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PubMed1989

pH dependence of the kinetic parameters for the pyrophosphate-dependent phosphofructokinase reaction supports a proton-shuttle mechanism.

The pH dependence of kinetic parameters for the pyrophosphate-dependent phosphofructokinase from Propionibacterium freudenreichii suggests that the enzyme catalyzes its reaction via general acid-base catalysis with the use of a proton shuttle. The base is required unprotonated in both reaction directions. In the direction of fructose 6-phosphate phosphorylation the base accepts a proton from the hydroxyl at C-1 of F6P and then donates it to protonate the leaving phosphate. Whether this occurs in one or two steps cannot be deduced from the present data. The maximum velocity of the reaction is pH independent in both reaction directions while V/K profiles exhibit pKs for binding groups (including enzyme and reactant functional groups) as well as pKs for enzyme catalytic groups. These data suggest that reactants bind only when correctly protonated and only to the correctly protonated form of the enzyme. Specifically, the requirement for two enzyme epsilon-amino groups in the protonated form for reactant binding was detected as was the requirement for the ionized phosphates of fructose 6-phosphate, fructose 1,6-bisphosphate, MgPPi and HPO4(2-). The protonation state of enzyme and reactant binding groups is in agreement with data obtained previously [Cho, Y.-K., & Cook, P. F. (1988) J. Biol. Chem. 263, 5135].

Binding Sites↗
PubMed1989

Synthesis and properties of azidonitrophenyl pyrophosphate, a photoaffinity probe of the nucleotide binding sites of mitochondrial F1-ATPase.

4-Azido-2-nitrophenyl pyrophosphate (azido-PPi) labeled with 32P in the alpha position was prepared and used to photolabel beef heart mitochondrial F1. Azido-PPi was hydrolyzed by yeast inorganic pyrophosphatase, but not by mitochondrial F1-ATPase. Incubation of F1 with [alpha-32P]azido-PPi in the dark under conditions of saturation resulted in the binding of the photoprobe to three sites, two of which exhibited a high affinity (Kd = 2 microM), the third one having a lower affinity (Kd = 300 microM). Mg2+ was required for binding. As with PPi [Issartel et al. (1987) J. Biol. Chem. 262, 13538-13544], the binding of 3 mol of azido-PPi/mol of F1 resulted in the release of one tightly bound nucleotide. ADP, AMP-PNP, and PPi competed with azido-PPi for binding to F1, but Pi and the phosphate analogue azidonitrophenyl phosphate did not. The binding of [32P]Pi to F1 was enhanced at low concentrations of azido-PPi, as it was in the presence of low concentrations of PPi. Sulfite, which is thought to bind to an anion-binding site on F1, inhibited competitively the binding of both ADP and azido-PPi, suggesting that the postulated anion-binding site of F1 is related to the exchangeable nucleotide-binding sites. Upon photoirradiation of F1 in the presence of [alpha-32P]azido-PPi, the photoprobe became covalently bound with concomitant inactivation of F1. The plots relating the inactivation of F1 to the covalent binding of the probe were rectilinear up to 50% inactivation.(ABSTRACT TRUNCATED AT 250 WORDS)

Adenosine Diphosphate↗
PubMed1990

Guanylate cyclase from bovine rod outer segments: solubilization, partial purification, and regulation by inorganic pyrophosphate.

In spite of its pivotal role in visual transduction, very little is known about guanylate cyclase of retinal photoreceptor cells. The enzyme has not yet been purified principally because of the difficulty in solubilizing it. We report here a simple method for solubilization of 67% of the cyclase activity from the retinal rod disk membranes (RDM). With Nonidet P-40 as detergent, the solubilization of cyclase is favored by a high concentration of KCl and exclusion of manganese. The solubilized and the residual insoluble enzymes are both highly unstable but could be partially stabilized by dithiothreitol. They were both insensitive to calcium, calmodulin, and atrial natriuretic factor. They also responded similarly to varying the manganese concentration in the assay. For the activity in both fractions, the Km for GTP was about 230 microM, Line-weaver-Burk plots showed that substrate binding was cooperative, and Hill plots suggested that there are two substrate binding sites. Cumulatively, these observations showed that while the entire activity could not be solubilized, the solubilized and the residual insoluble activities probably belonged to the same enzyme. Partial purification resolved the solubilized enzyme into two activities refered to as enzymes 1 and 2. Both had substrate saturation kinetics similar to the solubilized enzyme and were inhibited competitively by inorganic pyrophosphate, one of the products of the cyclase reaction. The Ki for PPi for enzyme 1 was 70-100 microM and 150-200 microM for enzyme 2. cGMP at concentrations up to 800 microM had no influence on the activity of either enzyme.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗
PubMed1980

Biochemistry of terminal deoxynucleotidyltransferase: identification, characterization, requirements, and active-site involvement in the catalysis of associated pyrophosphate exchange and pyrophosphorolytic activity.

Terminal deoxynucleotidyltransferase (TdT) has been found to catalyze both pyrophosphate exchange and pyrophosphorolysis reactions. Both reactions are strongly inhibited by antiserum to TdT. The reactions require the presence of a divalent cation, a single- or double-stranded oligomeric or polymeric DNA or RNA, and deoxyribonucleoside triphosphates (for PPi exchange only). Of the three divalent cations tested, Mg2+ and Co2+ are equally effective, while Mn2+ neither is used for catalysis nor inhibits the Mg2+-catalyzed reactions. Ribonucleoside triphosphates have been found to support the PPi exchange reaction to a minor extent and have no inhibitory effect on the catalysis mediated by dNTPs. Inhibition studies, using SH group inhibitors, Zn chelator, and a substrate binding site specific reagent, revealed that PPi exchange and pyrophosphorolysis reactions may be distinguished by differences in their sensitivity to inhibition by various reagents. While the PPi exchange reaction is strongly inhibited by sulfhydryl reagents, o-phenanthroline, and pyridoxal phosphate, the pyrophosphorolysis reaction is insensitive to these reagents. In addition, the pyrophosphorolysis reaction is also found not to require a free 3'-OH terminus of a primer. This difference in the susceptibility of the two reactions indicates that discrete active-site structures exist in TdT which catalyze PPi exchange and pyrophosphorolysis reactions.

Binding Sites↗
PubMed1979

Mechanistic studies on deoxyribonucleic acid dependent ribonucleic acid polymerase from Escherichia coli using phosphorothioate analogues. 1. Initiation and pyrophosphate exchange reactions.

The diastereomers of adenosine 5'-O-(1-thiotriphosphate) (ATP alpha S) and adenosine 5'-O-(2-thiotriphosphate) (ATP beta S) can replace adenosine triphosphate (ATP) in the initiation reaction catalyzed by deoxyribonucleic acid (DNA) dependent ribonucleic acid (RNA) polymerase from Escherichia coli. In both cases, the Sp diastereomer is a better initiator than the Rp isomer. The diasteromers of 3'-uridyl 5'-adenosyl ,O-phosphorothioate [Up(S)A] can replace UpA in the primed initiation reaction catalyzed by RNA polymerase; however, the Rp diastereomer is a better initiator than the Sp isomer. By using ATP or CpA as initiator and UTP alpha S, isomer A, as substrate, we determined the stereochemical courses of both the initiation and primed initiation reactions, respectively, with T7 DNA template and found them to proceed with inversion of configuration. Determination of the stereochemical course of the pyrophosphate exchange reaction catalyzed by RNA polymerase provides evidence that this reaction is the reverse of the phosphodiester bond-forming reaction.

DNA-Directed RNA Polymerases↗
PubMed1979

p-(Bromoacetamido)phenyl uridyl pyrophosphate: an active-site-directed irreversible inhibitor for uridine diphosphate galactose 4-epimerase.

The synthesis of p-(bromoacetamido)phenyl uridyl pyrophosphate (BUP) is described. This compound is an active-site-directed irreversible inhibitor of Escherichia coli UDP-galactose 4-epimerase. The inactivation follows pseudo-first-order kinetics at pH 8.5 in nonnucleophilic buffers, and a saturation effect is seen in the pseudo-first-order rate constant as the concentration of BUP is increased. The half-saturation parameter for BUP in the inactivation is 0.21 +/- 0.02 mM, which compares favorably with the inhibition constant of 0.3 +/- 0.05 mM for BUP acting as a competitive reversible inhibitor of the enzyme. The inactivation rate is slow, however, with a minimum half-time of 12 h at pH 8.5 and 27 degrees C. Both specific alkylation and nonspecific alkylation by BUP occur, but nonspecific alkylation is faster than the inactivation and the rate of inactivation correlates well with the rate of covalent incorporation of one molecule of [14C]BUP at the active site.

Binding Sites↗
PubMed1979

Uridine diphosphate galactose 4-epimerase. Alkylation of enzyme-bound diphosphopyridine nucleotide by p-(bromoacetamido)phenyl uridyl pyrophosphate, an active-site-directed irreversible inhibitor.

When UDP-galactose 4-epimerase is inactivated by p-(bromoacetamido)phenyl uridyl pyrophosphate (BUP), the diphosphopyridine nucleotide (DPN) associated with this enzyme as a tightly bound coenzyme cannot be reduced by substrates or by UMP-activated reduction by glucose. Upon acid denaturation of the inactivated enzyme, the DPN released corresponded to 15-30% of that released from the native enzyme. When the enzyme is inactivated by [14C]BUP, about 80% of the radioactivity bound at the active site is released from the protein upon acid denaturation. When epimerase-[3H]DPN is inactivated with [14C]BUP, the 3H and 14C released from the protein upon denaturation of the complex cochromatograph on DEAE-Sephadex. Experiments with [nicotinamide-4-3H]DPN and [adenine-2,8-3H]DPN show that it is the adenine ring that is alkylated. The data suggest that the adenine ring of DPN in epimerase-DPN may be oriented near the glycosyl-binding subsite of this enzyme. Since the nicotinamide ring must also be near this site, it appears that the DPN may not be in an extended conformation when it is bound at the active site of UDP-galactose 4-epimerase from Escherichia coli.

Alkylation↗
PubMed1976

Uridine 5'-(5-thio-alpha-D-glucopyranosyl pyrophosphate): chemical synthesis and activation of rat liver glycogen synthetase.

Uridine 5'-(5-thio-alpha-D-glucopyranosyl pyrophosphate), UDPTG, appears to be a potent activator of rat liver glycogen synthetase a even though it is not a substrate. At 1.0 mM, UDPTG causes over 400% activation of glycogen synthetase a activity. Activation by UDPTG is accompanied by normalization of the otherwise sigmoidal kinetics for UDPG with glycogen synthetase a and a decrease in the apparent Km for UDPG from approximately 2.0 to 0.62 mM. UDPTG inhibits catalytic activity at higher concentrations. At the concentrations examined, UDPTG has no effect on glycogen synthetase b activity. The use of glycogen synthetase free from glycogen synthetase b phosphatase and the selective inhibition of glycogen synthetase b phosphatase by 100 mM NaF-indicate that conversion of synthetase b to a is not responsible for the activation. Moreover, the use of the colorimetric assay for glycogen synthetase activity precludes effects of UDPTG on glycogen phosphorylase activity. UDPTG, chemically synthesized in 60% yield, is characterized by chromatographic and electrophoretic procedures, by its uv spectra, and by analysis of products after chemical and enzymatic hydrolysis.

Animals↗
PubMed2003

Temperature dependence of the backbone dynamics of ribonuclease A in the ground state and bound to the inhibitor 5'-phosphothymidine (3'-5')pyrophosphate adenosine 3'-phosphate.

The interaction of the dinucleotide inhibitor 5'-phosphothymidine(3',5')pyrophosphate adenosine 3'-phosphate (pTppAp) with bovine pancreatic ribonuclease A (RNase A) was characterized by calorimetry and solution NMR spectroscopy. Calorimetric data show that binding of pTppAp to RNase A is exothermic (DeltaH = -60.1 +/- 4.1 kJ/mol) with a dissociation constant of 16 nM at 298 K. At this temperature, the binding results in an entropy loss (TDeltaS = -16.8 +/- 7.3 kJ/mol) that is more favorable than that with the product analogue, 2'-CMP (TDeltaS = -31.3 +/- 0.9 kJ/mol). Temperature-dependent calorimetric experiments give a DeltaC(p) for ligand binding of -230 +/- 100 J/mol K. Binding of pTppAp results in noticeable effects on the backbone amide chemical shifts and dynamics. Amide backbone (15)N NMR spin-relaxation studies were performed on both apo RNase A and RNase A/pTppAp as a function of temperature. At each temperature, the model-free-determined order parameters, S(2), were significantly higher for RNase A/pTppAp than for the apo enzyme indicating a decrease in the conformational entropy of the protein upon ligand binding. Furthermore, the magnitude of this difference varies along the amino acid sequence specifically locating the entropic changes. The temperature dependence of S(2) at each residue enabled assessment of the local heat capacity changes (DeltaC(p)) from ligand binding. In an overall, average sense, DeltaC(p) for the protein backbone, determined from the NMR dynamics measurements, did not differ between apo RNase A and RNase A/pTppAp indicating that backbone dynamics contribute little to DeltaC(p) for protein-ligand interactions in this system. However, residue-by-residue comparison of the temperature-dependent change in entropy (DeltaS(B)) between free and bound forms reveals nonzero contributions to DeltaC(p) at individual sites. The balance of positive and negative changes reveals a redistribution of energetics upon binding. Furthermore, experiment and semiempirical estimates suggest that a large negative DeltaC(p) should accompany binding of pTppAp, and we conclude that this contribution must arise from factors other than amide backbone dynamics.

Adenosine Monophosphate↗
PubMed2003

Biosynthesis of the thiazole moiety of thiamin pyrophosphate (vitamin B1).

While most of the proteins required for the biosynthesis of thiamin pyrophosphate have been known for more than a decade, the reconstitution of this biosynthesis in a defined biochemical system has been difficult due to the novelty of the chemistry involved. Here we demonstrate the first successful enzymatic synthesis of the thiazole moiety of thiamin from glycine, cysteine, and deoxy-D-xylulose-5-phosphate using overexpressed Bacillus subtilis ThiF, ThiS, ThiO, ThiG, and a NifS-like protein. This has facilitated the identification of the biochemical function of each of the proteins involved: ThiF catalyzes the adenylation of ThiS; NifS catalyzes the transfer of sulfur from cysteine to the acyl adenylate of ThiS; ThiO catalyzes the oxidation of glycine to the corresponding imine; and ThiG catalyzes the formation of the thiazole phosphate ring. The complex oxidative cyclization reaction involved in the biosynthesis of the thiamin thiazole has been greatly simplified by replacing ThiF, ThiS, ThiO, and NifS with defined biosynthetic intermediates in a reaction where ThiG is the only required enzyme.

Bacillus subtilis↗
PubMed1997

Chemical cross-linking of the human immunodeficiency virus type 1 Tat protein to synthetic models of the RNA recognition sequence TAR containing site-specific trisubstituted pyrophosphate analogues.

A chemical ligation procedure has been developed for the synthesis of oligoribonucleotides carrying a trisubstituted pyrophosphate (tsp) linkage in place of a single phosphodiester. Good yields of tsp were obtained when a single 2'-deoxynucleoside 5' to the tsp was used in the ligation reaction. A tsp linkage was found to be reasonably stable to hydrolysis but cleaved by treatment with ethylenediamine or lysine to give phosphoamidate adducts. A model human immunodeficiency virus type 1 (HIV-1) TAR RNA duplex containing an activated tsp was able to bind to HIV-1 Tat protein with only 3-fold reduced affinity and to a Tat peptide (residues 37-72) with identical affinity compared to that of an unmodified duplex. Tsps incorporated at sites previously identified as being in close proximity to Tat protein were able to cross-link to Tat peptide (37-72) to form a covalent phosphoamidate conjugate. Endopeptidase cleavage followed by MALDI-TOF (matrix-assisted laser desorption ionization time of flight) mass spectrometric analysis provided strong evidence that a TAR duplex containing a tsp replacing the phosphate at 38-39 had reacted specifically with Lys51 in the basic region of Tat peptide (37-72). The new chemical cross-linking method may be generally useful for identifying lysines in close proximity to phosphates in basic RNA-binding domains of proteins.

Amino Acid Sequence↗
PubMed1998

Identification and purification of diphosphoinositol pentakisphosphate kinase, which synthesizes the inositol pyrophosphate bis(diphospho)inositol tetrakisphosphate.

Diphosphoinositol pentakisphosphate (PP-IP5) and bis(diphospho)inositol tetrakisphosphate (bis-PP-IP4) were recently identified as inositol phosphates which possess pyrophosphate bonds. The molecular mechanisms that regulate the cellular levels of these compounds are not yet characterized. To pursue this question, we have previously purified an inositol hexakisphosphate (IP6) kinase from rat brain supernatants [Voglmaier, S. M., et al. (1996) Proc. Natl. Acad. Sci. U.S.A. 93, 4305-4310]. We now report the identification and purification of another novel kinase, diphosphoinositol pentakisphosphate (PP-IP5) kinase, which uses PP-IP5 as a substrate to form bis(diphospho)inositol tetrakisphosphate (bis-PP-IP4) in soluble fractions of rat forebrain. The purified protein, a monomer of 56 kDa, displays high affinity (Km = 0.7 microM) and selectivity for PP-IP5 as a substrate. The purified enzyme also can transfer a phosphate from bis-PP-IP4 to ADP to form ATP. This ATP synthase activity is an indication of the high phosphoryl group transfer potential of bis-PP-IP4 and may represent a physiological role for PP-IP5 and bis-PP-IP4.

Animals↗
PubMed1999

Mutagenesis of the phosphatase sequence motif in diacylglycerol pyrophosphate phosphatase from Saccharomyces cerevisiae.

Diacylglycerol pyrophosphate (DGPP) phosphatase, encoded by the DPP1 gene, is a membrane-associated enzyme in the yeast Saccharomyces cerevisiae. The enzyme removes the beta phosphate from DGPP to form phosphatidate. The substrate and product of the DGPP phosphatase reaction play roles in lipid signaling and in cell metabolism. The deduced primary structure of the DGPP phosphatase protein contains a three-domain phosphatase sequence motif. In this work, we examined the hypothesis that the phosphatase sequence motif in the enzyme is involved in the DGPP phosphatase reaction. The amino acid residues Arg(125), His(169), and His(223) in domains 1, 2, and 3, respectively, of the phosphatase sequence motif were changed to alanine residues by site-directed mutagenesis. The mutant DPP1(R125A), DPP1(H169A), and DPP1(H223A) alleles were cloned into a yeast shuttle vector and then expressed in a dpp1Delta lpp1Delta double mutant that lacks DGPP phosphatase activity. Northern blot and immunoblot analyses showed that the mutations in the phosphatase sequence motif did not affect the expression of the enzyme. The DGPP phosphatase activities of the R125A, the H169A, and the H223A mutant enzymes were 0.05, 9, and 0.03%, respectively, of the DGPP phosphatase activity of the wild-type enzyme. Enzymes with mutations in more than one domain of the phosphatase sequence motif had no measurable DGPP phosphatase activity. The R125A and H233A mutant DGPP phosphatase enzymes had reduced V(max) and elevated K(m) values for DGPP when compared with the wild-type enzyme. The H169A mutant enzyme had reduced V(max) and K(m) values when compared with the control. The specificity constants (V(max)/K(m)()) for DGPP of the R125A mutant and H233A mutant enzymes were 4610-fold and 15 367-fold lower, respectively, when compared to the wild-type enzyme. The studies reported here indicated that the phosphatase sequence motif played an important role in the reaction catalyzed by the S. cerevisiae DGPP phosphatase.

Amino Acid Motifs↗
PubMedDate not supplied

Analysis of the spin exchange interactions in the three phases of vanadium pyrophosphate, (VO)2P2O7, in terms of spin-orbital interaction energy.

The spin exchange interactions in the ambient-pressure orthorhombic (APO), high-pressure orthorhombic (HPO), and ambient-pressure monoclinic (APM) phases of the vanadium pyrophosphate, (VO)2P2O7, were analyzed by calculating the spin-orbital interaction energies delta e-delta e0 of their spin dimers. The anisotropy of the spin exchange interactions in the HPO phase is well explained by the delta e-delta e0 values. For the APO phase, the reported crystal structure does not provide accurate enough delta e-delta e0 values to conclude unambiguously which of the V1-V2 and V3-V4 chains has a larger spin gap and which of the bridged and edge-sharing spin dimers has a stronger spin exchange interaction in the V1-V2 and V3-V4 chains. The APM phase is predicted to exhibit essentially two spin gaps, with a large spin gap for the V8-V5-V7-V6 chain and a very small one for the V4-V2-V3-V1 chain.

Journal Article↗
PubMed2002

Flux growth of vanadyl pyrophosphate, (VO)(2)P(2)O(7), and spin dimer analysis of the spin exchange interactions of (VO)(2)P(2)O(7) and vanadyl hydrogen phosphate, VO(HPO(4)).0.5H(2)O.

Large transparent blue crystals of vanadyl pyrophosphate, (VO)(2)P(2)O(7), were grown from a phosphorus pentoxide flux, and the single-crystal X-ray structure of (VO)(2)P(2)O(7) was determined with high precision. On the basis of spin dimer analysis, we examined the spin exchange interactions of (VO)(2)P(2)O(7) and its precursor VO(HPO(4)).0.5H(2)O. Our analysis of (VO)(2)P(2)O(7) using two high-precision crystal structures shows unambiguously that the V3-V4 chain has a larger spin gap than does the V1-V2 chain and that the super-superexchange (V-O...O-V) interaction is stronger than the superexchange (V-O-V) interaction in the V3-V4 chain while the opposite is true in the V1-V2 chain. Our analysis of VO(HPO(4)).0.5H(2)O reveals that the superexchange interaction must dominate over the super-superexchange interaction, in disagreement with the conclusion from a powder neutron scattering study of VO(DPO(4)).0.5D(2)O.

Journal Article↗
PubMed1996

Copper(II) Complexes of the Hexaaza Macrocyclic Ligand 3,6,9,16,19,22-Hexaaza-27,28-dioxatricyclo[22.2.1.1(11,14)]octacosa-1(26),11,13,24-tetraene and Their Interaction with Oxalate, Malonate, and Pyrophosphate Anions.

The hexaaza macrocyclic ligand 3,6,9,16,19,22-hexaaza-27,28-dioxatricyclo[22.2.1.1(11,14)]octacosa-1(26),11,13,24-tetraene (BFBD), forms both mono- and dinuclear complexes, as well as several protonated and hydroxo chelates, with Cu(II) ions. These cationic species can bind inorganic and organic anions through coordination and hydrogen bonding. Stability constants of the mono- and dinuclear Cu(II) complexes of BFBD and their interaction with oxalate, malonate, and pyrophosphate anions have been measured potentiometrically. The nature of the bonding between the hosts and the guests is discussed. The crystal structures of two new dinuclear Cu(II) complexes, determined by X-ray crystallography, are also reported. [BFBDCu(2)(Cl)(3)]ClO(4).0.5H(2)O crystallizes in the monoclinic system, space group P2(1)/n, with a = 13.267(2) Å, b = 12.155(6) Å, c = 18.461 0 Å, beta = 90.86(2) degrees, and Z = 4. Each Cu(II) ion is coordinated by three nitrogen atoms from the diethylenetriamine unit of the macrocyclic ligand and two chloride anions, forming a square pyramidal geometry. [BFBDCu(2)(Ox)](BF(4))(1.8)Cl(0.2) crystallizes in the triclinic system, space group P1, with a = 6.772(1) Å, b = 10.646(2) Å, c = 11.517(2) Å, alpha = 64.74(3) degrees, beta = 79.79(3) degrees, gamma = 81.94(3) degrees, and Z = 1. The environment of each copper is intermediate between square pyramidal and trigonal pyramidal. The oxalate anion bridges in a bis-bidentate fashion between two Cu(II) ions.

Journal Article↗
PubMed2002

Exchange interactions in the three phases of vanadyl pyrophosphate (VO)(2)P(2)O(7).

The magnetic exchange constants of vanadyl pyrophosphate (VO)(2)P(2)O(7) have been calculated on the basis of a combined DFT/broken symmetry approach. The three reported phases, ambient-pressure orthorhombic, ambient-pressure monoclinic, and high-pressure orthorhombic, have been explicitly considered. Calculations have been performed on four types of model clusters extracted from the crystal lattices. The singularity of each phase is clearly reflected through the number and values of exchange parameters. Our results show that the exchange interactions can be described in first approximation within the alternating antiferromagnetic chain model. The largest exchange coupling along the chain occurs through O-P-O bridges. The interchain interactions are much weaker and are of ferromagnetic nature.

Journal Article↗