Regulation of UDPG pyrophosphorylase in Acetabularia mediterranea

The kinetic properties of UDPG pyrophosphorylase (glucosyl-1-phosphate uridyl transferase, EC 2.7.7.9) suggest that it may play a key role in the regulation of metabolism in Acetabularia mediterranea. The enzyme-catalyzed reaction is readily reversible in vitro, and has been assayed in both directions. The enzyme shows substrate inhibition by UDPG and UTP at substrate concentrations in excess of 2 mM. The kinetic behavior of the enzyme is consistent with the hypothesis that it catalyzes an ordered bisubstrate biproduct reaction in which G-1-P is the leading substrate, and UTP is the leading product. A plot of initial velocity vs. PPi concentration is sigmoid, indicating a cooperative homotropic effect. PGAL inhibits the reaction in the direction: UTP + G-1-P leads to UDPG + PPi It has no effect on the reverse reaction. The responses of the enzyme may serve to regulate the allocation of G-1-P between anabolic and catabolic pathways.     

Studies on the Fermentative Production and Metabolism of Uridine Coenzymes

Enzyme activities involved in the galactose metabolism of Torulopsis Candida grown on a. lactose medium were investigated with the cell-free extract and ammonium sulfate fraction. Remarkable activities of galactokinase, galactose-1-phosphate uridylyltransferase and UDPG pyrophosphorylase were detected, whereas UDPGal pyrophosphorylase activity was weak. UDPGal formation proceeded by the cell-free extract along a coupling reaction catalyzed by UDPG pyrophosphorylase and galactose-1-phosphate uridylyltransferase where UDPG or glucose-l-phosphate acted as a catalyst.

The mechanism of UDPGal accumulation under the fermentative condition could be explained by a concerted inhibition of UDPGal-4- epimerase activity by 5′-UMP and galactose present as fermentation substrates.     

An Enzymatic Preparation of UDP (U-13C) Glucose

Uniformly labeled uridine diphosphoglucose (UDP(U-¹³C)G) was prepared by a two-step enzymatic synthesis. (U-¹³C) G-6-P was prepared quantitatively by incubating (U-¹³C) glucose, ATP, MgS0₄, and hexokinase. UDP(U-¹³C) Glucose was prepared by incubation of (U-¹³C)G-6-P with UDPG pyrophosphorylase, phosphoglucomutase, inorganic pyrophosphatase, UTP, and glucose-1, 6-diphosphate in pH 7.5, 100 mM Tris-HCl buffer. After purification over Biogel P-2 and subsequent preparative HPLC, UDP (U-¹³C)G was obtained in 50% yield. UDP(U-¹³C)G was characterized by ¹³C NMR and FAB-MS.     

Biochemical Studies on “Bakanae” Fungus. Part 54

Phosphate compounds in potato tubers were fractionated by ion-exchange chromatography. By the use of radio-phosphorus, the following compounds were tentatively identified to be present in potato tubers: G-1-P, G-6-P, F-6-P, FDP, PGA, AMP, UMP, ADP, UDPX, UDPG and ATP. When the tubers were stored at a low temperature, the contents of organic phosphate compounds showed a considerable increase over those of potatoes stored at a high temperature. However, the relative composition of each component was not much influenced by the storage temperature except ATP which showed a great increase at a lower temperature.     

Enzymes of galactose utilization in the rat tapeworm, Hymenolepis diminuta.

1. Crude enzyme preparations from Hymenolepis diminuta contained galactokinase, galactose 1-phosphate uridyl transferase and UDPgalactose 4-epimerase activity, although their specific activities were low. 2. Galactose 1-phosphate non-competitively inhibited galactose phosphorylation. This inhibition, together with the low specific activities of the enzymes in the pathway of galactose utilization, probably accounts for the inadequacy of galactose as a main nutritive carbohydrate for development of the worm.     

Nuclear magnetic resonance studies of the solution conformation of nucleoside diphosphohexoses and their components.

The solution conformations of UDPG, UDPGN, UDPGal, UDPM, UDPGluc, UDPGalc, ADPG, ADPM, GDPG, GDPM, and CDPG and their components Glu-1-P, Gal-1-P, Man-1-P, Gluc-1-P, Galc-1-P, ADP, GDP, UDP, and CDP are studied by high resolution fast Fourier transform nuclear magnetic resonance spectroscopy with iterative computer line shape simulation. The following results were observed. (1) The six-membered ring is in 4C1 chair form with the C(5')-C(6') bond in gg equilibrium tg equilibrium for the derivatives of glucose and mannose and gt equilibrium tg for those of galactose. (2) No conformational preference can be detected for C(1')-O(1') bond in hexose-1'-P moiety. (3) Chemical shift dependencies for the pyranoid ring protons and their structural and conformational relations are: (a) axial proton is at higher field than equatorial: (b) the shielding effect of a gauche vicinal hydroxyl group is stronger than a trans vicinal; (c) the vicinity of a hydroxyl group located more than three bonds away tends to shift the proton downfield. (4) The conformation of the nucleoside 5'-diphosphate part is [anti, 2E equilibrium 3E, g'g' equilibrium g't', g'g' equilibrium g'/t'], with slight variation of each conformation occuring for individual compounds. (5) No significant interactions are detected between the hexose and nucleoside parts in the nucleoside diphosphohexoses, and the hexose and nucleoside components display the same conformational preference as they become integrated to form nucleoside diphosphohexoses.     

Catabolism of d-fructose and d-ribose by Pseudomonas doudoroffii

1. The 1-P-fructokinase (1-PFK) and 6-P-fructokinase (6-PFK) from Pseudomonas doudoroffii were partially purified by a combination of (NH₄)₂SO₄ fractionation and DEAE-Sephadex column chromatography. The pH optima of these enzymes were 9.0 and 8.5, respectively.
2. When the concentrations of the substrates of the 1-PFK reaction were varied, Michaelis-Menten kinetics were observed. The Kms for d-fructose-1-P (F-1-P) and ATP were 3.03×10^-4 M and 3.39×10^-4 M, respectively. Variation of MgCl₂ at fixed concentrations of F-1-P and ATP resulted in sigmoidal kinetics; about 10 mM MgCl₂ was necessary for maximal activity. Activity of 1-PFK was inhibited when the ratio of ATP: Mg⁺⁺ was higher than 0.5, suggesting that ATP: 2Mg⁺⁺ was the substrate and that free ATP was inhibitory. Although an absolute requirement for K⁺ or NH ₊ ⁴ could not be demonstrated, these cations stimulated the rate of the reaction. Activity of 1-PFK was not significantly affected by 3 mM AMP, cyclic-AMP, P_i, d-fructose-6-P (F-6-P), ADP, P-enolpyruvate (PEP), pyruvate, citrate, or l-glutamate.
3. Sigmoidal kinetics were observed for 6-PFK when the concentration of F-6-P was increased and the level of ATP was kept constant. Activity of 6-PFK was increased by ADP, inhibited by PEP, and unaffected by 3 mM AMP, cyclic-AMP, P_i, F-1-P, pyruvate, or citrate.

     

Activity of the enzymes involved in the synthesis of exopolysaccharide precursors in an overproducing mutant ropy strain of Streptococcus thermophilus

The activities of some enzymes belonging to the Leloir pathway, phosphoglucomutase, UDP-glucose pyrophosphorylase, UDP-galactose 4-epimerase and galactose 1-P uridyl transferase, were studied in a wild ropy, a non-ropy and an overproducing mutant ropy strain of Streptococcus thermophilus. These activities were assayed over successive culture transfers along with exocellular polysaccharide (EPS) production. The overproducing mutant ropy strain showed increments in polysaccharide production over successive culture transfers, as opposed to reductions in production by the wild ropy strain. The observed variations among strains in the enzyme activities that were analysed in relation to EPS production suggest their involvement in the synthesis of sugar-nucleotide EPS precursors.     

Changes in 32P-phosphorus compounds during translocation in Laminaria digitata (L.) lamouroux

³²P was applied to a Laminaria digitata thallus and the pattern of ³²P phosphorylated compounds was studied, as a function of time, in the different tissues involved in translocation, i.e. source, pathway and sinks. The results showed that, 3 hours after absorption by the uptake region (lamina), the bulk of the radioactivity was incorporated into organic compounds (70 to 80% of total ³²P taken up), hexose monophosphates being the heaviest labelled. Further change in that region was marked by an accumulation of ³²P in the inorganic pool (65 to 70% after 13 days). Conversely, the ³²P pattern in the medulla of the stipe, which initially showed a similar pattern to the uptake region, did not vary during translocation. The pattern of ³²P distribution into sinks (growing stipe peripheral tissue or hapteron) leads to accumulation of the radioactive element in inorganic and acid-insoluble fractions. These results are discussed in terms of comparative distribution of ³²P in the different parts of the thallus and suggest that phosphate moves as Pi in that alga.Abbreviations TCA trichloroacetic acid - Po organic phosphate - Po sol acid-soluble organic phosphate fraction - Po insol acidinsoluble organic phosphate fraction - Pi morganic phosphate fraction - P lip lipidic phosphate - Np protein nitrogen - ATP adenosine triphosphate - ADP adenosine diphosphate - PEP phosphoenolpyruvic acid - PGA phosphoglyceric acid - G-1-P glucose-1-phosphate - G-6-P glucose-6-phosphate - UDPG uridine diphosphoglucose     

Purification and steady state kinetic mechanism of glycogen synthase-D from human polymorpho-nuclear leukocytes

Summary The authors' work on the purification and steady state kinetic investigation of the enzyme glycogen synthase D (UDP-glucose: glycogen 4--glucosyl-transferase, EC 2.4.1.11) from human polymorphonuclear leukocytes is reviewed. The main features of the kinetic mechanism for catalysis of the reaction UDPG + glycogen_n UDP + glycogen_(n+1) are: (i) Lineweaver-Burk plots in both substrates are linear, exhibiting intersecting patterns; (ii) UDP is a competitive, respectively noncompetitive, inhibitor towards the substrates UDPG and glycogen; (iii) the essential activator glucose-6-phosphate (G-6-P) showed an intersecting pattern towards glycogen and an equilibrium ordered pattern towards UDPG. These features identify in this case the mechanism as a rapid equilibrium random bi-bi mechanism, with G-6-P adding to the enzyme prior to the substrate UDPG. New results on the influence of the modifiers NaCl, Ca⁺⁺, Mn⁺⁺, Mg⁺⁺, HPO₄ ^–-, SO₄ ^–-, and ATP on the enzyme are reported. Interpreting the observations in terms of the established mechanism, the following results are obtained: The effect of salt (NaCl) is nonspecific and fairly small, probably reflecting a general action of the electrolyte medium on the conformation of the enzyme. Divalent cations affect only the rate limiting step, i.e. the interconversion of the quaternary enzyme-substrate-activator complexes. The anions interact exclusively with the G-6-P binding site of the enzyme. The dissociation constants for the enzyme-modifier complexes are determined, and a kinetic mechanism for the action of the anions is proposed, leading to activation or inhibition, depending on the concentration of G-6-P.An invited article     

Glyceraldehyde-3-phosphate dehydrogenases from Euglena gracilis. Purification and physical and chemical characterization.

NAD⁺-dependent and NADP⁺-dependent glyceraldehyde-3-phosphate (G-3-P) dehydrogenases were isolated from Euglena gracilis and characterized as to their physical and chemical parameters. NAD⁺-G-3-P dehydrogenase was found to have a strong resemblance to similar enzymes from muscle tissue. It has a molecular weight of about 140,000, four subunits of identical size and charge, and a single species of NH₂-terminal amino acid. Two sulfhydryl groups per subunit are present, one of which is directly involved in the catalytic activity and is rapidly titratable. The enzyme also exhibits the “half the sites reactivity” of sulfhydryl groups as defined by O. P. Malhotra and S. A. Bernhard ((1968) J. Biol. Chem. 243, 1243). The pH and temperature optima are also similar to those of the enzymes from muscle tissue, as are the reaction kinetics and the strict specificity for NAD⁺.NADP⁺-dependent G-3-P dehydrogenase is different in many respects. Its molecular weight is slightly lower (~136,000) than that of the NAD⁺ enzyme, though it also consists of four subunits. It has a higher affinity for the reverse reaction substrates, in line with its probable function in vivo in CO₂ fixation. There is only one sulfhydryl group per subunit, and that is not involved in activity, suggesting a difference in reaction mechanisms between the two enzymes. The NADP⁺-dependent enzyme exhibits activation by ATP, whereas the NAD⁺-dependent enzyme is competitively inhibited by this nucleotide.The greatest difference observed is in the physical characteristics of the enzymes. NADP⁺-G-3-P dehydrogenase was highly hydrophobic. Its solubility in a 10% aqueous solution of p-dioxane was approximately four to five times that of the NAD⁺-enzyme. Isolation of the enzyme was accomplished by fractionation in 1,2-dimethoxyethane, which also stabilized the enzymatic activity, as did aqueous p-dioxane. The high axial ratio of the NADP⁺-enzyme (~9) coupled with its very low degree of hydration as well as the high degree of amidation of the dicarboxylic amino acids (>90%) indicates that the exterior of the enzyme molecule is probably hydrophobic in nature. This is in agreement with its in vivo hydrophobic environment in the chloroplast membrane and explains the lability of the enzyme once extracted into an aqueous environment as well as its stabilization in solvents.     

The Suppression of Stareh Synthesis and the Accumulation of Uridine Diphosphoglucose in Cucumber Leaves due to Ammonium Toxicity

This work is a study of the metabolic disorder due to ammonium toxicity in cucumber (Cucumis sativus L. cv. suisei No. 2) leaves. The cucumber was cultured with 20 and 200 mg/l NH₃-N for 5 days. In the first half of this experiment, the plant leaves were photosynthesized for 3 hours to study the distribution of ¹⁴C in starch and other fractions. The incorporation of photosynthesized ¹⁴C into not only starch but also other higher polymers was suppressed by ammonium toxicity. On the other band, the rate of ¹⁴C incorporation in 80 % ethanol soluble fraction was higher in the treatment of 200 mg/l NH₃-N. In the latter half of experiment, phosphate esters in the loaves were analyzed by column chromatography. The opposing contents of uridine diphosphoglucose (UDPG) and the uridine compound containing sugar or sugar derivative (UDPX) were determined by different ammonia levels. Toxicity of ammonia resulted in an increase of UDPG and a decrease of UDPX. The level of ATP was not changed so much. The content of glucose-6-phosphate (G-6-P) in injured plants was lower than that of normal plants, while ghicose-1-phosphate (G-1-P) and fructose-6–phosphate (F-6-P) were higher in injured plants. These results further suggested the disorder of carbohydrate metabolism due to ammonium toxicity which was reported previously.     

An Enzymatic Preparation of UDP (U-13C) Glucose

Uniformly labeled uridine diphosphoglucose (UDP(U-¹³C)G) was prepared by a two-step enzymatic synthesis. (U-¹³C) G-6-P was prepared quantitatively by incubating (U-¹³C) glucose, ATP, MgS0₄, and hexokinase. UDP(U-¹³C) Glucose was prepared by incubation of (U-¹³C)G-6-P with UDPG pyrophosphorylase, phosphoglucomutase, inorganic pyrophosphatase, UTP, and glucose-1, 6-diphosphate in pH 7.5, 100 mM Tris-HCl buffer. After purification over Biogel P-2 and subsequent preparative HPLC, UDP (U-¹³C)G was obtained in 50% yield. UDP(U-¹³C)G was characterized by ¹³C NMR and FAB-MS.     

E. coli galactose-1-phosphate uridyl transferase: N-terminal and C-terminal sequences

Summary A modified procedure for the purification of E. coli galactose-1-phosphate uridyl transferase (E.C. 2.7.6.12) was developed which reproducibly gives pure enzyme. The purified enzyme was shown to be a dimeric protein with a subunit molecular weight of 41,000 and its amino acid composition and content of free sulfhydryl groups were determined. The N-terminal and C-terminal amino acid sequences were found to be NH₂-thr-gln-phe-asn-pro-val-asp and -ser(val leu)-ala-COOH respectively. This N-terminal sequence allowed the identification of the start of the transferase gene in the DNA sequence determined by GRINDLEY. Furthermore it appears to define a nine base intercistronic region between the epimerase and transferase genes.Abbreviations Cyclic AMP Cyclic adenosine 2¹5¹ monophosphate - DPN Diphosphopyridine nucleotide - UDP Uridine diphosphate - EDTA Ethylene diamine tetra acetic acid - SDS sodium dodecyl sulfate - NEM N-ethylmaleimide     

Isolation and regulatory properties of two glutamate dehydrogenases from the cellular slime mold Dictyostelium discoideum.

Two distinct glutamate dehydrogenases are present in amoebae of the cellular slime mold Dictyostelium discoideum. One enzyme has been extracted from a crude mitochondrial fraction, and the other from an extramitochondrial cytoplasmic fraction. Both enzymes have been partially purified and characterized. The mitochondrial enzyme can utilize both NAD⁺ and NADP⁺ as coenzyme, while the extramitochondrial is NAD⁺ specific. When the mitondrial enzyme is assayed in the presence of either a rate-limiting or saturating concentration of glutamate, its activity is stimulated by both AMP and ADP and is inhibited by ATP. When the extramitochondrial enzyme is assayed in the presence of a rate-limiting concentration of glutamate, its activity is sensitive to modulation by a number of intermediates in carbohydrate metabolism and is inhibited by ADP, ATP, GTP, and CTP.     

Characterization of hypothetical protein VNG0128C from Halobacterium NRC-1 reveals GALE like activity and its involvement in Leloir pathway of galactose metabolism

VNG0128C, a hypothetical protein from Halobacterium NRC-1, was chosen for detailed insilico and experimental investigations. Computational exercises revealed that VNG0128C functions as NAD⁺ binding protein. The phylogenetic analysis with the homolog sequences of VNG0128C suggested that it could act as UDP-galactose 4-epimerase. Hence, the VNG0128C sequence was modeled using a suitable template and docking studies were performed with NAD and UDP-galactose as ligands. The binding interactions strongly indicate that VNG0128C could plausibly act as UDP-galactose 4-epimerase. In order to validate these insilico results, VNG0128C was cloned in pUC57, subcloned in pET22b⁺, expressed in BL21 cells and purified using nickel affinity chromatography. An assay using blue dextran was performed to confirm the presence of NAD binding domain. To corroborate the epimerase like enzymatic role of the hypothetical protein, i.e. the ability of the enzyme to convert UDP-galactose to UDP-glucose, the conversion of NAD to NADH was measured. The experimental assay significantly correlated with the insilico predictions, indicating that VNG0128C has a NAD⁺ binding domain with epimerase activity. Consequently, its key role in nucleotide-sugar metabolism was thus established. Additionally, the work highlights the need for a methodical characterization of hypothetical proteins (less studied class of biopolymers) to exploit them for relevant applications in the field of biology.     

Effect of ligands on Drosophila phosphorylase a as monitored by its enzymic inactivation

The dephosphorylation of Drosophila phosphorylase a with the catalytic subunit of fruit-fly protein phosphatase-1 was inhibited by AMP, IMP, ADP, ATP, glucose-6-P, glucose-1-P and UDPG. Glucose, caffeine and glycogen did not influence the reaction. The inhibitory effect of AMP was reduced by glucose and caffeine. The above ligands acted through the modification of phosphorylase a conformation. This conclusion was drawn from the ligands' effect on the dephosphorylation of phosphohistone by Drosophila phosphatase-1 and on the tryptic digestion of fruit-fly phosphorylase a.     

Structure of an antibiotic-synthesizing UDP-glucuronate 4-epimerase MoeE5 in complex with substrate

The epimerase MoeE5 from Streptomyces viridosporus converts UDP-glucuronic acid (UDP-GlcA) to UDP-galacturonic acid (UDP-GalA) to provide the first sugar in synthesizing moenomycin, a potent inhibitor against bacterial peptidoglycan glycosyltransferases. The enzyme belongs to the UDP-hexose 4-epimerase family, and uses NAD⁺ as its cofactor. Here we present the complex crystal structures of MoeE5/NAD⁺/UDP-GlcA and MoeE5/NAD⁺/UDP-glucose, determined at 1.48 Å and 1.66 Å resolution. The cofactor NAD⁺ is bound to the N-terminal Rossmann-fold domain and the substrate is bound to the smaller C-terminal domain. In both crystals the C4 atom of the sugar moiety of the substrate is in close proximity to the C4 atom of the nicotinamide of NAD⁺, and the O4 atom of the sugar is also hydrogen bonded to the side chain of Tyr154, suggesting a productive binding mode. As the first complex structure of this protein family with a bound UDP-GlcA in the active site, it shows an extensive hydrogen-bond network between the enzyme and the substrate. We further built a model with the product UDP-GalA, and found that the unique Arg192 of MoeE5 might play an important role in the catalytic pathway. Consequently, MoeE5 is likely a specific epimerase for UDP-GlcA to UDP-GalA conversion, rather than a promiscuous enzyme as some other family members.     

Nucleotide allosteric regulation of the glutamate dehydrogenases of Teladorsagia circumcincta and Haemonchus contortus

The expression of glutamate dehydrogenase (GDH; EC 1.4.1.3) in L3 of the nematode Haemonchus contortus was confirmed by detecting GDH mRNA, contrary to earlier reports. The enzyme was active in both L3 and adult H. contortus homogenates either with NAD⁺/H or NADP⁺/H as co-factor. Although it was a dual co-factor GDH, activity was greater with NAD⁺/H than with NADP⁺/H. The rate of the aminating reaction (glutamate formation) was approximately three times higher than for the deaminating reaction (glutamate utilisation). GDH provides a pathway for ammonia assimilation, although the affinity for ammonia was low. Allosteric regulation by GTP, ATP and ADP of L3 and adult H. contortus and Teladorsagia circumcincta (Nematoda) GDH depended on the concentration of the regulators and the direction of the reaction. The effects of each nucleotide were qualitatively similar on the mammalian and parasite GDH, although the nematode enzymes were more responsive to activation by ADP and ATP and less inhibited by GTP under optimum assay condition. GTP inhibited deamination and low concentrations of ADP and ATP stimulated weakly. In the reverse direction, GTP was strongly inhibitory and ADP and ATP activated the enzyme.     

Purification, properties, and isozyme pattern of galactose-1-phosphate uridyl transferase from calf liver.

Galactose-1-phosphate uridyl transferase was purified approximately 2000-fold from calf liver with a yield of 15%. The purification procedure involved ammonium sulfate fractionation, calcium phosphate-gel adsorption, and chromatography on DEAE-cellulose, hydroxylapatite, and Sephadex columns. The purified product demonstrated five protein bands on polyacrylamide-gel electrophoresis. Each band had transferase activity as five peaks of activity were observed on preparative polyacrylamide-gel electrophoresis. Galactose-1-phosphate uridyl transferase showed no requirement for divalent metals for activity. In contrast, it was inhibited by Mg²⁺ and other divalent metals. The purified enzyme but not the crude preparation was stimulated by sulfhydryl compounds. The enzyme was completely inhibited by low concentrations of p-hydroxymercuribenzoate.