ribulose-5-phosphate and 6-phosphogluconic-acid

The enzyme 6-phosphogluconate dehydrogenase catalyzes the conversion of 6-phosphogluconate to ribulose-5-phosphate. It represents an important reaction in the oxidative pentose phosphate pathway, producing a ribose precursor essential for nucleotide and nucleic acid synthesis. We succeeded, for the first time, to determine the three-dimensional structure of this enzyme from an acetic acid bacterium, Gluconacetobacter diazotrophicus (Gd6PGD). Active Gd6PGD, a homodimer (70 kDa), was present in both the soluble and the membrane fractions of the nitrogen-fixing microorganism. The Gd6PGD belongs to the newly described subfamily of short-chain (333 AA) 6PGDs, compared to the long-chain subfamily (480 AA; e.g., Ovis aries, Homo sapiens). The shorter amino acid sequence in Gd6PGD induces the exposition of hydrophobic residues in the C-terminal domain. This distinct structural feature is key for the protein to associate with the membrane. Furthermore, in terms of function, the short-chain 6PGD seems to prefer NAD

Topics: Amino Acid Sequence; Animals; Bacterial Proteins; Biocatalysis; Gluconacetobacter; Gluconates; Humans; Models, Chemical; Models, Molecular; Molecular Structure; NAD; NADP; Phosphogluconate Dehydrogenase; Phylogeny; Protein Domains; Protein Multimerization; Ribulosephosphates; Sequence Homology, Amino Acid

Giardia lamblia, due to the habitat in which it develops, requires a continuous supply of intermediate compounds that allow it to survive in the host. The pentose phosphate pathway (PPP) provides essential molecules such as NADPH and ribulose-5-phosphate during the oxidative phase of the pathway. One of the key enzymes during this stage is 6-phosphogluconate dehydrogenase (6 PGDH) for generating NADPH. Given the relevance of the enzyme, in the present work, the 6pgdh gene from G. lamblia was amplified and cloned to produce the recombinant protein (Gl-6 PGDH) and characterize it functionally and structurally after the purification of Gl-6 PGDH by affinity chromatography. The results of the characterization showed that the protein has a molecular mass of 54 kDa, with an optimal pH of 7.0 and a temperature of 36-42 °C. The kinetic parameters of Gl-6 PGDH were K

Topics: Amino Acid Motifs; Binding Sites; Cloning, Molecular; Gene Expression; Geobacillus stearothermophilus; Giardia lamblia; Gluconates; Humans; Kinetics; Models, Molecular; NADP; Pentose Phosphate Pathway; Phosphogluconate Dehydrogenase; Protein Binding; Protein Conformation, alpha-Helical; Protein Conformation, beta-Strand; Protein Interaction Domains and Motifs; Protozoan Proteins; Recombinant Proteins; Ribulosephosphates; Structural Homology, Protein; Substrate Specificity; Thermodynamics

Dental caries is initiated by demineralization of the tooth surface through acid production by sugar metabolism of supragingival plaque microflora. To elucidate the sugar metabolic system, we used CE-MS to perform metabolomics of the central carbon metabolism, the EMP pathway, the pentose-phosphate pathway, and the TCA cycle in supra- gingival plaque and representative oral bacteria, Streptococcus and Actinomyces. Supragingival plaque contained all the targeted metabolites in the central carbon metabolism, except erythrose 4-phosphate in the pentose-phosphate pathway. After glucose rinse, glucose 6-phosphate, fructose 6-phosphate, fructose 1,6-bisphosphate, dihydroxyacetone phosphate, and pyruvate in the EMP pathway and 6-phosphogluconate, ribulose 5-phosphate, and sedoheptulose 7-phosphate in the pentose-phosphate pathway, and acetyl CoA were increased. Meanwhile, 3-phosphoglycerate and phosphoenolpyruvate in the EMP pathway and succinate, fumarate, and malate in the TCA cycle were decreased. These pathways and changes in metabolites observed in supragingival plaque were similar to the integration of metabolite profiles in Streptococcus and Actinomyces.

Topics: Acetyl Coenzyme A; Actinomyces; Adult; Bacteriological Techniques; Carbon; Citric Acid Cycle; Dental Plaque; Dihydroxyacetone Phosphate; Female; Fructosediphosphates; Fructosephosphates; Fumarates; Gluconates; Glucose; Glucose-6-Phosphate; Glyceric Acids; Glycolysis; Humans; Malates; Male; Metabolomics; Pentose Phosphate Pathway; Phosphoenolpyruvate; Pyruvic Acid; Ribulosephosphates; Streptococcus; Streptococcus mutans; Succinic Acid; Sugar Phosphates

Rhodobacter sphaeroides phosphoribulokinase (PRK) is inactivated upon exposure to pyridoxal phosphate/sodium borohydride, suggesting a reactive lysine residue. Protection is afforded by a combination of the substrate ATP and the allosteric activator NADH, suggesting that the targeted lysine maps within the active site. PRK contains two invariant lysines, K53 and K165. PRK-K53M retains sensitivity to pyridoxal phosphate, implicating K165 as the target of this reagent. PRK-K165M retains wild-type structure, as judged by titration with effector NADH and the tight-binding alternative substrate trinitrophenyl-ATP. The catalytic activity of K165M and K165C mutants is depressed by >10(3)-fold. Residual activity of K165M is insensitive to pyridoxal phosphate, confirming K165 as the target of this reagent. The decreased catalytic efficiency of K165 mutants approaches the effect measured for a mutant of D169, which forms a salt-bridge to K165. K165M exhibits a 10-fold increase in S()1(/)()2 (ATP) and a 10(2)-fold increase in K(m) (Ru5P). To evaluate the contribution to Ru5P binding of K165 in comparison with this substrate's interaction with invariant H45, R49, R168, and R173, PRKs mutated at these positions have been used to determine relative K(i) values for 6-phosphogluconate, a competitive inhibitor with respect to Ru5P. Elimination of the basic side chain of K165, R49, and H45 results in increases in K(m) (Ru5P) which correlate well with the magnitude of increases in K(i) (phosphogluconate). In contrast, while mutations eliminating charge from R168 and R173 result in enzymes with substantial increases in K(m) (Ru5P), such mutant enzymes exhibit only small increases in K(i) (phosphogluconate). These observations suggest that K165, R49, and H45 are major contributors to Ru5P binding.

Topics: Amino Acid Sequence; Binding Sites; Catalysis; Cysteine; Gluconates; Kinetics; Lysine; Methionine; Models, Molecular; Molecular Sequence Data; Mutagenesis, Site-Directed; Phosphotransferases (Alcohol Group Acceptor); Pyridoxal Phosphate; Rhodobacter sphaeroides; Ribulosephosphates

The identity of a number of phosphorus-containing metabolites present in Synechocystis sp. PCC 6308 has been confirmed by 31P NMR spectroscopy. The presence of D-ribulose 1,5-bisphosphate (RuBP); DL-glyceraldehyde 3-phosphate (GlyP); D(-)3-phosphoglyceric acid (3PGA); D-ribulose 5-phosphate (Ru5P);6-phosphogluconic acid (6PGA); phosphoenolpyruvate (PEP); inorganic phosphate (Pi); uridine diphosphoglucose (UDPG); ADP and ATP were demonstrated by the pH dependence of their 31P NMR chemical shifts in spectra of perchloric acid cell extracts. Intracellular pH of cells was determined to be 7.5-7.7.

Topics: Adenosine Diphosphate; Adenosine Triphosphate; Cyanobacteria; Gluconates; Glyceraldehyde 3-Phosphate; Glyceric Acids; Hydrogen-Ion Concentration; Intracellular Fluid; Magnetic Resonance Spectroscopy; Phosphates; Phosphoenolpyruvate; Phosphorus; Ribulosephosphates; Uridine Diphosphate Glucose

[2-18O]Ribulose 5-phosphate was prepared and shown to be converted enzymically by 6-phosphogluconate dehydrogenase from sheep liver into 6-phosphogluconate with complete retention of the heavy isotope. This finding unequivocally excludes the possibility of a Schiff-base mechanism for the enzyme. The involvement of metal ions has already been excluded, and other possible mechanisms are discussed. The enzyme was purified by an improved large-scale procedure, which is briefly described.

Topics: Animals; Decarboxylation; Gluconates; Liver; Mass Spectrometry; Models, Chemical; Oxidation-Reduction; Phosphogluconate Dehydrogenase; Ribulosephosphates; Sheep

Topics: Gluconates; Pentoses; Phosphates; Ribosemonophosphates; Ribulosephosphates; Yeasts