Crystal structure of bacterial L-arabinose 1-dehydrogenase in complex with L-arabinose and NADP

L-Arabinose 1-dehydrogenase (AraDH) is responsible for the first step of the non-phosphorylative L-arabinose pathway from bacteria, and catalyzes the NAD(P)⁺-dependent oxidation of L-arabinose to L-arabinonolactone. This enzyme belongs to the so-called Gfo/Idh/MocA protein superfamily, but has a very poor phylogenetic relationship with other functional members. We previously reported the crystal structures of AraDH without a ligand and in complex with NADP⁺. To clarify the underlying catalytic mechanisms in more detail, we herein elucidated the crystal structure in complex with L-arabinose and NADP⁺. In addition to the previously reported five amino acid residues (Lys91, Glu147, His153, Asp169, and Asn173), His119, Trp152, and Trp231 interacted with L-arabinose, which were not found in substrate recognition by other Gfo/Idh/MocA members. Structure-based site-directed mutagenic analyses suggested that Asn173 plays an important role in catalysis, whereas Trp152, Trp231, and His119 contribute to substrate binding. The preference of NADP⁺ over NAD⁺ was significantly subjected by a pair of Ser37 and Arg38, whose manners were similar to other Gfo/Idh/MocA members.