Pyruvate dehydrogenase complex
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201356573
2008-03-27T16:46:48Z
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'''Pyruvate dehydrogenase complex''' (PDC) is a complex of three [[enzyme]]s 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 alpha-keto acid dehydrogenase complex|branched-chain oxo-acid dehydrogenase multi-enzyme]] complexes.
==Reaction==
The reaction catalysed by pyruvate dehydrogenase complex is:
{{Enzymatic Reaction
|foward_enzyme=pyruvate dehydrogenase complex
|reverse_enzyme=
|substrate=[[pyruvate]]
|product=[[acetyl CoA]]
|reaction_direction_(foward/reversible/reverse)=foward
|minor_foward_substrate(s)= [[Coenzyme A|CoA-SH]] '''+''' NAD<sup>+</sup>
|minor_foward_product(s)= CO<sub>2</sub> '''+''' NADH '''+''' H<sup>+</sup>
|minor_reverse_substrate(s)=
|minor_reverse_product(s)=
|substrate_image=pyruvate_wpmp.png
|product_image=acetyl_co-A_wpmp.png
}}
==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:
{| class="wikitable"
! Enzyme !! Abbrev. !! [[Cofactor]](s) !! # subunits
|-
| [[pyruvate dehydrogenase|pyruvate dehydrogenase]]<br>({{EC number|1.2.4.1}}) || E1 || [[thiamine|TPP (thiamine pyrophosphate)]] || 24
|-
| [[dihydrolipoyl transacetylase|dihydrolipoyl transacetylase]]<br>({{EC number|2.3.1.12}}) || E2 || [[lipoic acid|lipoate]]<br>[[coenzyme A|coenzyme A]] || 24
|-
| [[dihydrolipoyl dehydrogenase|dihydrolipoyl dehydrogenase]]<br>({{EC number|1.8.1.4}}) || E3 || [[FAD]]<br>[[nicotinamide adenine dinucleotide|NAD]]<sup>+</sup> || 12
|}
=== Pyruvate dehydrogenase (E1) ===
Initially, [[pyruvate]] and [[thiamine|thiamine pyrophosphate]] (TPP) are bound by [[pyruvate dehydrogenase]] subunits. The [[thiazole|thiazolium]] ring of TPP is in a [[zwitterion]]ic form, and the [[anion]]ic 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 is attached to a [[lysine]] residue. In a ring-opening S<sub>N</sub>2-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 [[lipoic acid|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 FADH<sub>2</sub>. Then, a [[nicotinamide adenine dinucleotide|NAD<sup>+</sup>]] [[cofactor]] oxidizes FADH<sub>2</sub> back to its FAD resting state, producing NADH.
==Regulation==
Pyruvate dehydrogenase is inhibited when one or more of the three following ratios are increased: [[Adenosine triphosphate|ATP]]/[[Adenosine diphosphate|ADP]], [[NADH]]/NAD<sup>+</sup> and [[acetyl-CoA]]/[[Coenzyme A|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 [[eukaryote|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 transport|active]], consuming [[energy]]. Passive diffusion of pyruvate into the mitochondria is impossible because it is 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 [[prokaryote]]s, 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, 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.
===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.
==See also==
* [[Pyruvate dehydrogenase deficiency]]
==Related links==
* http://www.dentistry.leeds.ac.uk/biochem/MBWeb/mb1/part2/krebs.htm#animat1 - animation of the general mechanism of the PDH complex (link on upper right) at [[University of Leeds]]
* {{MeshName|Pyruvate+Dehydrogenase+Complex}}
{{Multienzyme complexes}}
{{Mitochondrial enzymes}}
{{Citric acid cycle enzymes}}
[[Category:EC 1.2.1]]
[[Category:Cellular respiration]]
[[de:Pyruvat-Dehydrogenase]]
[[fr:Pyruvate déshydrogénase]]
[[it:Piruvato deidrogenasi (complesso enzimatico)]]
[[ja:ピルビン酸デヒドロゲナーゼ複合体]]
[[sl:Kompleks piruvat-dehidrogenaza]]
[[zh:丙酮酸去氫酶複合物]]