Crystal structure of l‐rhamnose 1‐dehydrogenase involved in the nonphosphorylative pathway of l‐rhamnose metabolism in bacteria

Abstract

Several microorganisms can utilize l‐rhamnose as a carbon and energy source through the nonphosphorylative metabolic pathway, in which l‐rhamnose 1‐dehydrogenase (RhaDH) catalyzes the NAD(P)⁺‐dependent oxidization of l‐rhamnose to l‐rhamnono‐1,4‐lactone. We herein investigated the crystal structures of RhaDH from Azotobacter vinelandii in ligand‐free, NAD⁺‐bound, NADP⁺‐bound, and l‐rhamnose‐ and NAD⁺‐bound forms at 1.9, 2.1, 2.4, and 1.6 Å resolution, respectively. The significant interactions with the 2′‐phosphate group of NADP⁺, but not the 2′‐hydroxyl group of NAD⁺, were consistent with a preference for NADP⁺ over NAD⁺. The C5‐OH and C6‐methyl groups of l‐rhamnose were recognized by specific residues of RhaDH through hydrogen bonds and hydrophobic contact, respectively, which contribute to the different substrate specificities from other aldose 1‐dehydrogenases in the short‐chain dehydrogenase/reductase superfamily.