Tertiary structure of a Nif11-like leader peptide mediates protein-protein interactions with a RiPP biosynthetic enzyme

Abstract

Ribosomally synthesized and post-translationally modified peptides (RiPPs) are produced from precursor peptides that typically contain a short, unstructured N-terminal leader region that engages RiPP biosynthetic enzymes through peptide-protein contacts. A distinct subclass of leader peptides, the nitrogen-fixing protein 11-like leader peptides (Nif11-LPs), are unusually long and conspicuously enriched in cyanobacteria. No atomic structures of Nif11-LPs have been reported. Here, we report the solution structure of MppEleader, a Nif11-LP from the marine cyanobacterium Moorena producens PAL. MppEleader adopts a bipartite architecture with a rigid N-terminal tetrahelical bundle stabilized around a hydrophobic nucleus, followed by a dynamic, largely disordered C-terminal region containing a conserved L(X)L motif. We show that the -ketoglutarate/non-heme iron enzyme MppG dihydroxylates the macrocyclized MppEcore peptide in a strictly leader-dependent manner. NMR titrations and structure-guided mutagenesis demonstrate that both the tetrahelical hydrophobic nucleus and the L(X)L motif of MppE make direct, functionally required contacts with MppG, including its RiPP recognition element (RRE) domain. An AlphaFold3-guided structural model rationalizes these contacts. Together, these findings establish a tertiary structure-dependent protein-protein interaction paradigm for RiPP core peptide modification, distinguishing Nif11-LP recognition from canonical short-leader mechanisms and expanding the understanding of substrate recognition in RiPP biosynthesis.