Structural Biochemistry/Enzyme Catalytic Mechanism/Dehydrogenases

Dehydrogenases

Dehydrogenases catalyze the oxidation of alcohols to carbonyl compounds by using either NAD+ or NADP+. Some dehydrogenases are specific for one coenzyme. This reaction can be reduced by NADH or NADPH. In the oxidation of the alcohol, one in dehydrogenases transferred to the 4 position of the nicotinamide ring of the NAD+ by removing two hydrogens. Therefore, the carbonyl group was made from the reaction. This reaction is stereospecific. The enzyme can either attack either side of the ring, resulting in different conformations and characteristics. The enzyme with the syn conformation will catalyze the reaction to reduce carbonyls groups more rapidly. The enzyme with the anti conformation is less reactive than the previous enzyme. Different types of dehydrogenases exist, some of which are briefly mentioned below.

1. The alcohol dehydrogenases

The alcohol dehydrogenase catalyzes the reaction of alcohols to aldehydes and ketones by using NAD+ as a coenzyme. It also has the zinc ion sites at the bottom of the enzyme. The zinc ion binds on NAD+ by during the catalysis. Mechanistically, the coenzyme binds to the enzyme by oxidizing the alcohol in the enzyme. The enzyme-NADH complex is dissociated to be rate determining.

2. L-Lactate dehydrogenase

L-lactate dehydrogenase oxidizes the reversible reaction of L-lactate to pyruvate by using NAD+ as a coenzyme. The alcohol group becomes the carbonyl group of the enzyme. L-lactate or pyruvate is binded to the enzyme through the coenzyme. Therefore, the coenzyme always binds on the enzyme first. Other substrates may bind to the enzyme as well. Lactate dehydrogenase is especially important for the role that it plays in glycolysis. In order for glycolysis to occur, NAD+ must be available. Under anaerobic conditions, there is not sufficient NAD+ available for glycolysis to occur because it is all stuck in the NADH form (the insufficient amount of oxygen means that no oxygen is present to receive electrons from the end of the electron transport chain). Lactate dehydrogenase allows for the occurrence of glycolysis by helping in the conversion of NADH to NAD+. Lactate dehydrogenase does this by converting pyruvate to lactate. The figure below explains this reaction.

   O  O                OH  O                               
   ‖  ‖                |   ‖                                

H3C – C – CO- + NADH ↔ H3C – CH – CO- + NAD+

Pyruvate             Lactate
                         

As is shown, two electrons are removed from NADH and a proton is added in order for lactate to be formed and for NADH to be oxidized to NAD+.

3. Malate dehydrogenase

Malactate dehydrogenase oxidizes malate to oxaloactate in areversible reaction. NADH and NAD+ bind with equal affinity. In other words, it catalyzes, by means of NAD+ or NADP, the dehydrogenation of malate to oxaloacetate or the decarboxylation of maleate to pyruvate.

4. Glutamate Dehydrogenase

Glutamate dehydrogenase catalyzes the conversion of the nitrogen atom in glutamate into ammonium ions by oxidative deamination (See Reaction Scheme Below). In oxidative deamination, the reaction starts by dehydrogenation of the Carbon-Nitrogen bond, which then leads to an imine intermediate known as the Schiff-base intermediate. The first step utilizes glutamate dehydrogenase (GDH)and utilizes the coenzyme NAD+, which is reduced to NADH [1]. Next, hydrolysis of the Schiff base leads to α-ketoglutarate and the free ammonium ion. The reaction is driven in the forward direction due to quick removal of the ammonium ion. Glutamate dehydrogenase is located in the mitochondria of cells. Glutamate dehydrogenase is unique because, in some organisms, it is capable of using either NAD+ or NADP+ in its catalytic reactions. This ability is unique because NADPH is used as the reductant in biosynthetic reactions, while NAD+ is usually used as the oxidant in most catabolic reaction, and glutamine dehydrogenase is not specific to either.

Reference

Alan Fersht, Enzyme Structure and Mechanism.

Jeremy M. Berg, John L. Tymoczko, Lubert Stryer. Biochemistry (6ed). New York. W.H. Freeman and Company, 2007, 2002.

Aaron Coleman, Meredith Gould, Jose Luis Stephano. Biochemical Techniques. Hayden-McNeil Publishing, 2013.