Refined crystal structures of Zn(II)- and Cu(II)-alcohol dehydrogenase : a comparative study

University dissertation from Stockholm : Stockholm University

Abstract: The crystal structure of the ternary complex of horse liver alcohol dehydrogenase (LADH) with the coenzyme NADH and inhibitor dimethyl sulphoxide (DMSO) (space group PI) has been refined by simulated annealing with molecular dynamics and restrained positional refinement using the program system XPLOR. The resulting crystallographic R- factor is 17. 1 V, for 62 440 reflections in the resolution range 10.0 to 1.8 A.The structure of the active site Cut 11)-substituted LADH complex with NADH and DMSO (space group P2^ ) was solved by molecular replacement and refined to a crystallographic R-factor of 15.6 for 40 796 reflections in the resolution range 12.0 to 2.1 A.The refinement of the two structures demonstrated that the conformational transition from the open to the closed form of LADH induces asymmetry between the two subunits of the dimer. The asymmetry is a result of a relative shift of the catalytic domains with respect to each other. In the Cutll)-substituted LADH the catalytic domains are also rotated relative to each other by an angle of 1.2°.The coordination geometry of the Cu(II) and Zn(II) ions in the active site is compared. The distances from the metal to the protein ligands (Cys46, His67 and Cysl74) are similar for both the Zn(II) and Cu(II) ions. The distances of the oxygen of the inhibitor DMSO to the Cu(II) ion in the two subunits of the enzyme are 3.12 A and 3.44 A, which are considerably larger than the respective distances to the Zn(II) ion - 2. 19 A and 2.15 A. The coordination geometry of the Cut II) ion in LADH is closely related to that of the blue (type I) copper proteins.