2012 Protein of the Year

pyruvate decarboxylase

Pyruvate decarboxylase (PDC) plays a particularly important role in ethanol fermentation in yeast and other microorganisms.  Glucose is first converted to pyruvate via glycolysis.  PDC, with help from its cofactors Mg²⁺ and thiamine pyrophosphate (TPP), then catalyzes the decarboxylation of pyruvate to acetaldehyde and carbon dioxide.  After PDC does this, alcohol dehyrdrogenase completes the two-step fermentation process and converts acetaldehyde to ethanol.  Therefore, PDC plays a crucial role in the regulation and production of ethanol, an infamous alcohol known throughout the world.

PDC is a homotetramer.  This is flawless symmetry at its best!  It occurs as a dimer of dimers.  The two dimers interact loosely to form a loose tetramer.  There are two active sites shared between the monomers of each dimer, thus resulting in a total of 4 active sites altogether.  The enzyme has parallel beta-sheets in a beta-alpha-beta structure.  Each dimer contains 563 residue subunits for a total of 2252 subunits in the entire tetramer.  Take a look at the two figures below to see this spectacular symmetry.

The figure below shows one of the four active sites of PDC.  Displayed are the cofactors Mg²⁺ and TPP, as well as key amino acids: Glu-51, Glu-477, Asp-444, and Asp-28.  Glu-51 and Glu-477 aid in cofactor binding (Glu-477 contributes solely to the stability of TPP. It's the lower-right corner Glu in the figure below).  Asp-444 and Asp-44 stabilize the Mg²⁺ ion.

To ensure that only pyruvate binds to the active site, two Cys-221 and two His-92 trigger a conformational change, which inhibits or activates the enzyme depending on the bound substrate (see figure below).  If the substrate is pyruvate, the enzyme is activated.  The conformational change is thought to involve a 1,2 nucleophilic addition, thus resulting in the formation of a thioketal, which transforms the enzyme from its inactive to active state.

Positions of His and Cys residues in respect to active sites (TPP and Mg) that participate in conformation changes when interacting with pyruvate substrate.

PDC is present in brewer’s and baker’s yeast.  The CO₂ produced by pyruvate decarboxylation in brewer’s yeast is responsible for the characteristic carbonation of champagne.  In baker’s yeast, the CO₂ produced mixes with fermentable sugar and causes the dough to rise.  Without PDC, we would not have the same champagne and beer that we humans adore, and our bread would look like this:

 

Without pyruvate decarboxylase, life would surely be one giant FAIL.

References

Baburina I, Dikdan G, Guo F, Tous GI, Root B, Jordan F (February 1998). "Reactivity at the substrate activation site of yeast pyruvate decarboxylase: inhibition by distortion of domain interactions". Biochemistry 37 (5): 1245–55. 

Dyda F, Furey W, Swaminathan S, Sax M, Farrenkopf B, Jordan F (June 1993). "Catalytic centers in the thiamin diphosphate dependent enzyme pyruvate decarboxylase at 2.4-A resolution". Biochemistry 32 (24): 6165–70. 

Nelson, D. L., & Cox, M. M. (2008). Lehninger: Principles of Biochemistry (5th ed., p. 547-549). New York, NY: W.H. Freeman and Company.

Some Recent Literature

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.  The Journal of Biological Chemistry.  1998

                The authors present a crystal structure of pyruvate decarboxylase (PDC) from the Zymomonas mobilis bacterium.  The presented PDC is one that has yet to be observed.  The pyruvate decarboxylase from the bacterium, ZmPDC, was determined by molecular displacement methods.  ZmPDC is a homotetramer.  Each monomer can be further divided into three domains: PYR, R, and PP.  Each domain has open alpha/beta topology.  At the dimer-dimer interface, they interpreted some residual electron density as citrate molecules.   The four citrates might contribute to the tetramer assembly by electrostatic interactions and hydrogen bonds to protein side chains.  A quaternary structure comparison of PDC from Z. mobilis and PDC from yeast shows structural differences that may be related to the differences in their kinetic behavior. 

Hokyoung S., Kyunghun M., Jungkwan, L. , Gyung, J., Jin-Cheol K., & Yin-Won, L.  Differential roles of pyruvate decarboxylase in aerial and embedded mycelia of the ascomycete Giberrela zeae.  FEMS Microbiology Letters. 2012

                The researchers knocked out the three PDC genes in the fungus Giberrela zeae.  In particular, they looked at PDC1 and its role in the pyruvate-acetaldehyde-acetate (PAA) pathway.  The PAA pathway is important for its role in lipid production.  When PDC1 was knocked out, lipid accumulation declined in the aerial, but not the embedded mycelia.  Therefore, PDC1 may function as a key enzyme in lipid production in the aerial mycelia, and it mat function differently in the embedded mycelia, where it is believed to be involved in energy generation by ethanol fermentation.  This is the first description of different physiological roles in the aerial and embedded mycelia for the same metabolic process in filamentous fungi.  PDC1 and the PPA pathway are important for lipid production in the aerial mycelia.  However, embedded mycelia seem to utilize them via ethanol fermentation for growth.

Kondo, T., Tezuka, H., Ishii, J., Matsuda, F., Ogino, C., and Kondo, A.  Genetic engineering to enhance the Ehrlich pathway and alter carbon flux for increased isobutanol production from glucose by Saccharomyces cerevisiae.  Journal of Biotechnology.  2012

Recently, much attention has been given to the production of higher alcohols by engineered bacteria.  Saccharomyces cerevisiae has much potential as a producer of alcohols due to its tolerance to low pH among other things.  Since the bacterium does not naturally produce alcohols significantly, the researchers sought to genetically engineer a way to increase production of the alcohol isobutanol.  Knocking out the PDC1 gene (see above), along with modification of culture conditions and enhancing the Ehrlich pathway, resulted in a 13-fold increase in isobutanol concentration.  The Ehrlich pathway was enhanced by overexpressing 2-keto acid decarboxylase, alcohol dehydrogenase, and IIv2.

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