Pyruvate dehydrogenase (lipoamide) beta, also known as pyruvate dehydrogenase E1 component subunit beta, mitochondrial or PDHE1-B is an enzyme that in humans is encoded by the PDHB gene. The pyruvate dehydrogenase (PDH) complex is a nuclear-encoded mitochondrial multienzyme complex that catalyzes the overall conversion of pyruvate to acetyl-CoA and CO2, and provides the primary link between glycolysis and the tricarboxylic acid (TCA) cycle. The PDH complex is composed of multiple copies of three enzymatic components: pyruvate dehydrogenase (E1), dihydrolipoamide acetyltransferase (E2) and lipoamide dehydrogenase (E3). The E1 enzyme is a heterotetramer of two alpha and two beta subunits. This gene encodes the E1 beta subunit. Mutations in this gene are associated with pyruvate dehydrogenase E1-beta deficiency.
Structure The PDH genes that comprise the E1 subunit are 1.36 kilobases long (alpha) and 1.69 kb long (beta). The PDHB gene has a total of 10 exons and 9 introns. All intron-exon splice junctions follow the standard GT/AG rule. There was an Alu family found in introns 2 and 8. The 5' flanking region gene contains a "CAAT" consensus promoter sequence but no "TATA" sequence. The transcription start site is an adenine residue located 132 bases upstream from the initiation codon in exon 1. The mRNA species that results from transcription of PDHB has been experimentally determined, via Northern blotting, to be 1.6 kb in length, although another fragment 5.5 kb long was also identified. The PDHB gene encodes a precursor protein that has 359 amino acid residues and a final mature protein that has 329 amino acids, and is part of the pyruvate dehydrogenase multienzyme complex. Two of the mature PDHB proteins come together with two PDHA 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. Specifically, the catalytic residue has been identified on the PDHB subunit, the 89th residue, which is a glutamate. In forming the entire PDH complex, the 289th beta residue, aspartic acid, interacts with the 276th residue of the E2 complex, a lysine. 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. 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.
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. Additionally, PDHB interacts with Prolyl-hydroxylase PHD3 to regulate the cellular PDH activity.
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