Pyruvate dehydrogenase (lipoamide) alpha 2 explained

Pyruvate dehydrogenase (lipoamide) alpha 2, also known as pyruvate dehydrogenase E1 component subunit alpha, testis-specific form, mitochondrial or PDHE1-A type II, is an enzyme that in humans is encoded by the PDHA2 gene.^{[1] [2]}

Structure

Two mature PDHA proteins come together with two PDHB proteins to form a heterotetrameric E1 subunit. Crystal Structures allowed for a model in which the enzyme undergoes a 2-A shuttle-like motion of its heterodimers to perform the catalysis.^[3] The protein encoded by the human PDHA2 gene is part of the pyruvate dehydrogenase multienzyme complex. The entire human complex is 9.5 MDa in size, and has been described as 60-meric, meaning there are over 60 components that are assembled to make the entire complex. These subunits are conserved across many species, as the function of this complex is essential for the generation of ATP for all eukaryotes.^[4] Each component is responsible for the catalysis of one step in this pathway; this complex exists for the purpose of channeling the intermediates of each reaction to the next enzyme, thus greatly increasing the rate of reaction.^[5]

Function

The pyruvate dehydrogenase complex is responsible for the oxidative decarboxylation of pyruvate, with the final product being Acetyl CoA. Overall the complex catalyzes five reactions, with the overall reaction being:

Pyruvate + CoA + NAD⁺ → acetyl-CoA + CO₂

There are three different coenzymes required throughout the 5 steps that this complex carries out: thiamine pyrophosphate (TPP), lipoamide, and coenzyme A. This step is only one of the central metabolic pathway carried out by eukaryotes, in which glucose is oxidized to form carbon dioxide, water, and ATP. The E1 complex specifically uses the TPP cofactor to cleave the Calpha-C(=O) bond of pyruvate, and then transfer the acetyl group to the TPP coenzyme, thus resulting in an intermediate, hydroxylethyl-Tpp*E1, and producing CO₂. The thiazolium ring on the TPP is ideal for adding to carbonyl groups and acting as an electron sink, or a group that can pull electrons from a reaction and stabilize an electron-deficient intermediate.

Regulation

The activity of the PDH complex in mammalian tissues is largely determined by the phosphorylation of certain subunits within the complex. As such, the absolute amounts of site-specific kinases and phosphates expressed in the mitochondria directly affect PDH activity.^[6]

As this gene is mostly inactive, save for in testis tissue, a methylation mechanism is in place that inactivates this gene in somatic cells. Removing the methyl group from the coding region has shown to activate the enzyme in vitro.^[7]

Clinical significance

Mutations in the PDHA2 gene have been known to cause one form of pyruvate dehydrogenase deficiency. Pyruvate dehydrogenase deficiency is characterized by the buildup of a chemical called lactic acid in the body and a variety of neurological problems. Signs and symptoms of this condition usually first appear shortly after birth, and they can vary widely among affected individuals. The most common feature is a potentially life-threatening buildup of lactic acid (lactic acidosis), which can cause nausea, vomiting, severe breathing problems, and an abnormal heartbeat. People with pyruvate dehydrogenase deficiency usually have neurological problems as well. Most have delayed development of mental abilities and motor skills such as sitting and walking. Other neurological problems can include intellectual disability, seizures, weak muscle tone (hypotonia), poor coordination, and difficulty walking. Some affected individuals have abnormal brain structures, such as underdevelopment of the tissue connecting the left and right halves of the brain (corpus callosum), atrophy of the exterior part of the brain known as the cerebral cortex, or patches of damaged tissue (lesions) on some parts of the brain. Because of the severe health effects, many individuals with pyruvate dehydrogenase deficiency do not survive past childhood, although some may live into adolescence or adulthood. Mutations primarily manifest in the PDHA1 gene.

In women, this deficiency can be much harder to detect. This is because of the chance that there will be a skewed X inactivation pattern enzyme measurement in fibroblasts, meaning that the enzyme activity measurement may not be entirely accurate. Because the clinical presentation of this disorder overlaps heavily with deficiencies in oxidative phosphorylation, it is recommended to perform a detailed biochemical analysis on a muscle biopsy in females with a suspected pyruvate dehydrogenase deficiency, followed by molecular genetic analysis of the PDHA1 gene.^[8]

The methylation as a form of regulation shows promise as a therapy for those with PDH deficiency due to mutations in other genes, as the gene has been activated in vitro via demethylation.^[9]

Further reading

• Jacobia SJ, Korotchkina LG, Patel MS . Differential effects of two mutations at arginine-234 in the alpha subunit of human pyruvate dehydrogenase. . Arch. Biochem. Biophys. . 395 . 1 . 121–8 . 2001 . 11673873 . 10.1006/abbi.2001.2576 .
• Olsen JV, Blagoev B, Gnad F, etal . Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. . Cell . 127 . 3 . 635–48 . 2006 . 17081983 . 10.1016/j.cell.2006.09.026 . 7827573 . free .
• Caruso M, Maitan MA, Bifulco G, etal . Activation and mitochondrial translocation of protein kinase Cdelta are necessary for insulin stimulation of pyruvate dehydrogenase complex activity in muscle and liver cells. . J. Biol. Chem. . 276 . 48 . 45088–97 . 2001 . 11577086 . 10.1074/jbc.M105451200 . free .
• Datta U, Wexler ID, Kerr DS, etal . Characterization of the regulatory region of the human testis-specific form of the pyruvate dehydrogenase alpha-subunit (PDHA-2) gene. . Biochim. Biophys. Acta . 1447 . 2–3 . 236–43 . 1999 . 10542321 . 10.1016/s0167-4781(99)00158-x.
• Gerhard DS, Wagner L, Feingold EA, etal . The Status, Quality, and Expansion of the NIH Full-Length cDNA Project: The Mammalian Gene Collection (MGC) . Genome Res. . 14 . 10B . 2121–7 . 2004 . 15489334 . 528928 . 10.1101/gr.2596504 .
• Pinheiro A, Faustino I, Silva MJ, etal . Human testis-specific PDHA2 gene: methylation status of a CpG island in the open reading frame correlates with transcriptional activity . Mol. Genet. Metab. . 99 . 4 . 425–30 . 2010 . 20005141 . 10.1016/j.ymgme.2009.11.002 .
• Fitzgerald J, Hutchison WM, Dahl HH . Isolation and characterisation of the mouse pyruvate dehydrogenase E1 alpha genes . Biochim. Biophys. Acta . 1131 . 1 . 83–90 . 1992 . 1581363 . 10.1016/0167-4781(92)90102-6 .
• Strausberg RL, Feingold EA, Grouse LH, etal . Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences . Proc. Natl. Acad. Sci. U.S.A. . 99 . 26 . 16899–903 . 2002 . 12477932 . 139241 . 10.1073/pnas.242603899 . 2002PNAS...9916899M . free .
• Venter JC, Adams MD, Myers EW, etal . The sequence of the human genome . Science . 291 . 5507 . 1304–51 . 2001 . 11181995 . 10.1126/science.1058040 . 2001Sci...291.1304V . free .
• Liu S, Baker JC, Andrews PC, Roche TE . Recombinant expression and evaluation of the lipoyl domains of the dihydrolipoyl acetyltransferase component of the human pyruvate dehydrogenase complex . Arch. Biochem. Biophys. . 316 . 2 . 926–40 . 1995 . 7864652 . 10.1006/abbi.1995.1124 .
• Brown RM, Dahl HH, Brown GK . Pyruvate dehydrogenase E1 alpha subunit genes in the mouse: mapping and comparison with human homologs . Somat. Cell Mol. Genet. . 16 . 5 . 487–92 . 1990 . 2122529 . 10.1007/BF01233198 . 24587303 .

Notes and References

1. Web site: Entrez Gene: pyruvate dehydrogenase (lipoamide) alpha 2.
2. Dahl HH, Brown RM, Hutchison WM, Maragos C, Brown GK . A testis-specific form of the human pyruvate dehydrogenase E1 alpha subunit is coded for by an intronless gene on chromosome 4 . Genomics . 8 . 2 . 225–32 . October 1990 . 2249846 . 10.1016/0888-7543(90)90275-Y.
3. Ciszak. EM. Korotchkina. LG. Dominiak. PM. Sidhu. S. Patel. MS. Structural basis for flip-flop action of thiamin pyrophosphate-dependent enzymes revealed by human pyruvate dehydrogenase.. The Journal of Biological Chemistry. 6 June 2003. 278. 23. 21240–6. 12651851. 10.1074/jbc.m300339200. free. 2060/20030106063. free.
4. Hiromasa. Y. Fujisawa. T. Aso. Y. Roche. TE. Organization of the cores of the mammalian pyruvate dehydrogenase complex formed by E2 and E2 plus the E3-binding protein and their capacities to bind the E1 and E3 components.. The Journal of Biological Chemistry. 20 February 2004. 279. 8. 6921–33. 14638692. 10.1074/jbc.m308172200. free.
5. Book: Principles of Biochemistry . Chapter 17, Citric Acid Cycle . Donald J. . Voet . Judith G. . Voet . Charlotte W. . Pratt . Wiley . 2010 . 978-0-470-23396-2 . 550 . 4th . vanc .
6. Kolobova. E. Tuganova. A. Boulatnikov. I. Popov. KM. Regulation of pyruvate dehydrogenase activity through phosphorylation at multiple sites.. The Biochemical Journal. 15 August 2001. 358. Pt 1. 69–77. 11485553. 10.1042/0264-6021:3580069. 1222033.
7. Korotchkina. LG. Sidhu. S. Patel. MS. Characterization of testis-specific isoenzyme of human pyruvate dehydrogenase.. The Journal of Biological Chemistry. 7 April 2006. 281. 14. 9688–96. 16436377. 10.1074/jbc.m511481200. free.
8. Willemsen. M. Rodenburg. RJ. Teszas. A. van den Heuvel. L. Kosztolanyi. G. Morava. E. Females with PDHA1 gene mutations: a diagnostic challenge.. Mitochondrion. June 2006. 6. 3. 155–9. 16713755. 10.1016/j.mito.2006.03.001.
9. Pinheiro. A. Nunes. MJ. Milagre. I. Rodrigues. E. Silva. MJ. de Almeida. IT. Rivera. I. Demethylation of the coding region triggers the activation of the human testis-specific PDHA2 gene in somatic tissues.. PLOS ONE. 2012. 7. 6. e38076. 22675509. 10.1371/journal.pone.0038076. 3365900. 2012PLoSO...738076P. free.