Crystal structure of l-2-keto-3-deoxyrhamnonate 4-dehydrogenase involved in the non-phosphorylating pathway of l-rhamnose metabolism by bacteria.

In the non-phosphorylative l-rhamnose and l-fucose pathways in bacteria, the C4-OH groups of the l-2-keto-3-deoxyrhamnonate (l-KDR) and l-2-keto-3-deoxyfuconate (l-KDF) intermediates are oxidized by different NAD+-dependent dehydrogenases, which belong to the same superfamily: l-KDRDH and l-KDFDH, respectively. To further elucidate their opposite stereospecificities, we herein investigated the crystal structures of l-KDRDH (from Herbaspirillum huttiense) in ligand-free and NAD+-bound forms. The interactions between the side chains of Asp39 and Gln18, and the 2'- and/or 3'-hydroxyl group(s) of NAD+ were consistent with strict specificity for NAD+. In a binding model for the substrate, Asn151 and Arg247 interacted with the C1 carboxyl and/or C5 hydroxyl group(s) of l-KDR with the acrylic α-keto form, which differed from l-KDFDH, which recognizes l-KDF with the cyclic hemiketal. A comparison of gene clusters on the bacterial genome and biochemical characterization suggested that l-KDRDH functions as a novel 4-hydroxy-2-oxopentanoate dehydrogenase in the degradation of aromatic compounds.