Comparative kinetic studies of Mg2+-activated hydrolysis of tripolyphosphate and pyrophosphate by inorganic pyrophosphatase]

Computer analysis of P3 and pyrophosphate conversion rate dependence on substrate and metal-activator concentrations reveals the identity of kinetic patterns. Dissociation and catalytical constants for the enzyme combinations with two types of metal-substrates complexes, MS and M2S, at pH 9.0 are by one to two orders of magnitude "poorer" for P3 as compared to PPi. Optimal pH value for the hydrolysis of P3 is by 2 units higher than this for the hydrolysis of PPi. pH profiles for the kinetic parameters in the pH range 8.0--9.5 differ considerably for the two substrates, presumably due to the existence of additional catalitically important ionisations in the reaction with P3.     

Purification and kinetic properties of human erythrocyte Mg2+-dependent inorganic pyrophosphatase

Inorganic pyrophosphatase (pyrophosphate phosphohydrolase, EC 3.6.1.1) from human erythrocyte hemolysates has been purified up to 10 000-fold. The purified enzyme is homogenous and has a specific activity of 79.75 mumol PPi hydrolysed.min-1.mg-1 at pH 8 and 37 degrees C. It was confirmed that it is a dimer with a molecular weight of 42 000, composed of two identical protomers. From kinetic studies, it is proposed that human erythrocyte inorganic pyrophosphatase activity depends on free Mg2+ concentration in different ways. This ion constitutes part of the substrate (the Mg.PPi complex; Km = 1.4.10(-4) M) and probably acts as an allosteric activator (kinetic activation constant: KMg2+a = 7.5.10(-4) M). Equilibrium binding studies performed in the absence of PPi showed 4 binding sites for Mg2+, all having the same high affinity (dissociation constant: KMg2+d = 4.10(-6) M). Since the concentration of free Mg2+ in red blood cells is very low and may vary with the oxygenation state, it is likely that in vivo erythrocyte pyrophosphatase activity is regulated.     

Mechanism of Ca2+-induced inhibition of Escherichia coli inorganic pyrophosphatase

The causes of inhibition of Escherichia coli inorganic pyrophosphatase (PPase) by Ca2+ were investigated. The interactions of several mutant pyrophosphatases with Ca2+ in the absence of substrate were analyzed by equilibrium dialysis. The kinetics of Ca2+ inhibition of hydrolysis of the substrates MgPPi and LaPPi by the native PPase and three mutant enzymes (Asp-42-Asn, Ala, and Glu) were studied. X-Ray data on E. coli PPase complexed with Ca2+ or CaPPi solved at atomic resolution were analyzed. It was shown that, in the course of the catalytic reaction, Ca2+ replaces Mg2+ at the M2 site, which shows higher affinity for Ca2+ than for Mg2+. Different properties of these cations account for active site deformation. Our findings indicate that the filling of the M2 site with Ca2+ is sufficient for PPase inhibition. This fact proves that Ca2+ is incapable of properly activating the H2O molecule for nucleophilic attack on PPi. It was also demonstrated that Ca2+, as a constituent of the non-hydrolyzable substrate analog CaPPi, competes with MgPPi at the M3 binding site. As a result, Ca2+ is a powerful inhibitor of all known PPases. Other possible reasons for the inhibitory effect of Ca2+ on the enzyme activity are also considered.     

Identification of new protein complexes of Escherichia coli inorganic pyrophosphatase using pull-down assay

Inorganic pyrophosphatase (PPase) is a conserved and essential enzyme catalyzing the hydrolysis of pyrophosphate PP_i. Its activity is required to promote a lot of thermodynamically unfavorable reactions including biosynthesis of activated precursors of sugars and amino acids. Several protein partners of PPase were found so far in Escherichia coli by large-scale approaches. Functional role of these interactions was not studied. In this paper we report the identification of three protein partners of E. coli PPase not found earlier. Pull-down assay on the Ni²⁺-chelating column using 6His-tagged PPase as bait was used to isolate PPase complexes from stationary-phase cells. Of several isolated protein components, five were identified by MALDI-TOF mass-spectrometry: two chaperones (DnaK and GroEL) and three enzymes of carbohydrate and amino acid metabolism (FbaB, fructose-1,6-bisphosphate aldolase, class I; GadA, l-glutamate decarboxylase; and KduI, 5-keto-4-deoxyuronate isomerase). These three proteins were cloned, expressed and purified in 6His-tagged and/or tag-free forms. Their binary interactions with PPase were verified by independent approaches. Initial characterization of the complexes indicates that PPase may stabilize its protein partners against unfolding or degradation. Comparative analysis of the PPase protein partners allowed an insight into its possible involvement in the cell metabolic regulation.     

Properties and regulation of Mg2+-dependent chloroplast inorganic pyrophosphatase from Sorghum vulgare leaves

A Mg2+ dependent inorganic pyrophosphatase from chloroplasts of Sorghum vulgare has been purified 275-fold to electrophoretic purity with an overall recovery of about 25% activity. Estimations of native and monomeric relative molecular weights by size exclusion chromatography and denaturing electrophoresis suggest that the holoenzyme is a monomer of 42 +/- 1.5 kDa. A high specificity for tetrasodium pyrophosphate (PPi) as substrate has been observed, as the other phosphoesters tested were virtually unaffected. The Mg2+:PPi ratio of 5:1 at pH 8.0 shifts to 2.5:1.0 at pH 9.0 and 10:1 at pH 7.0. None of the divalent cations tested could substitute for Mg2+. Further, in the presence of Mg2+, these divalent cations inhibit the catalytic hydrolysis of PPi. EDTA rapidly and irreversibly inactivates the purified enzyme in a biphasic manner. Of the metabolites tested, Pi and L-malate significantly inhibited the catalytic activity of the enzyme. Malate inhibits the enzyme through an allosteric mechanism. A Hill plot of this inhibition shows that at least two molecules of malate bind to each molecule of the purified enzyme. The likely physiological significance of this result is discussed.     

Kinetic studies of asparagine synthetase from rat liver: role of Mg2+ in enzyme catalysis

The kinetic mechanism of asparagine synthetase from rat liver has been studied. The mechanism of the reaction in the presence of high concentrations of total Mg2+ (50 mM) was suggested to be a uni-uni-bi-ter ping-pong-type without abortive complexes; glutamine binds first followed by glutamate release, and aspartate and ATP bind in order followed by ordered release of PPi, AMP, and asparagine. But, it is indicated that in the presence of 0.5-2.0 mM excess Mg2+ over ATP the binding of substrates after the release of glutamate is in a rapid equilibrium system such as ordered Mg2+ and random aspartate-MgATP. Mg2+ was demonstrated to have two roles in the catalysis; to modify the enzyme and to form a complex of MgATP.     

Kinetic studies of the interaction of uranyl ions with inorganic pyrophosphatase from baker's yeast.

Kinetic measurements were performed to test the effect of uranyl ions on the enzymatic hydrolysis of pyrophosphate. A strong inhibition of the enzyme was found. From a Dixon-plot an inhibition competitive to the substrate magnesium pyrophosphate and an inhibitory constant of Ki = 3 . 10(-7) M was deduced.     

Use of inorganic pyrophosphatase as a marker in enzyme immunoassays

A technique of heterogeneous enzyme immunoassay with the E. coli inorganic pyrophosphatase as marker enzyme and Malachite green dye and acidic molybdate as color reagent is developed. Color change (light-yellow/greenish blue) is extremely suitable for visual perception, in some cases making unnecessary the measuring device. Assays with pyrophosphatase are 5-10 times more sensitive than with peroxidase. Further advantages of pyrophosphatase include high thermostability, insensitivity to sodium azide, low value of Michaelis constant (5 microM), substrate stability. Examples are given of use of the pyrophosphatase for assays of human alpha-fetoprotein and immunoglobulin.     

H(+)-translocating inorganic pyrophosphatase of plant vacuoles. Inhibition by Ca2+, stabilization by Mg2+ and immunological comparison with other inorganic pyrophosphatases.

The effects of divalent cations, especially Ca2+ and Mg2+, on the proton-translocating inorganic pyrophosphatase purified from mung bean vacuoles were investigated to compare the enzyme with other pyrophosphatases. The pyrophosphatase was irreversibly inactivated by incubation in the absence of Mg2+. The removal of Mg2+ from the enzyme increased susceptibility to proteolysis by trypsin. Vacuolar pyrophosphatase required free Mg2+ as an essential cofactor (K0.5 = 42 microM). Binding of Mg2+ stabilizes and activates the enzyme. The formation of MgPPi is also an important role of magnesium ion. Apparent Km of the enzyme for MgPPi was about 130 microM. CaCl2 decreased the enzyme activity to less than 60% at 40 microM, and the inhibition was reversed by EGTA. Pyrophosphatase activity was measured under different conditions of Mg2+ and Ca2+ concentrations at pH 7.2. The rate of inhibition depended on the concentration of CaPPi, and the approximate Ki for CaPPi was 17 microM. A high concentration of free Ca2+ did not inhibit the enzyme at a low concentration of CaPPi. It appears that for Ca2+, at least, the inhibitory form is the Ca2(+)-PPi complex. Cd2+, Co2+ and Cu2+ also inhibited the enzyme. The antibody against the vacuolar pyrophosphatase did not react with rat liver mitochondrial or yeast cytosolic pyrophosphatases. Also, the antibody to the yeast enzyme did not react with the vacuolar enzyme. Thus, the catalytic properties of the vacuolar pyrophosphatase, such as Mg2+ requirement and sensitivity to Ca2+, are common to the other pyrophosphatases, but the vacuolar enzyme differs from them in subunit mass and immunoreactivity.     

Functionally important lysine residues in inorganic pyrophosphatase from E. coli. I. Interaction of inorganic pyrophosphatase with pyridoxal-5'-phosphate

Interaction of inorganic pyrophosphatase from E. coli with pyridoxal-5'-phosphate includes binding of the reagent at the active site through the phosphate group and then a reversible modification of one lysine residue in each of the enzyme's subunit. In the equilibrium state the protein's molecules contain both inactive modified and native subunits. A stable secondary amine is formed upon the sodium borohydride reduction of the modified protein.     

Kinetic studies of Escherichia coli AlkB using a new fluorescence-based assay for DNA demethylation

The Escherichia coli AlkB protein catalyzes the direct reversal of alkylation damage to DNA; primarily 1-methyladenine (1mA) and 3-methylcytosine (3mC) lesions created by endogenous or environmental alkylating agents. AlkB is a member of the non-heme iron (II) α-ketoglutarate-dependent dioxygenase superfamily, which removes the alkyl group through oxidation eliminating a methyl group as formaldehyde. We have developed a fluorescence-based assay for the dealkylation activity of this family of enzymes. It uses formaldehyde dehydrogenase to convert formaldehyde to formic acid and monitors the creation of an NADH analog using fluorescence. This assay is a great improvement over the existing assays for DNA demethylation in that it is continuous, rapid and does not require radioactively labeled material. It may also be used to study other demethylation reactions including demethylation of histones. We used it to determine the kinetic constants for AlkB and found them to be somewhat different than previously reported values. The results show that AlkB demethylates 1mA and 3mC with comparable efficiencies and has only a modest preference for a single-stranded DNA substrate over its double-stranded DNA counterpart.     

Fluoride inhibition of inorganic pyrophosphatase. IV. Evidence for metal participation in the active center and a four-site model of metal effect on catalysis.

Atomic spectroscopy of native yeast inorganic pyrophosphatase (pyrophosphate phosphohydrolase, EC 3.6.1.1) after gel filtration showed that it only binds activating Mg2% in an easily dissociable manner. Formation of a covalent intermediate between the enzyme and an entire substrate molecular in the presence of fluoride, however, dramatically strengthened the binding of two Mg2+ per subunit and eliminated at neutral pH the effect of added metals on protein fluorescence but not on the absorption spectrum, suggesting that different mental binding sites influence the two spectra. This conclusion was confirmed by spectra studied on native enzyme. A third, low-affinity site for Mg2+ was found on the enzyme pH greater than 8. A model of enzyme-substrate-metal interactions was proposed, according to which the fluorescence-controlling site belongs to the active center and substrate can only be bound to it as a 1 : 1 complex with metals.     

Kinetic studies of 18O exchange from inorganic phosphate catalyzed by Mg2+-activated unadenylylated glutamine synthetase (E. coli w).

Oxygen-18 exchange out of [¹⁸O]Pi catalyzed by Mg²⁺-activated unadenylated glutamine synthetase from $\text{E.}$$\text{coli}$ was followed by ³¹P-NMR in the presence of the other substrates, ADP and L-glutamine. The pattern of the ${}^{16}\text{O}{}^{18}\text{O}$ in the species P¹⁸O₄, P¹⁸O₃¹⁶O₁, P¹⁸O₂¹⁶O₂, P¹⁸O₁¹⁶O₃, P¹⁶O₄ during the exchange followed a binomial distribution consistent with indiscriminate removal of any of the four oxygens of P_i. The rate constant for ${}^{16}\text{O}{}^{18}\text{O}$ exchange was 410±40 min^?1 while the rate constant for net reaction (ATP formation) was 62±4 min^?1. Thus exchange proceeds ～7 times faster than net reaction, a finding in accord with that of Stokes and Boyer ($\text{J.}$$\text{Biol.}$$\text{Chem.}$ (1976) $\text{251}$, 5558) for the Mn²⁺-activated adenylylated glutamine synthetase. A model for the overall catalytic events first derived from rapid kinetic fluorescence experiments (Rhee and Chock, Proc. Natl. Acad. Sci. USA, (1976) $\text{73}$, 476) was successfully used to fit the oxygen exchange data in this paper.