Pyruvate decarboxylase

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Pyruvate decarboxylase
Pyruvate decarb 1.svg
Reaction catalyzed by pyruvate decarboxylase:
pyruvate + thiamine pyrophosphate (TPP) → hydroxyethyl-TPP + CO2
Identifiers
EC no. 4.1.1.1
CAS no. 9001-04-1
Databases
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BRENDA BRENDA entry
ExPASy NiceZyme view
KEGG KEGG entry
MetaCyc metabolic pathway
PRIAM profile
PDB structures RCSB PDB PDBe PDBsum
Gene Ontology AmiGO / QuickGO
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NCBI proteins

Pyruvate decarboxylase is an enzyme (EC 4.1.1.1) that catalyses the decarboxylation of pyruvic acid to acetaldehyde. It is also called 2-oxo-acid carboxylase, alpha-ketoacid carboxylase, and pyruvic decarboxylase. [1] In anaerobic conditions, this enzyme participates in the fermentation process that occurs in yeast, especially of the genus Saccharomyces , to produce ethanol by fermentation. It is also present in some species of fish (including goldfish and carp) where it permits the fish to perform ethanol fermentation (along with lactic acid fermentation) when oxygen is scarce. [2] Pyruvate decarboxylase starts this process by converting pyruvate into acetaldehyde and carbon dioxide. [3] Pyruvate decarboxylase depends on cofactors thiamine pyrophosphate (TPP) and magnesium. This enzyme should not be mistaken for the unrelated enzyme pyruvate dehydrogenase, an oxidoreductase (EC 1.2.4.1), that catalyzes the oxidative decarboxylation of pyruvate to acetyl-CoA.

Contents

Structure

Pyruvate decarboxylase occurs as a dimer of dimers with two active sites shared between the monomers of each dimer. The enzyme contains a beta-alpha-beta structure, yielding parallel beta-sheets. It contains 563 residue subunits in each dimer; the enzyme has strong intermonomer attractions, but the dimers loosely interact to form a loose tetramer. [4]

Active site residues

Each active site has 20 amino acid residues, including the acidic Glu-477, which interacts with the TPP ring, and Glu-51, which participates with the binding of the cofactor. These glutamates also stabilize the ylid of TPP, acting as proton donors. The nonpolar environment around this Glu 477 is nonpolar, which contributes to a higher than normal pKa (normal Glu and Asp pKa's are around 4.6 in small proteins). [5]

The lipophilic residues Ile-476, Ile-480 and Pro-26 contribute to the nonpolarity of the area around Glu-477. The only other negatively charged residue apart from TPP coenzyme is the Asp-28, which also aids in increasing the pKa of Glu-477. Thus, the environment of the enzyme must allow for the protonation of the gamma-carboxyl group of Glu-477 to be around pH 6. [5]

The aminopyrimidine ring on TPP acts as a base, once in its imine form, to pull off the C2 proton from TPP to form the nucleophile ylide. [4] This must occur because the enzyme has no basic side chains present to deprotonate the TPP C2. A mutation at the active site involving these Glu can result in the inefficiency or inactivity of the enzyme. This inactivity has been proven in experiments in which either the N1' and/or 4'-amino groups are missing. In NMR analysis, it has been determined that when TPP is bound to the enzyme along with the substrate-analog pyruvamide, the rate of ylid formation is greater than the normal enzyme rate. Also, the rate of mutation of Glu 51 to Gln reduces this rate significantly. [4]

Residues Asp-444 and Asp-28 bind Mg2+. Two Cys-221 (more than 20 Ångstroms away from each site) and His-92 trigger a conformational change, which inhibits or activates the enzyme depending on the substrate availability. If the substrate bound in the active site is pyruvate, the enzyme is activated by a conformational change in this regulatory site. [6] The conformational change involves a 1,2 nucleophilic addition. This reaction, the formation of a thioketal, transforms the enzyme from its inactive to active state.

Inhibition of the site is done by a XC6H4CH=CHCOCOOH class of inhibitors/substrate analogues, as well as by the product of decarboxylation from such compounds as cinnamaldehydes. Other potential nucleophilic sites for the inhibitor include Cys-152, Asp-28, His-114, His-115, and Gln-477. [6]

The normal catalytic rate of pyruvate decarboxylase is kcat = 10 s−1. However, the rate of the enzyme with a Glu-51 mutation to Gln is 1.7 s−1. [4]

TPP prosthetic group

The cofactor TPP is the prosthetic group to the enzyme. The CH center located between the sulfur and nitrogen atoms on thiazole ring is acidic. Upon deprotonation, it generates an ylide, and becomes negatively charged as a carbanion. This can react as a nucleophile at the ketone carbon of pyruvic acid. [3] During the decarboxylation of pyruvate, the TPP stabilizes the carbanion intermediates as an electrophile by noncovalent bonds. [4] Specifically, the pyridyl nitrogen N1' and the 4'-amino group of TPP are essential for the catalytic function of the enzyme-TPP complex. [5]

Mechanism

Pyruvate decarboxylase mechanism.svg

The enzyme splits pyruvate into carbon dioxide and acetaldehyde. The reaction proceeds by attack of the nucleophilic thiazole carbon on the keto group. The intermediate loses carbon dioxide, giving an enol, in an irreversible step. Subsequently, free acetaldehyde is released and the TPP is regenerated. [7]

Yeast

In yeast, pyruvate decarboxylase acts independently during anaerobic fermentation and releases the 2-carbon fragment as acetaldehyde plus carbon dioxide. Pyruvate decarboxylase creates the means of CO2 elimination, which the cell dispels. The enzyme is also means to create ethanol, which is used as an antibiotic to eliminate competing organisms. [4] The enzyme is necessary to help the decarboxylation of alpha-keto acids because there is a build-up of negative charge that occurs on the carbonyl carbon atom in the transition state; therefore, the enzyme provides the suitable environment for TPP and the alpha-keto acid (pyruvate) to meet. [4]

Related Research Articles

Pyruvic acid (IUPAC name: 2-oxopropanoic acid, also called acetoic acid) (CH3COCOOH) is the simplest of the alpha-keto acids, with a carboxylic acid and a ketone functional group. Pyruvate, the conjugate base, CH3COCOO, is an intermediate in several metabolic pathways throughout the cell.

<span class="mw-page-title-main">Active site</span> Active region of an enzyme

In biology and biochemistry, the active site is the region of an enzyme where substrate molecules bind and undergo a chemical reaction. The active site consists of amino acid residues that form temporary bonds with the substrate, the binding site, and residues that catalyse a reaction of that substrate, the catalytic site. Although the active site occupies only ~10–20% of the volume of an enzyme, it is the most important part as it directly catalyzes the chemical reaction. It usually consists of three to four amino acids, while other amino acids within the protein are required to maintain the tertiary structure of the enzymes.

<span class="mw-page-title-main">Acetaldehyde dehydrogenase</span> Class of enzymes

Acetaldehyde dehydrogenases are dehydrogenase enzymes which catalyze the conversion of acetaldehyde into acetyl-CoA. This can be summarized as follows:

<span class="mw-page-title-main">Pyruvate dehydrogenase complex</span> Three-enzyme complex

Pyruvate dehydrogenase complex (PDC) is a complex of three enzymes that converts pyruvate into acetyl-CoA by a process called pyruvate decarboxylation. Acetyl-CoA may then be used in the citric acid cycle to carry out cellular respiration, and this complex links the glycolysis metabolic pathway to the citric acid cycle. Pyruvate decarboxylation is also known as the "pyruvate dehydrogenase reaction" because it also involves the oxidation of pyruvate.

<span class="mw-page-title-main">Thiamine pyrophosphate</span> Chemical compound

Thiamine pyrophosphate (TPP or ThPP), or thiamine diphosphate (ThDP), or cocarboxylase is a thiamine (vitamin B1) derivative which is produced by the enzyme thiamine diphosphokinase. Thiamine pyrophosphate is a cofactor that is present in all living systems, in which it catalyzes several biochemical reactions.

Aromatic <small>L</small>-amino acid decarboxylase Class of enzymes

Aromatic L-amino acid decarboxylase, also known as DOPA decarboxylase (DDC), tryptophan decarboxylase, and 5-hydroxytryptophan decarboxylase, is a lyase enzyme, located in region 7p12.2-p12.1.

<span class="mw-page-title-main">Aspartate transaminase</span> Enzyme involved in amino acid metabolism

Aspartate transaminase (AST) or aspartate aminotransferase, also known as AspAT/ASAT/AAT or (serum) glutamic oxaloacetic transaminase, is a pyridoxal phosphate (PLP)-dependent transaminase enzyme that was first described by Arthur Karmen and colleagues in 1954. AST catalyzes the reversible transfer of an α-amino group between aspartate and glutamate and, as such, is an important enzyme in amino acid metabolism. AST is found in the liver, heart, skeletal muscle, kidneys, brain, red blood cells and gall bladder. Serum AST level, serum ALT level, and their ratio are commonly measured clinically as biomarkers for liver health. The tests are part of blood panels.

Carboxy-lyases, also known as decarboxylases, are carbon–carbon lyases that add or remove a carboxyl group from organic compounds. These enzymes catalyze the decarboxylation of amino acids, beta-keto acids and alpha-keto acids.

<span class="mw-page-title-main">Oxaloacetate decarboxylase</span> Enzyme

Oxaloacetate decarboxylase is a carboxy-lyase involved in the conversion of oxaloacetate into pyruvate.

<span class="mw-page-title-main">Amino acid synthesis</span> The set of biochemical processes by which amino acids are produced

Amino acid biosynthesis is the set of biochemical processes by which the amino acids are produced. The substrates for these processes are various compounds in the organism's diet or growth media. Not all organisms are able to synthesize all amino acids. For example, humans can synthesize 11 of the 20 standard amino acids. These 11 are called the non-essential amino acids).

Oxidative decarboxylation is a decarboxylation reaction caused by oxidation. Most are accompanied by α- Ketoglutarate α- Decarboxylation caused by dehydrogenation of hydroxyl carboxylic acids such as carbonyl carboxylic acid, malic acid, isocitric acid, etc.

<span class="mw-page-title-main">Pyruvate dehydrogenase</span> Class of enzymes

Pyruvate dehydrogenase is an enzyme that catalyzes the reaction of pyruvate and a lipoamide to give the acetylated dihydrolipoamide and carbon dioxide. The conversion requires the coenzyme thiamine pyrophosphate.

<span class="mw-page-title-main">Neurophysin II</span> Cleavage product of the arginine vasopressin gene

Neurophysin II is a carrier protein with a size of 19,687.3 Da and is made up of a dimer of two virtually identical chains of amino acids. Neurophysin II is a cleavage product of the AVP gene. It is a neurohypophysial hormone that is transported in vesicles with vasopressin, the other cleavage product, along axons, from magnocellular neurons of the hypothalamus to the posterior lobe of the pituitary. Although it is stored in neurosecretory granules with vasopressin and released with vasopressin into the bloodstream, its biological action is unclear. Neurophysin II is also known as a stimulator of prolactin secretion.

Malate dehydrogenase (oxaloacetate-decarboxylating) (NADP<sup>+</sup>) Enzyme

Malate dehydrogenase (oxaloacetate-decarboxylating) (NADP+) (EC 1.1.1.40) or NADP-malic enzyme (NADP-ME) is an enzyme that catalyzes the chemical reaction in the presence of a bivalent metal ion:

<span class="mw-page-title-main">Phosphoenolpyruvate mutase</span> Enzyme

In enzymology, a phosphoenolpyruvate mutase is an enzyme that catalyzes the chemical reaction

<span class="mw-page-title-main">Cystathionine beta-lyase</span> Enzyme

Cystathionine beta-lyase, also commonly referred to as CBL or β-cystathionase, is an enzyme that primarily catalyzes the following α,β-elimination reaction

<span class="mw-page-title-main">2-Dehydro-3-deoxy-phosphogluconate aldolase</span> Class of enzymes

The enzyme 2-dehydro-3-deoxy-phosphogluconate aldolase, commonly known as KDPG aldolase, catalyzes the chemical reaction

<span class="mw-page-title-main">Arginine decarboxylase</span>

The enzyme Acid-Induced Arginine Decarboxylase (AdiA), also commonly referred to as arginine decarboxylase, catalyzes the conversion of L-arginine into agmatine and carbon dioxide. The process consumes a proton in the decarboxylation and employs a pyridoxal-5'-phosphate (PLP) cofactor, similar to other enzymes involved in amino acid metabolism, such as ornithine decarboxylase and glutamine decarboxylase. It is found in bacteria and virus, though most research has so far focused on forms of the enzyme in bacteria. During the AdiA catalyzed decarboxylation of arginine, the necessary proton is consumed from the cell cytoplasm which helps to prevent the over-accumulation of protons inside the cell and serves to increase the intracellular pH. Arginine decarboxylase is part of an enzymatic system in Escherichia coli, Salmonella Typhimurium, and methane-producing bacteria Methanococcus jannaschii that makes these organisms acid resistant and allows them to survive under highly acidic medium.

<span class="mw-page-title-main">Diaminopimelate decarboxylase</span> Enzyme decarboxylates diaminopimelate, forming L-lysine

The enzyme diaminopimelate decarboxylase (EC 4.1.1.20) catalyzes the cleavage of carbon-carbon bonds in meso 2,6 diaminoheptanedioate to produce CO2 and L-lysine, the essential amino acid. It employs the cofactor pyridoxal phosphate, also known as PLP, which participates in numerous enzymatic transamination, decarboxylation and deamination reactions.

<span class="mw-page-title-main">Aldehyde ferredoxin oxidoreductase</span>

In enzymology, an aldehyde ferredoxin oxidoreductase (EC 1.2.7.5) is an enzyme that catalyzes the chemical reaction

References

  1. "NiceZyme View of ENZYME: EC 4.1.1.1". ExPASy Proteomics Server.
  2. Aren van Waarde; G. Van den Thillart; Maria Verhagen (1993). "Ethanol Formation and pH-Regulation in Fish". Surviving Hypoxia. CRC Press. pp. 157−170. hdl:11370/3196a88e-a978-4293-8f6f-cd6876d8c428. ISBN   0-8493-4226-0.
  3. 1 2 Tadhg P. Begley; McMurry, John (2005). The organic chemistry of biological pathways. Roberts and Co. Publishers. p. 179. ISBN   0-9747077-1-6.
  4. 1 2 3 4 5 6 7 PDB: 1pyd ; 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. doi:10.1021/bi00075a008. PMID   8512926.
  5. 1 2 3 Lobell M, Crout DH (1996). "Pyruvate Decarboxylase: A Molecular Modeling Study of Pyruvate Decarboxylation and Acyloin Formation". J. Am. Chem. Soc. 118 (8): 1867–1873. doi:10.1021/ja951830t.
  6. 1 2 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. doi:10.1021/bi9709912. PMID   9477950.
  7. H., Garrett, Reginald (2013). Biochemistry. Grisham, Charles M. (5th ed.). Belmont, CA: Brooks/Cole, Cengage Learning. ISBN   9781133106296. OCLC   777722371.{{cite book}}: CS1 maint: multiple names: authors list (link)