Pyruvate, NADH, and ATP are the products of glycolysis. Under anaerobic conditions, pyruvate undergoes fermentation to oxidize NADH to
NAD+, so glycolysis can continue. In alcoholic fermentation, which occurs in some yeast, this is a two-step process. The first involves the Enzyme pyruvate decarboxylase (PDC). The pyruvate is decarboxylated to an acetaldehyde. This acetaldehyde then undergoes a reaction catalyzed by alcohol dehydrogenase to produce ethanol; this is the step in which the NAD+ is restored [1].
Structure
Pyruvate decarboxylase is a homotetramer. Each identical subunit consists of approximately alternating α-helices and β-sheets, and 2 domains exist within each 60kDa subunit. This means its SCOP category is alpha and beta protein [2]. Being a homotetramer, pyruvate PDC has 4 identical active sites that are green surrounding the ligands when the previous link is selected.
Active Site
The active site of PDC consists of Glu 477, Asp28, His114, and His 115 as well as the thiamine diphosphate cofactor. Hydrogen bonding occurs between the substrate and Asp28, His114, and Thr73. In the catalytic step of the reaction mechanism, Glu 473, shown in red, donates a proton to the pyruvate. The scene shows the close proximity of this residue to the pyruvate. The negative charge of the Glu residue following the protonation of the substrate leads to the destabilization of the pyruvate carboxylate group. Next the carboxyl group leaves, using thyiamine diphosphate as an electron sink (described below). Following decarboxylation in the final step of the mechanism, release of acetaldehyde, a proton is transferred to the Glu477 residue from a cofactor. After the protonation in a concerted step, a water molecule donates a proton to the substrate while receiving a proton from Glu477. As the proton is taken from the substrate, the electrons move to form a carbonyl, which leads to the release of the acetaldehyde.
Regulation
PDC is regulated by substrate activation. This means that if substrate is not present in the pathway, the protein will be "off." The residue that is bound to start a cascade of events resulting in the activation of the enzyme is C 221[3] which is highlighted in pink in the scene. This process allows the enzyme to be on when its function is necessary and off when it would not be catalyzing the reaction even if it were on.
ThDP an Important Cofactor
Thiamine diphosphate (ThDP) is an important cofactor in alpha decarboxylation reactions. The structure of ThDP is bent when bound to the protein. This kink brings the 4'N of ThDP in close enough proximity to C2 to deprotonate it, forming a reactive ylid [4]. Glutamic acid 51 on the other side of ThDP forms a hydrogen bond with ThDP to increase the basicity of 4'N. In the decarboxylation reaction, C2 of ThDP is deprotonated, and attacks C2 of the pyruvate (this structure has pyruvamide instead of pyruvate), resulting in a covalent bond between ThDP and the pyruvate. This allows the ThDP to act as an electron sink for the decarboxylation reaction.
↑Dobritzsch D, Konig S, Schneider G, Lu G. High resolution crystal structure of pyruvate decarboxylase from Zymomonas mobilis. Implications for substrate activation in pyruvate decarboxylases. J Biol Chem. 1998 Aug 7;273(32):20196-204. PMID:9685367
↑Sergienko EA, Jordan F. Catalytic acid-base groups in yeast pyruvate decarboxylase. 3. A steady-state kinetic model consistent with the behavior of both wild-type and variant enzymes at all relevant pH values. Biochemistry. 2001 Jun 26;40(25):7382-403. PMID:11412092
