Comparative Enzymology of the Adenosine Triphosphate Sulfurylases from Leaf and Swollen Hypocotyl Tissue of Beta vulgaris: Multiple Enzyme Forms in Hypocotyl Tissue

ATP sulfurylase activity was partially purified from the swollen hypocotyl of beetroot (Beta vulgaris); activity was measured by sulfate-dependent PPi-ATP exchange. The ATP sulfurylase activity was separated from pyrophosphatase and ATPase activities which interfere with the assay of ATP sulfurylase activity. The ATP sulfurylase activity from hypocotyl tissue was invariably resolved into two approximately equal activities (hypocotyls I and II) by ion exchange chromatography and polyacrylamide gradient gel electrophoresis. Both enzymes catalyzed selenate- and sulfate-dependent PPi-ATP exchange; the affinity of hypocotyl II for these substrates was greater than for hypocotyl I. It is unlikely that the two activities arise by allelic variation or as an artifact of purification; they are most probably isoenzymes. Studies of the subcellular localization of the two hypocotyl enzymes were inconclusive.     

Ribonucleoside Triphosphate-Dependent Pyrophosphate Exchange of Reovirus Cores

Reovirus cores catalyze a ribonucleoside triphosphate (rNTP)-dependent pyrophosphate exchange reaction in the presence of all four rNTP species. When rNTP species are tested individually, only guanosine-5'-triphosphate supports pyrophosphate exchange.     

Subcloning, expression, and purification of the enterobactin biosynthetic enzyme 2,3-dihydroxybenzoate-AMP ligase: demonstration of enzyme-bound (2,3-dihydroxybenzoyl)adenylate product

The gene coding for the enzyme 2,3-dihydroxybenzoate-AMP ligase (2,3DHB-AMP ligase), responsible for activating 2,3-dihydroxybenzoic acid in the biosynthesis of the siderophore enterobactin, has been subcloned into the multicopy plasmid pKK223-3 and overproduced in a strain of Escherichia coli. The protein is an alpha 2 dimer with subunit molecular mass of 59 kDa. The enzyme catalyzes the exchange of [32P]pyrophosphate with ATP, dependent upon aromatic substrate with a turnover number of 340 min-1. The enzyme also releases pyrophosphate upon incubation with 2,3-dihydroxybenzoic acid and ATP; an initial burst corresponding to 0.7 nmol of pyrophosphate released per nanomole of enzyme is followed by a slower, continuous release with a turnover number of 0.41 min-1. The 1000-fold difference in rates observed between ATP-pyrophosphate exchange and continuous pyrophosphate release, as well as the close to stoichiometric amount of pyrophosphate released, suggests that intermediates are accumulating on the enzyme surface. Such intermediates have been observed and correspond to enzyme-bond (2,3-dihydroxybenzoyl)adenylate product.     

Phenylalanyl-tRNA synthetase of baker's yeast. Modulation of adenosine triphosphate-pyrophosphate exchange by transfer ribonucleic acid

Native and modified phenylalanine transfer ribonucleic acid (tRNAPhe) can modulate phenylalanine-dependent adenosine triphosphate--inorganic [32P]pyrophosphate (ATP--[32P]PPi) exchange activity via inhibition of adenylate synthesis. Inhibition is visualized if concentrations of L-phenylalanine, ATP, and pyrophosphate are subsaturating. In the proposed mechanism, tRNAPhe is a noncompetitive inhibitor at conditions where only one of the two active sites per molecule of enzyme is occupied by L-phenylalanine, ATP, and pyrophosphate. At saturating concentrations of these reactants, both active sites are occupied and, according to the model, inhibition is eliminated. Occupation by these reactants is assumed to follow homotropic negative cooperativity. The type of effects depends on modification of tRNAPhe. Native tRNAPhe, tRNA2'-dAPhe, and tRNAoxi-redPhe are inhibitors, tRNAPhepCpC has no effect, and tRNAoxPhe is an activator. Kinetics of activation by tRNAoxPhe are slow, following the time course of Schiff base formation and subsequent reduction by added cyanoborohydride. Besides showing that a putative enzyme amino group is nonessential for substrate binding and adenylate synthesis, this result may suggest that an enzyme amino group could interact with the 3'-terminal adenyl group of cognate tRNA. In the case of asymmetrical occupation of the enzyme active sites by all of the small reactants ATP, L-phenylalanine, and pyrophosphate, the interaction with the amino group might trigger the observed noncompetitive inhibition of the pyrophosphate exchange by tRNAPhe.     

Stereochemistry at C-1 of geranyl pyrophosphate and neryl pyrophosphate in the cyclization to (+)- and (-)-bornyl pyrophosphate

(1R)-1-3H-labeled and (1S)-1-3H-labeled geranyl pyrophosphate and neryl pyrophosphate were prepared from the corresponding 1-3H-labeled aldehydes by a combination of enzymatic and synthetic procedures. Following admixture with the corresponding 2-14C-labeled internal standard, each substrate was converted to (+)-bornyl pyrophosphate and (-)-bornyl pyrophosphate by cell-free enzyme preparations from sage (Salvia officinalis) and tansy (Tanacetum vulgare), respectively. Each pyrophosphate ester was hydrolyzed, and the resulting borneol was oxidized to camphor. The stereochemistry of labeling at C-3 of the derived ketone was determined by base-catalyzed exchange, taking advantage of the known selective exchange of the exo-alpha-protons. By comparison of such exchange rates to those of product generated from (1RS)-2-14C,1-3H2-labeled substrate, it was demonstrated that geranyl pyrophosphate was cyclized to bornyl pyrophosphate with net retention of configuration at C-1 of the acyclic precursor, whereas neryl pyrophosphate was cyclized to product with inversion of configuration at C-1. The observed stereochemistry is consistent with a reaction mechanism whereby geranyl pyrophosphate is first stereospecifically isomerized to linalyl pyrophosphate which, following rotation about C-2-C-3 to the cisoid conformer, cyclizes from the anti-endo configuration. Neryl pyrophosphate cyclizes either directly or via the linalyl intermediate without the attendant rotation.     

Effect of adenine nucleotides and pyrophosphate on the exchange of transferrin-bound carbonate.

1. ATP, ADP and pyrophosphate accelerate the exchange of carbonate of the transferrin-iron-carbonate ternary complex, while AMP, cyclic AMP and phosphate have no effect. 2. ATP promotes carbonate exchange without removing iron from transferrin, whereas pyrophosphate effectiely attacks both the anion and iron components of the ternary complex. 3. Transferrin readily takes over iron from its ATP or pyrophosphate complex. 4. Neither ATP nor pyrophosphate can substitute for carbonate of the ternary complex. These results fit in well with the concept that ATP may play a direct role in the iron uptake by reticulocytes.     

Iron transfer from transferrin to ferritin mediated by pyrophosphate

There is no significant iron exchange from transferrin to ferritin in the absence of reducing and chelating agents. Pyrophosphate can release iron from transferrin and can be isolated as a ferric pyrophosphate complex by ion exchange chromatography. We have established that pyrophosphate alone can mediate iron exchange from transferrin to ferritin. Under these conditions, iron is incorporated directly into ferritin as Fe(III).     

Isotope exchange as a probe of the kinetic mechanism of pyrophosphate-dependent phosphofructokinase

Data obtained from isotope exchange at equilibrium, exchange of inorganic phosphate against forward reaction flux, and positional isotope exchange of 18O from the bridge position of pyrophosphate to a nonbridge position all indicate that the pyrophosphate-dependent phosphofructokinase from Propionibacterium freudenreichii has a rapid equilibrium random kinetic mechanism. The maximum rates of isotope exchange at equilibrium for the [14C]fructose 1,6-bisphosphate in equilibrium fructose 6-phosphate, [32P]Pi in equilibrium MgPPi, and Mg[32P]PPi in equilibrium fructose 1,6-bisphosphate exchange reactions increasing all four possible substrate-product pairs in constant ratio are identical, consistent with a rapid equilibrium mechanism. All exchange reactions are strongly inhibited at high concentrations of the fructose 6-phosphate (F6P)/Pi and MgPPi/Pi substrate-product pairs and weakly inhibited at high concentrations of the MgPPi/fructose 1,6-bisphosphate (FBP) pair suggesting three dead-end complexes, E:F6P:Pi, E:MgPPi:Pi, and E:FBP:MgPPi, in agreement with initial velocity studies [Bertagnolli, B.L., & Cook, P.F. (1984) Biochemistry 23, 4101]. Neither back-exchange by [32P]Pi nor positional isotope exchange of 18O-bridge-labeled pyrophosphate was observed under any conditions, suggesting that either the chemical interconversion step or a step prior to it limits the overall rate of the reaction.     

The phosphate-pyrophosphate exchange and hydrolytic reactions of the membrane-bound pyrophosphatase of Rhodospirillum rubrum: effects of Mg2+, phosphate, and pyrophosphate

The relation that exists between the Pi-PPi exchange reaction and pyrophosphate hydrolysis by the membrane-bound pyrophosphatase of chromatophores of Rhodospirillum rubrum was studied. The two reactions have a markedly different requirement for added Mg2+. Optimal rates of hydrolysis were attained at 1 mM Mg2+ with 0.67 mM pyrophosphate; the rate od hydrolysis correlated with the concentration of Mg-pyrophosphate, which indicated that the latter was the substrate for hydrolysis. The Pi-PPi exchange reaction rate was low at concentrations of added Mg2+ below 1 mM (0.67 mM pyrophosphate), but increased as the concentration of Mg2+ in the medium was increased. The Pi-PPi exchange reaction depends on the concentration of MgHPO4, which suggests that this is the substrate in the exchange reaction. However, it is likely that free Mg2+ also exerts a favorable effect on the Pi-PPi exchange reaction. The optimal concentration for the Pi-PPI exchange reaction was approx 240 microM, which suggests that the concentration of the hydrolyzable substrates modulates the kinetic characteristics of the enzyme.     

Mechanism of the pyrophosphate migration in the enzymatic cyclization of geranyl and linalyl pyrophosphates to (+)- and (-)-bornyl pyrophosphates

Soluble enzymes from sage (Salvia officinalis) and tansy (Tanacetum vulgare), which catalyze the cyclization of geranyl pyrophosphate and the presumptive intermediate linalyl pyrophosphate to the (+) and (-) enantiomers, respectively, of 2-bornyl pyrophosphate, were employed to evaluate mechanistic alternatives for the pyrophosphate migration in monoterpene cyclization reactions. Separate incubation of [1-3H2,alpha-32P]- and [1-3H2,beta- 32P]geranyl and (+/-)-linalyl pyrophosphates with partially purified preparations of each enantiomer-generating cyclase gave [3H, 32P]bornyl pyrophosphates, which were selectively hydrolyzed to the corresponding bornyl phosphates. Measurement of 3H:32P ratios of these monophosphate esters established that two ends of the pyrophosphate moiety retained their identifies in the cyclization of both precursors to both products and also indicated that there was no appreciable exchange with exogenous inorganic pyrophosphate in the reaction. Subsequent incubations of each cyclase with [8,9-14C,1-18O]geranyl pyrophosphate and with (1E)-(+/-)-[1-3H,3-18O]linalyl pyrophosphate gave the appropriate (+)- or (-)-bornyl pyrophosphates, which were hydrolyzed in situ to the corresponding borneols. Analysis of the derived benzoates by mass spectrometry demonstrated each of the product borneols to possess an 18O enrichment essentially identical with that of the respective acyclic precursor. The absence of P alpha-P beta interchange and the complete lack of positional 18O isotope exchange of the pyrophosphate moiety are compatible with tight ion pairing of intermediates in the coupled isomerization-cyclization of geranyl pyrophosphate and establish a remarkably tight restriction on the motion of the transiently generated pyrophosphate anion with respect to its cationic terpenyl reaction partner.     

The influence of diphosphonic analogues of inorganic pyrophosphate on reactions catalyzed by DNA-dependent RNA-polymerase II

Diphosphonic analogues of inorganic pyrophosphate were studied for their influence both on RNA pyrophosphorolysis and pyrophosphate exchange, catalyzed by purified DNA-dependent RNA-polymerase II from calf thymus. Methylene-, oxyethylene-and aminomethylenediphosphonic acids are shown to compete with PPi for incorporation into nucleoside triphosphate. They activate RNA pyrophosphorolysis in the concentration of 2 mM, but to a less extent than PPi does.     

A nonradioactive high-throughput assay for screening and characterization of adenylation domains for nonribosomal peptide combinatorial biosynthesis

Adenylation domains are critical enzymes that dictate the identity of the amino acid building blocks to be incorporated during nonribosomal peptide (NRP) biosynthesis. NRPs display a wide range of biological activities and are some of the most important drugs currently used in clinics. Traditionally, activity of adenylation domains has been measured by radioactive ATP-[³²P]pyrophosphate (PP_i) exchange assays. To identify adenylation domains for future combinatorial production of novel NRPs as potential drugs, we report a convenient high-throughput nonradioactive method to measure activity of these enzymes. In our assay, malachite green is used to measure orthophosphate (P_i) concentrations after degradation by inorganic pyrophosphatase of the PP_i released during aminoacyl-AMP formation by action of the adenylation domains. The assay is quantitative, accurate, and robust, and it can be performed in 96- and 384-well plate formats. The performance of our assay was tested by using NcpB-A₄, one of the seven adenylation domains involved in nostocyclopeptide biosynthesis. The kinetics of pyrophosphate release monitored by this method are much slower than those measured by a traditional ATP-[³²P]PP_i exchange assay. This observation indicates that the formation of the adenylated amino acid and its release are the rate-limiting steps during the catalytic turnover.     

A simplified assay of enzymes catalyzing ATP-pyrophosphate exchange reactions.

The ATP-pyrophosphate exchange reaction is a widely used method for determination of the activity of enzymes forming enzyme-adenylate intermediates in the course of their catalytic action (1–4). For separation of the labeled ATP formed in the enzyme-catalyzed reaction from the labeled pyrophosphate, the adsorption of ATP on activated Norit is generally used. This method, however, is rather time consuming (considering the extensive washings required for the removal of pyrophosphate from Norit), and its reproducibility is highly dependent on pretreatment of charcoal with acid, Another method of separation applies anion-exchange paper (5). According to our experience, separation on DEAE-cellulose paper (Whatman DE 81) is not sufficient.     

Tightly bound pyrophosphate in Escherichia coli inorganic pyrophosphatase

Hexameric inorganic pyrophosphatase of Escherichia coli contains about 1 mol/mol of 'structural' pyrophosphate, which survives gel filtration and prolonged incubation with Mg2+, does not exchange with medium phosphate and pyrophosphate but is removed with 0.8 M perchloric acid. The site of pyrophosphate binding seems to be another than the active site. An additional 0.9 mol of enzyme-bound pyrophosphate is formed in the presence of phosphate and Mg2+ but this pyrophosphate is in fast equilibrium with medium phosphate and appears to be bound to the active site.     

Creatine phosphate inhibition of adenylate deaminase is mainly due to pyrophosphate.

Inhibition of rat skeletal muscle adenylate deaminase by creatine phosphate reported previously is due to inorganic pyrophosphate present as a contaminant in commercial preparations of creatine phosphate. This conclusion is based on the following evidence: a compound that inhibits adenylate deaminase can be separated from commercially prepared creatine phosphate by ion exchange chromatography; the inhibition by "creatine phosphate" and by the separated inhibitory compound is relieved by treatment with inorganic pyrophosphatase; inhibition by inorganic pyrophosphate is similar to that produced by unpurified creatine phosphate; and pyrophosphate is present in commercially available creatine phosphate in amounts sufficient to account for the inhibition. Some commercial preparations of creatine phosphate contain much less pyrophosphate than others; these preparations are only weakly inhibitory. Inorganic triphosphate is a more powerful inhibitor of the enzyme than pyrophosphate; it may also be present as a contaminant in creatine phosphate.     

Energy-linked Adenosine Diphosphate Accumulation by Corn Mitochondria: II. Phosphate and Divalent Cation Requirement

The requirement for phosphate and Mg²⁺ in energy-linked [³H] ADP accumulation by corn mitochondria has been studied. Arsenate will fully substitute for phosphate; sulfate partially substitutes; acetate, bicarbonate, and pyrophosphate are ineffective. Phosphate is also taken up by the mitochondria, but the ADP/Pi ratio varies widely with experimental treatments. ADP does not exchange with endogenous labeled phosphate, although Pi/³²Pi exchange occurs.     

Ligand binding and enzymic catalysis coupled through subunits in tyrosyl-tRNA synthetase.

The interaction of the tyrosyl-tRNA synthetase from Bacillus stearothermophilus with its substrates in the aminoacyl adenylation reaction has been studied by stopped-flow fluorescence. The observed changes have been assigned to their chemical and physical processes by comparison with equilibrium dialysis, pyrophosphate exchange kinetics and rapid quenching and sampling techniques to give the rate constants for ligand binding, the formation of tyrosyl adenylate, and the reverse reaction. The stoichiometry of tyrosine and ATP binding in the catalytic process has been determined directly by equilibrium dialysis and equilibrium gel filtration under pyrophosphate exchange conditions, i.e., where a steady state has been set up in which the equilibrium position favors starting materials. It is shown that the rate-determining step in the formation of tyrosyl adenylate involves 1 mole each of tyrosine and ATP. A second mole of tyrosine and ATP bind to the aminoacyl adenylate complex stabilizing the high-energy intermediate. The enzyme tyrosyl adenylate complex that is isolated by gel filtration is in a different conformational state from that in the presence of tyrosine and ATP.     

Plasmid-encoded copper resistance and precipitation by Mycobacterium scrofulaceum.

A copper-tolerant Mycobacterium scrofulaceum strain was able to remove copper from culture medium by sulfate-dependent precipitation as copper sulfide. Such precipitation of copper sulfide was not observed in a derivative that lacks a 173-kilobase plasmid. In addition, the plasmid-carrying strain has a sulfate-independent copper resistance mechanism.