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Enzymic capacities of purified cauliflower bud plastids for lipid synthesis and carbohydrate metabolism.

Isolated cauliflower (Brassica oleracea) bud plastids, purified by isopycnic centrifugation in density gradients of Percoll, were found to be highly intact, to be practically devoid of extraplastidial contaminations, and to retain all the enzymes involved in fatty acid, phosphatidic acid, and monogalactosyldiacylglycerol synthesis. Purified plastids possess all the enzymes needed to convert triose phosphate to starch and vice versa, and are capable of conversion of glycerate 3-phosphate to pyruvate for fatty acid synthesis. They are also capable of oxidation of hexose phosphate and conversion to triose phosphate via the oxidative pentosephosphate pathway. Cauliflower bud plastids prove to be, therefore, biochemically very flexible organelles.

Journal Article↗

Phylogeny and ontogeny of the phosphoglycerate mutases.--V. Inactivation of phosphoglycerate mutase isozymes by histidine-specific reagents.

1. The three isozymes of glycerate-2,3-P2 dependent phosphoglycerate mutase present in tissues of mammals and reptiles were inactivated by both treatment with diethylpyrocarbonate and photooxidation with rose bengal. 2. Inactivation of type M isozyme purified from rabbit muscle was complete when two histidine residues per enzyme subunit were carboethoxylated. Hydroxylamine removed the carboethoxy groups, with partial recovery of the enzymatic activity. The cofactor protected the enzyme against inactivation. 3. The inactivation of rabbit muscle phosphoglycerate mutase by photooxidation with methylene blue and rose bengal was sharply pH dependent. The pH profile of enzyme inactivation followed the titration curve of histidine, suggesting that this amino acid was critical for enzyme activity. Glycerate-2,3-P2 did not protect phosphoglycerate mutase against photoinactivation.

Animals↗

Crystal structure of the binary complex of pig muscle phosphoglycerate kinase and its substrate 3-phospho-D-glycerate.

Pig muscle phosphoglycerate kinase has been crystallized from polyethyleneglycol in the presence of its substrate 3-phospho-D-glycerate (3-PG) and the structure has been determined at 2.0 A resolution. The structure was solved using the known structure of the substrate-free horse muscle enzyme and has been refined to a crystallographic R-factor of 21.5%. 3-Phospho-D-glycerate is bound to the N-domain of the enzyme through a network of hydrogen bonds to a cluster of basic amino acid residues and by electrostatic interactions between the negatively charged phosphate and these basic protein side chains. This binding site is in good agreement with earlier proposals [Banks et al., Nature (London) 279:773-777, 1979]. The phosphate oxygen atoms are hydrogen bonded to His-62, Arg-65, Arg-122, and Arg-170. The 2-hydroxyl group, which defines the D-isomer of 3PG, is hydrogen bonded to Asp-23 and Asn-25. The carboxyl group of 3-PG points away from the N-domain towards the C-domain and is hydrogen bonded via a water molecule to main chain nitrogen atoms of helix-14. The present structure of the 3-PG-bound pig muscle enzyme is compared with the structure of the substrate-free horse enzyme. Major changes include an ordering of helix-13 and a domain movement, which brings the N-domain closer to the ATP-binding C-domain. This domain movement consists of a 7.7 degree rotation, which is less than previously estimated for the ternary complex. Local changes close to the 3-PG binding site include an ordering of Arg-65 and a shift of helix-5.

Adenosine Triphosphate↗

Quantitative organic acid analysis in cerebrospinal fluid and plasma: reference values in a pediatric population.

Quantitative reference values for the concentrations of organic acids in cerebrospinal fluid (CSF) and plasma, as well as ratios of individual organic acids between CSF and plasma, were determined in twenty-three pairs of samples from pediatric patients. Twenty-six organic acids were present and quantifiable in all or the majority of plasma and CSF specimens (limit of detection 1 mumol/l). There were substantial differences between subgroups of organic acids, best reflected by the ratios of individual acids between CSF and plasma. Metabolites related to fatty acid oxidation were present in CSF in substantially lower amounts than in plasma. Organic acids related to carbohydrate and energy metabolism and to amino acid degradation were present in CSF in equal or slightly lower amounts than in plasma. Finally, some organic acids were found in substantially higher amounts in CSF than in plasma, e.g. glycolate, glycerate, 2,4-dihydroxybutyrate, citrate and isocitrate. Quantitation of organic acids in CSF and plasma should aid diagnosis and monitoring of treatment of patients with organic acid disorders.

Acids↗

Model of early self-replication based on covalent complementarity for a copolymer of glycerate-3-phosphate and glycerol-3-phosphate.

Glyceraldehyde-3-phosphate acts as the substrate in a model of early self-replication of a phosphodiester copolymer of glycerate-3-phosphate and glycerol-3-phosphate. This model of self-replication is based on covalent complementarity in which information transfer is mediated by a single covalent bond, in contrast to multiple weak interactions that establish complementarity in nucleic acid replication. This replication model is connected to contemporary biochemistry through its use of glyceraldehyde-3-phosphate, a central metabolite of glycolysis and photosynthesis.

Evolution, Molecular↗

The catalytic bimodality of mammalian phosphoglycerate mutase.

Rabbit muscle phosphoglycerate mutase, presumed to manifest an absolute cofactor requirement for activity, has been found to express catalysis (3 +/- 1% of optimum) in the absence of added D-glycerate-2,3-P2. Isotope experiments indicate that this catalysis proceeds through a binary phosphoryl enzyme-glycerate intermediate which dissociates into free enzyme and monophosphoglycerate. 32P-Labeled phosphoglycerate mutase is formed by reaction with either D-32P-glycerate-3-P or D-U32P-glycerate-2,3-P2. In each case, the acid lability and alkali stability of the covalent adduct, phosphoenzyme, is consistent with a phosphohistidyl residue having been formed within the active site. D-[U-14C]Glycerate reacts with phosphoenzyme to generate D-[U-14C]monophosphoglycerate which, in turn, can react further with phosphoenzyme to yield D-[U-14C]glycerate-2,3-P2. The pH profile for the cofactor-independent activity exhibits an optimum at 6.0 as opposed to 7.0 when D-glycerate-2,3-P2 is present in the reaction medium. Bisubstrate kinetics (pH 7.0, 23 degrees C) with D-glycerate-3-P concentration as the variable, yields a family of reciprocal plots which is in accord with a modified ping-pong mechanism when D-glycerate-2,3-P2 concentrations are greater than 10(-1) Km (where Km = 0.33 microM). Progressively diminishing concentrations (much less than Km) of D-glycerate-2,3-P2 produce curvilinear reciprocal plots that approach linearity as a limit in accordance with single substrate kinetics.

2,3-Diphosphoglycerate↗

Ozonation Products of Organosolvolytic Extracts from Vegetal Materials.

The ozonation of lignin in an organic solution was used to produce oxyaromatic compounds. Corn (Zea mays) stalk and poplar (Populus deltoides) wood lignin solutions (organosolvolytic juices) obtained from their respective autohydrolyzed materials and an organosolv lignin were treated with ozone, and the time course trend of the identified reaction products was studied. GC/MS and GC/FID were used to identify and quantify (internal standard method) the reaction products. The following acids were identified: glycolic, oxalic, malic, glyceric, p-hydroxybenzoic, and vanillic. In addition, p-hydroxybenzaldehyde, vanillin, syringaldehyde, and hydroquinone were also identified. All the oxyaromatic aldehydes reached maximum yields at short reaction times (between 1 and 8 min). These results were used to determine the ratio between the different phenylpropane units of their constitutive lignins. The ratio of p-hydroxyphenyl:guaiacyl:syringyl units for corn stalk, poplar wood, and organosolv lignins was 5.3:2:1, 0.1:1:1.1, and 0:1:1.1, respectively.

Journal Article↗

Genetic basis of primary hyperoxaluria type II.

Primary hyperoxaluria Type II (PH2) is a rare monogenic disease characterized by excessive urinary oxalate and L-glycerate excretion. The severity of clinical complications in PH2 patients can range from none to end-stage renal failure secondary to massive deposits of calcium oxalate crystals in the kidney. The disease is a result of the absence of an enzyme with glyoxylate reductase and hydroxypyruvate reductase activities (GRHPR). Recent breakthroughs have occurred in our understanding of the molecular basis of PH2. In this article, we briefly review the literature concerning the clinical and biochemical characteristics of the disease and the enzyme associated with it. We describe the identification of the cDNA for the GRHPR enzyme using the expressed sequence tag database, the characterization of the human GRHPR gene, and the identification of mutations in patients with PH2. Insights gained from the molecular biology underlying this disease as they relate to relevant clinical issues such as potential therapeutic strategies are discussed.

Alcohol Oxidoreductases↗

Isolation, characterization, and structure of a mutant 89 Arg----Cys bisphosphoglycerate mutase. Implication of the active site in the mutation.

Bisphosphoglycerate mutase (EC 5.4.2.4.) is a trifunctional enzyme which displays synthase, mutase, and phosphatase activities. The purification, characterization, and structural study of an abnormal form of the enzyme, isolated from a patient which we reported earlier (Rosa, R., Prehu, M. O., Beuzard, Y., and Rosa, J. (1978) J. Clin. Invest. 62, 907-915), is described. The abnormal enzyme, present at 50% of the level of the normal enzyme as estimated by immunological methods, showed elevated electrophoretic mobility and hybridized with erythrocyte phosphoglycerate mutase (EC 5.4.2.1.) in the same manner as the normal control. The mutant enzyme was unstable at 55 degrees C and could be protected against thermal instability by 0.5 mM glycerate 2,3-bisphoshate but not by either glycerate 3-phosphate or glycolate 2-phosphate. Two of the three functions of the mutant enzyme were distinct from those of the normal protein. The specific activity of the synthase was 0.57% of normal and that of the mutase 4.1%. By contrast, the specific phosphatase activity was not affected by the mutation. However, the phosphatase activity of the mutated protein was markedly less stimulated by glycolate-2-phosphate than that of the control. High performance liquid chromatography analysis of tryptic peptides derived from the mutant enzyme showed an abnormal profile with the absence of two peaks normally containing the T12 and T13 peptides and without the appearance of a supplementary peak. Amino acid sequence and mass spectrometric analysis demonstrated the substitution of Arg----Cys residue in position 89 producing an uncleaved T12-T13 present in the same peak as the T6. Considered together, our data suggest that Arg-89 is located at or near the active site of bisphosphoglycerate mutase and that this residue is probably involved in the binding of monophosphoglycerates.

Amino Acid Sequence↗

Synthesis of GDP-mannose and mannosylglycerate from labeled mannose by genetically engineered Escherichia coli without loss of specific isotopic enrichment.

We report the construction of an Escherichia coli mutant that harbors two compatible plasmids and that is able to synthesize labeled 2-O-alpha-D-mannosyl-D-glycerate from externally added labeled mannose without the loss of specific isotopic enrichment. The strain carries a deletion in the manA gene, encoding phosphomannose isomerase. This deletion prevents the formation of fructose-6-phosphate from mannose-6-phosphate after the uptake of mannose from the medium by mannose-specific enzyme II of the phosphotransferase system (PtsM). The strain also has a deletion of the cps gene cluster that prevents the synthesis of colanic acid, a mannose-containing polymer. Plasmid-encoded phosphomannomutase (cpsG) and mannose-1-phosphate guanylyltransferase (cpsB) ensure the formation of GDP-mannose. A second plasmid harbors msg, a gene from Rhodothermus marinus that encodes mannosylglycerate synthase, which catalyzes the formation of 2-O-alpha-D-mannosyl-D-glycerate from GDP-mannose and endogenous glycerate. The rate-limiting step in 2-O-alpha-D-mannosyl-D-glycerate formation is the transfer of GDP-mannose to glycerate. 2-O-alpha-D-mannosyl-D-glycerate can be released from cells by treatment with cold-water shock. The final product is formed in a yield exceeding 50% the initial quantity of labeled mannose, including loss during preparation and paper chromatography.

Carbon Radioisotopes↗

Hyperoxaluria in L-glyceric aciduria: possible nonenzymic mechanism.

Hydroxypyruvate inhibited the oxidation of [1-14C]glyoxylate to [14C] oxalate whether catalyzed by a purified preparation of glycolic acid oxidase from human liver, lactate dehydrogenase, a human liver extract, or a lobe of rat liver. It also brought about the nonenzymic decarboxylation of [1-14C]glyoxylate when it was present in the above assay systems. Radioactive isotope dilution and high-performance liquid chromatography analysis revealed the autooxidation of hydroxypyruvate to oxalate on standing in buffered solution at pH 7.4. In view of these observations, the current hypothesis of the role of lactate dehydrogenase in inducing hyperoxaluria in L-glyceric aciduria has been reexamined, and a possible nonenzymic mechanism by which oxalate may originate from hydroxypyruvate under such conditions has been proposed.

Amino Acid Metabolism, Inborn Errors↗

Cytotoxic and anti-HIV principles from the rhizomes of Begonia nantoensis.

Three new compounds: begonanline (1). nantoamide (2). and methyl (S)-glycerate (3). as well as forty-four known compounds have been isolated and characterized from the rhizomes of Begonia nantoensis. The structures of these compounds were determined by spectral analyses and/or X-ray crystallography. Among them, cucurbitacin B (4). dihydrocucurbitacin B (5). cucurbitacin E (6). dihydrocucurbitacin E (7). cucurbitacin I (8). and (-)-auranamide (9). showed cytotoxicity against four human cancer cell lines. 3beta,22alpha-Dihydroxyolean-12-en-29-oic acid (10), indole-3-carboxylic acid (11), 5,7-dihydroxychromone (12), and (-)-catechin (13) demonstrated significant activity against HIV replication in H9 lymphocyte cells.

Anti-HIV Agents↗

Multiplicity of interactions between dromedary hemoglobin and solvent components. A structural and functional study.

The interaction of dromedary hemoglobin with various solvent components [2-(p-chlorophenoxy)-2-methylpropionic acid (CFA), 2,3-bisphospho-D-glycerate (glycerate-2,3-P2) and chloride] has been studied. 1. CFA greatly lowers the oxygen affinity of dromedary hemoglobin. 2. The oxygen-linked CFA binding sites are probably located in the deoxy derivative at the alpha cleft, while in the oxy form and in the presence of two other effectors (glycerate-2,3-P2 and chloride) additional, structurally and possibly functionally relevant binding site(s) should be considered. 3. Both CFA and glycerate-2,3-P2 stabilize the deoxy-like tertiary structure in the oxy derivative. 4. Chloride appears to be fundamental to obtain quaternary structural changes. 5. Interaction energy, retained in the protein when the three ligands (CFA, glycerate-2,3-P2 and chloride) are bound to the oxy form, favours intermediates not stable if only one or two allosteric effector(s) is (are) present on the protein. 6. The oxygen affinity appears to be related to both tertiary and quaternary structural changes, while cooperatively is largely invariant with solvent conditions. In conclusion, the functional properties of dromedary hemoglobin do not depend in any simple way on the variety of stabilized conformations.

2,3-Diphosphoglycerate↗

Crystal structure of the binary complex of ribulose-1,5-bisphosphate carboxylase and its product, 3-phospho-D-glycerate.

The crystal structure of the binary complex of non-activated ribulose-1,5-bisphosphate carboxylase/oxygenase from Rhodospirillum rubrum and its product 3-phospho-D-glycerate has been determined to 2.9-A resolution. This structure determination confirms the proposed location of the active site (Schneider, G., Lindqvist, Y., Brändén, C.-I., and Lorimer, G. (1986) EMBO J. 5, 3409-3415) at the carboxyl end of the beta-strands of the alpha/beta-barrel in the carboxyl-terminal domain. One molecule of 3-phosphoglycerate is bound per active site. All oxygen atoms of 3-phosphoglycerate form hydrogen bonds to groups of the enzyme. The phosphate group interacts with the sidechains of residues Arg-288, His-321, and Ser-368, which are conserved between enzymes from different species as well as with the main chain nitrogens from residues Thr-322 and Gly-323. These amino acid residues constitute one of the two phosphate binding sites of the active site. The carboxyl group interacts with the side chains of His-287, Lys-191, and Asn-111. Implications of the activation process for the binding of 3-phosphoglycerate are discussed.

Binding Sites↗

Phosphate free perfusion prevents washout of tissue creatine in Langendorff perfused rabbit heart.

Rabbit hearts were perfused with Krebs-Henseleit bicarbonate buffer supplemented with 15 mM glucose and 10 mU/ml of insulin +/- Pi. At the end of 60 min the hearts were freeze-clamped and the content of ATP, creatine phosphate, creatine, lactate, pyruvate, DHAP and 3-P glycerate were determined enzymatically in neutralized perchloric acid tissue extracts. The free cytosolic ADP and Pi and the cytosolic NAD+ redox and phosphorylation potentials were calculated from the measured metabolite concentrations. Pi free perfusion resulted in increased creatine, free cytosolic ADP and cytosolic phosphorylation potential, decreased calculated free Pi and no change in cardiac ATP and creatine phosphate content. The increase in the cytosolic phosphorylation potential was due to the lowering of cytosolic free Pi. The increase in ADP was due to the increase in creatine. The increase in creatine appeared to be due to an inhibition of creatine efflux from the heart during Pi free perfusion which was mediated by an enhanced Na+ electrochemical gradient.

Adenosine Diphosphate↗

Characterization of the interaction of yeast enolase with polynucleotides.

Yeast enolase is inhibited under certain conditions by DNA. The enzyme binds to single-stranded DNA-cellulose. Inhibition was used for routine characterization of the interaction. The presence of the substrate 2-phospho-D-glycerate reduces inhibition and binding. Both yeast enolase isozymes behave similarly. Impure yeast enolase was purified by adsorption onto a single-stranded DNA-cellulose column followed by elution with substrate. Interaction with RNA, double-stranded DNA, or degraded DNA results in less inhibition, suggesting that yeast enolase preferentially binds single-stranded DNA. However, yeast enolase is not a DNA-unwinding protein. The enzyme is inhibited by the short synthetic oligodeoxynucleotides G6, G8 and G10 but not T8 or T6, suggesting some base specificity in the interaction. The interaction is stronger at more acid pH values, with an apparent pK of 5.6. The interaction is prevented by 0.3 M KCl, suggesting that electrostatic factors are important. Histidine or lysine reverse the inhibition at lower concentrations, while phosphate is still more effective. Binding of single-stranded DNA to enolase reduces the reaction of protein histidyl residues with diethylpyrocarbonate. The inhibition of yeast enolase by single-stranded DNA is not total, and suggests the active site is not directly involved in the interaction. Binding of substrate may induce a conformational change in the enzyme that interferes with DNA binding and vice versa.

Animals↗

Transient and equilibrium kinetic studies on yeast 3-phosphoglycerate kinase. Evidence that an intermediate containing 1,3-bisphosphoglycerate accumulates in the steady state.

The structure of the key glycolytic enzyme 3-phosphoglycerate kinase (PGK) is known in detail, but there is little information on its reaction pathway. We have studied its equilibrium and transient kinetics in the direction of 1,3-bisphosphoglycerate (1,3-bis-P-glycerate) production: ATP + 3-P-glycerate<==>ADP + 1,3-bis-P-glycerate. We devised a sensitive method for following this production. PGK is mixed with 3-P-glycerate and [gamma-32P]ATP in a rapid flow quench apparatus. The reaction mixtures are aged for 4 ms or more and then quenched in acid in which any [1-32P]-1,3-P-glycerate decomposes to 3-P-glycerate and 32Pi, which is determined specifically. The Pi reflects accurately the 1,3-bis-P-glycerate in the original reaction mixture, and the kcat obtained is identical to that obtained by the conventional linked assay method with glyceraldehyde-3-phosphate dehydrogenase. This does not support the postulate of a rapid direct transfer of the 1,3-bis-P-glycerate between the kinase and the dehydrogenase [Srivastava, D. K., & Bernhard, S. A. (1986) Science 234, 1081-1086]. We fitted our data to a simple scheme with the formation of binary complexes, the interconversion of substrates to products via ternary complexes, and the release of products. Because of the high turnover of PGK, the work was carried out under cryoenzymic conditions with 40% ethylene glycol in the buffer. The glycol decreased kcat from 80 to 8.5 s-1 (pH 7.5, 4 degrees C), but the Km for 3-P-glycerate and ATP and the equilibrium constants in the scheme were little affected. We carried out two types of experiment.(ABSTRACT TRUNCATED AT 250 WORDS)

Adenosine Triphosphate↗

Electrophoretic clean-up of organic acids from coffee for the GC/MS analysis.

The clean-up presented here includes a free flow field step electrophoresis followed by ultrafiltration. Thus, organic acids can be separated from non-acidic and high-molecular compounds in roasted and instant coffee. The acids are identified by gas chromatography/mass spectrometry after freeze-drying and trimethylsilylation. With the method presented, 31 acids could be identified in commercial roasted coffee blends and in instant coffee, among them for the first time in coffee: 3-hydroxypropionic, 2-oxobutyric, glyceric, 2,4-dihydroxybutyric, 5-hydroxymethylfuran-2-carboxylic and 2-hydroxyglutaric acid.

Journal Article↗