Insights into substrate binding by D-2-ketoacid dehydrogenases from the structure of Lactobacillus pentosus D-lactate dehydrogenase

Background: D-Lactate dehydrogenases (D-LDHs) and L-lactate dehydrogenases (L-LDHs) catalyze a reaction differing only in the chirality of the product. Both enzymes utilize the same kind of amino acid side chains in substrate binding and catalysis. Models based on D-LDH-related enzymes propose that these side chains assume identical roles in both enzymes with their active sites related by a simple geometrical relationship such as a mirror plane. Results: The crystal structure of the homodimeric D-LDH from Lactobacillus pentosus has been determined to 2.6 Angstrom resolution by multiple isomorphous replacement methods and the resulting molecular model refined to an R-factor of 19.1%. Topologically, the enzyme is closely related to other D-2-ketoacid dehydrogenase enzymes. Each subunit comprises two domains enclosing a deep cleft containing the active site. Substrate binding and domain closure have been modelled. Conclusions: Comparison of the D-LDH structure with other members of the protein family and with the L-specific enzyme has confirmed that no overall structural relationship exists between the L-LDH and D-LDH enzymes - they belong to distinct protein classes. The small size of the ketoacid substrate and the very restricted number of functionally appropriate side chains will constrain the choice of amino acids and their placement in the active site. Our models imply that although the same kinds of amino acids are involved in substrate binding their exact chemical role might differ in the two dehydrogenases.