In this article, we will try to explain in an accessible manner what the pyruvate dehydrogenase complex and the biochemistry of the process are, to reveal the composition of enzymes and coenzymes, to indicate the role and significance of this complex in nature and human life. In addition, the possible consequences of violation of the functional purpose of the complex and the time of their manifestation will be considered.
Familiarization with the concept
Pyruvate dehydrogenase complex (PDH) is a protein-type complex whose role is to oxidize pyruvate as a result of decarboxylation. This complex contains 3 enzymes, as well as two proteins necessary for the implementation of auxiliary functions. In order for the pyruvate dehydrogenase complex to function, certain cofactors are required. There are five of them: CoA, nicotinamide adenine dinucleotide, flavin adenine dinucleotide, thiamine pyrophosphate and lipoate.
Localization of PDH in bacterial organisms is concentrated in the cytoplasm, eukaryotic cells store it in the matrix on mitochondria.
Relationship with pyruvate decarboxylation
The significance of the pyruvate dehydrogenase complex lies in the oxidation reaction of pyruvate. Consider the essence of this process.
The mechanism of pyruvate oxidation under the influence of decarboxylation is a biochemical process in which the CO 2 molecule is split off in the singular, followed by the addition of this molecule to pyruvate subjected to decarboxylation and belonging to coenzyme A (CoA). This creates acetyl-KoA. This phenomenon takes an intermediate place between the processes of glycolysis and the tricarboxylic acid type cycle. The pyruvate dicarboxylation process is carried out with the participation of a complex MPC, which, as previously mentioned, comprises three enzymes and two auxiliary proteins.
The role of coenzymes
For the pyruvate dehydrogenase complex, enzymes play a crucial role. However, they can begin their work only in the presence of five coenzymes or groups of the prosthetic type, which were listed above. The process itself will ultimately lead to the fact that the acyl group will be included in CoA-acetyl. Speaking about coenzymes, it is necessary to know that four of them belong to derivative vitamins: thiamine, riboflavin, niacin and pantothenic acid.
Flavin adenine dinucleotide and nicotinamide adenine indinucleotide are involved in electron transfer, and thiamine pyrophosphate, many known as pyruvate decarboxyl coenzyme, enters into a fermentation reaction.
Thiol group activation
Acetylation coenzyme (A) - contains a thiol-type group (-SH), which is very active, it is critical and necessary in order for CoA to function as a substance that can transfer the acyl group to the thiol and form a thioether. Thiol esters (thioesters) - have a fairly high rate of hydrolytic energy of a free nature, because they have a high potential for the transfer of the acyl group to a variety of acceptor molecules. That is why acetyl CoA is periodically called activated CH 3 COOH.
Electron transfer
In addition to the four cofactors of the nature of vitamin derivatives, there is the 5th cofactor of the pyruvate dehydrogenase complex, called lipoatom. It is characterized by 2 groups of the thiol type, capable of undergoing reversible oxidation, which results in the formation of a disulfide bond (-SS-), which is similar to how this process proceeds between amino acid and cysteine ββresidues in proteins. The ability to oxidize and recover gives the lipoate the opportunity to be a carrier of not only the acyl group, but also electrons.
Enzymatic set
Of the enzymes, the pyruvate dehydrogenase complex includes three main components. The first enzyme is pyruvate dehydrosenase (E 1 ). The second enzyme is dihydrolipoyl dehydrogenase (E 3 ). The third is dihydrolipoyl transacetylase (E 2 ). The pyruvate dehydrogenase complex includes these enzymes, storing them in a large number of copies. The number of copies of each enzyme can be different, and therefore the size of the complex can vary greatly. The PDH complex in mammals reaches about 50 nanometers in diameter. This is 5-6 times larger than the diameter of the ribosome. Such complexes are very large, so they can be distinguished in an electron microscope.
The gram-positive bacterium bacillus stearothermophilus in its PDH has sixty identical copies of the dihydrolipoyltransacetylase, which, in turn, create a pentagonal-type dodecahedron with a diameter of approximately 25 nanometers. Gram-positive bacterium Escherichia coli contains twenty-four copies of E 2 , cat. attaches to itself a prosthetic group of lipoate, and it establishes a bond of the amide type with the amino group of the lysine residue included in E 2 .
Dihydrolipoyltransacetylase is built upon the interaction of 3 domains with functional differences. These are: the amino terminal lipoil domain containing a lysine residue and bound to the lipoate; a binding domain (central E 1 - and E 3 - ); an internal acyltransferase domain including active type acyltransferase centers.
The pyruvate dehydrogenase complex of yeast has only one domain of the lipoyl type, the mammals of such domains have two, and the bacteria of E. coli - three. The linker sequence of amino acids, which consist of twenty to thirty amino acid residues, is shared by E 2 , with the residues of alanins and proline alternating with amino acid residues that are charged. These linkers most often have extended forms. This feature affects the fact that they share 3 domains.
Relationship of origin
E 1 with its active center establishes a connection with the TTR, and the active center E 3 with FAD. The human body contains the enzyme E 1 in the form of a tetramer, which consists of four subunits: two E 1 alpha and two E 1 beta. Regulatory proteins are presented as protein kinases and phosphoprotein phosphatases. This type of structure (E 1 - E 2 - E 3 ) remains an element of conservatism in evolutionary doctrine. Complexes with a similar structure and device can participate in a variety of reactions other than standard ones, for example, when Ξ±-ketoglutarate is subjected to oxidation during the Krebs cycle, Ξ±-keto acid is also oxidized, which was formed due to the catabolic utilization of branched type amino acids: valine, leucine and isoleucine.
Pyruvate dehydrogenase complex has the enzyme E 3 , which is found in other complexes. The similarity of the protein structure, cofactors and also reaction mechanisms indicates a common origin. The lipoate attaches to lysine E 2 , and a βhandβ is created, which is able to move from the active center E 1 to the active centers E 2 and E 3 , which is approximately 5 nm.
Eukaryotes in the pyruvate dehydrogenase complex contain twelve subunits of E3BP (E 3 - non-catalytic binding protein). The location of this protein is not known exactly. There is a hypothesis that this protein replaces a subset of the subunit. E 2 in cow PDH.
Contact with microorganisms
The complex under consideration is inherent in some types of bacteria of the anaerobic type. However, the number of bacterial organisms with PDH in their structure is small. The functions performed by the complex in bacteria, as a rule, are reduced to general processes. For example, the role of the pyruvate dehydrogenase complex in the bacterium Zymonomonas mobilis is alcoholic fermentation. Pyruvate bacteria in the amount of up to 98% will be spent precisely for such purposes. The remaining few percent are oxidized to carbon dioxide, nicotinamide adenine dinucleotide, acetyl CoA, etc. The structure of the pyruvate dehydrogenase complex in Zimomonas mobilis is interesting. In this microorganism, it contains four enzymes: E 1 alpha, E 1 beta, E 2 and E 3 . In the PDH of this bacterium there is a lipoyl domain inside E 1 beta, which makes it unique. The core of the complex is represented by E 2 , and the organization of the complex itself takes the form of a pentagonal dodecahedron. Zimomonas mobilis does not have a whole series of enzymes in the tricarboxylic acid cycle, and therefore its PDH deals only with anabolic functions.
PDH in man
Man, like other living organisms, has genes involved in the coding of PDH. The E 1 alpha - PDHA 1 gene is localized on the X chromosome. The mechanism of action of the pyruvate dehydrogenase complex is extremely important, which follows from the fact that there are more than thirty mutants of the mutant type in the above gene, and each of the mutations leads to PDH deficiency. Symptoms of the disease can vary greatly from lactic acidosis problems of a mild nature to fatal malformations of the body. Men whose X-chromosome includes a similar allele will have an early death at a very young age. Females also experience this disease, but to a lesser extent, and the problem itself is the inactivation of any X chromosome.
Mutation Issues
E 1 beta - PDHB - is located on the third chromosome. Only two mutants of the mutant type are known for this gene, which, being in the homozygous position, lead to death throughout the year, which is associated with malformations.
There are probably other similar alleles that can cause death before the full development of the body. E 2 - DLAT - focused on the eleventh chromosome. Humanity is aware of two alleles of this gene that will create problems in the future, however, a proper diet can compensate for this. There is a high probability that the fetus will die inside the womb due to other mutations of this gene. E 3 - dld - is located on the seventh chromosome and includes a large number of alleles. A rather large percentage of them leads to the appearance of diseases of a genetic nature, which will be associated with a violation of amino acid metabolism.
Conclusion
We examined how important the pyruvate dehydrogenase complex is for living organisms. The reactions occurring in it are directed, first of all, to the decarboxylation of pyruvate by oxidation, and PDH itself is highly specialized, but under different conditions, if there are certain reasons, it can also perform functions of a different nature, for example, to participate in fermentation. We also found that protein-type complexes that are involved in pyruvate oxidation consist of five enzymes that remain functional only if there are five cofactors. Any changes in the algorithm of the complex mechanism of decarboxylation can cause serious pathologies and even lead to the death of the individual.