A vitamin K-dependent carboxylase orthologue is involved in antibiotic biosynthesis

Vitamin K-dependent carboxylase (VKDC) enzymes modify glutamate residues in mammalian vitamin K-dependent proteins, generating γ-carboxyglutamic acids with malonate moieties that mediate important physiological responses such as blood coagulation. Proteins with sequence similarity to mammalian VKDC are also found in bacteria; however, their function remains unknown. The antibiotic malonomycin from Streptomyces rimosus contains an unusual malonate group, of unknown origin, that is essential for its biological activity. Here, we show that a bacterial VKDC orthologue (MloH) is responsible for the malonic acid moiety in malonomycin. Using CRISPR/Cas9 gene editing, complementation and mutagenesis experiments, this VKDC-like enzyme was shown to α-carboxylate an aspartyl residue within a hybrid polyketide–nonribosomal peptide intermediate during malonomycin biosynthesis. This study reveals a highly unusual biosynthetic pathway to malonic acid-containing metabolites, providing a functional role for VKDC-like proteins in prokaryotes and a vitamin K-dependent carboxylation reaction with a non-proteinogenic substrate.