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The binding of NAD to liver alcohol dehydrogenase has been studied in four different ternary complexes by using crystallographic methods. These complexes crystallize isomorphously in a triclinic crystal form which contains the whole dimer of the enzyme in the asymmetric unit. This form of the enzyme has been refined at 2.9-A resolution to a crystallographic R factor of 0.22. NAD binds in essentially the same way in these complexes. The binding site is located at the central part of the coenzyme binding domain. The adenine ring binds with hydrophobic interactions between two isoleucine side chains. Both ribose rings have 2E(C2'-endo) puckering, and each ribose makes three hydrogen bonds to the enzyme. The pyrophosphate bridge has hydrogen bonds to the side chains of arginine-47 and -369 and to main chain nitrogen atoms from the amino ends of two alpha-helices. The nicotinamide ring is in van der Waals contact with the active-site zinc atom and with the sulfur atoms of its cysteine ligands. The carboxamide group is about 30 degrees out of the plane of the nicotinamide ring and hydrogen bonds to main chain atoms of residues 292,317, and 319. The overall conformation of the NAD molecule is similar to that observed for other dehydrogenases, but differs in details. In the presence of the coenzyme, the enzyme undergoes a large conformational change from an open to a closed form. This conformational change has three major effects: to create favorable binding interactions with groups of the enzyme, to enclose the coenzyme and gain binding energy for the coenzyme by reducing the accessible surface area, and to close off one entrance to the active site. As a comparison, ADP-ribose binding has been studied in the open form of the enzyme. The adenosine moiety binds in a similar way as NAD, while the rest of the molecule has different interactions.
Eklund et al. (Sat,) studied this question.