Pyruvate dehydrogenase complex Totally Explained

Everything about Pyruvate Dehydrogenase Complex totally explained

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.

Reaction

The reaction catalysed by pyruvate dehydrogenase complex is:
Structure & function in eukaryotes Pyruvate dehydrogenase complex is located in the mitochondrial matrix of eukaryotes. It consists of a total of 60 subunits, organized into three functional proteins:

Enzyme	Abbrev.	Cofactor(s)	# subunits
pyruvate dehydrogenase	E1	TPP (thiamine pyrophosphate)	24
dihydrolipoyl transacetylase	E2	lipoate coenzyme A	24
dihydrolipoyl dehydrogenase	E3	FAD NAD⁺	12

Pyruvate dehydrogenase (E1)

Initially, pyruvate and thiamine pyrophosphate (TPP) are bound by pyruvate dehydrogenase subunits. The thiazolium ring of TPP is in a zwitterionic form, and the anionic C2 carbon performs a nucleophilic attack on the C2 (ketone) carbonyl of pyruvate. The resulting hemithioacetal undergoes Decarboxylation to produce an acyl anion equivalent (see cyanohydrin or aldehyde-dithiane umpolung chemistry, as well as benzoin condensation). This anion attacks S1 of an oxidized lipoate species that's attached to a lysine residue. In a ring-opening S_N2-like mechanism, S2 is displaced as a sulfide or sulfhydryl moiety. Subsequent collapse of the tetrahedral hemithioacetal ejects thiazole, releasing the TPP cofactor and generating a thioacetate on S1 of lipoate. The E1-catalyzed process is the rate-limiting one of the whole pyruvate dehydrogenase complex.

Dihydrolipoyl transacetylase (E2)

At this point, the lipoate-thioester functionality is translocated into the dihydrolipoyl transacetylase (E2) active site, where a transacylation reaction transfers the acetyl from the "swinging arm" of lipoyl to the thiol of coenzyme A. This produces acetyl-CoA, which is released from the enzyme complex and subsequently enters the citric acid cycle.

Dihydrolipoyl dehydrogenase (E3)

The dihydrolipoate, still bound to a lysine residue of the complex, then migrates to the dihydrolipoyl dehydrogenase (E3) active site where it undergoes a flavin-mediated oxidation, identical in chemistry to disulfide isomerase. First, FAD oxidizes dihydrolipoate back to its lipoate resting state, producing FADH₂. Then, a NAD⁺ cofactor oxidizes FADH₂ back to its FAD resting state, producing NADH.

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 pyruvate dehydrogenase kinase (PDK) and pyruvate dehydrogenase 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.

Localization of pyruvate decarboxylation

In eukaryotic cells the pyruvate decarboxylation occurs inside the mitochondria, after transport of the substrate, pyruvate, from the cytosol. The transport of pyruvate into the mitochondria is via a transport protein and is active, consuming energy. Passive diffusion of pyruvate into the mitochondria is impossible because it's a polar molecule.
On entry to the mitochondria the pyruvate decarboxylation occurs, producing acetyl CoA. This irreversible reaction traps the acetyl CoA within the mitochondria (there is no transporter for acetyl CoA). The carbon dioxide produced by this reaction is nonpolar and small, and can diffuse out of the mitochondria and out of the cell.
In prokaryotes, which have no mitochondria, this reaction is either carried out in the cytosol, or not at all.

Structural differerences between species

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

Gram-negative bacteria

In Gram-negative bacteria, for example 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.

Gram-positive bacteria and eukaryotes

In contrast, in Gram-positive bacteria (for example 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 isn't 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.

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