Dephosphorylated NPr of the nitrogen PTS regulates lipid A biosynthesis by direct interaction with LpxD

► We identified LpxD as a binding partner of NPr of the Escherichia coli nitrogen PTS. ► LpxD shows a preferential interaction with dephosphorylated NPr. ► LpxD catalyzes biosynthesis of the bacterial endotoxin lipid A and lipopolysaccharide. ► A npr mutant shows increased lipopolysaccharide synthesis and rifampin resistance.