Modeling studies of conformational changes in the substrate-binding loop in Drosophila alcohol dehydrogenase

Three-dimensional structures of seven short-chain dehydrogenases/reductases show that these enzymes share common structural features. Sequence alignment studies of Drosophila alcohol dehydrogenase (DADH), with an unknown 3D-structure, and four short-chain dehydrogenases/reductases with known X-ray structures suggest that DADH shares the same structural features. However, the substrate binding regions, which are located in the C-terminal region of these enzymes, share little sequence homology, because of the wide variety of substrates used. X-ray structures of short-chain dehydrogenases/reductases indicate that conformational changes occur in a loop, in the C-terminal region, upon substrate binding. This substrate-binding loop is located between a strand and a helix and may contain one or two small helices. Secondary structure predictions and modeling studies of this substrate-binding loop in DADH predict that the two helices may also be present in this enzyme. The naturally occurring variants of Drosophila melanogaster alleloenzymes ADH-S and ADH-F differ in a replacement of threonine by lysine at position 192, which is located at a central position in the substrate-binding loop. The positive charge of lysine may move significantly on substrate binding, resulting in a direct charge interaction with NAD+ in the enzyme-substrate complex, explaining a very strong influence of pH on the binding of ADH-S for the NAD+ analogue Cibacron Blue. This indicates that the ADH S/F polymorphism has a direct influence on the catalytic properties of the enzyme.