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Ryoikibetsu Shokogun Shirizu 1998
Review
Topics: Biomarkers; Diagnosis, Differential; Female; Humans; Lactic Acid; Male; Metabolism, Inborn Errors; Mutation; Prognosis; Pyruvate Decarboxylase; Pyruvic Acid
PubMed: 9590062
DOI: No ID Found -
BMC Research Notes May 2021Zymomonas mobilis is an alpha-proteobacterium with a rapid ethanologenic pathway, involving Entner-Doudoroff (E-D) glycolysis, pyruvate decarboxylase (Pdc) and two...
OBJECTIVE
Zymomonas mobilis is an alpha-proteobacterium with a rapid ethanologenic pathway, involving Entner-Doudoroff (E-D) glycolysis, pyruvate decarboxylase (Pdc) and two alcohol dehydrogenase (ADH) isoenzymes. Pyruvate is the end-product of the E-D pathway and the substrate for Pdc. Construction and study of Pdc-deficient strains is of key importance for Z. mobilis metabolic engineering, because the pyruvate node represents the central branching point, most novel pathways divert from ethanol synthesis. In the present work, we examined the aerobic metabolism of a strain with partly inactivated Pdc.
RESULTS
Relative to its parent strain the mutant produced more pyruvate. Yet, it also yielded more acetaldehyde, the product of the Pdc reaction and the substrate for ADH, although the bulk ADH activity was similar in both strains, while the Pdc activity in the mutant was reduced by half. Simulations with the kinetic model of Z. mobilis E-D pathway indicated that, for the observed acetaldehyde to ethanol production ratio in the mutant, the ratio between its respiratory NADH oxidase and ADH activities should be significantly higher, than the measured values. Implications of this finding for the directionality of the ADH isoenzyme operation in vivo and interactions between ADH and Pdc are discussed.
Topics: Alcohol Dehydrogenase; Metabolic Engineering; Pyruvate Decarboxylase; Respiration; Zymomonas
PubMed: 34049566
DOI: 10.1186/s13104-021-05625-5 -
PloS One 2023Understanding metabolism in the pathogen Candida glabrata is key to identifying new targets for antifungals. The thiamine biosynthetic (THI) pathway is partially...
Understanding metabolism in the pathogen Candida glabrata is key to identifying new targets for antifungals. The thiamine biosynthetic (THI) pathway is partially defective in C. glabrata, but the transcription factor CgPdc2 upregulates some thiamine biosynthetic and transport genes. One of these genes encodes a recently evolved thiamine pyrophosphatase (CgPMU3) that is critical for accessing external thiamine. Here, we demonstrate that CgPdc2 primarily regulates THI genes. In Saccharomyces cerevisiae, Pdc2 regulates both THI and pyruvate decarboxylase (PDC) genes, with PDC proteins being a major thiamine sink. Deletion of PDC2 is lethal in S. cerevisiae in standard growth conditions, but not in C. glabrata. We uncover cryptic cis elements in C. glabrata PDC promoters that still allow for regulation by ScPdc2, even when that regulation is not apparent in C. glabrata. C. glabrata lacks Thi2, and it is likely that inclusion of Thi2 into transcriptional regulation in S. cerevisiae allows for a more complex regulation pattern and regulation of THI and PDC genes. We present evidence that Pdc2 functions independent of Thi2 and Thi3 in both species. The C-terminal activation domain of Pdc2 is intrinsically disordered and critical for species differences. Truncation of the disordered domains leads to a gradual loss of activity. Through a series of cross species complementation assays of transcription, we suggest that there are multiple Pdc2-containing complexes, and C. glabrata appears to have the simplest requirement set for THI genes, except for CgPMU3. CgPMU3 has different cis requirements, but still requires Pdc2 and Thi3 to be upregulated by thiamine starvation. We identify the minimal region sufficient for thiamine regulation in CgTHI20, CgPMU3, and ScPDC5 promoters. Defining the cis and trans requirements for THI promoters should lead to an understanding of how to interrupt their upregulation and provide targets in metabolism for antifungals.
Topics: Saccharomyces cerevisiae; Candida glabrata; Transcription Factors; Fungal Proteins; Pyruvate Decarboxylase; Thiamine; Carboxy-Lyases; Promoter Regions, Genetic; Intrinsically Disordered Proteins; Gene Expression Regulation, Fungal
PubMed: 37285346
DOI: 10.1371/journal.pone.0286744 -
Annals of the New York Academy of... 1982
Review
Topics: Acetylation; Amino Acids; Apoenzymes; Arginine; Carboxy-Lyases; Chemical Phenomena; Chemistry; Circular Dichroism; Lysine; Macromolecular Substances; Plants; Protein Conformation; Protein Denaturation; Pyruvate Decarboxylase; Saccharomyces cerevisiae; Serine; Structure-Activity Relationship; Sulfhydryl Compounds; Thiamine Pyrophosphate; Triticum; Tryptophan; Tyrosine
PubMed: 6805384
DOI: 10.1111/j.1749-6632.1982.tb31203.x -
Biochimica Et Biophysica Acta Jun 1998Pyruvate decarboxylase (EC 4.1.1.1) is a thiamin diphosphate-dependent enzyme that catalyzes the penultimate step in alcohol fermentation. The enzyme is widely... (Review)
Review
Pyruvate decarboxylase (EC 4.1.1.1) is a thiamin diphosphate-dependent enzyme that catalyzes the penultimate step in alcohol fermentation. The enzyme is widely distributed in plants and fungi but is rare in prokaryotes and absent in animals. Here we review its structure and properties with particular emphasis on how site-directed mutagenesis of the enzyme from Zymomonas mobilis has assisted us to understand the function of critical residues.
Topics: Amino Acid Sequence; Binding Sites; Catalysis; Kinetics; Molecular Sequence Data; Mutagenesis, Site-Directed; Pyruvate Decarboxylase; Pyruvic Acid; Thiamine Pyrophosphate; Zymomonas
PubMed: 9655927
DOI: 10.1016/s0167-4838(98)00077-6 -
Preparative Biochemistry & Biotechnology 2022has good reproductive ability in both haploid and diploid forms, a pyruvate decarboxylase plays an important role in cell metabolism. In this study, 1 and 5 double...
has good reproductive ability in both haploid and diploid forms, a pyruvate decarboxylase plays an important role in cell metabolism. In this study, 1 and 5 double knockout strains of H14-02 (a type) and H5-02 (α type) were obtained by the Cre/loxP technique. The effects of the deletion of 1 and 5 on the metabolites of the two haploid strains were consistent. In H14-02, the ethanol conversion decreased by 30.19%, the conversion of glycerol increased by 40.005%, the concentration of acetic acid decreased by 43.54%, the concentration of acetoin increased by 12.79 times, and the activity of pyruvate decarboxylase decreased by 40.91% compared to those in the original H14 strain. The original haploid strain H14 produced a small amount of acetoin but produced very little 2,3-butanediol. However, H14-02 produced 1.420 ± 0.063 g/L 2,3-BD. This study not only provides strain selection for obtaining haploid strains with a high yield of 2,3-BD but also lays a foundation for haploid to be used as a new tool for genetic research and breeding programs.
Topics: Acetoin; Butylene Glycols; Carboxy-Lyases; Ethanol; Gene Deletion; Gene Expression Regulation, Fungal; Gene Knockout Techniques; Glycerol; Haploidy; Pyruvate Decarboxylase; Saccharomyces cerevisiae; Saccharomyces cerevisiae Proteins
PubMed: 33881948
DOI: 10.1080/10826068.2021.1910958 -
Acta Chemica Scandinavica (Copenhagen,... Aug 1992Pyruvate decarboxylase (PDC) catalyzes the decarboxylation of pyruvate anion by a factor of around 10(12), compared with the non-enzymic decarboxylation by thiamine,... (Review)
Review
Pyruvate decarboxylase (PDC) catalyzes the decarboxylation of pyruvate anion by a factor of around 10(12), compared with the non-enzymic decarboxylation by thiamine, under standard state conditions of 1 mM pyruvate and thiamine diphosphate (TDP), pH 6.2. Free-energy diagrams constructed on the basis of earlier measurements for the enzymic and non-enzymic reactions give some information on catalysis by PDC. PDC stabilizes the reactant state preceding TDP addition to pyruvate by 76 kJ mol-1 and the transition state for the addition by 83 kJ mol-1. PDC stabilizes the reactant state preceding decarboxylation (presumably alpha-lactyl-TDP) by 27 kJ mol-1 and the transition state for decarboxylation by 68 kJ mol-1. In addition, the free-energy diagrams reveal a leveling of reactant-state free energies in the enzymic reaction compared with the non-enzymic reaction, in that the former are nearly equal to each other. The enzyme-bound transition-state energies are similarly leveled. The energetic leveling of reactant states has been noted by Albery, Knowles and their coworkers in many enzymic reactions and termed 'matched internal thermodynamics.' They showed that the result would arise naturally (and inevitably) in the 'evolution to perfection' of enzymes, when the evolutionary process was treated by a deterministic model. The critical assumption of this model was the validity of a Marcus-type or Brønsted-type linear free-energy relationship between rate and equilibrium constants for reactions occurring wholly within enzyme complexes. Here a completely stochastic simulation of molecular evolution, with no deterministic assumptions, is shown to reproduce both 'matched internal thermodynamics' and the 'matched internal kinetics' or leveling of transition-state energies noted here. The Albery-Knowles result is thus more general than might have been supposed.
Topics: Biological Evolution; Catalysis; Computer Simulation; Models, Chemical; Pyruvate Decarboxylase; Pyruvates; Pyruvic Acid; Thermodynamics
PubMed: 1497997
DOI: 10.3891/acta.chem.scand.46-0778 -
Acta Crystallographica. Section F,... Sep 2016Pyruvate decarboxylase (PDC; EC 4.1.1.1) is a thiamine pyrophosphate- and Mg(2+) ion-dependent enzyme that catalyses the non-oxidative decarboxylation of pyruvate to...
Pyruvate decarboxylase (PDC; EC 4.1.1.1) is a thiamine pyrophosphate- and Mg(2+) ion-dependent enzyme that catalyses the non-oxidative decarboxylation of pyruvate to acetaldehyde and carbon dioxide. It is rare in bacteria, but is a key enzyme in homofermentative metabolism, where ethanol is the major product. Here, the previously unreported crystal structure of the bacterial pyruvate decarboxylase from Zymobacter palmae is presented. The crystals were shown to diffract to 2.15 Å resolution. They belonged to space group P21, with unit-cell parameters a = 204.56, b = 177.39, c = 244.55 Å and Rr.i.m. = 0.175 (0.714 in the highest resolution bin). The structure was solved by molecular replacement using PDB entry 2vbi as a model and the final R values were Rwork = 0.186 (0.271 in the highest resolution bin) and Rfree = 0.220 (0.300 in the highest resolution bin). Each of the six tetramers is a dimer of dimers, with each monomer sharing its thiamine pyrophosphate across the dimer interface, and some contain ethylene glycol mimicking the substrate pyruvate in the active site. Comparison with other bacterial PDCs shows a correlation of higher thermostability with greater tetramer interface area and number of interactions.
Topics: Amino Acid Sequence; Bacterial Proteins; Catalytic Domain; Cations, Divalent; Cloning, Molecular; Crystallography, X-Ray; Escherichia coli; Ethylene Glycol; Gene Expression; Halomonadaceae; Kinetics; Magnesium; Models, Molecular; Protein Binding; Protein Conformation, alpha-Helical; Protein Conformation, beta-Strand; Protein Interaction Domains and Motifs; Protein Multimerization; Pyruvate Decarboxylase; Pyruvic Acid; Recombinant Proteins; Substrate Specificity; Thiamine Pyrophosphate
PubMed: 27599861
DOI: 10.1107/S2053230X16012012 -
Archaea (Vancouver, B.C.) 2014The hyperthermophilic archaeon Thermococcus guaymasensis produces ethanol as a metabolic end product, and an alcohol dehydrogenase (ADH) catalyzing the reduction of...
The hyperthermophilic archaeon Thermococcus guaymasensis produces ethanol as a metabolic end product, and an alcohol dehydrogenase (ADH) catalyzing the reduction of acetaldehyde to ethanol has been purified and characterized. However, the enzyme catalyzing the formation of acetaldehyde has not been identified. In this study an enzyme catalyzing the production of acetaldehyde from pyruvate was purified and characterized from T. guaymasensis under strictly anaerobic conditions. The enzyme had both pyruvate decarboxylase (PDC) and pyruvate ferredoxin oxidoreductase (POR) activities. It was oxygen sensitive, and the optimal temperatures were 85°C and >95°C for the PDC and POR activities, respectively. The purified enzyme had activities of 3.8 ± 0.22 U mg(-1) and 20.2 ± 1.8 U mg(-1), with optimal pH-values of 9.5 and 8.4 for each activity, respectively. Coenzyme A was essential for both activities, although it did not serve as a substrate for the former. Enzyme kinetic parameters were determined separately for each activity. The purified enzyme was a heterotetramer. The sequences of the genes encoding the subunits of the bifunctional PDC/POR were determined. It is predicted that all hyperthermophilic β -keto acids ferredoxin oxidoreductases are bifunctional, catalyzing the activities of nonoxidative and oxidative decarboxylation of the corresponding β -keto acids.
Topics: Acetaldehyde; DNA, Archaeal; Enzyme Inhibitors; Enzyme Stability; Ethanol; Hydrogen-Ion Concentration; Kinetics; Molecular Sequence Data; Oxygen; Protein Multimerization; Pyruvate Decarboxylase; Pyruvate Synthase; Pyruvic Acid; Sequence Analysis, DNA; Temperature; Thermococcus
PubMed: 24982594
DOI: 10.1155/2014/349379 -
Biochimica Et Biophysica Acta Jun 1998The crystal structures of pyruvate decarboxylase from the yeast Saccharomyces uvarum and Saccharomyces cerevisiae have been determined at 2.4 and 2.3 A resolution,... (Review)
Review
The crystal structures of pyruvate decarboxylase from the yeast Saccharomyces uvarum and Saccharomyces cerevisiae have been determined at 2.4 and 2.3 A resolution, respectively. These structures provide details about the protein fold and domain assembly within subunits, about subunit assembly to form dimers and about dimer assembly to form tetramers. They also provide a clear picture of the active site centered on the thiamin diphosphate cofactor, and have allowed amino acids critical for catalysis and involved in stabilization of the unusual cofactor conformation to be identified. The structural information has enabled identification of the site of allosteric activation to be centered on Cys-221, and suggests that a six residue segment leading from the regulatory site to the catalytic site may be involved in transmission of a binding signal. The importance of several amino acids within this segment in the regulatory process, as well as some involved in stabilizing and activating the cofactor has been confirmed by analyzing the behavior of recombinant enzymes with single point mutations introduced at these sites. Additional structures have been determined for pyruvate decarboxylase in multiple crystal forms, some of which were obtained from crystals grown with known allosteric activators present in the media. Currently four distinct types of tetramers have been observed, with each showing a different mode of association of dimers to form the tetramers. In some of the cases involving the presence of allosteric activators drastic changes in the mode of dimer assembly to form tetramers is seen.
Topics: Allosteric Regulation; Binding Sites; Crystallography, X-Ray; Macromolecular Substances; Models, Molecular; Molecular Structure; Protein Conformation; Pyruvate Decarboxylase; Saccharomyces; Structure-Activity Relationship; Thiamine Pyrophosphate
PubMed: 9655915
DOI: 10.1016/s0167-4838(98)00073-9