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PubMed1995

Effect of hemimethylation and methylation of adenine on the structure and stability of model DNA duplexes.

Enzymatic methylation of adenine underlies a variety of biological regulatory mechanisms in Escherichia coli. We present here structural and thermodynamic characterization of a non-self-complementary DNA decamer duplex containing the dam sequence 5'-GATC in the unmethylated, hemimethylated (both forms), and methylated states. Differential scanning calorimetry measurements show that the free energies for adenine methylation of the decamer duplex are +1.1 and +2.0 kcal/mol for hemimethylation, respectively, and +3.3 kcal/mol for full methylation. In all cases, a large unfavorable enthalpy change is partially compensated by a favorable entropy term. CD spectroscopy indicates an overall conformational difference between the unmethylated decamer duplex and its methylated analogs. Reaction with diethyl pyrocarbonate (DEPC), a purine-specific probe sensitive to conformation, is enhanced in the vicinity of the methylation site of the duplex, consistent with loosening of base pairing at this site. Comparison of the scission patterns of these decamer duplexes by the reactive probes methidiumpropyl-EDTA.FeII [MPE.FeII] and CuI(o-phenanthroline)2 [(OP)2CuI] indicates that the methylation site of the decamer duplex represents a site of enhanced reactivity for these agents. On the basis of these thermodynamics and structural features, we suggest that the methylated base pair exists in two different helical states, which require local transient opening of the duplex for interconversion.

Adenine↗
PubMed1991

The Z-Z junction: the boundary between two out-of-phase Z-DNA regions.

The boundary between two segments of Z-DNA that differ in the phase of their syn-anti alternation about the glycosidic bond is termed a Z-Z junction. Using chemical probes and two-dimensional gel electrophoresis, we examined a Z-Z junction consisting of the sequence d[(CG)8C(CG)8] inserted into a plasmid and used energy minimization techniques to devise a three-dimensional model that is consistent with the available data. We show that both alternating CG segments undergo the B-Z transition together to form a Z-Z junction. The junction is very compact, displaying a distinctive reactivity signature at the two base pairs at the junction. In particular, the 5' cytosine of the CC dinucleotide at the junction is hyperreactive toward hydroxylamine, and the two guanines of the GG dinucleotide on the complementary strand are less reactive toward diethyl pyrocarbonate than are the surrounding Z-DNA guanines. Statistical mechanical treatment of the 2-D gel data yields a delta G for forming the Z-Z junction equal to 3.5 kcal, significantly less than the cost of a B-Z junction and approximately equal to the cost of a base out of alternation (i.e., a Z-DNA pyrimidine in the syn conformation). The computer-generated model shows little distortion of the Z helix outside of the central two base pairs, and the energy of the structure and the steric accessibility of the reactive groups are consistent with the data.

Base Sequence↗
PubMed1984

[Poly(A) RNA distribution and the polysome-monosome ratio in the lymphocytes of healthy persons and chronic lympholeukemia patients].

Intact polysomes from lymphocytes of donors and patients with chronic lymphocytic leukemia (CLL) were isolated using diethyl pyrocarbonate. It has been shown that only 3/4 of ribisomes are bound to polysomes of a comparatively small size. Poly(A) RNA of the postmitochondrial fraction is largely associated with polysomes. Cyclohexamide treatment results in recruitment of monosomes into polysomes and in a shift of ribosomes in larger polysomes. There are no differences in the polysome content and size, the effect of cyclohexamide treatment and the distribution of the polysomal and non-polysomal poly(A) RNA in normal and CLL lymphocytes. It is suggested that during the transition of resting lymphocytes into the growth state, when protein synthesis increases, the mobilization of mRNP and ribosomes into polysomes is not essential.

Cell Fractionation↗
PubMed1988

Selective inhibition of histidine-modified pancreatic alpha-amylase by proteinaceous inhibitor from Phaseolus vulgaris.

Chemical modification of two histidine residues of porcine pancreatic alpha-amylase (EC 3.2.1.1) by diethyl pyrocarbonate in the presence of a high concentration of maltotriose caused a decrease of amylase activity and an increase of maltosidase activity (hydrolysis of p-nitrophenyl-alpha-maltoside). By binding a proteinaceous inhibitor from Phaseolus vulgaris (white kidney bean) with the modified enzyme, the amylase activity was further decreased but the maltosidase activity was retained to about 100% that of the native enzyme. Both amylase and maltosidase activities of the native enzyme were almost completely inhibited by the proteinaceous inhibitor. The increase of maltosidase activity by histidine modification was due to an increase of kcat, whereas the Km value was not changed; but binding of the proteinous inhibitor affected mainly the Km value of the modified enzyme.

Animals↗
PubMed1992

Chemical modification of cysteinyl, lysyl and histidyl residues of mouse liver 17 beta-hydroxysteroid dehydrogenase.

Monomeric 17 beta-hydroxysteroid dehydrogenase from mouse liver was rapidly inactivated by 5,5'-dithiobis(2-nitrobenzoic acid) and 2,4,6-trinitrobenzene-1-sulfonate, and the absorption spectra of the inactivated enzymes indicated that cysteine and lysine residues were modified. The kinetics of inactivation and spectrophotometric quantification of the modified residues suggested that complete inactivation was caused by modification of two cysteine residues or one lysine residue per active site. The inactivation by the two reagents was protected by NADP+ and some coenzyme analogs, but not by a steroid substrate, testosterone. Moreover, chemical modification by diethyl pyrocarbonate also produced inactivation of the enzyme, and showed a difference spectrum with a peak at 242 nm characteristic of N-carbethoxyhistidine residues, which decreased with the addition of hydroxylamine. The inactivation by this reagent, following pseudo-first-order kinetics, was protected partially by either NADP+ or testosterone and completely in the presence of both the coenzyme and substrate. The results suggest the presence of essential cysteine and lysine residues at or near the coenzyme-binding site and that of essential histidine residue(s) in the catalytic region of the active site of mouse liver 17 beta-hydroxysteroid dehydrogenase.

17-Hydroxysteroid Dehydrogenases↗
PubMed1983

Structural analysis of RNA molecules involved in plasmid copy number control.

DNA replication of the plasmid ColE1 and its relatives is controlled mainly by a small plasmid-encoded transcript known as RNA11. We have studied the conformation of RNA1 molecules from two related but compatible plasmids, ColE1 and RSF1030, using T1 ribonuclease, S1 nuclease, cobra venom nuclease, and diethyl pyrocarbonate modification as probes for secondary structure. Both RNA1 molecules contain three double-stranded stems, three single-stranded loops, and an exposed 5' tail. All loops in both molecules show similar sensitivities to the probes used, as do stems 1 and 3. The region comprising stem 2 of each RNA1 molecule contains the most sequence differences as well as the most structural changes of any region in the two molecules. The structure of the RNA1 molecule encoded by a recessive high copy number mutant of ColE1 was also investigated. Structural alterations involving the first stem and loop of the molecule are proposed to be responsible for the inability of the mutant RNA1 to function in vivo.

Base Sequence↗
PubMed1989

On the role of histidine and tyrosine residues in E. coli asparaginase. Chemical modification and 1H-nuclear magnetic resonance studies.

The relative importance of tyrosine and histidine residues for the catalytic action of Escherichia coli asparaginase (L-asparagine amidohydrolase, EC 3.5.1.1) was studied by chemical modification and 1H-NMR spectroscopy. We show that, under appropriate reaction conditions, N-bromosuccinimide (NBS) as well as diazonium-1H-tetrazole (DHT) inactivate by selectively modifying two tyrosine residues per asparaginase subunit without affecting histidyl moieties. We further show that diethyl pyrocarbonate (DEP), a reagent considered specific for histidine, also modifies tyrosine residues in asparaginase. Thus, inactivation of the enzyme by DEP is not indicative of histidine residues being involved in catalysis. In 1H-nuclear magnetic resonance (NMR) spectra of asparaginase signals from all three histidine residues were identified. By measuring the pH dependencies of these resonances, pKa values of 7.0 and 5.8 were derived for two of the histidines. Titration with aspartate which tightly binds to the enzyme at low pH strongly reduced the signal amplitude of the pKa 7 histidyl moiety as well as those of resonances of one or more tyrosine residues. This suggests that tyrosine and histidine are indeed constituents of the active site.

Asparaginase↗
PubMed1990

Evidence for the importance of a carboxyl group in the binding of ligands to the D2 dopamine receptor.

A series of group specific modifying reagents were tested for their effects on [3H]spiperone binding to brain D2 dopamine receptors to identify amino acid residues at the binding site of the D2 dopamine receptor that are critical for ligand binding. The dependence of ligand binding to the receptor on the pH of the incubation medium was also examined. N-Acetylimidazole, 5,5'-dithiobis(2-nitrobenzoic acid), 1,2-cyclohexanedione, and acetic anhydride had no specific effect on [3H]spiperone binding, indicating the lack of participation of tyrosine, free sulphydryl, arginine, or primary amino groups in ligand binding to the receptor. N,N'-Dicyclohexylcarbodiimide (DCCD) potently reduced the number of [3H]spiperone binding sites, indicating that a carboxyl group is involved in ligand binding to the receptor. The effects of DCCD could be prevented by prior incubation of the receptor with D2 dopamine receptor selective compounds. The pH-binding profile for [3H]spiperone binding indicated the importance of an ionising group of pKa 5.2 for ligand binding which may be the same carboxyl group. Diethyl pyrocarbonate, the histidine modifying reagent, also inhibited [3H]spiperone binding, reducing the affinity of the receptor for this ligand but the effects were not at the ligand binding site. From the effects of pH changes on ligand binding some evidence was obtained for a second ionising group (pKa 7.0) that specifically affects the binding of substituted benzamide drugs to the receptor. It is concluded that the D2 dopamine receptor binding site contains separate but over-lapping binding regions for antagonists such as spiperone and substituted benzamide drugs. The former region contains an important carboxyl group; the latter region contains another group that may be a second carboxyl group or a histidine.

Acetic Anhydrides↗
PubMed1991

Differential effect of pH on thromboxane A2/prostaglandin H2 receptor agonist and antagonist binding in human platelets.

The effects of changes in pH on the binding of agonists and antagonists to the human platelet thromboxane A2/prostaglandin H2 (TXA2/PGH2) receptor were determined. Competition binding studies were performed with the TXA2/PGH2 mimetic [1S-1 alpha,2 beta (5Z), 3 alpha(1E,3R*),4 alpha)]-7-[3-(3-hydroxy-4'-iodophenoxy)-1-buteny) 7-oxabicyclo-[2.2.1]-heptan-2-yl]-5-heptenoic acid ([125I]BOP). The pH optimum for binding of [125I] BOP to washed human platelets was broad with a range of pH 4-6 in contrast to that of the TXA2/PGH2 receptor antagonist 9,11-dimethyl-methano-11,12-methano-16-(3-iodo-4-hydroxyl)-13-aza-15 alpha,beta-omega-tetranorthromboxane A2 ([125I]PTA-OH) which was 7.4. Scatchard analysis of [125I]BOP binding in washed platelets at pH 7.4, 6.0, and 5.0 revealed an increase in affinity (Kd = 1.16 +/- 0.06, 0.64 +/- 0.09, and 0.48 +/- 0.05 nM, respectively) and an increase in the number of receptors (Bmax = 2807 +/- 415, 5397 +/- 636, and 7265 +/- 753 sites/platelet, respectively). The potency of I-BOP to induce shape change in washed platelets at pH 6.0 was also significantly increased from an EC50 value of 0.34 +/- 0.016 nM at pH 7.4 to 0.174 +/- 0.014 nM at pH 6.0 (n = 6, p less than 0.05). In contrast, the EC50 value for thrombin was unaffected by the change in pH. In competition binding studies with [125I]BOP, the affinity of the agonists U46619 and ONO11113 were increased at pH 6.0 compared to 7.4. In contrast, the affinity of the TXA2/PGH2 receptor antagonists I-PTA-OH, SQ29548, and L657925 were either decreased or unchanged at pH 6.0 compared to 7.4. Diethyl pyrocarbonate and N-bromosuccinimide, reagents used to modify histidine residues, reversed the increase in affinity of [125I]BOP at pH 6.0 to values equivalent to those at pH 7.4. In solubilized platelet membranes, the effects of NBS were blocked by coincubation with the TXA2/PGH2 mimetic U46619. The results suggest that agonist and antagonist binding characteristics are different for the TXA2/PGH2 receptor and that histidine residue(s) may play an important role in the binding of TXA2/PGH2 ligands to the receptor.

15-Hydroxy-11 alpha,9 alpha-(epoxymethano)prosta-5↗
PubMed1988

Evidence of histidine phosphorylation in isocitrate lyase from Escherichia coli.

Escherichia coli isocitrate lyase (EC 4.1.3.1.) can be phosphorylated in vitro by an ATP-dependent reaction. The enzyme becomes phosphorylated by an endogenous kinase when partially purified sonic extracts are incubated with [gamma-32P]ATP. Treatment of isocitrate lyase with diethyl pyrocarbonate, a histidine-modifying reagent, blocked incorporation of [32P]phosphate from [gamma-32P]ATP. The isoelectric point of the enzyme was altered by treatment with phosphoramidate, a histidine phosphorylating agent, which suggests that isocitrate lyase can be phosphorylated at a histidine residue(s). Immunoprecipitated 32P-labeled isocitrate lyase was subjected to alkaline hydrolysis, mixed with chemically synthesized phosphohistidine standards, and analyzed by anion exchange chromatography. Characterization of the phosphoamino acid was based on the demonstration that the 32P-labeled product from alkali-hydrolyzed isocitrate lyase comigrated with synthetic 1-phosphohistidine. In addition, loss of catalytic activity after treatment with potato acid phosphatase indicates that catalytically active isocitrate lyase is the phosphorylated form of the enzyme.

Acid Phosphatase↗
PubMed1999

Evidence that histidine-163 is critical for catalytic activity, but not for substrate binding to Escherichia coli agmatinase.

Agmatinase (agmatine ureohydrolase, EC 3.5.3.11) from Escherichia coli was inactivated by diethyl pyrocarbonate (DEPC) and illumination in the presence of Rose bengal. Protection against photoinactivation was afforded by the product putrescine, and the dissociation constant of the enzyme-protector complex (12 mM) was essentially equal to the K(i) value for this compound acting as a competitive inhibitor of agmatine hydrolysis. Upon mutation of His163 by phenylalanine, the agmatinase activity was reduced to 3-5% of wild-type activity, without any change in K(m) for agmatine or K(i) for putrescine inhibition. The mutant was insensitive to DEPC and dye-sensitized inactivations. We conclude that His163 plays an important role in the catalytic function of agmatinase, but it is not directly involved in substrate binding.

Catalysis↗
PubMed1988

Role of basic amino acids in the interaction of bindin with sulfated fucans.

Bindin, the acrosomal sperm adhesion protein of the sea urchin Strongylocentrotus purpuratus, binds specifically and with high affinity (Kd = 10(-8) M) to egg sulfated fucans in the high ionic strength milieu of seawater (0.55 M salt). Previous studies indicated that the negatively charged sulfate groups of the polysaccharide are critical for binding which suggested a binding mechanism involving basic residues of bindin. We found that the binding of fucan to bindin or polyarginine is stable at the ionic strength of seawater, whereas the binding of fucan to polylysine or polyhistidine is inhibited by 50% or more at this ionic strength. Group-specific modification of either arginine, lysine, or histidine residues of bindin results in a substantial inactivation of fucan binding activity. Preincubation of bindin with fucan can almost completely protect bindin from inactivation by arginine-specific reagents, butanedione and phenylglyoxal, but only moderately slowed the inactivation by the histidine reagent diethyl pyrocarbonate. In contrast, prior fucan binding could not prevent loss of activity by the reaction of citraconic anhydride with lysine residues. Other sulfated polysaccharides which do not interact strongly with bindin did not protect binding from phenylglyoxal-mediated inactivation when 800-3000-fold more polysaccharide than fucan was used during the preincubation before modification. We found that the larger and more hydrophobic arginine-modifying reagents, camphorquinone-10-sulfonic acid and cyclohexanedione, fail to inactivate fucan binding, suggesting that essential arginine residues may reside in an environment with restricted accessibility to these reagents. Parallel kinetic studies monitoring [14C]phenylglyoxal incorporation and fucan binding inactivation indicate that several of the four total arginine residues may be critical for fucan binding.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗
PubMed2000

Mutation of histidine 286 of the human P2X4 purinoceptor removes extracellular pH sensitivity.

1. Effects of external pH on the human P2X4 purinoceptor, an ATP-activated ion channel, were studied using the Xenopus oocyte expression system. 2. Changing the external pH from 7.4 to 6.5 significantly reduced, whilst an increase to pH 8 enhanced, maximum ATP-activated current amplitude, without changing the current- voltage relationship of the ATP-activated current. 3. Diethyl pyrocarbonate (DEPC; 10 mM) treatment of P2X4-injected oocytes had no effect on the pH sensitivity of the ATP-activated current. 4. Site-directed mutagenesis of histidine 286 (H286) to alanine completely abolished the pH sensitivity of the P2X4 receptor at all agonist concentrations. ATP potency showed a small (fourfold) leftward shift. Mutagenesis of the other three histidines present in the P2X4 sequence had no effect on pH sensitivity. 5. The results show that pH modulation of P2X4 in the pathophysiological range is mediated by protonation of H286. This provides direct confirmation that pH sensitivity resides in the P2X4 channel protein rather than the agonist species.

Adenosine Triphosphate↗
PubMed1981

Structure-function relationships of sea anemone toxin II from Anemonia sulcata.

Chemical modifications of sea anemone toxin II from Anemonia sulcata have been used to study the residues involved in its toxic action on crabs and mice and in its binding properties to the Na+ channel of rat brain synaptosomes. Guanidination of th epsilon-amino groups of lysines 35, 36, and 46 with O-methylisourea hydrogen sulfate did not change the net charge of the toxin molecule and had no effect upon its toxic and binding properties. Either acetylation or fluorescamine treatment of the toxin that destroyed the positive charges of the three epsilon-amino groups and of the alpha-amino function of Gly produced an almost complete loss of toxicity and a considerable decrease in the binding activity. Iodination of the toxin on His induced practically no loss of toxic or binding properties. Carbethoxylation of both histidines 32 and 37 with diethyl pyrocarbonate provoked an important decrease of both the toxicity and the binding activity. Modifications of the guanidine side chain of Arg with 1,2-cyclohexanedione fully destroyed both toxicity and binding of the toxin to the Na+ channel. Modification of the carboxylate functions of Asp, Asp, and of the COOH-terminal Gln with glycine ethyl ester in the presence of a soluble carbodiimide completely abolished the toxicity but left the affinity for the sea anemone toxin receptor unchanged. The antagonist character of this carboxylate-modified derivative was further confirmed by electrophysiological and Na+ flux experiments. The theoretical and practical significance of these results are discussed.

Acetic Anhydrides↗
PubMed2001

Structure-function analysis of the ArsA ATPase: contribution of histidine residues.

The ArsA ATPase is the catalytic subunit of the ArsAB oxyanion pump in Escherichia coli that is responsible for extruding arsenite or antimonite from inside the cell, thereby conferring resistance. Either antimonite or arsenite stimulates ArsA ATPase activity. In this study, the role of histidine residues in ArsA activity was investigated. Treatment of ArsA with diethyl pyrocarbonate (DEPC) resulted in complete loss of catalytic activity. The inactivation could be reversed upon subsequent incubation with hydroxylamine, suggesting specific modification of histidine residues. ATP and oxyanions afforded significant protection against DEPC inactivation, indicating that the histidines are located at the active site. ArsA has 13 histidine residues located at position 138, 148, 219, 327, 359, 368, 388, 397, 453, 465, 477, 520, and 558. Each histidine was individually altered to alanine by site-directed mutagenesis. Cells expressing the altered ArsA proteins were resistant to both arsenite and antimonite. The results indicate that no single histidine residue plays a direct role in catalysis, and the inhibition by DEPC may be caused by steric hindrance from the carbethoxy group.

Antimony↗
PubMed2001

Purification and characterization of the maize amyloplast stromal 112-kDa starch phosphorylase.

A plastidic 112-kDa starch phosphorylase (SP) has been identified in the amyloplast stromal fraction of maize. This starch phosphorylase was purified 310-fold from maize endosperm and characterized with respect to its enzymological and kinetic properties. The purification procedure included ammonium sulfate fractionation, Sephacryl 300 HR chromatography, affinity starch adsorption, Q-Sepharose, and Mono Q chromatography. The procedure resulted in a nearly homogeneous enzyme preparation as determined by native and SDS-polyacrylamide gel electrophoresis. Anti-SP antibodies recognized the purified 112-kDa SP enzyme and N-terminal amino acid sequence analysis confirmed that the purified enzyme is the amyloplast stromal 112-kDa SP. Analysis of the purified enzyme by Superose 6 gel filtration chromatography indicated that the native enzyme consisted of two identical subunits. The pH optimum for the enzyme was 6.0 in the synthetic direction and 5.5 in the phosphorolytic direction. SP activity was inhibited by thioreactive agents, diethyl pyrocarbonate, phenylglyoxal, and ADP-glucose. The activation energies for the synthetic and phosphorolytic reactions were 11.1 and 16.9 kcal/mol, respectively, and the enzyme was thermally labile above 50 degrees C. Results of kinetic experiments indicated that the enzyme catalyzes its reaction via a sequential Bi Bi mechanism. The Km value for amylopectin was eight-fold lower than that of glycogen. A kinetic analysis indicated that the phosphorolytic reaction was favored over the synthetic reaction when malto-oligosaccharides (4 to 7 units) were used as substrates. The specificity constants (Vmax/Km) of the enzyme measured in either the synthetic or the phosphorolytic directions increased with increasing chain length.

Adenosine Diphosphate Glucose↗
PubMed1994

Spectroscopic and kinetic studies of the histidine residues of bovine low-molecular-weight phosphotyrosyl protein phosphatase.

The role of the two conserved histidine residues in the low-molecular-weight phosphotyrosyl protein phosphatases was investigated using site-directed mutagenesis of the recombinant bovine heart enzyme. His-66 and His-72 were individually mutated to alanine and to asparagine. A double mutant, containing only alanines in place of the histidines, was also created. The 1H NMR spectra of the purified proteins revealed no apparent tertiary structure alterations. Microscopic pKas for the two histidines were determined from a pH titration of the wild-type enzyme using 1H NMR spectroscopy and an MLEV-17 spectral editing scheme to more readily follow shifts in the specific histidine resonance peaks. His-66 titrates with an apparent pKa of 8.4 while for His-72 the value is 9.2. Since earlier chemical modification experiments indicated that the wild-type enzyme was inactivated by the histidine-selective modification reagent diethyl pyrocarbonate (DEP), the histidine mutants were tested for sensitivity to DEP. Both of the histidine single mutants were inactivated by DEP, and surprisingly, the double mutant containing no histidines was also readily inactivated by DEP. Thus, for this protein, modification by DEP is not specific for histidine residues. Kinetic studies of the mutant proteins reveal that neither histidine is essential in the catalytic mechanism. His-66 mutants showed virtually identical catalytic properties compared to wild-type enzyme, whereas His-72 mutants had reduced specific activity and higher phosphate Ki and lower Km values at pH5 and higher. It is proposed that His-72, although not essential for catalysis, may serve a significant structural role at the enzyme active site.

Animals↗
PubMed2001

Evidence for essential histidines in human pituitary glutaminyl cyclase.

Glutaminyl cyclase (QC, EC 2.3.2.5) catalyzes the formation of the pyroglutamyl residue present at the amino terminus of numerous secretory peptides and proteins. Treatment with diethyl pyrocarbonate inactivated recombinant human QC with the apparent modification of three essential histidine residues. Comparisons of the protein sequences of QC from a variety of eukaryotic species show four completely conserved histidine residues. Mutation of each of these residues to glutamine resulted in two mutant enzymes that were inactive (H140Q and H330Q), suggesting a role in catalysis, and two that exhibited increased Km values (H307Q and H319Q), suggesting a role in substrate binding. Consistent with these results is the prediction that QC possesses a zinc aminopeptidase domain in which the four histidines identified here are present in the active site. Mammalian glutaminyl cyclases may, therefore, have structural and catalytic similarities to a family of bacterial zinc aminopeptidases.

Amino Acid Sequence↗