There are three different enzyme components in the pyruvate dehydrogenase complex. Pyruvate dehydrogenase (EC 1.2.4.1) is responsible for the oxidation of pyruvate, dihydrolipoyl transacetylase (this enzyme; EC 2.3.1.12) transfers the acetyl group to coenzyme A (CoA), and dihydrolipoyl dehydrogenase (EC 1.8.1.4) regenerates the lipoamide. Because dihydrolipoyl transacetylase is the second of the three enzyme components participating in the reaction mechanism for conversion of pyruvate into acetyl CoA, it is sometimes referred to as E2.
In humans, dihydrolipoyl transacetylase enzymatic activity resides in the pyruvate dehydrogenase complex component E2 (PDCE2) that is encoded by the DLAT (dihydrolipoamide S-acetyltransferase) gene.[5]
Nomenclature
The systematic name of this enzyme class is acetyl-CoA:enzyme N6-(dihydrolipoyl)lysine S-acetyltransferase.
The cubic catalytic core structure made up of 24 dihydrolipoyl transacetylase subunits.[6]The dodecahedral catalytic core structure made up of 60 dihydrolipoyl transacetylase subunits from Geobacillus stearothermophilus: 3D electron microscopy map (left) and X-ray diffraction structure (right).[7]
All dihydrolipoyl transacetylases have a unique multidomain structure consisting of (from N to C): 3 lipoyl domains, an interaction domain, and the catalytic domain (see the domain architecture at Pfam). All the domains are connected by disordered, low complexity linker regions.
Depending on the species, multiple subunits of dihydrolipoyl transacetylase enzymes can arrange together into either a cubic or dodecahedral shape. These structure then form the catalytic core of the pyruvate dehydrogenase complex which not only catalyzes the reaction that transfers an acetyl group to CoA, but also performs a crucial structural role in creating the architecture of the overall complex.[7]
Cube
The cubic core structure, found in species such as Azotobacter vinelandii, is made up of 24 subunits total.[8][9] The catalytic domains are assembled into trimers with the active site located at the subunit interface. The topology of this trimer active site is identical to that of chloramphenicol acetyltransferase. Eight of these trimers are then arranged into a hollow truncated cube. The two main substrates, CoA and the lipoamide (Lip(SH)2), are found at two opposite entrances of a 30 Å long channel which runs between the subunits and forms the catalytic center. CoA enters from the inside of the cube, and the lipoamide enters from the outside.[10]
Dodecahedron
In many species, including bacteria such as Geobacillus stearothermophilus and Enterococcus faecalis[7] as well as mammals such as humans[11] and cows,[12] the dodecahedral core structure is made up of 60 subunits total. The subunits are arranged in sets of three, similar to the trimers in the cubic core shape, with each set making up one of the 20 dodecahedral vertices.
Dihydrolipoyl transacetylase participates in the pyruvate decarboxylation reaction that links glycolysis to the citric acid cycle. These metabolic processes are important for cellular respiration—the conversion of biochemical energy from nutrients into adenosine triphosphate (ATP) which can then be used to carry out numerous biological reactions within a cell. The various parts of cellular respiration take place in different parts of the cell. In eukaryotes, glycolysis occurs in the cytoplasm, pyruvate decarboxylation in the mitochondria, the citric acid cycle within the mitochondrial matrix, and oxidative phosphorylation via the electron transport chain on the mitochondrial cristae. Thus pyruvate dehydrogenase complexes (containing the dihydrolipoyl transacetylase enzymes) are found in the mitochondria of eukaryotes (and simply in the cytosol of prokaryotes).
Mechanism
Dihydrolipoyl transacetylase mechanism
Pyruvate decarboxylation requires a few cofactors in addition to the enzymes that make up the complex. The first is thiamine pyrophosphate (TPP), which is used by pyruvate dehydrogenase to oxidize pyruvate and to form a hydroxyethyl-TPP intermediate. This intermediate is taken up by dihydrolipoyl transacetylase and reacted with a second lipoamide cofactor to generate an acetyl-dihydrolipoyl intermediate, releasing TPP in the process. This second intermediate can then be attacked by the nucleophilic sulfur attached to Coenzyme A, and the dihydrolipoamide is released. This results in the production of acetyl CoA, which is the end goal of pyruvate decarboxylation. The dihydrolipoamide is taken up by dihydrolipoyl dehydrogenase, and with the additional cofactors FAD and NAD+, regenerates the original lipoamide (with NADH as a useful side product).
Interactive pathway map
Click on genes, proteins and metabolites below to link to respective articles.[§ 1]
Primary biliary cirrhosis (PBC) is an autoimmune disease characterized by autoantibodies against mitochondrial and nuclear antigens. These are called anti-mitochondrial antibodies (AMA) and anti-nuclear antibodies (ANA), respectively. These antibodies are detectable in the sera of PBC patients and vary greatly with regards to epitope specificity from patient to patient. Of the mitochondrial antigens that can generate autoantibody reactivity in PBC patients, the E2 subunit of the pyruvate dehydrogenase complex, dihydrolipoyl transacetylase, is the most common epitope (other antigens include enzymes of the 2-oxoacid dehydrogenase complexes as well as the other enzymes of the pyruvate dehydrogenase complexes).[13] Recent evidence has suggested that peptides within the catalytic site may present the immunodominant epitopes recognized by the anti-PDC-E2 antibodies in PBC patients.[14] There is also evidence of anti-PDC-E2 antibodies in autoimmune hepatitis (AIH) patients.[15]
Pyruvate dehydrogenase deficiency
Pyruvate dehydrogenase deficiency (PDH) is a genetic disease resulting in lactic acidosis as well as neurological dysfunction in infancy and early childhood. Typically PDH is the result of a mutation in the X-linked gene for the E1 subunit of the pyruvate dehydrogenase complex. However, there have been a few rare cases in which a patient with PDH actually has a mutation in the autosomal gene for the E2 subunit instead. These patients have been reported to have much less severe symptoms, with the most prominent disease manifestation being episodic dystonia, though both hypotonia and ataxia were also present.[16]
^"Human PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
^"Mouse PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
^Leung PS, Watanabe Y, Munoz S, Teuber SS, Patel MS, Korenberg JR, Hara P, Coppel R, Gershwin ME (1993). "Chromosome localization and RFLP analysis of PDC-E2: the major autoantigen of primary biliary cirrhosis". Autoimmunity. 14 (4): 335–40. doi:10.3109/08916939309079237. PMID8102256.
^Mattevi A, Obmolova G, Kalk KH, Teplyakov A, Hol WG (Apr 1993). "Crystallographic analysis of substrate binding and catalysis in dihydrolipoyl transacetylase (E2p)". Biochemistry. 32 (15): 3887–901. doi:10.1021/bi00066a007. PMID8471601.
^de Kok A, Hengeveld AF, Martin A, Westphal AH (Jun 1998). "The pyruvate dehydrogenase multi-enzyme complex from Gram-negative bacteria". Biochimica et Biophysica Acta (BBA) - Protein Structure and Molecular Enzymology. 1385 (2): 353–66. doi:10.1016/S0167-4838(98)00079-X. PMID9655933.
^Hanemaaijer R, Westphal AH, Van Der Heiden T, De Kok A, Veeger C (Feb 1989). "The quaternary structure of the dihydrolipoyl transacetylase component of the pyruvate dehydrogenase complex from Azotobacter vinelandii. A reconsideration". European Journal of Biochemistry. 179 (2): 287–92. doi:10.1111/j.1432-1033.1989.tb14553.x. PMID2917567.
^Mattevi A, Obmolova G, Schulze E, Kalk KH, Westphal AH, de Kok A, Hol WG (Mar 1992). "Atomic structure of the cubic core of the pyruvate dehydrogenase multienzyme complex". Science. 255 (5051): 1544–50. Bibcode:1992Sci...255.1544M. doi:10.1126/science.1549782. PMID1549782.
^Head RA, Brown RM, Zolkipli Z, Shahdadpuri R, King MD, Clayton PT, Brown GK (Aug 2005). "Clinical and genetic spectrum of pyruvate dehydrogenase deficiency: dihydrolipoamide acetyltransferase (E2) deficiency". Annals of Neurology. 58 (2): 234–41. doi:10.1002/ana.20550. PMID16049940. S2CID38264402.
Further reading
Mattevi A, Obmolova G, Kalk KH, Teplyakov A, Hol WG (Apr 1993). "Crystallographic analysis of substrate binding and catalysis in dihydrolipoyl transacetylase (E2p)". Biochemistry. 32 (15): 3887–901. doi:10.1021/bi00066a007. PMID8471601.
Matsumura S, Kita H, He XS, Ansari AA, Lian ZX, Van De Water J, Yamamoto K, Tsuji T, Coppel RL, Kaplan M, Gershwin ME (Nov 2002). "Comprehensive mapping of HLA-A0201-restricted CD8 T-cell epitopes on PDC-E2 in primary biliary cirrhosis". Hepatology. 36 (5): 1125–34. doi:10.1053/jhep.2002.36161. PMID12395322. S2CID20687454.
Suzuki Y, Yoshitomo-Nakagawa K, Maruyama K, Suyama A, Sugano S (Oct 1997). "Construction and characterization of a full length-enriched and a 5'-end-enriched cDNA library". Gene. 200 (1–2): 149–56. doi:10.1016/S0378-1119(97)00411-3. PMID9373149.
Head RA, Brown RM, Zolkipli Z, Shahdadpuri R, King MD, Clayton PT, Brown GK (Aug 2005). "Clinical and genetic spectrum of pyruvate dehydrogenase deficiency: dihydrolipoamide acetyltransferase (E2) deficiency". Annals of Neurology. 58 (2): 234–41. doi:10.1002/ana.20550. PMID16049940. S2CID38264402.
Bogdanos DP, Pares A, Baum H, Caballeria L, Rigopoulou EI, Ma Y, Burroughs AK, Rodes J, Vergani D (Jun 2004). "Disease-specific cross-reactivity between mimicking peptides of heat shock protein of Mycobacterium gordonae and dominant epitope of E2 subunit of pyruvate dehydrogenase is common in Spanish but not British patients with primary biliary cirrhosis". Journal of Autoimmunity. 22 (4): 353–62. doi:10.1016/j.jaut.2004.03.002. PMID15120760. S2CID6619201.
Maruyama K, Sugano S (Jan 1994). "Oligo-capping: a simple method to replace the cap structure of eukaryotic mRNAs with oligoribonucleotides". Gene. 138 (1–2): 171–4. doi:10.1016/0378-1119(94)90802-8. PMID8125298.
