Crystallography of liver alcohol dehydrogenase complexed with substrates

Abstract

Horse liver alcohol dehydrogenase was crystallized at pH 7 and 5 °C from an equilibrium mixture containing predominantly NAD + and p-bromobenzyl alcohol and lower concentrations of NADH and p-bromobenzaldehyde. It is assumed from the results of kinetic studies in solution that most of the enzyme was complexed with NAD + and p-bromobenzyl alcohol. A ternary complex with NAD + and trifluoroethanol (an unreactive alcohol) and complexes with NAD + or NADH and 2-methyl-2,4-pentanediol (the crystallization agent, which partially occupies the substrate-binding pocket) were also crystallized. All of these complexes formed triclinic crystals that were isomorphous with the enzyme-NADH-dimethylsulfoxide complex, which has been solved to a resolution of 4.5 Å. X-ray diffractometer data (at 4.5 Å) were used to compute electron density difference maps, which showed that both subunits of the dimeric enzyme bound p-bromobenzyl alcohol or trifluoroethanol in a substrate binding pocket that was close to the position occupied by dimethylsulfoxide. These complexes appeared to have the same protein and coenzyme structure as the complex with NADH and dimethylsulfoxide. Since the dimethylsulfoxide appeared to be ligated to the catalytic zinc atom, it was not possible to see a direct connection between the alcohols and the zinc ion in these difference maps. However, maps computed from the differences in amplitudes between the NAD +-alcohol complexes and NAD(H)-methylpentanediol complexes and the phases from the NADH-dimethylsulfoxide complex showed continuous electron density from the bromo or trifluoromethyl positions of the substrates to the zinc ion. Using the structure of the orthorhombic form of apoenzyme, which has been solved to a resolution of 2.4 Å, as a guide for interpreting the various maps, we constructed a provisional model of the active site. This model led us to conclude that the oxygen of either alcohol is directly ligated to the zinc ion (2 Å), while carbon 1 of the alcohol is 3.5 Å from carbon 4 of the nicotinamide ring. Studies at higher resolution are required to confirm these conclusions and to reveal further details.