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PubMed1976

Purification and characterization of phosphoglycerate mutase from methanol-grown Hyphomicrobium X and Pseudomonas AM1.

Phosphoglycerate mutase has been purified from methanol-grown Hyphomicrobium X and Pseudomonas AMI by acid precipitation, heat treatment, ammonium sulphate fractionation, Sephadex G-50 gel filtration and DEAE-cellulose column chromatography. The purification attained using the Hyphomicrobium X extract was 72-fold, and using the Pseudomonas AMI extract, 140-fold. The enzyme purity, as shown by analytical polyacrylamide gel electrophoresis, was 50% from Hyphomicrobium X and 40% from Pseudomonas AMI. The enzyme activity was associated with one band. The purified preparations did not contain detectable amounts of phosphoglycerate kinase, phosphopyruvate hydratase, phosphoglycerate dehydrogenase or glycerate kinase activity. The molecular weight of the enzymic preparation was 32000 +/- 3000. The enzyme from both organisms was stable at low temperatures and, in the presence of 2,3-diphosphoglyceric acid, could withstand exposure to high temperatures. The enzyme from Pseudomonas AMI has a broad pH optimum at 7-0 to 7-6 whilst the enzyme from Hyphomicrobium X has an optimal activity at pH 7-3. The cofactor 2,3-diphosphoglyceric acid was required for maximum enzyme activity and high concentrations of 2-phosphoglyceric acid were inhibitory. The Km values for the Hyphomicrobium X enzyme were: 3-phosphoglyceric acid, 6-0 X 10(-3) M: 2-phosphoglyceric acid, 6-9 X 10(-4) M; 2,3-diphosphoglyceric acid, 8-0 X 10(-6) M; and for the Pseudomonas AMI ENzyme: 3-4 X 10(-3) M, 3-7 X 10(-4) M and 10 X 10(-6) M respectively. The equilibrium constant for the reaction was 11-3 +/- 2-5 in the direction of 2-phosphoglyceric acid to 3-phosphoglyceric acid and 0-09 +/- 0-02 in the reverse direction. The standard free energy for the reaction proceeding from 2-phosphoglyceric acid to 3-phosphoglyceric acid was -5-84 kJ mol(-1) and in the reverse direction +5-81 kJ mol(-1).

Bacteria↗
PubMed2005

D-Serine-induced nephrotoxicity: a HPLC-TOF/MS-based metabonomics approach.

HPLC-MS-based metabonomic analysis was used to investigate urinary metabolic perturbations associated with D-serine-induced nephrotoxicity. D-Serine causes selective necrosis of the proximal straight tubules in the rat kidney accompanied by aminoaciduria, proteinuria and glucosuria. Alderely Park (Wistar-derived) rats were dosed with either D-serine (250 mg/kg ip) or vehicle (deionised water) and urine was collected at 0-12, 12-24, 24-36 and 36-48 h post-dosing. Samples were analysed using a Waters Alliance HT 2795 HPLC system coupled to a Waters Micromass Q-ToF-micro equipped with an electrospray source operating in either positive or negative ion mode. Changes to the urinary profile were detected at all time points compared to control. In negative ion mode, increases were observed in serine (m/z=103.0077), m/z=104.0376 (proposed to be hydroxypyruvate) and glycerate (m/z=105.0215), the latter being metabolites of D-serine. Furthermore, an increase in tryptophan, phenylalanine and lactate and decreases in methylsuccinic acid and sebacic acid were observed. Positive ion analysis revealed a decrease in xanthurenic acid, which has previously been assigned and reported using HPLC-MS following exposure to mercuric chloride and cyclosporine A. A general aminoaciduria, including proline, methionine, leucine, tyrosine and valine was also observed as well as an increase in acetyl carnitine. Investigation of additional metabolites altered as a result of exposure to D-serine is on-going. Thus, HPLC-MS-based metabonomic analysis has provided information concerning the mechanism of D-serine-induced renal injury.

Animals↗
PubMed1995

Identification and gene expression of anaerobically induced enolase in Echinochloa phyllopogon and Echinochloa crus-pavonis.

Enolase (2-phospho-D-glycerate hydrolase, EC 4.2.1.11) has been identified as an anaerobic stress protein in Echinochloa oryzoides based on the homology of its internal amino acid sequence with those of enolases from other organisms, by immunological reactivity, and induction of catalytic activity during anaerobic stress. Enolase activity was induced 5-fold in anoxically treated seedlings of three flood-tolerant species (E. oryzoides, Echinochloa phyllopogon, and rice [Oryza sativa L.]) but not in the flood-intolerant species (Echinochloa crus-pavonis). A 540-bp fragment of the enolase gene was amplified by polymerase chain reaction from cDNAs of E. phyllopogon and maize (Zea mays L.) and used to estimate the number of enolase genes and to study the expression of enolase transcripts in E. phyllopogon, E. crus-pavonis, and maize. Southern blot analysis indicated that only one enolase gene is present in either E. phyllopogon or E. crus-pavonis. Three patterns of enolase gene expression were observed in the three species studied. In E. phyllopogon, enolase induction at both the mRNA and enzyme activity levels was sustained at all times with a further induction after 48 h of anoxia. In contrast, enolase was induced in hypoxically treated maize root tips only at the mRNA level. In E. crus-pavonis, enolase mRNA and enzyme activity were induced during hypoxia, but activity was only transiently elevated. These results suggest that enolase expression in maize and E. crus-pavonis during anoxia are similarly regulated at the transcriptional level but differ in posttranslational regulation, whereas enolase is fully induced in E. phyllopogon during anaerobiosis.

Amino Acid Sequence↗
PubMedDate not supplied

[Anticoagulate activity of phosphatidyl-ethanolamine and phosphatidyl-serine deacylation products].

The water-methanol phase products obtained by slight alkali deacylation of a phosphatidyl-ethanolamine and phosphatidyl serine mixture, reveal a higher specific anticoagulating activity than the base mix. In the composition of the water-methanol phase glycerin, serine, ethanolamine, phosphoryl-serine, phosphoryl-ethanolamine, glyceryl-phosphoryl-ethanolamine and glyceryl-phosphoryl-serine were detected by the method of thin-layer paper chromatography. The only substance, glycerly-phosphoryl-serine, possesses an inhibitory activity. Therefore, anticoagulative activity of phosphatidyl-serine is not connected with the presence of the fatty acid residue in its molecule, it is due to the glyceryl-phosphoryl-serine residue. The further glyceryl-phosphoryl-serine degradation is accompanied by the disappearance of the anticoagulative activity.

Anticoagulants↗
PubMed1963

GLYCOLIC ACID OXIDATION BY ESCHERICHIA COLI ADAPTED TO GLYCOLATE.

Furuya, Akira (University of Illinois College of Medicine, Chicago) and James A. Hayashi. Glycolic acid oxidation by Escherichia coli adapted to glycolate. J. Bacteriol. 85:1124-1131. 1963.-A procedure is described for extraction and partial purification of glycolic acid oxidase from Escherichia coli adapted to grow on glycolate as the sole carbon source. Enzyme activity was assayed by oxygen uptake and by reduction of 2,6-dichlorophenol-indophenol. Glyoxylic acid was the product of glycolate oxidation by the enzyme. Enzyme activity, which diminishes rapidly on storage, shows a maximum at pH 6 to 7. We were unable to show any cofactor requirement. Compounds which inhibited glycolate oxidation and their order of inhibitory activity were: p-hydroxymercuribenzoate > sodium azide > iodoacetate and o-phenanthroline > ethylenediaminetetraacetic acid. Tests of enzyme specificity showed that the following compounds were oxidized, but at different rates: glycolate, d-lactate, l-lactate, dl-alpha-hydroxybutyrate, dl-malate, and dl-glycerate. Citrate, tartrate, and dl-beta-hydroxybutyrate were not oxidized. Potassium cyanide stimulated oxygen uptake when glycolate and lactate were oxidized. Whether the oxidations were due to different oxidases or to a single oxidase with a wide range of specificities was tested by observing the oxidation of glycolate, d-lactate, and l-lactate under various conditions. Ammonium sulfate fractionation of a crude extract did not change the relative ability to oxidize the three acids. However, the three oxidative capacities diminished at different rates during storage at 0 C for 6 days. The partially purified glycolic oxidase preparations were probably mixtures of several different oxidases.

Azides↗
PubMed1989

Post-translational modifications in the large subunit of ribulose bisphosphate carboxylase/oxygenase.

Two adjacent N-terminal tryptic peptides of the large subunit of ribulose bisphosphate carboxylase/oxygenase [3-phospho-D-glycerate carboxy-lyase (dimerizing), EC 4.1.1.39] from spinach, wheat, tobacco, and muskmelon were removed by limited tryptic proteolysis. Characterization by peptide sequencing, amino acid composition, and tandem mass spectrometry revealed that the N-terminal residue from the large subunit of the enzyme from each plant species was acetylated proline. The sequence of the penultimate N-terminal tryptic peptide from the large subunit of the spinach and wheat enzyme was consistent with previous primary structure determinations. However, the penultimate N-terminal peptide from the large subunit of both the tobacco and muskmelon enzymes, while identical, differed from the corresponding peptide from spinach and wheat by containing a trimethyllysyl residue at position 14. Thus, tryptic proteolysis occurred at lysine-18 rather than lysine-14 as with the spinach and wheat enzymes. A comparison of the DNA sequences for the large subunit of ribulose bisphosphate carboxylase/oxygenase indicates that the N terminus has been post-translationally processed by removal of methionine-1 and serine-2 followed by acetylation of proline-3. In addition, for the enzyme from tobacco and muskmelon a third post-translational modification occurs at lysine-14 in the form of N epsilon-trimethylation.

Amino Acid Sequence↗
PubMed1991

D-lactate dehydrogenase is a member of the D-isomer-specific 2-hydroxyacid dehydrogenase family. Cloning, sequencing, and expression in Escherichia coli of the D-lactate dehydrogenase gene of Lactobacillus plantarum.

The gene encoding D-lactate dehydrogenase (D-lactate: NAD+ oxidoreductase, EC 1.1.1.28) of Lactobacillus plantarum has been sequenced, and expressed in Escherichia coli cells with an inducible expression plasmid, in which the 5'-noncoding region of the gene was replaced with the tac promoter. Comparison of the sequence of D-lactate dehydrogenase with L-lactate dehydrogenases, including the L. plantarum L-lactate dehydrogenase, showed no significant homology. In contrast, the D-lactate dehydrogenase is homologous to E. coli D-3-phosphoglycerate dehydrogenase and Lactobacillus casei D-2-hydroxyisocaproate dehydrogenase. This indicates that D-lactate dehydrogenase is a member of a new family of 2-hydroxyacid dehydrogenases recently proposed, being distinct from L-lactate dehydrogenase and L-malate dehydrogenase, and strongly suggests that the new family consists of D-isomer-stereospecific enzymes. In the reductive reaction, the enzyme showed a broad substrate specificity, although pyruvate was the most favorable of all 2-ketocarboxylic acids tested. In particular, hydroxypyruvate is effectively reduced by the enzyme, the reaction rate, and Km value being comparable to those in the case of pyruvate, indicating that the enzyme has not only D-lactate dehydrogenase activity but also D-glycerate dehydrogenase activity. The conserved residues in this family appear to be the residues involved in the substrate binding and the catalytic reaction, and thus to be targets for site-directed mutagenesis.

Alcohol Oxidoreductases↗
PubMed1975

Effect of various concentrations of protein in chick diet upon the metabolic enzymes of glycine and serine.

The effect of feeding low protein diets with and without 2% glycine or 2% L-serine to chicks upon the enzymes concerned in the matabolism of glycine and serine has been determined. D-3-phosphoglycerate dehydrogenase (EC 1.1.1.s), hosphoserine phosphatase (EC 3.1.3.3), and serine hydroxymethyltransferase (EC 2.1.2.1) activities were significantly increased in livers from chicks fed 75% protein diets as compared to liver enzyme activities from chicks fed either 24% chick starter, 2% or 25% protein diets. Phosphoserine phosphatase activity was significantly higher in kidney tissue of chicks fed 75% protein diets. Livers from chicks fed 25% protein diets had a higher activity for D-3-phosphoglycerate dehydrogenase and phosphoserine phosphatase than did those fed chick starter or 2% protein diets. D-3-phosphoglycerate dehydrogenase and phosphoserine phosphatase activities were higher in livers from chicks fed 2% protein, 2% protein + 2% glycine, and 2% protein + 2% L-serine diets when compared to those from chicks fed low protein diets with supplemental methionine or cysteine. Serine dehydratase (EC 4.2.1.13), glycerate dehydrogenase (EC 1.1.1.29) and hydroxypyruvate-P: L-glutamate transaminase activities remained constant in livers from chicks fed all experimental diets. The uric acid concentration was significantly increased in plasma from chicks fed the high protein diets which suggests that D-3-phosphoglycerate dehydrogenase, phosphoserine phosphatase and serine hydroxymethyltransferase activities were increased because of the high requirement for glycine in uric acid formation. The 75% protein diet provided three times as much glycine as the 25% protein diet which may have met the increased need for glycine for uric acid formation.

Alcohol Oxidoreductases↗
PubMed1970

Biosynthesis of amino acids in Clostridium pasteurianum.

1. Clostridium pasteurianum was grown on a synthetic medium with the following carbon sources: (a) (14)C-labelled glucose, alone or with unlabelled aspartate or glutamate, or (b) unlabelled glucose plus (14)C-labelled aspartate, glutamate, threonine, serine or glycine. The incorporation of (14)C into the amino acids of the cell protein was examined. 2. In both series of experiments carbon from exogenous glutamate was incorporated into proline and arginine; carbon from aspartate was incorporated into glutamate, proline, arginine, lysine, methionine, threonine, isoleucine, glycine and serine. Incorporations from the other exogenous amino acids indicated the metabolic sequence: aspartate --> threonine --> glycine right harpoon over left harpoon serine. 3. The following activities were demonstrated in cell-free extracts of the organism: (a) the formation of aspartate by carboxylation of phosphoenolpyruvate or pyruvate, followed by transamination; (b) the individual reactions of the tricarboxylic acid route to 2-oxoglutarate from oxaloacetate; glutamate dehydrogenase was not detected; (c) the conversion of aspartate into threonine via homoserine; (d) the conversion of threonine into glycine by a constitutive threonine aldolase; (e) serine transaminase, phosphoserine transaminase, glycerate dehydrogenase and phosphoglycerate dehydrogenase. This last activity was abnormally high. 4. The combined evidence indicates that in C. pasteurianum the biosynthetic role of aspartate and glutamate is generally similar to that in aerobic and facultatively aerobic organisms, but that glycine is synthesized from glucose via aspartate and threonine.

Alcohol Oxidoreductases↗
PubMed1981

Metabolites of glucose in the blood of patients with renal failure.

The blood concentrations of pyruvate and of some of its metabolites and the red cell 2,3-diphosphoglycerate concentration were compared with the severity of uraemia in 103 patients with renal failure. In chronic renal failure 2,3-butylene glycol was distinctly elevated, and a positive linear correlation (2p Less Than 0.001) with the urea was found. The values were even higher in corresponding patients with uraemic pericarditis, but,--taking into account their relation to the urea--,they were not elevated in acute renal failure. Acetaldehyde, acetoin and acetate behaved in part likewise. Severe uraemia, which clinically was demonstrated by uraemic pericarditis, was characterized biochemically, without regard to the urea, by very elevated values of 2,3-butylene glycol and acetaldehyde and of the pyruvate: lactate ratio. In addition, the chronic patients who were not undergoing regular haemodialysis, did not show the expected rise of 2,3-diphospho-glycerate along with progressive anaemia. The data suggest that the uraemic state is characterized by the impairment of the oxidative glucose metabolism between pyruvate and the tricarbonic acid cycle more precisely than by the blood urea.

2,3-Diphosphoglycerate↗
PubMed2003

Reverse protonation is the key to general acid-base catalysis in enolase.

The pH dependence of enolase catalysis was studied to understand how enolase is able to utilize both general acid and general base catalysis in each direction of the reaction at near-neutral pHs. Wild-type enolase from yeast was assayed in the dehydration reaction (2-phospho-D-glycerate --> phosphoenolpyruvate + H(2)O) at different pHs. E211Q, a site-specific variant of enolase that catalyzes the exchange of the alpha-proton of 2-phospho-D-glycerate but not the complete dehydration, was assayed in a (1)H/(2)H exchange reaction at different pDs. Additionally, crystal structures of E211Q and E168Q were obtained at 2.0 and 1.8 A resolution, respectively. Analysis of the pH profile of k(cat)/K(Mg) for wild-type enolase yielded macroscopic pK(a) estimates of 7.4 +/- 0.3 and 9.0 +/- 0.3, while the results of the pD profile of the exchange reaction of E211Q led to a pK(a) estimate of 9.5 +/- 0.1. These values permit estimates of the four microscopic pK(a)s that describe the four relevant protonation states of the acid/base catalytic groups in the active site. The analysis indicates that the dehydration reaction is catalyzed by a small fraction of enzyme that is reverse-protonated (i.e., Lys345-NH(2), Glu211-COOH), whereas the hydration reaction is catalyzed by a larger fraction of the enzyme that is typically protonated (i.e., Lys345-NH(3)(+), Glu211-COO(-)). These two forms of the enzyme coexist in a constant, pH-independent ratio. The structures of E211Q and E168Q both show virtually identical folds and active-site architectures (as compared to wild-type enolase) and thus provide additional support to the conclusions reported herein. Other enzymes that require both general acid and general base catalysis likely require reverse protonation of catalytic groups in one direction of the reaction.

Acids↗
PubMed1997

Thermoterrabacterium ferrireducens gen. nov., sp. nov., a thermophilic anaerobic dissimilatory Fe(III)-reducing bacterium from a continental hot spring.

A strain of a thermophilic, anaerobic, dissimilatory, Fe(III)-reducing bacterium, Thermoterrabacterium ferrireducens gen. nov., sp. nov. (type strain JW/AS-Y7T; DSM 11255), was isolated from hot springs in Yellowstone National Park and New Zealand. The gram-positive-staining cells occurred singly or in pairs as straight to slightly curved rods, 0.3 to 0.4 by 1.6 to 2.7 microns, with rounded ends and exhibited a tumbling motility. Spores were not observed. The temperature range for growth was 50 to 74 degrees C with an optimum at 65 degrees C. The pH range for growth at 65 degrees C was from 5.5 to 7.6, with an optimum at 6.0 to 6.2. The organism coupled the oxidation of glycerol to reduction of amorphous Fe(III) oxide or Fe(III) citrate as an electron acceptor. In the presence as well as in the absence of Fe(III) and in the presence of CO2, glycerol was metabolized by incomplete oxidation to acetate as the only organic metabolic product; no H2 was produced during growth. The organism utilized glycerol, lactate, 1,2-propanediol, glycerate, pyruvate, glucose, fructose, mannose, and yeast extract as substrates. In the presence of Fe(III) the bacterium utilized molecular hydrogen. The organism reduced 9,10-anthraquinone-2,6-disulfonic acid, fumarate (to succinate), and thiosulfate (to elemental sulfur) but did not reduce MnO2, nitrate, sulfate, sulfite, or elemental sulfur. The G + C content of the DNA was 41 mol% (as determined by high-performance liquid chromatography). The 16S ribosomal DNA sequence analysis placed the isolated strain as a member of a new genus within the gram-type-positive Bacillus-Clostridium subphylum.

Bacillus↗
PubMed1969

Distribution of enzymes in mesophyll and parenchyma-sheath chloroplasts of maize leaves in relation to the C4-dicarboxylic acid pathway of photosynthesis.

1. Mesophyll and parenchyma-sheath chloroplasts of maize leaves were separated by density fractionation in non-aqueous media. 2. An investigation of the distribution of photosynthetic enzymes indicated that the mesophyll chloroplasts probably contain the entire leaf complement of pyruvate,P(i) dikinase, NADP-specific malate dehydrogenase, glycerate kinase and nitrite reductase and most of the adenylate kinase and pyrophosphatase. The fractionation pattern of phosphopyruvate carboxylase suggested that this enzyme may be associated with the bounding membrane of mesophyll chloroplasts. 3. Ribulose diphosphate carboxylase, ribose phosphate isomerase, phosphoribulokinase, fructose diphosphate aldolase, alkaline fructose diphosphatase and NADP-specific ;malic' enzyme appear to be wholly localized in the parenchyma-sheath chloroplasts. Phosphoglycerate kinase and NADP-specific glyceraldehyde phosphate dehydrogenase, on the other hand, are distributed approximately equally between the two types of chloroplast. 4. After exposure of illuminated leaves to (14)CO(2) for 25sec., labelled malate, aspartate and 3-phosphoglycerate had similar fractionation patterns, and a large proportion of each was isolated with mesophyll chloroplasts. Labelled fructose phosphates and ribulose phosphates were mainly isolated in fractions containing parenchyma-sheath chloroplasts, and dihydroxyacetone phosphate had a fractionation pattern intermediate between those of C(4) dicarboxylic acids and sugar phosphates. 6. These results indicate that the mesophyll and parenchyma-sheath chloroplasts have a co-operative function in the operation of the C(4)-dicarboxylic acid pathway. Possible routes for the transfer of carbon from C(4) dicarboxylic acids to sugars are discussed.

Aldehyde-Lyases↗
PubMed1993

Is glycolysis impaired in erythrocytes of diabetic rats?

In erythrocytes from diabetic rats the generation of radioactive metabolites from 3H- or 14C-labeled D-glucose occurs at a lower rate than in cells from control animals, while the total production of L-lactic acid is the same in both cell types. The radioisotopic anomaly is not corrected by agents causing phosphofructokinase activation and is not attributable to interference of metabolites generated from either glycogen or 2,3-diphospho-D-glycerate. It is mimicked by preincubating the erythrocytes at a high concentration of D-glucose and suppressed in diabetic rats treated with insulin in order to lower the blood glucose concentration prior to sacrifice. These findings suggest isotopic dilution of the 3H- or 14C-labeled tracer by endogenous unlabeled D-glucose. The influence of factors such as the concentration of erythrocytes in the incubation medium, the concentration of extracellular D-glucose, and the length of incubation upon radioactive metabolic variables is also compatible with the postulated phenomenon of isotopic dilution.

1-Methyl-3-isobutylxanthine↗
PubMed1994

[Optimal structure of the multienzyme system of the tricarboxylic acid cycle of E. coli during growth on various carbon sources].

The optimal structure (stoichiometry) of the tricarboxylic acid cycle multienzyme system of E. coli has been computed using experimental data for the E. coli biomass monomeric content and the results of the steady-state metabolic fluxes calculation. The calculation was performed for the cases of E. coli growth on acetate, glycolate, glycerate, glutamate, glucose, gluconate and pyruvate as carbon sources. The possible self-control mechanisms make it possible to optimize the cellular multienzyme system structure for each of the carbon sources under study. The relationship between the optimal structure and the maximal specific rate of the cell growth is discussed.

Carbon↗