Pyruvate dehydrogenase complex

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Pyruvate dehydrogenase complex (PDC) is a complex of three enzymes that transform 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.

This multi-enzyme complex is related structurally and functionally to the oxoglutarate dehydrogenase and branched-chain oxo-acid dehydrogenase multi-enzyme complexes.

The reaction catalysed by pyruvate dehydrogenase complex is:

pyruvate	pyruvate dehydrogenase		acetyl CoA

	CoA + NAD⁺	CO₂ + NADH + H⁺

1 Structure & function (in eukaryotes)
- 1.1 Cofactors
- 1.2 Regulation
2 Structural differerences between species
- 2.1 Gram-negative bacteria
- 2.2 Gram-positive bacteria and eukaryotes
3 See also
4 Related links

[edit] Structure & function (in eukaryotes)

Pyruvate dehydrogenase complex is located in the mitochondrial matrix of eukaryotes. It consists of three functional protein subunits, which may aggregate into larger clusters:

E1, Pyruvate dehydrogenase (acetyl-transferring)(EC 1.2.4.1)
E2, Dihydrolipoyl transacetylase (EC 2.3.1.12)
E3, Dihydrolipoyl dehydrogenase (EC 1.8.1.4)

E1 catalyses the rate-limiting reaction within PDC. It requires thiamine pyrophosphate (TPP) as a cofactor and catalyses the decarboxylation of pyruvate. The TPP remains bound to the acetate through a thioester bond. This bond brings the acetate in proximity to an oxidized lipoyllysine, to which it becomes esterified. The acetate is trans-esterified from the sulfide of the lipoyl 'swinging arm' to coenzyme A (CoA), where it forms acetyl-CoA. The reduced lipoyllysine becomes reoxidized, by concomitant reduction of flavin adenine dinucleotide (FAD) present in E3. FADH then reduces nicotinamide adenine dinucleotide (NAD), returning the pyruvate dehydrogenase complex to is original redox state. The acetyl-CoA is free to enter the TCA cycle.

[edit] Cofactors

5 different cofactors are required for this complex:

TPP (Thiamine pyrophosphate) - Hydroxyethyl Carrier
CoA (Coenzyme A) - Substituted onto the Acetyl group to form Acetyl-CoA
R-Lipoic acid - Utilized as a Lysine Tether to transport Acetyl group to active site for CoA addition
FAD (Flavin Adenine Dinucleotide) - Oxidizing agent to oxidize the lipoyllysine sulfaring to repeat process.
NAD (Nicotinamide adenine dinucleotide)- Oxidizes FADH₂ in order to repeat process. NADH is then used for oxidative phosphorylation or may be used somewhere else in the cytosol.

Multiple copies of each different cofactor may be necessary for proper function of this complex.

[edit] Regulation

Pyruvate dehydrogenase is inhibited when one or more of the three following ratios are increased: ATP/ADP, NADH/NAD⁺ and acetyl-CoA/CoA.

In eukaryotes PDC is tightly regulated by its own specific PDC kinase (PDK) and phosphatase (PDP). PDK phosphorylates three specific serine residues on E1 with different affinities. Phosphorylation of any one of them renders E1 (and in consequence the entire complex) inactive. Dephosphorylation of E1 by PDP reinstates complex activity.

Products of the reaction act as allosteric inhibitors of the PDH complex, but they also act on PDH kinase, activating it. Substrates in turn inhibit the PDH complex.

During starvation, PDK increases in amount in most tissues, including skeletal muscle, via increased gene transcription. Under the same conditions, the amount of PDP decreases. The resulting inhibition of PDC prevents muscle and other tissues from catabolizing glucose and gluconeogenesis precursors. Metabolism shifts toward fat utilization, while muscle protein breakdown to supply gluconeogenesis precursors is minimized, and available glucose is spared for use by the brain.

Calcium ion has a role in regulation of PDH complex in muscle tissue, because it activates PDH phosphatase, stimulating glycolysis on its release into the cytosol - during muscle contraction.

[edit] Structural differerences between species

PDC is a large complex composed of multiple copies of 3 or 4 subunits depending on species.

[edit] Gram-negative bacteria

In Gram-negative bacteria, e.g. Escherichia coli, PDC consists of a central octahedral core made up from 24 molecules of dihydrolipoyl transacetylase (E2).

Up to 24 copies of pyruvate decarboxylase (E1) and 12 molecules of dihydrolipoyl dehydrogenase (E3) bind to the outside of the E2 core.

[edit] Gram-positive bacteria and eukaryotes

In contrast, in Gram-positive bacteria (e.g. Bacillus stearothermophilus) and eukaryotes the central PDC core contains 60 E2 molecules arranged into an icosahedron.

Eukaryotes also contain 12 copies of an additional core protein, E3 binding protein (E3BP). The exact location of E3BP is not completely clear. Cryo-electron microscopy has established that E3BP binds to each of the icosahedral faces in yeast. However, it has been suggested that it replaces an equivalent number of E2 molecules in the bovine PDC core.

Up to 60 E1 or E3 molecules can associate with the E2 core from Gram-positive bacteria - binding is mutually exclusive. In eukaryotes E2 is specifically bound by E2, while E3 associates with E3BP. It is thought that up to 30 E1 and 6 E3 enzymes are present, although the exact number of molecules can vary in vivo and often reflects the metabolic requirements of the tissue in question.