Sequence specificity of isolated DNA-adenine methylases from Mycobacterium smegmatis (butyricum) and Shigella sonnei 47 cells

A set of four individual DNA-adenine methylases differing in pI (isoelectric point) values (MMbu4.2, MMbu6.4, MMbu7.3, and MMbu8.7), and a sole methylating enzyme with the same base specificity (MSso9.5) are present in M. smegmatis (butyricum) and Sh. sonnei 47 cells, respectively. The sequence specificity of each of those was studied 'in vitro' by a combined approach that comprised isostich (purine tract) analysis and identification of the immediate neighbourhood of the methylated base within the sequence methylated. The MSso9.5 recognition site has been established as the hexanucleotide 'palindromic' 5'-G-A-A-T-T-C-3' sequence which is structurally similar to the analogous MEco RI recognition site. However, in contrast to MEco RI, MSso9.5 methylates the 5'-end adenine residue in the sequence and thus it appears to be an isometimer of MEco RI. By means of the same approach, the partial nucleotide sequences methylated by each of the four individual M. butyricum enzymes were determined. MMbu7.3 and MMbu8.7 exhibit the identical sequence specificity upon methylation of the degenerative trinucleotide 5'-Py-A-Py-3' sequence and thus these enzymes are assumed to represent the different molecular forms of the methylase. MMbu4.2 methylates the 5'-G-G-A-3' sequence and thus it is of a great value as the tool for negating effects of the RBam HI and RAva II-type restriction. MMbu6.4 is of a particular interest on account of its unique DNA methylation pattern which is distinguished in the pronounced clustering of purine bases in the 5'-Pu-Pu-Pu-Pu-Pu-3' sequence methylated.

Quantitative aspects of metal ion binding to certain transfer RNA anticodon loop modified nucleosides

Magnesium and manganese ions bind strongly to the unusual transfer RNA anticodon loop nucleotides, N-[(9-beta-D-ribofuranosyl-9H-purin-6-yl)carbamoyl]-L-threonine 5'-monophosphate (pt6A) and uridine-5-oxyacetic acid 5'-monophosphate (pV). Potentiometric measurements have shown that the delta G for metal ion-pt6A complex formation is 2-3-times more exothermic than for AMP. Electron-nuclear longitudinal dipolar relaxation data yielded manganese-ligand atom distances which permit a three-dimensional construct of the complex in which metal is coordinated to the phosphate, carboxylate of the threonine side-chain (with the nucleotide in the anti glycosidic conformation) and N7 of the adenine ring. Similarly, manganese binds strongly to pV, involving phosphate and carboxylate functions. It is possible that a facet of the functional role of these unusual residues is to chelate magnesium ions and in so doing permit optimum anticodon loop conformational stability and stability of tRNA-mRNA-ribosome complexes.

Investigation of enzyme-substrate complexes by affinity chromatography. Application to pig heart citrate synthase

The relative affinities of Sepharose gels, to which coenzyme A (CoA-SH) and CoA-SH analogues were bound through a well defined site, for citrate synthase were determined. The relative eluting power of coenzyme derivatives for the CoA-SH-gel and the Matrex Gel Blue-bound enzyme was measured, and the influence of oxaloacetate on the binding of the enzyme investigated. From the results, the contributions of different parts of the coenzyme to its binding in the active site and kinetic concepts are derived and found to be in complete agreement with corresponding data for citrate synthase obtained from kinetic measurements reported in the literature. It is demonstrated for some other CoA-SH-specific enzymes that affinity chromatography is of value as an additional tool for the comparative investigation of binding sites of enzymes which depend on the same coenzyme.

Studies on the dynamic syn-anti equilibrium in purine nucleosides and nucleotides with the aid of 1H and 13C NMR spectroscopy

Analyses of 1H and 13C NMR spectra have been utilized to extend studies on the dynamic equilibrium syn-anti about the glycosidic bond of purine nucleosides and nucleotides. With the aid of chemically synthesized model analogous in fixed syn and anti conformations, and the introduction of appropriate corrections for the conformation of the exocyclic chain of the sugar moiety, it is possible to evaluate quantitatively the relative populations of the syn and anti conformers from the experimentally observed chemical shifts of H(2') and C(2'). The resulting agreement between the data based on H(2') chemical shifts with those deduced from C(2') chemical shifts extends the validity of this procedure, and furnishes more accurate results than those previously based on uncorrected H(2') chemical shifts alone. The overall findings are briefly compared with those derived from measurements of proton relaxation times and the Overhauser effect, as well as by X-ray diffraction in the solid state. Attention is drawn to the potential utility of the results, including chemical shift data, in studies on interactions of nucleosides and nucleotides with appropriate enzyme systems.

Immobilization of xanthine oxidase to controlled pore-glass. Application to high-performance liquid chromatography

Immobilized xanthine oxidase (XO) was prepared by intermolecular cross-linking to controlled pore-glass using glutaraldehyde. The performance of enzyme reactors packed with the immobilized XO were considered theoretically and investigated experimentally. Using a post-column reactor packed with the immobilized XO, simultaneous determinations of hypoxanthine and xanthine by reversed-phase high-performance liquid chromatography were achieved.

Fluorescence quenching and spin label electron spin resonance studies of stacking self-association in aqueous solutions of 2-aminopurine riboside and its 5'-mono- and -diphosphate

The autoassociation of 2-aminopurine riboside (rn2Pur) and its 5'-mono- (P-rn2Pur) and 5'-diphosphate (PP-rn2Pur) in neutral aqueous solutions was investigated using fluorescence quenching and ESR spin-label methods within the range 276-358 K. Respective equilibrium constants and thermodynamic functions were derived therefrom assuming two models of infinite autoassociation: (i) an isodesmic one (K2 = K3 = ... Kp), and (ii) one in which K2 no equal to K2 = K4 ... Kp. Comparative analysis of these data and that of the parent 2-aminopurine, obtained previously, allowed us to formulate the following conclusions: (1) the mechanism of autoassociation of rn2Pur varies with temperature in such a way that a T = 318 K the isodesmic model is fulfilled (K2 = Kp); at high temperatures Kp/K2 greater than 1, i.e. the process is cooperative, while at lower temperatures it becomes anticooperative (Kp/K2 greater less than 1); (2) at 298 K the tendency to autoassociation decreases in the order; rn2Pur greater than P-rn2Pur greater than PP-rn2Pur; (3) rn2Pur forms highly packed complexes with the bases stacked and the ribofuranose residues interacting via hydrogen bonds or water bridges; (4) autoassociation of P-rn2Pur and PP-rn2Pur is mainly governed by stacking of the bases, while the ribose phosphate residues attain a trans configuration corresponding to the lowest electrostatic repulsion between charged phosphate groups; even at high ionic strength (I = 0.8), a positive electrostatic contribution to the free enthalpy of autoassociation is observed; (5) the two methods employed gave similar results for P-rn2Pur, but somewhat different ones for rn2Pur because the presence of the spin label (nitroxide stable radical) at the 2'(3')-OH group of the ribose residues prevents its interaction via hydrogen bonding with an unlabeled one of an adjacent nucleoside.

Reaction of bovine pancreatic ribonuclease A with 6-chloropurine riboside 5'-monophosphate. Nuclear magnetic resonance studies of the corresponding S-peptide

The n.m.r. spectra of native S-peptide and of S-peptide II, a derivative obtained after reaction of bovine pancreatic ribonuclease A with 6-chloropurine riboside 5'-monophosphate, both in D2O and in urea-d4, were obtained with a 270 MHz Fourier transform spectrometer. From these spectra it was possible to assign most of the proton resonances of the peptide and the position of the labelling group, the alpha-NH2 of Lys-1, was also deduced.

Complex formation of carnosine with purine nucleotides in aqueous solution

This 1H-NMR study provides experimental evidence for an intermolecular interaction between the dipeptide carnosine (beta-alanyl-L-histidine) and the purine nucleoside 5'-monophosphates 5'-AMP, 5'-GMP. From the observed upfield shifts of the purine nucleotide and imidazole proton resonances it is concluded that the interaction is of the stacking type and that it involves the purine base of the nucleotide and the histidine moiety of carnosine. Apparent microscopic equilibrium constants and complex shifts are obtained with a microscopic model which considers the formation of both 1:1 and 1:2 complexes. The stacking pattern for complex formation between the histidine moiety of carnosine and the adenine moiety of 5'-AMP is constructed by fitting the experimental 5'-AMP complex shifts to the calculated isoshielding contours for histidine.

NMR studies in the syn-anti dynamic equilibrium in purine nucleosides and nucleotides

The syn in equilibrium anti equilibrium conformation about the glycosidic bond of purine nucleosides and 5'-nucleotides in different solvent systems has been investigated by means of 1H NMR spectroscopy. Quantitative values for the conformer populations were improved, relative to previous results, by a detailed study of, and a resultant derived correction for, the influence of the sugar exocyclic group conformation on the chemical shifts of the sugar ring protons. This was achieved with the aid of nucleosides and nucleotides fixed in the conformations gauche-trans [derivatives of 8,5'-(R)-cyclo] and trans-gauche [derivatives of 8,5'-(S)-cyclo]. The results of 13C NMR confirmed those obtained by 1H NMR. The measured values of the vicinal coupling constants between H-1' and the C-8 and C-4 carbons were employed to evaluate approximately the glycosidic angles chi of the nucleosides in the conformations syn and anti. A critical examination is made of the applicability of relaxation methods, involving analysis of spin-lattice relaxation time of protons (T1) and the Overhauser effect, to determine the conformation of the base about the glycosidic bond; interpretations are provided for the lack of agreement between these methods and those based on chemical shifts in the present study. The foregoing resuls are also applied to an examination of the effect of the conformation of the base about the glycosidic bond on the enzymatic reactions catalyzed by 5'-nucleotidase and adenosine deaminase.

A DNase for apurinic/apyrimidinic sites associated with exonuclease III of Hemophilus influenzae

An endonuclease purified from Hemophilus influenzae made single strand breaks in DNA containing apurinic or apyrimidinic sites but had no detectable endonuclease activity on untreated native DNA. The new 5'-termini created at the cleavage sites were base-free deoxyribose 5-phosphate residues. The enzyme preparation also catalyzed the exonucleolytic release of 5'-mononucleotides from bihelical DNA and the hydrolysis of DNA 3'-terminal phosphomonoesters. The phosphatase-exonuclease activity was indistinguishable from that reported by Gunther and Goodgal (J. Biol. Chem. (1970) 245, 5341-5349) and resembled that of exonuclease III of Escherichia coli. The endonucleolytic and exonucleolytic activities could not be separated by electrophoresis, sedimentation, or gel filtration, and they were also affected simultaneously by mutation. The enzymatic activities appear to be functions of a single monomeric protein (M(r) = 30,000).

Acceptor specificity of ATP:nucleoside-5'-phosphate pyrophosphotransferase from Streptomyces adephospholyticus. Synthesis of the 3'-pyrophosphates of pyrimidine nucleotides, some oligoribonucleotides, 5'-diphosphonucleosidic coenzymes and mG-5'-ppp-5'-Am

ATP: nucleoside-5'-phosphate pyrophosphotransferase [EC 2.7.6.4] of Streptomyces adephospholyticus synthesizes not only 3'-pyrophosphates of 5'-purine ribomononucleotides but also those of pyrimidine mononucleotides, some short oligonucleotides, a variety of 5'-diphosphonucleosidic coenzymes and mG-5'-ppp-5'-Am.

Proton NMR and spin lattice relaxation study of nucleoside di- and triphosphates in neutral aqueous solutions

The average conformations of adenosine, inosine and guanosine di- and triphosphates in neutral aqueous solution have been investigated by 1H vicinal couplings, chemical shifts and T1 relaxation time measurements at 250 MHz. Comparison of chemical shifts with those of the corresponding nucleotide monophosphates suggests that the beta-phosphate group is in all cases oriented towards the base and close to H3'. The vicinal coupling constants indicate that the proportion of the S conformer of the ribose moiety is 55--60% and that the gauche-gauche rotamer of the CH2-OP exocyclic group is predominant. The preferential orientations of the base have been determined by minimization of the standard deviation about the mean of the molecular reorientation correlation times derived from the H8, H1', H2' and H3' relaxation times and computed interproton distances. The problem of the correlation between the syn-anti equilibrium and the N equilibrium S interconversion has been examined. Typical magnetization recovery curves after a 180 degree pulse have been simulated in the case of ATP, taking into account cross relaxation effects. It is shown that in most of the molecules under consideration the syn orientation of the base is predominant whereas for ATP the syn and anti are equivalent.

Human endonuclease specific for apurinic/apyrimidinic sites in DNA. Partial purification and characterization of multiple forms from placenta

Six chromatographically distinct forms of endonuclease active on apurinic and apyrimidinic sites in DNA have been purified away from DNA phosphatases, DNA N-glycosidases, and other DNases of human placenta. The forms seem to be monomeric proteins of 27,000 to 31,000 daltons, and although catalytically similar, they can be distinguished from one another on the basis of substrate Km and the effects of small molecules such as ATP. Analysis of enzymatic activity on a spectrum of damaged DNA substrates indicates that the enzyme forms probably act at an appreciable rate only adjacent to the phosphodiester bond of a deoxyribose lacking a base (purine or pyrimidine) in duplex DNA; such sites can be formed by treating the DNA with acid, alkylating agents, DNA N-glycosidases, and, probably, x-rays and OsO4. The incision is made so as to form a deoxyribose 5'-phosphate and a 3'-hydroxynucleotide.

Purine metabolic cycle in normal and leukemic leukocytes

Purine metabolism and reutilization pathways were studied as they applied to normal and leukemic leukocytes. The enzyme activities were expressed in terms of the quantity of protein extracted and per 10(10) cells. Whereas the protein extracted and the enzyme activities from normal lymphocytes were relatively constant, considerable variation was noted in cases of chronic lymphocytic leukemia (CLL). This variability in the properties of the leukemic cells suggests that the difference may be useful in the subclassification of the leukemias. The studies of the complete enzyme system were done with 300 million cells. The extraction of 350,000 normal lymphocytes/mul gave a soluble protein concentration of 1.46+/-0.16 mg protein per ml, and the yield from the same number of CLL lymphocytes varied between 0.72 and 8.32 mg protein per ml. The 5'-nucleotidase activity gave an inverse correlation with the amount of extractable protein. In individual cases of CLL, the protein concentrations and the 5'-nucleotidase activities were found on either side of the normal values. In most cases, the adenosine deaminase of CLL lymphocytic cell extracts was lower than normal, and the adenosine kinase was higher; in the CLL cells, these two enzymes gave a positive correlation with one another. Little or no difference was observed in the activities of the purine nucleoside phosphorylases in extracts of normal or leukemic lymphocytes and granulocytes. The hypoxanthine-guanine and adenine phosphoribosyltransferase activities increased in the leukemic granulocytes but almost always showed a decrease in the CLL lymphocytes when compared with the normal cells. Most of the leukemic cells had greater than normal activities of the enzymes synthesizing phosphoribosyl pyrophosphate when tested with the purines. The total nucleotide produced from adenine and guanine with adenine- and hypoxanthine-guanine phosphoribosyltransferase was about equal in normal and leukemic lymphocytes, but the proportion of the adenosine 5'-triphosphate in the product was much greater with the leukemic cells. This suggested that the ribosyltransferase activities were the same in both types of cells, but the nucleoside kinases and the nucleoside diphosphate kinases were more active in the leukemic cells. Inosine monophosphate dehydrogenase was less active than normal in the CLL cell extracts and was not directly related to the amount of inosine monophosphate generated from hypoxanthine.

[A general method for the determination of the conformation of nucleotides bound to an enzyme site. Interaction between glycogen phsophorylase b and nucleoside-5'-monophosphates]

The conformation of 5' nucleotides in the active site of glycogen phosphorylase b has been deduced from T2 relaxation time of protons H1, H8 and H2. It is shown by deuterium substitution of the purine ring in position 8 that the orientation of the base is anti in the case of strong activators like adenosine 5'-monophosphate, and syn in that of weak activators like inosine 5'-monophosphate.

Conformational properties of dinucleoside monophosphates in solution: dipurines and dipyrimidines

In order to obtain information about the conformational features in a polyribonucleotide at the nearest neighbor level, detailed nuclear magnetic resonance studies of the dinucleoside monophosphates ApA, ApG, GpA, UpU, CpC, UpC, and CpU were undertaken. Proton spectra were recorded at 100, 220, 270, or 300 MHz for D2O solutions, 0.01-0.03 M, pD 7.4 at 20+/-2 degrees C. Spectra of ApA, ApG, UpU, and UpC were also recorded in the temperature range of 70-90 degrees C. Unambiguous signal assignments of all proton resonances were made with the aid of selectively deuterated dimers. Complete, accurate sets of nuclear magnetic resonance (NMR) parameters were derived for each nucleotidyl unit by simulation-iteration methods. A complete set of chemical shift and coupling constant data was also obtained for all the constituent monomeric units at a concentration and ionization state comparable to that of the dimers. Conformational properties were evaluated quantitatively for most of the bonds in the dinucleoside monophosphates using procedures developed in earlier studies. All of the dimers have a flexible conformational framework in aqueous solution. While flexibility is allowed and alternate conformations are accessible, these molecules nevertheless attempt to achieve conformational identity by showing preferences--sometimes overwhelming preferences--for certain orientations. Thus the ribose rings exist as equilibrium mixtures of C2'-endo in equilibrium C3'-endo conformers with a bias for the C3'-endo pucker in most cases. The C4'-C5' bonds of both nucleotidyl units show significant preference (70-85%) for a gg conformation. Similarly, the dominant conformer (80-90%) about C5'-O5' is g'g'. Even though an unambiguous determination of the orientation about C3'-O3' cannot be made, there is suggestive evidence that the orientation of the 3' phosphate group is coupled to the ribose conformational equilibrium and it is likely that a 3Eg- in equilibrium 2Eg+ equilibrium exists with a bias for the 3Eg- coupled conformation in which the H3'-C3'-O3'-P dihedral angle is about 34-38 degrees. The individual nucleotidyl units in the dimers differ in several key ways from corresponding monomer conformations. Specifically, the ribose equilibrium C2'-endo in equilibrium C3'-endo shifts in favor of C3'-endo upon dimerization, the only exception being UpU. The C4'-C5' and C5'-O5' bonding network in the dimer forms a stable conformational unit and no correlation exists in the dimers between the conformational preference of this fragment and ribose conformer population. The temperature data for the dimers and dimerization data clearly indicate that the transition C2'-endo leads to C3'-endo is directly related to XCN changes brought about by dimerization and stacking...

Reactivity and selectivity in light-induced free radical reactions of 2-propanol with purine and pyrimidine mononucleotides and dinucleoside monophosphates

Photoalkylation reactions with 2-propanol, initiated with di-tert-butyl peroxide, of a variety of purine and pyrimidine mononucleotides and dinucleoside monophosphates lead to the substitution of an alpha-hydroxyisopropyl group for the H-8 atom of adenosine and the addition of the alcohol across the 5,6-double bond of the pyrimidines. Adenosine moieties blocked at their 3'-hydroxyl group are alkylated faster than those blocked at their 5'-hydroxyl. The reactivity of the uridine moieties of 3'-UMP, 5'-UMP, and uridylyl-(3',5')-uridine is not affected by the location of the phosphate group. However, the uridine moiety of uridylyl-(3',5')-adenosine is modified faster than that of adenylyl-(3',5')-uridine. It is suggested that steric hindrance imposed by the phosphate group determines the reactivity of adenosine moieties, while base stacking involving adenosine determines the reactivity of uridine moieties. These two effects play a major role in controlling the nature and degree of the selectivity of these photoalkylation reactions for either adenosine or uridine. Cytidine has been found to be inert in these reactions.

Occurrence of pppApp-synthesizing activity in actinomycetes and isolation of purine nucleotide pyrophosphotransferase

The occurrence of adenosine 5'-triphosphate-3'diphosphate-synthesizing activity was detected in five strains of actinomycetes; Streptomyces morookaensis, Streptomyces aspergilloides, Streptomyces hachijoensis, tactinomyces violascens and Streptoverticillium septatum, out of 825 strains of actinomycetes, bacteria, fungi and fungi imperficti. Purine nucleotide pyrophosphotransferase were extracellularly excreted associating with the cell growth, and were purified partially or to apparent homogeneiety from the culture filtrate. The enzymes are a monomeric protein with molecular weight of 18,000-26,000 and synthesize adenosine, guanosine and inosine 5'-phosphate (mono, di or tri)-3'-diphosphate such as pApp, ppA pp, pppApp, pGpp, ppGpp, pppGpp, and pppIpp by transferring a pyrophosphoryl group from the 5'-position of ATP, dATP and ppApp to the 3'-position of purine nucleotides in the presence of a divalent cation and in alkaline state.