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Arginine294 is essential for the inhibition of Anabaena PCC 7120 ADP-glucose pyrophosphorylase by phosphate.

Treatment of ADP-glucose pyrophosphorylase (EC 2.7.7.27) from the cyanobacterium Anabaena PCC 7120 with phenylglyoxal in 50 mM Hepes, pH 8.0, at 25 degrees C resulted in a time- and concentration-dependent loss of enzyme activity. Phosphate, the inhibitor, protected the enzyme from inactivation most effectively, while 3-P-glycerate, fructose-1,6-P2, pyridoxal-P, and ATP plus magnesium were also good protectors. After incubation with 2 mM phenylglyoxal for 1 h, the modified enzyme had a 10-fold lower apparent affinity for phosphate in the absence of the activator, 3-P-glycerate, than that of the wild-type enzyme. This result has implicated the involvement of an arginine residue at the allosteric sites, most probably the inhibitor-binding site, of ADP-glucose pyrophosphorylase from the cyanobacterium Anabaena PCC 7120. In order to identify the arginine residue, five arginine residues, which are conserved in all higher-plant and cyanobacterial enzymes but not in enteric bacterial enzymes, were individually converted to alanine by site-directed mutagenesis. The mutant enzymes, R66A, R105A, R294A, and R385A, were purified, and the properties of these mutants were compared with the wild-type enzyme. Substitution of arginine294 with alanine resulted in an enzyme with more than 100-fold or 40-fold lower affinity for the inhibitor, phosphate, in the absence or presence of 3-P-glycerate, respectively. This mutation had no or lesser impact on the kinetic constants for the substrates and the activator, 3-P-glycerate.

Adenosine Triphosphate↗

Tartrate dehydrogenase reductive decarboxylation: stereochemical generation of diastereotopically deuterated hydroxymethylenes.

Tartrate dehydrogenase catalyzes the reductive decarboxylation of meso-tartrate to glycerate. Concomitant with the ketonization of the intermediate enolate the C3 hydroxymethylene of glycerate necessarily acquires a proton from solvent. In D2O, the proton is shown to be added stereospecifically to form (2R,3R)-[3-2H]glycerate. The 1H-NMR assignments of the diastereotopic C3 protons of glycerate were confirmed by the enzymatic conversion of [1R-2H]fructose-6-phosphate to (2R,3R)-[3-2H]glycerate. The decarboxylation-protonation occurs with retention of configuration, implying that the general acid is positioned on the same face of the intermediate as the departing carboxylate. The stereochemically pure (2R,3R)-[3-2H]glycerate is readily synthesized and serves as a chiral hydroxymethylene synthon as demonstrated by the synthesis of (2S,3R)-[3-2H]serine.

Alcohol Oxidoreductases↗

Solution-phase and solid-phase syntheses of enzyme inhibitor RK-682 and antibiotic agglomerins.

The enzyme inhibitor RK-682 (5R)-(+)-1 was prepared in solution and on a solid support from (2R)-glycerates in five steps and ca. 40% overall yield. Key steps were a ring-closing tandem addition-Wittig alkenation reaction of the respective protected or immobilized glycerates with the ylide Ph(3)PCCO and the 3-acylation of the tetronic acids thus obtained with palmitic acid. A similar route extended by a mesylation-elimination sequence led to antibiotic agglomerins A-C 2 featuring 3-acyl-5-methylidenetetronic acid structures.

4-Butyrolactone↗

Biosynthesis of mannosylglycerate in the thermophilic bacterium Rhodothermus marinus. Biochemical and genetic characterization of a mannosylglycerate synthase.

The biosynthetic reaction scheme for the compatible solute mannosylglycerate in Rhodothermus marinus is proposed based on measurements of the relevant enzymatic activities in cell-free extracts and in vivo (13)C labeling experiments. The synthesis of mannosylglycerate proceeded via two alternative pathways; in one of them, GDP mannose was condensed with D-glycerate to produce mannosylglycerate in a single reaction catalyzed by mannosylglycerate synthase, in the other pathway, a mannosyl-3-phosphoglycerate synthase catalyzed the conversion of GDP mannose and D-3-phosphoglycerate into a phosphorylated intermediate, which was subsequently converted to mannosylglycerate by the action of a phosphatase. The enzyme activities committed to the synthesis of mannosylglycerate were not influenced by the NaCl concentration in the growth medium. However, the combined mannosyl-3-phosphoglycerate synthase/phosphatase system required the addition of NaCl or KCl to the assay mixture for optimal activity. The mannosylglycerate synthase enzyme was purified and characterized. Based on partial sequence information, the corresponding mgs gene was identified from a genomic library of R. marinus. In addition, the mgs gene was overexpressed in Escherichia coli with a high yield. The enzyme had a molecular mass of 46,125 Da, and was specific for GDP mannose and D-glycerate. This is the first report of the characterization of a mannosylglycerate synthase.

Amino Acid Sequence↗

Conversion of glycerate to serine in intact spinach leaf peroxisomes.

Intact spinach (Spinacia oleracea L.) leaf peroxisomes converted glycerate to serine in the presence of NAD and alanine. The reaction proceeded optimally at pH9. Addition of oxaloacetate or alpha-ketoglutarate plus aspartate enhanced the conversion about three-fold. Alteration of the concentration of one of the reaction components, consisting of 2 mM glycerate, 0.2 mM NAD, 0.5 mM oxaloacetate, and 2 mM alanine, revealed half-saturation constants of 0.45 mM for glycerate, 0.06 mM for NAD, 0.02 mM for oxaloacetate, and 0.33 mM for alanine. The conversion proceeded with the formation of hydroxypyruvate followed by serine; hydroxypyruvate did not accumulate to a high amount in the presence or absence of alanine. The amino group donor could be alanine (half-saturation constant, 0.33 mM), glycine (0.45 mM), or asparagine (0.67 mM); the three amino acids produced roughly similar Vmax values. The results indicate that, in the conversion of glycerate to serine, the transamination is catalyzed by a hydroxypyruvate aminotransferase with characteristics unknown among all other studied leaf peroxisomal aminotransferases. The peroxisomal membrane is sparsely permeable to NAD/NADH, and the participation of the peroxisomal malate dehydrogenase in an electron shuttle system across the membrane in the regeneration of NAD/NADH is suggested.

Alanine↗

Hyperoxaluria in L-glyceric aciduria: possible pathogenic mechanism.

The effect of hydroxypyruvate on synthesis of oxalate and glycolate from glyoxylate was studied in in vitro preparations from normal human erythrocytes and leukocytes, rat liver, and with purified lactate dehydrogenase from beef heart. In the presence of reduced nicotinamide adenine dinucleotide, hydroxypyruvate stimulated the oxidation of glyoxylate to oxalate and decreased the reduction of glyoxylate to glycolate. These findings may explain the hyperoxaluria seen in L-glyceric aciduria (type II primary hyperoxaluria).

Alcohol Oxidoreductases↗

Normal glycine transport in cultured diploid fibroblasts from hyperglycinaemic subjects.

The glycine uptake in cultured fibroblasts was studied in three children with non-ketotic hyperglycinaemia, one child with D-glyceric acidaemia and hyperglycinaemia and in six normal children, using an improved assay system giving individual protein correction. It was shown that all hyperglycinaemic children had normal uptake rates and kinetic characteristics similar to the controls.

Amino Acid Metabolism, Inborn Errors↗

Excretion of short-chain N-acylglycines in the urine of a patient with D-glyceric acidemia.

Five urine samples were collected in clinically quiet periods over a period of one year from a patient suffering from D-glyceric acidemia, and investigated for presence or absence of glycine-conjugates. The findings of isovalerylglycine, 2-methylbutyrylglycine, isobutyrylglycine, and tiglylglycine are interpreted as indications of intracelluar accumulations of isovaleryl-CoA, 2-methylbutyryl-CoA and isobutyryl-CoA. Similarly, the findings of elevated amounts of butyric acid and hexanoic acid together with butyrylglycine, hexanoylglycine, and suberic acid suggest intracellular accumulations of straight-chain acyl-CoA's. It is therefore suggested that this child has a common derangement in his acyl-CoA dehydrogenase (in addition to his primary defect). As possible secondary consequences of this, two points can be mentioned: firstly hyperglycinemia, from which the patient suffered, and secondly, diminished tendency to ketosis, a condition from which the child never suffered, not even in connection with severe intercurrent disease.

Amino Acid Metabolism, Inborn Errors↗

Biotransformations of glafenine in the rat and in man.

The biotransformations of a therapeutic dose of the non-narcotic analgesic, glafenine, have been studied in the rat and in man. In the rat, the ester bond is extensively hydrolysed to give glafenic acid which is the major metabolite excreted in bile and in urine. Two minor pathways have been identified one leading by hydroxylation of the benzene ring of glafenine or glafenic acid in para of the amino-substituent to the corresponding phenols, the other, by oxidation of the quinoline nitrogen of glafenic acid, to its N-oxide. In vivo this N-oxide is partly reduced into the parent compound. Hydroxyglafenic acid is the product of both direct oxidation of glafenic acid and hydrolysis of hydroxyglafenine. The glyceric esters are conjugated as glucuro-ethers and/or sulfo-esters and the carboxylic metabolites as acyl glucuronides. The conjugation rate, high for glafenine, its phenol homologue and glafenic acid, is low for hydroxyglafenic acid and the N-oxide. The analogous urinary excretion patterns in man and in the rat suggest a similarity in the biotransformation of glafenine in these two species.

Animals↗

A carboxylate oxygen of the substrate bridges the magnesium ions at the active site of enolase: structure of the yeast enzyme complexed with the equilibrium mixture of 2-phosphoglycerate and phosphoenolpyruvate at 1.8 A resolution.

The equilibrium mixture of yeast enolase with substrate, 2-phospho-D-glycerate (2-PGA), and product, phosphoenolpyruvate (P-enolpyruvate), has been crystallized from solutions of poly(ethylene glycol) (PEG) at pH 8.0. Crystals belong to the space group C2 and have unit cell dimensions a = 121.9 A, b = 73.2 A, c = 93.9 A, and beta = 93.3 degrees. The crystals have one dimer per asymmetric unit. Crystals of the equilibrium mixture and of the enolase complex of phosphonoacetohydroxamate (PhAH) are isomorphous, and the structure of the former complex was solved from the coordinates of enolase-(Mg2+)2-PhAH [Wedekind, J. E., Poyner, R. R., Reed, G. H., & Rayment, I. (1994) Biochemistry 33, 9333-9342]. The current crystallographic R-factor is 17.7% for all recorded data (92% complete) to 1.8 A resolution. The electron density map is unambiguous with respect to the positions and liganding of both magnesium ions and with respect to the stereochemistry of substrate/product binding. Both magnesium ions are complexed to functional groups of the substrate/product. The higher affinity Mg2+ coordinates to the carboxylate side chains of Asp 246, Glu 295, and Asp 320, both carboxylate oxygens of the substrate/product, and a water molecule. One of the carboxylate oxygens of the substrate/product also coordinates to the lower affinity Mg2+-thus forming a mu-carboxylato bridge. The other ligands of the second Mg2+ are a phosphoryl oxygen of the substrate/product, two water molecules, and the carbonyl and gamma-oxygens of Ser 39 from the active site loop. The intricate coordination of both magnesium ions to the carboxylate group suggests that both metal ions participate in stabilizing negative charge in the carbanion (aci-carboxylate) intermediate. The epsilon-amino group of Lys 345 is positioned to serve as the base in the forward reaction whereas the carboxylate side chain of Glu 211 is positioned to interact with the 3-OH of 2-PGA. The structure provides a candid view of the catalytic machinery of enolase.

Binding Sites↗

Hydroxypyruvate-mediated regulation of oxalate synthesis by lactate dehydrogenase and its relevance to primary hyperoxaluria type II.

Hydroxypyruvate (HP) brought about the decarboxylation of [1-14C] glyoxylate nonenzymically at all pH values considered. The rate of decomposition of glyoxylate increased with each increase in the concentrations of the reactants, the pH, and temperature and on the addition of the cations Fe2+, Mn2+, Mg2+, Zn2+, Co2+, and Cu2+. The addition of HP to a purified preparation of lactate dehydrogenase (LDH) catalyzing the oxidation of [1-14C]glyoxylate to [14C]oxalate in the presence of either NAD or NADH inhibited the production of oxalate. These observations have their implications in L-glyceric aciduria (primary hyperoxaluria type II), a syndrome characterized by the accumulation of HP and recurrent oxalosis. They suggest that the accumulating HP may reduce the contribution of intracellular glyoxylate to the formation of oxalate by competitively inhibiting the liver LDH. The involvement of liver LDH in oxalate synthesis and its postulated induction by HP and NAD in vivo are, therefore, reexamined.

Amino Acid Metabolism, Inborn Errors↗

Calculated effects of the chemical environment of 2-phospho-D-glycerate on the pKa of its carbon-2 and correlations with the proposed mechanism of action of enolase.

The mechanism of action of enolase requires drastic lowering of the pK of the alpha carbon of the substrate to enable removal of the alpha hydrogen. Calculations suggest this is done primarily by rotation of the carboxyl ("carbon-1") of the substrate around the carbon-1 carbon-2 bond by 90 degrees so that its oxygen atoms lie in the plane formed by the three carbon atoms and secondarily by effectively neutralizing the negative charges on the carboxylate and phosphate. These predictions are in very good agreement with the proposed mechanism of action of enolase which is based on X-ray crystallographic data.

Amino Acid Sequence↗

A transport system for phosphoenolpyruvate, 2-phosphoglycerate, and 3-phosphoglycerate in Salmonella typhimurium.

Salmonella typhimurium strain LT-2 was found to utilize phosphoenolpyruvate, 2-phosphoglycerate, and 3-phosphoglycerate as sole sources of carbon and energy for growth, but Escherichia coli strains did not. The following evidence suggests that this growth difference was due to the presence in Salmonella cells of an inducible phosphoglycerate permease distinct from previously studied transport systems: (a) The ability of cells to take up 3-phospho[14-C]glycerate was induced by growth in the presence of phosphoenolpyruvate, 2-phosphoglycerate, or 3-phosphoglycerate, but not glycerate, alpha-glycerophosphate, or other carbon sources tested. (b) Uptake of 3-phospho[14-C]glycerate was strongly inhibited by the three nonradioactive inducers of 3-phosphoglycerate uptake, but not by glycerate or alpha-glycerophosphate. (c) Mutants which lost the ability to utilize and take up 3-phosphoglycerate simultaneously lost the ability to utilize 2-phosphoglycerate and phosphoenolpyruvate, but not other compounds tested. (d) Mutant strains which constitutively synthesized the phosphoglycerate transport system could use both phosphoglycerates and phosphoenolpyruvate as sole sources of phosphate at low substrate concentrations. (e) A strain lacking alkaline and acid phosphatases could still grow with 3-phosphoglycerate as sole carbon source. Maximal rates of 3-phospho[14-C]glycerate uptake occurred at pH 6 in the presence of an exogenous energy source. The apparent Km for 3-phosphoglycerate uptake under these conditions was about 10-minus 4 M. The maximal uptake rate (but not the Km) was dependent on potassium ions. Although synthesis of the phosphoglycerate transport system appeared to be under adenosine 3:5-monophosphate control, glucose repressed induction only slightly. The genes controlling synthesis of the phosphoglycerate transport system (pgt genes) appeared to map at about 74 min on the Salmonella chromosome.

Biological Transport↗

Site-directed mutagenesis of lysine382, the activator-binding site, of ADP-glucose pyrophosphorylase from Anabaena PCC 7120.

Previous studies have shown that a highly conserved lysyl residue (Lys 419) near the C-terminus of Anabaena ADP-glucose pyrophosphorylase is involved in the binding of 3-P-glycerate, the allosteric activator [Charng, Y., Iglesias, A. A., & Preiss, J. (1994) J. Biol. Chem. 269, 24107-24113]. Phosphopyridoxylation of the K419R mutant enzyme modified another conserved lysyl residue (Lys382), suggesting that this residue might be also located within the activator-binding site [Charng, Y., Iglesias, AA., & Preiss, J. (1994) J. Biol. Chem. 269, 24107-24113]. Site-directed mutagenesis of Lys382 of the Anabaena enzyme was performed to determine the role of this residue. Replacing Lys382 with either arginine, alanine, or glutamine produced mutant enzymes with apparent affinities for 3-P-glycerate 10-160-fold lower than that of the wild-type enzyme. The glutamic acid mutant enzyme was inhibited by 3-P-glycerate. These mutations had lesser impact on the kinetic constants for the substrates and inhibitor, P(i), and on the thermal stability. These results indicate that both the charge and size of the residue at position 382 influence the binding of 3-P-glycerate. Site-directed mutagenesis was also performed to obtain a K382R-K419R double mutant. The apparent affinity for 3-P-glycerate of this double-mutant enzyme was 104-fold lower than that of the wild-type enzyme, and the specificity for activator of this mutant enzyme was altered. The K382R-K419R enzyme could not be phosphopyridoxylated, suggesting that other lysine residues are not involved in the binding of 3-P-glycerate.

Allosteric Regulation↗

Mechanism of catalysis of the cofactor-independent phosphoglycerate mutase from Bacillus stearothermophilus. Crystal structure of the complex with 2-phosphoglycerate.

The structure of the complex between the 2, 3-diphosphoglycerate-independent phosphoglycerate mutase (iPGM) from Bacillus stearothermophilus and its 3-phosphoglycerate substrate has recently been solved, and analysis of this structure allowed formulation of a mechanism for iPGM catalysis. In order to obtain further evidence for this mechanism, we have solved the structure of this iPGM complexed with 2-phosphoglycerate and two Mn(2+) ions at 1. 7-A resolution. The structure consists of two different domains connected by two loops and interacting through a network of hydrogen bonds. This structure is consistent with the proposed mechanism for iPGM catalysis, with the two main steps in catalysis being a phosphatase reaction removing the phosphate from 2- or 3-phosphoglycerate, generating an enzyme-bound phosphoserine intermediate, followed by a phosphotransferase reaction as the phosphate is transferred from the enzyme back to the glycerate moiety. The structure also allowed the assignment of the function of the two domains of the enzyme, one of which participates in the phosphatase reaction and formation of the phosphoserine enzyme intermediate, with the other involved in the phosphotransferase reaction regenerating phosphoglycerate. Significant structural similarity has also been found between the active site of the iPGM domain catalyzing the phosphatase reaction and Escherichia coli alkaline phosphatase.

Amino Acid Sequence↗

Molecular and structural characterization of NADPH-dependent d-glycerate dehydrogenase from the enteric parasitic protist Entamoeba histolytica.

Putative NADPH-dependent GDH (L-glycerate dehydrogenase) of the protozoan parasite Entamoeba histolytica (EhGDH) has been characterized. The EhGDH gene encodes a protein of 318 amino acids with a calculated isoelectric point of 6.29 and a molecular mass of 35.8 kDa. EhGDH showed highest identities with GDH from epsilon-proteobacteria. This close kinship was also supported by phylogenetic analyses, suggesting possible lateral transfer of the gene from epsilon-proteobacteria to E. histolytica. In contrast with the implications from protein alignment and phylogenetic analysis, kinetic studies revealed that the amoebic GDH showed biochemical properties similar to those of mammalian GDH, i.e. a preference for NADPH as cofactor and higher affinities towards NADPH and beta-hydroxypyruvate than towards NADP+ and L-glycerate. Whereas the amino acids involved in nucleotide binding and catalysis are totally conserved in EhGDH, substitution of a negatively charged amino acid with a non-charged hydroxy-group-containing amino acid is probably responsible for the observed high affinity of EhGDH for NADP+/NADPH. In addition, the amoebic GDH, dissimilar to the bacterial and mammalian GDHs, lacks glyoxylate reductase activity. Native and recombinant EhGDH showed comparable subunit structure, kinetic parameters and elution profiles on anion-exchange chromatography. We propose that the GDH enzyme is likely to be involved in regulation of the intracellular concentration of serine, and, thus, also in controlling cysteine biosynthesis located downstream of serine metabolic pathways in this protist.

Amino Acid Sequence↗

Structure of the R65Q mutant of yeast 3-phosphoglycerate kinase complexed with Mg-AMP-PNP and 3-phospho-D-glycerate.

The structure of a ternary complex of the R65Q mutant of yeast 3-phosphoglycerate kinase (PGK) with magnesium 5'-adenylylimidodiphosphate (Mg-AMP-PNP) and 3-phospho-D-glycerate (3-PG) has been determined by X-ray crystallography to 2.4 angstrom resolution. The structure was solved by single isomorphous replacement, anamalous scattering, and solvent flattening and has been refined to an R-factor of 0.185, with rms deviations from ideal bond distance and angles of 0.009 angstrom and 1.78 degrees, respectively. PGK consists of two domains, with the 3-PG bound to a "basic patch" of residues from the N-terminal domain and the Mg-AMP-PNP interacting with residues from the C-terminal domain. The two ligands are separated by approximately 11 angstrom across the interdomain cleft. The model of the R65Q mutant of yeast PGK is very similar to the structures of PGK isolated from horse, pig, and Bacillus stearothermophilus (rms deviations between equivalent alpha-carbons in the individual domains < 1.0 angstrom) but exhibits substantial variations with a previously reported yeast structure (rms deviations between equivalent alpha-carbons in the individual domains of 2.9-3.2 angstrom). The most significant tertiary structural differences among the yeast R65Q, equine, porcine, and B. stearothermophilus PGK structures occur in the relative orientations of the two domains. However, the relationships between the observed conformations of PGK are inconsistent with a "hinge-bending" behavior that would close the interdomain cleft. It is proposed that the available structural and biochemical data on PGK may indicate that the basic patch primarily represents the site of anion activation and not the catalytically active binding site for 3-PG.

Adenylyl Imidodiphosphate↗