of RiPP recognition elements.

ABSTRACT: Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a large class of natural products with wide-ranging structural and functional diversity. Central to many RiPP biosynthetic pathways is the RiPP Recognition Element (RRE), a structurally conserved peptide-binding domain that enables class-independent genome mining. Bioinformatic tools, such as RRE-Finder, have leveraged this domain to identify novel RiPPs, but accuracy has been limited by high false-positive rates. To improve accuracy, we assessed whether structure-based searching of the AlphaFold database with the rapid tertiary structure alignment tool Foldseek could reduce false-positive rates and identify previously unretrievable, sequence-divergent RREs. We used these divergent RREs to build 11 new Foldseek-

SUBMITTER: Bregman MH 

PROVIDER: S-EPMC12710340 | biostudies-literature | 2025 Dec

REPOSITORIES: biostudies-literature