Pyruvate dehydrogenase complex


Pyruvate dehydrogenase complex

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.

Contents

Reaction

The reaction catalysed by pyruvate dehydrogenase complex is:

pyruvate pyruvate dehydrogenase complex acetyl CoA
Pyruvate wpmp.png   Acetyl co-A wpmp.png
CoA-SH + NAD+ CO2 + NADH + H+
Biochem reaction arrow foward YYNN horiz med.png
 
 

Structure & function in eukaryotes

Pyruvate dehydrogenase complex is organized in cubic symmetry in prokaryotes, having 60 subunits in three functional proteins.[1] Pyruvate dehydrogenase complex is located in the mitochondrial matrix of eukaryotes. It is organized in dodecahedral symmetry, and consists of a total of 96 subunits, organized into three functional proteins in the human enzyme[2]:

Enzyme Abbrev. Cofactor(s) # subunits prokaryotes # subunits eukaryotes
pyruvate dehydrogenase
(EC 1.2.4.1)
E1 TPP (thiamine pyrophosphate) 24 30
dihydrolipoyl transacetylase
(EC 2.3.1.12)
E2 lipoate
coenzyme A
24 60
dihydrolipoyl dehydrogenase
(EC 1.8.1.4)
E3 FAD
NAD+
12 12
PDC Mechanism with pyruvate (R=H)

Pyruvate decarboxylase(E1)

Initially, pyruvate and thiamine pyrophosphate (TPP or vitamin B1) 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 is attached to a lysine residue. In a ring-opening SN2-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 step 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. E2 can also be known as lipoamide reductase-transacetylase.

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), deactivating and activating it respectively.

  • 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 PDC, because they activate PDK. Substrates in turn inhibit PDK, and thus, reactivating PDC.

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 PDC in muscle tissue, because it activates PDP, stimulating glycolysis on its release into the cytosol - during muscle contraction.

Localization of pyruvate decarboxylation

In eukaryotic cells the Swanson conversion 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 carries a negative charge.

On entry to the mitochondria the pyruvate decarboxylation occurs, producing acetyl CoA. This irreversible reaction traps the acetyl CoA within the mitochondria (the acetyl-CoA can only be transported out of the mitochondrial matrix under conditions of high oxaloacetate via the citrate shuttle, a TCA intermediate that is normally sparse). 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, e.g. Escherichia coli, PDC consists of a central cubic core made up from 24 molecules of dihydrolipoyl transacetylase (E2).

Up to 24 copies of Pyruvate dehydrogenase (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.[3] 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 E1 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

References

  1. ^ Mattevi, A., Obmolova, G., Schulze, E., Kalk, K.H., Westphal, A.H., de Kok, A., Hol, W.G. (1992) Atomic structure of the cubic core of the pyruvate dehydrogenase multienzyme complex. Science 255, 1544-1550.
  2. ^ Smolle, M., Prior, A.E., Brown, A.E., Cooper, A., Byron, O., Lindsay, J.G. (2006) A new level of architectural complexity in the human pyruvate dehydrogenase complex. J. Biol. Chem. 281, 19772-19780.
  3. ^ Stoops, J.K., Cheng, R.H., Yazdi, M.A., Maeng, C.Y., Schroeter, J.P., Klueppelberg, U., Kolodziej, S.J., Baker, T.S., Reed, L.J. (1997) On the unique structural organization of the Saccharomyces cerevisiae pyruvate dehydrogenase complex. J. Biol. Chem. 272, 5757-5764.

Related links

3D structures


Wikimedia Foundation. 2010.

Look at other dictionaries:

  • pyruvate dehydrogenase complex — a multienzyme complex consisting of multimers of the three distinct enzymes: pyruvate dehydrogenase (acetyl transferring) [EC 1.2.4.1], dihydrolipoyllysine residue acetyltransferase [EC 2.3.1.12], and dihydrolipoyl dehydrogenase [EC 1.8.1.4]. The …   Medical dictionary

  • pyruvate dehydrogenase complex — py·ru·vate de·hy·dro·gen·ase com·plex (piґroo vāt de hiґdro jən ās komґpleks) see under complex …   Medical dictionary

  • Pyruvate dehydrogenase (lipoamide) alpha 1 — PDB rendering based on 1ni4 …   Wikipedia

  • Pyruvate dehydrogenase kinase — (also pyruvate dehydrogenase complex kinase, PDC kinase, or PDK; EC number|2.7.11.2) is a kinase enzyme which acts to inactivate the enzyme pyruvate dehydrogenase by phosphorylating it using ATP. PDK thus participates in the regulation of the… …   Wikipedia

  • Pyruvate dehydrogenase deficiency — Classification and external resources ICD 10 E74.4 ICD 9 271.8 …   Wikipedia

  • Pyruvate dehydrogenase — Crystallographic structure of pyruvate dehydrogenase (PDH). PH is a six domain dimer with α (blue), α’ (yellow), β (red), and β’ (teal) regions denoted by the different colors. Thiamine pyrophosphate (TPP) is shown in grey ball and stick form,… …   Wikipedia

  • Pyruvate dehydrogenase (acetyl-transferring) — In enzymology, a pyruvate dehydrogenase (acetyl transferring) (EC number|1.2.4.1) is an enzyme that catalyzes the chemical reaction:pyruvate + [dihydrolipoyllysine residue acetyltransferase] lipoyllysine ightleftharpoons [dihydrolipoyllysine… …   Wikipedia

  • pyruvate dehydrogenase (acetyl-transferring) — py·ru·vate de·hy·dro·gen·ase (ac·e·tyl trans·fer·ring) (piґroo vāt de hiґdro jən ās asґə təl transґfər ing) [EC 1.2.4.1] an enzyme of the oxidoreductase class that is a component of the multienzyme pyruvate… …   Medical dictionary

  • [pyruvate dehydrogenase (acetyl-transferring)] kinase — [py·ru·vate de·hy·dro·gen·ase (ac·e·tyl trans·fer·ring)] ki·nase (piґroo vāt de hiґdro jən ās asґə təl transґfər ing kiґnās) [EC 2.7.11.2] an enzyme of the transferase class that catalyzes the phosphorylation of …   Medical dictionary

  • [pyruvate dehydrogenase (acetyl-transferring)]-phosphatase — [py·ru·vate de·hy·dro·gen·ase (ac·e·tyl trans·fer·ring)] phos·pha·tase (piґroo vāt de hiґdro jən ās asґə təl transґfər ing fosґfə tās) [EC 3.1.3.43] an enzyme of the hydrolase class that catalyzes the… …   Medical dictionary


Share the article and excerpts

Direct link
Do a right-click on the link above
and select “Copy Link”

We are using cookies for the best presentation of our site. Continuing to use this site, you agree with this.