Refined crystal structure of liver alcohol dehydrogenase–NADH complex at 1.8 Å resolution

Abstract

The crystal structure of the ternary complex of horse liver alcohol dehydrogenase (LADH) with the coenzyme NADH and inhibitor dimethyl sulfoxide (DMSO) has been refined by simulated annealing with molecular dynamics and restrained positional refinement using the program X-PLOR. The two subunits of the enzyme were refined independently. The space group was P1 with cell dimensions a = 51.8, b = 44.5, c = 94.6 A, alpha = 104.8, beta = 102.3 and gamma = 70.6 degrees. The resulting crystallographic R factor is 17.3% for 62 440 unique reflections in the resolution range 10.0-1.8 A. A total of 472 ordered solvent molecules were localized in the structure. An analysis of secondary-structure elements, solvent content and NADH binding is presented.

Molecular dynamics simulations of alcohol dehydrogenase with a four‐ or five‐coordinate catalytic zinc ion

“…The average zinc-ligand distances in the molecular dynamics simulations of alcohol dehydrogenase are in excellent agreement with the crystal structure of the enzyme 4 Table VII show that DMSO binds more strongly to the zinc ion than water; the Zn-O distance is 2.12 Å for DMSO compared to 2.26 Å for H 2 O with similar basis sets (Table III).…”

“…Throughout, the coordinates of horse liver alcohol dehydrogenase in complex with NADH and dimethylsulfoxide at 1.8 Å resolution (R-factor=0.172) 4 were used. This is at present the most accurate structure of alcohol dehydrogenase.…”

“…The active site of the enzyme contains a zinc ion that is essential for catalysis. Crystallographic studies of the horse liver enzyme and its binary or ternary complexes with coenzyme and different substrates have shown that this zinc ion is bound to the enzyme through two cysteine and one histidine residue and that it, as a rule, is tetrahedrally four-coordinate with one water or substrate molecule (or the corresponding anions, depending on pH) as the fourth first-sphere ligand [2][3][4][5] .…”

The coordination chemistry of the structural zinc ion in alcohol dehydrogenase studied by ab initio quantum chemical calculations

“…Crystallographic studies of the horse liver enzyme (Eklund et al, 1981, Eklund & Brändén, 1983, Al-Karadaghi et al, 1994 have shown that the latter zinc ion is bound to the enzyme by four cysteine residues. As can be seen in Table 1, the coordination geometry around this zinc ion is almost tetrahedral, with small but reproducible differences between the ligands.…”

“…The enzyme has been thoroughly studied and the crystal structure is known for several complexes (Eklund et al, 1981, Eklund & Brändén, 1983, Al-Karadaghi et al, 1994. Furthermore, if all the cysteines are deprotonated, there are eight equivalent Zn-S bonds in the enzyme, which gives a very accurate estimate of the average Zn-S bond length.…”