The methyltransferase NmbA methylates the low-molecular weight thiol bacillithiol, and displays a specific structural architecture

Abstract

Low-molecular weight (LMW) thiols maintain the cellular redox balance, and play a protective role against reactive species, heavy metals, toxins, and antibiotics. Despite serving similar metabolic functions, structurally distinct LMW thiols are widespread in nature, with bacillithiol (BSH) being the predominant LMW thiol in bacteria. The LMW thiol N-methyl-BSH (N-Me-BSH) has been characterized in the green sulfur bacterium Chlorobaculum tepidum, unveiling the presence and role of a putative S-adenosyl-L-methionine (SAM)-dependent methyltransferase (MT), NmbA, catalyzing the final biosynthetic step of N-Me-BSH. In this work, we report biochemical evidence for NmbAs function as an MT of the N-atom of the BSH cysteine moiety, showing substrate specificity, which together with our bioinformatics analyses classifies NmbA and its outspread homologs as N-directed natural product MTs (NPMTs) of the LMW thiol BSH. We also present the crystal structure of NmbA, which shows that NmbA is a Class I SAM-dependent MT, however, displaying a unique three-dimensional architecture unlike that observed for other NPMTs. The NmbA active site adopts a narrow molecular basket structure due to an unusual organization of the variable Cap domain, which together with our docking calculations suggests that it may specifically accommodate the BSH substrate. Our studies provide a valuable overview of the phylogenetic distribution of N-Me-BSH in bacteria, accompanied by important functional and structural insight into a new class of NPMTs. Our findings contribute to the field of SAM-dependent MTs, as well as possible applications for targeting distinct bacterial defense mechanisms involving LMW thiols with potential environmental, biotechnological, and medical implications.