Alcohol Dehydrogenase ( 1AXE.pdb )

Biological Importance Active Site Reaction Mechanism
Secondary Structures & Structural Motifs Sequence References
Intro dance. Hydrophobic molecules, red. Polar molecules, yellow.
Secondary Structure. (1) Active Site with Phe93, Leu 57, Leu 116. (2) Stabilization of the alcohol's oxygen by a zinc atom.
(3) Zinc with Cys 46, Cys 174, and His 67. (4) NAD (5) Gly 210 and Asn 225.
(6) Pro 243, Asn 242, Val 268, Asp 223. (7) Try 178, Arg 47, Gly 292 and Val 203.  (8) Gly 292, Val 203, Try 178, Val 318, Arg 47, Pro 243, Asn 242, Val 268, Asp 223, Phe 21 and Asn 225 are purple. His 51 is red.
(9) Important atoms in mechanism. (10) Basic residues are red, acidic residues are blue and neutral are white. (11) Rossman Structure.
Biological Importance

Alcohol Dehydrogenase (ADH) is the primary enzyme responsible for the oxidation of ethanol, the fist step of ethanol elimination in humans. The majority of ingested ethanol is metabolized in the liver, to acetate. The rate-limiting step in this process is the oxidation of ethanol to acetaldehyde which is catalyzed by the NAD+ dependent alcohol dehydrogenase. In other words, Alcohol Dehydrogenase is an enzyme that makes it possible for humans to drink beer, wine, and other alcoholic beverages. Hence, it is very important enzyme in Isla Vista as well as other college towns. However, its "real" function is thought to be the conversion of alcohol generated by bacteria in the intestine to other metabolic products. Individuals with some mutant forms of ADH may be specially sensitive to alcohol, (Thank God I am not a mutant). The degree to which different individuals re sensitive to the effects of alcohol depends not only on the kinetic properties of the ADH isoenzymes expressed in the liver, but also on the absolute amounts of each isoenzyme. ADH represents 2-3% of the soluble protein in normal human liver, which suggests that, aside from its action on exogenous ethanol, it may serve an important though presently unknown function(s) in intermediate metabolism.

Active Site

Active Site 
This close-up of the active site shows the Zn2+ cation coordinated with two cysteine anion residues (-CH2-S), and a histidine residue (cyclic N-containing group). An acetaldehyde is coordinated to the zinc and th -OH group of a serine residue (not shown). Held in position, the acetaldehyde is reduced to CH3CH2OH when a hydride anion (H:-) is released from the NADH and a proton (H+)is released from the serine hydroxyl group (which in turn acquires a new proton by a series of relays of H+ from the enzyme surface).)
Lewis Structure drawing of the molecules in the Active Site 

ADH is a zinc-containing, cytosolic enzyme present in a wide variety of tissues. Liver and the stomach mucosal cell layer contain the highest concentrations of ADH. 

ADH binds two zinc ions, one structural and one catalytic. The catalytic zinc coordinates with two sulfur atoms from (3) Cys 46, Cys 174, and a nitrogen atom from His 67. An ionizable water molecule occupies the fourth position on the zinc. The water molecule is also bonded to the hydroxyl group of Thr 48 (Ser 48) Glu 68, a conserved amino acidThis position is located 0.5 nm from the catalytic zinc ion in the crystal structure, may intermittently coordinate to the zinc ion, and it probably facilitate the exchange of zinc ligands. The fifth and final zinc coordinate is, of course, the oxygen from the alcohol. In the active site there are three amino acids,(1) Phe 93, Leu 57 and Leu 116, that work in concert to provide the three point binding of the alcohol substrate. This binding accounts for the stereo-specific removal of the pro-R hydrogen. The structural zinc ion has four cysteine deprotonated ligands coordinating the atom. The nicotinamide ring of NAD+ is bound close to the zinc. In the oxidation of alcohol two hydrogen atoms are removed - one to the fourth position of AD+ and the other as a proton. The transfer to NAD+ is generally thought to be hydride transfe. (4) The NAD is bound by multiple residues off the (11)Rossman fold (p 146, fig 6-29 inVVP) which is characterized by five beta strands in a paralled arrangement flanked by alpha helices. Some of the residues that bind NAD include: (5) Gly 210, Asn 225, (6) Pro 243, Asn 242, Val 268, Asp 223, (7) Try 178, Arg 47, Gly 292, Val 203.

Reaction Mechanism

Oxidation Mechanism 
Alcohol Dehydrogenase, with coenzyme nicotinamide adenine dinucleotide (NAD), stereospecifically catalyzes the oxidation of ethanol to acetaldehyde and the reduction of acetaldehyde to ethanol. This is illustrated by the following equation.

NAD+
----------------------------------->
CH3CH2OH           Alcohol Dehydrogenase           CH3-(C=O)-H 
<------------------------------------
NADH

ADH catalyzes the oxidation of alcohols by reducing NAD with a hydride. (2) ADH also utilizes a zinc ion to electrostatically stabilize the alcohol oxygen, thus increasing the acidity of the alcohol's proton. In the pathway, His 51 (8)is activated by general base catalysis such that the histidine can then accept a proton from the NAD, which is turn draws a proton from Thr 48, 9again demonstating general base catalysis (although this is rather indirect since the substrate has not yet been involved). These proton transfers ready the threonine (which is negatively charged due to proton transfer to the NAD) for accepting a proton from the alcohol of the actual substrate. This is the first example of true base catalysis of actually involving the substrate. At the same time, since this oxidation is concerted, there is a hydride transfer to the NAD in its traditional hydride accepting region. Thus, the whole sequence essentially amounts to a transfer of a hydride to the NAD and the oxidation of an alcohol to an aldehyde. key points are the orientation of the amino acid proton acceptors and donors, as well as the position of the zinc ion in relation to the substrate such that it stabilizes a negative charge on the substrate thereby taking part in transition state stabilization.

Secondary Structures and Structural Motifs

Secondary Structure
The primary structure of Alcohol Dehydrogenase consists of two equivalent subunits with 374 residues each. Most of the amino acids in ADH participate in either forming alpha helices or beta sheets. Some form parallel or anti-parallel beta sheets. Some amino acids also form aniparallel beta barrels. There are also a series of alpha helixes. Most alpha helixes surround the beta sheets forming a structure called a Rossman fold.

Sequence

Complete Sequence

References
1) Bahnson, B., Colby, T., Chin, J., Goldstein, B., Kinman, P. : A link between protein structure and enzyme catalyzed hydrogen tunneling, www.pubmendcentral.nih.gov/b.cgi?pubmedid=937175 (1997)
2) Blair, A., and Valee, B.: SOme Catalytic Properties of Human Liver Alcohol Dehydrogenase, Biochem. J., 5, 2026 (1966)
3) Mourad, N., and Woronick, C.: Crystalization of Human Liver Alcohol Dehydrogenase Arch. Biochem. Biophys., 121, 431 (1697)
4) William R. Wiley, Environmental Molecular Sciences Laboratory, Studies of the Human Liver AlcoholDehydrogenase Isoenzymes by CIEF-ESI-FTICR www.emsl.pnl.gov:2028/docs/msd.annual_report1999/1573b-5e.html
5) Pictures From classweb.gmu.edu

Suhair Eirene Suadi
Copyright © 2000
Department Molecular, Cellular, and Developmental Biology
University of California ~ Santa Barbara

© Duane W. Sears and Holly I. Rich
Revised for Jmol: September 13, 2012