Catalytic, Computational, and Evolutionary Analysis of the D-Lactate Dehydrogenases Responsible for D-Lactic Acid Production in Lactic Acid Bacteria

D-Lactate dehydrogenase (D-LDH) catalyzes the reversible reaction pyruvate + NADH + H+ -> lactate + NAD(+), which is a principal step in the production of D-lactate in lactic acid bacteria. In this study, we identified and characterized the major D-LDH (D-LDH1) from three D-LDHs in Leuconostoc mesenteroides, which has been extensively used in food processing. A molecular simulation study of D-LDH1 showed that the conformation changes during substrate binding. During catalysis, Tyr101 and Arg235 bind the substrates by hydrogen bonds and His296 acts as a general acid/base for proton transfer. These residues are also highly conserved and have coevolved. Point mutations proved that the substrate binding sites and catalytic site are crucial for enzyme activity. Network and phylogenetic analyses indicated that D-LDH1 and the homologues are widely distributed but are most abundant in bacteria and fungi. This study expands the understanding of the functions, catalytic mechanism, and evolution of D-LDH.