Pyridoxal-5'-Phosphate-Dependent Enzyme GenB3 Catalyzes C-3',4'-Dideoxygenation in Gentamicin Biosynthesis

Abstract

Background: C-3',4'-dideoxygenation structure in gentamicin can prevent deactivation by aminoglycoside 3'-phosphotransferase (APH(3')) in drug-resistant pathogens. However, the enzyme catalyzing the dideoxygenation step in the gentamicin biosynthesis pathway remains unknown. Results: Here, we report GenP catalyzes 3′ phosphorylation of gentamicin biosynthesis intermediates JI-20A, JI-20Ba, and JI-20B. We further demonstrate that a pyridoxal-5′-phosphate (PLP)-dependent enzyme GenB3 uses these phosphorylated substrates to form 3',4'-dideoxy-4',5'-ene-6'-oxo products. The following C-6' transamination and GenB4 catalyzed reduction of 4',5' olefin lead to the formation of gentamicin C. To the best of our knowledge, GenB3 is the first PLP dependent enzyme catalyzing dideoxygenation in aminoglycoside biosynthesis. Conclusions: This discovery solves the long-standing puzzle in gentamicin biosynthesis, also enriches the chemistry of PLP dependent enzymes. Interestingly, these results demonstrate that to evade APH(3') deactivation from the pathogens, the gentamicin producers evolved a smart strategy, which utilized their own APH(3') to activate hydroxyls as leaving groups for the 3',4'-dideoxygenation in gentamicin biosynthesis.

Mechanistic Insights into Dideoxygenation in Gentamicin Biosynthesis

“…1). During the preparation of this manuscript, Zhou et al 25 published a paper on GenB3 with similar results to those described in this paper.…”