An electron paramagnetic resonance study on the mechanism-based inactivation of adenosylcobalamin-dependent diol dehydrase by glycerol and other substrates

Adenosylcobalamin-dependent diol dehydrase undergoes mechanism-based inactivation by glycerol or other substrates during catalysis. X-band electron paramagnetic resonance spectra of holoenzyme were measured at −130°C after reaction with such substrates. After short time of incubation, broad signals assigned to low-spin Co(II) of cob(II)alamin and doublet signals assigned to an organic radical intermediate derived from each substrate were observed with 1,2-propanediol, 1,2-ethanediol, glycerol and meso-2,3-butanediol with the magnitude of their exchange interaction (J-value) decreasing in this order. A substrate with the smaller magnitude of exchange interaction between low-spin Co(II) and an organic radical intermediate seems to be an efficient mechanism-based inactivator. Since the magnitude of exchange interaction decreases with the distance between radical species in a radical pair, these results suggest that a stabilizing effect of holoenzyme on radical intermediates during reactions decreases with the distance between Co(II) and a radical.     

The mechanism of action of ethanolamine ammonia-lyase, an adenosylcobalamin-dependent enzyme. The source of the third methyl hydrogen in the 5'-deoxyadenosine generated from the cofactor during catalysis.

Ethanolamine ammonia-lyase is an adenosylcobalamin-dependent enzyme which catalyzes the conversion of ethanolamine and propanolamine to ammonia and the corresponding aldehydes. A mechanism has been proposed for this and other adenosylcobalamin-dependent reactions which involves cleavage of the carbon-cobalt bond of the cofactor followed by abstraction of a substrate hydrogen atom by the adenosyl fragment to form 5'-deoxyadenosine. In support of this proposal, a previous study demonstrated that the deamination of propanolamine by ethanolamine ammonia-lyase is accompanied by the reversible cleavage of the carbon-cobalt bond of the cofactor, with the production of 5'-deoxyadenosine (Babior, B.M., Carty, T.J., and Abeles, R.H. (1974) J. Biol. Chem. 249, 1689-1695). The present study is concerned with the origin of the third hydrogen atom on the methyl group of the 5'-deoxyadenosine produced in that reaction. The 5'-deoxyadenosine isolated from an incubation mixture initially containing enzyme, [5',5'-D2]adenosylcobalamin, and [1,1-D2]propanolamine was chemically degraded so that the 4' and 5' carbon atoms were, respectively, converted to the carbonyl and methyl carbons of acetaldehyde. Analysis of the p-nitrophenylhydrazone of the acetaldehyde by gas-liquid chromatography-mass spectroscopy revealed 3 deuterium atoms/molecule, indicating that two of the methyl hydrogens originated from adenosylcobalamin and the third was donated by substrate. This observation provides further support for the participation of 5'-deoxyadenosine in the mechanism of adenosylcobalamin-dependent reactions.     

Chemical Studies on the Reaction Products of Glucose and Ammonia

A new imidazole compound was isolated as crystalline form from the reaction mixture of glucose and ammonia, and identified as 4(5)-(dl-glycero-2,3-dihydroxypropyl)imidazole. From the results the authors suggested that pentose may be formed in the reaction mixture not by direct fission of C-C bond of glucose but by recombination of glucose fragments, for example, of triose and glycolic aldehyde.

4(5)-[d-(-)-Glycero-2,3-dihydroxypropyl]imidazole was also newly prepared from d-xylose via 3-deoxy-d-pentosone.     

Human erythrocyte phosphoglycerate mutase: Evidence for normal catalysis in the absence of added 2,3-bisphospho-D-glycerate

Kinetic analyses indicate that human erythrocyte phosphoglycerate mutase catalyzes the normal, reversible isomerization of D-glycerate-3-P and D-glycerate-2-P in the absence of added D-glycerate-2,3-P₂. The reaction is impeded, however, by a potent inhibitor which occurs as a natural component of commericial D-glycerate-3-P. Inhibition may be overcome through substrate purification or by adding D-glycerate-2,3-P₂ to the reaction medium containing the contaminant. In surmounting the inhibition, bisphosphoglycerate performs as a non-essential activator and not as a cofactor. The latter concept is corroborated by the observation that D-glycerate-2,3-P₂ has absolutely no influence on mutase catalysis conducted in the presence of pure substrate. The data presented here and elsewhere, however, suggest that the red cell enzyme is readily phosphorylated by mono- as well as bisphosphoglycerate. Additional findings show that at concentrations in excess of 3mM, D-glycerate-3-P accelerates phosphoglycerate mutase catalysis in the absence of cofactor, suggesting that the mutase molecule possesses a normal catalytic site and an allosteric activator site.     

The active site of hydroxynitrile lyase from Prunus amygdalus: Modeling studies provide new insights into the mechanism of cyanogenesis

The FAD-dependent hydroxynitrile lyase from almond (Prunus amygdalus, PaHNL) catalyzes the cleavage of R-mandelonitrile into benzaldehyde and hydrocyanic acid. Catalysis of the reverse reaction-the enantiospecific formation of alpha-hydroxynitriles--is now widely utilized in organic syntheses as one of the few industrially relevant examples of enzyme-mediated C-C bond formation. Starting from the recently determined X-ray crystal structure, systematic docking calculations with the natural substrate were used to locate the active site of the enzyme and to identify amino acid residues involved in substrate binding and catalysis. Analysis of the modeled substrate complexes supports an enzymatic mechanism that includes the flavin cofactor as a mere "spectator" of the reaction and relies on general acid/base catalysis by the conserved His-497. Stabilization of the negative charge of the cyanide ion is accomplished by a pronounced positive electrostatic potential at the binding site. PaHNL activity requires the FAD cofactor to be bound in its oxidized form, and calculations of the pKa of enzyme-bound HCN showed that the observed inactivation upon cofactor reduction is largely caused by the reversal of the electrostatic potential within the active site. The suggested mechanism closely resembles the one proposed for the FAD-independent, and structurally unrelated HNL from Hevea brasiliensis. Although the actual amino acid residues involved in the catalytic cycle are completely different in the two enzymes, a common motif for the mechanism of cyanogenesis (general acid/base catalysis plus electrostatic stabilization of the cyanide ion) becomes evident.     

Properties of 2,3-Butanediol Dehydrogenases from Lactococcus lactis subsp. lactis in Relation to Citrate Fermentation

Two 2,3-butanediol dehydrogenases (enzymes 1 and 2; molecular weight of each, 170,000) have been partially purified from Lactococcus lactis subsp. lactis (Streptococcus diacetylactis) D10 and shown to have reductase activity with either diacetyl or acetoin as the substrate. However, the reductase activity with 10 mM diacetyl was far greater for both enzymes (7.0- and 4.7-fold for enzymes 1 and 2, respectively) than with 10 mM acetoin as the substrate. In contrast, when acetoin and diacetyl were present together, acetoin was the preferred substrate for both enzymes, with enzyme 1 showing the more marked preference for acetoin. meso-2,3-Butanediol was the only isomeric product, with enzyme 1 independent of the substrate combinations. For enzyme 2, both the meso and optical isomers of 2,3-butanediol were formed with acetoin as the substrate, but only the optical isomers were produced with diacetyl as the substrate. With batch cultures of strain D10 at or near the point of citrate exhaustion, the main isomers of 2,3-butanediol present were the optical forms. If the pH was sufficiently high (>pH 5), acetoin reduction occurred over time and was followed by diacetyl reduction, and meso-2,3-butanediol became the predominant isomer. Interconversion of the optical isomers into the meso isomer did occur. The properties of 2,3-butanediol dehydrogenases are consistent with diacetyl and acetoin removal and the appearance of the isomers of 2,3-butanediol.     

Substrate specificity of coenzyme B12-dependent diol dehydrase: glycerol as both a good substrate and a potent inactivator.

The substrate specificity of adenosylcobalamin-dependent diol dehydrase was further studied in detail using an enzyme preparation that appears homogeneous by ultracentrifugal and gel electrophoretical criteria. Besides 1,2-propanediol and 1,2-ethanediol, glycerol, 1,2- and 2,3-butanediol were found to serve as substrate for the enzyme, whereas 1,3-propanediol was not. Of the substrate analogs tested, glycerol displayed some striking features: it was dehydrated to β-hydroxypropionaldehyde with concomitant inactivation of the enzyme. Although the initial velocity with glycerol was comparable to that with 1,2-propanediol, the dehydration reaction ceased almost completely within 3 min accompanying rapid, irreversible inactivation of the holoenzyme. 1,2- and 2,3-Butanediol were converted to butyraldehyde and methyl ethyl ketone, respectively, at a rate much lower than that with 1,2-propanediol. 2,3-Butanediol is the only compound, other than 1,2-diols, known at present to show a considerable substrate activity.     

Maillard Reaction Products Formed from d-Glucose and Glycine and the Formation Mechanisms of Amides as Major Components

Equimolar aqueous solutions of d-glucose and glycine were heated at 50°C and 95°C at pH 6.7. The headspace volatiles and the ether extracts from the reaction mixture were analyzed by gas chromatography and gas chromatography-mass spectrometry, using a fused silica capillary column. The major components formed were identified as diacetyl, furfuryl alcohol, two pyrroles, one pyranone and two amides. In order to elucidate the formation mechanisms of the amides formed from amino-carbonyl reactions, two model systems were adopted. N-Butylacetamide and N-butylformamide were formed as major components from diacetyl-butylamine and glyoxalbutylamine systems, respectively. The results obtained suggest that such α-dicarbonyls as 3-deoxyosone, 1-deoxy-d-erythro-2,3-hexodiulose and diacetyl generated in the amino-carbonyl reaction react with amino compounds, amides then being formed by cleavage of the C-C bond in the a-dicarbonyls.     

Separation of Racemic frommeso-2,3-Butanediol

2,3-Butanediol containing less than 3% of themesoform has been obtained from samples containing up to 50% of themesoform. The diacetate was obtained by esterification with acetic anhydride in the presence of traces of sulfuric acid as a catalyst and was then purified. When the diacetate was held at 4°C, crystals of racemic 2,3-butanediol diacetate formed, and these were separated by filtration. The diacetate was then transformed back to 2,3-butanediol by transesterification with methanol in the presence of sodium methylate as a catalyst. The resulting 2,3-butanediol contained less than 3% of themesoform. For an original batch of 2,3-butanediol containing 50%dland 50%meso,this method can isolate up to 70% of the racemate content. If the original 2,3-butanediol contains too muchmesoform, racemic 2,3-butanediol diacetate does not crystallize, but 2,3-butanediol containing up to 60% of themesoform can be enriched up to 70% racemate by distillation.     

A novel type of meso-diaminopimelic acid-based peptidoglycan and novel poly (erythritol phosphate) teichoic acids in cell walls of two coryneform isolates from the surface flora of French cooked cheeses

The primary structure of the peptidoglycan and the teichoic acids of two coryneform isolates from the surface flora of French cooked cheeses, CNRZ 925 and CNRZ 926, have been determined. In the peptidoglycan, meso-diaminopimelic acid was localized in position three of the peptide subunit. It contained an d-glutamyl-d-aspartyl interpeptide bridge, connecting meso-diaminopimelic acid and d-alanine residues of adjacent peptide subunits. The -carboxyl group of d-glutamic acid in position two of peptide subunits was substituted with glycine amide. The teichoic acid pattern and composition differed between the strains: both contained an erythritol teichoic acid and strain CNRZ 925 also contained an N-acetylglucosaminylphosphate polymer. The erythritol teichoic acids differed in terms of the quality and quantity of substituents, but they both had N,N-diacetyl-2,3-diamino-2,3-dideoxyglucuronic acid in common.Abbreviations DNP dinitrophenyl - Ery erythritol - Gal galactose - GlcN glucosamine - GlcNAc N-acetylglucosamine - GlcUANAc₂ N,N-diacetyl-2,3-diamino-2,3-dideoxyglucuronic acid - Hex UANAc₂ N,N-diacetyl-2,3-diamino-2,3-dideoxyhexuronic - acid m-Dpm, meso-diaminopimelic acid - Mur muramic acid - MurNAc N-acetylmuramic acid     

Aminopyrimidines and Derivatives. 271.-Synthesis,Anticancer and Antimicrobiological Activities of 7-Glycopyranosyl-Pyrrolo[2,3-D]Pyrimidines2

Abstract

Reaction between 4-(O-acetyl-β-D-glycopyranosylamino)-6-oxopyrimidines 1 and chloroacetaldehyde leads to the corresponding 7-glycopyranosyl-4-oxopyrrolo [2,3-d]pyrimidines 3 in moderate yields. The reaction of 1a yields also 4-glucopyranosylaminofuro[2,3-d] pyrimidine 2. The anticancer and antimicrobiological activities of these products are noticed.     

Nucleosides,III1 Synthesis and Properties of 2-Trifluoromethyl-Naphthimidazole-Ribonucleoside

Abstract

The fusion reaction between 2-trifluoromethylnaphth[2,3-d]imidazole (1) and 1-0-acetyl-2,3,5-tri-O-benzoyl-D-ribofuranose (2) leads to 2,3′,5′-tri-O-benzoyl-1-β-D-ribofuranosylnaphth[2,3-d]imidazole (3). Debenzoylation of (3) gives the corresponding nucleoside 1-β-D-ribofuranosyl -2-trifluoromethylnaphth[2,3-d]imidazole (4). Structural proofs are based on elementary analysis, UV-and ¹H-NMR spectra.     

Synthesis of Tubercidin, 6-Chlorotubercidin and Related Nucleosides

Abstract

Tubercidin (7-deazaadenosine, 1a) and several 6-chlorotuber-cidin derivatives were synthesized including 4-amino-6-chloro-7-β-D-ribofuranosylpyrrolo[2,3-d]pyrimidine-3′,5′-cycyclic phosphate 9. Isolation of a side product found in the glycosylation step of the reaction sequence proved to be the N-1 ribosyl-attached isomer as shown by X-ray diffraction analysis. All derivatives were tested for in vitro antiviral and antitumor activity.     

Isotope effects in the transient phases of the reaction catalyzed by ethanolamine ammonia-lyase: determination of the number of exchangeable hydrogens in the enzyme-cofactor complex

Transient phases of the reaction catalyzed by ethanolamine ammonia-lyase (EAL) from Salmonella typhimurium have been investigated by stopped-flow visible spectrophotometry and deuterium kinetic isotope effects. The cleavage of adenosylcobalamin (coenzyme B(12)) to form cob(II)alamin (B(12r)) with ethanolamine as the substrate occurred within the dead time of the instrument whenever coenzyme B(12) was preincubated with enzyme prior to mixing with substrate. The rate was, however, slowed sufficiently to be measured with perdeutero ethanolamine as the substrate. Optical spectra indicate that, during the steady states of the reactions with ethanolamine and with S-2-aminopropanol as substrates, approximately 90% of the active sites contain B(12r). Reformation of the carbon-cobalt bond of the cofactor occurs following depletion of substrate in the reaction mixtures, and the rate constant for this process reflects k(cat) of the respective substrates. This late phase of the reaction also exhibits (2)H isotope effects similar to those measured for the overall reaction with (2)H-labeled substrates. With unlabeled substrates, the rate of cofactor reassembly is independent of the number of substrate molecules turned over in the steady-state phase. However, with (2)H-labeled substrates, kinetic isotope effects appear in the reassembly phase, and these isotope effects are maximal after only approximately 2 equiv of substrate/active site are processed. With 5'-deuterated coenzyme B(12) and deuterated substrate, the isotope effect on reassembly is independent of the number of substrate molecules that are turned over. These results indicate that the pool of exchangeable hydrogens in the enzyme-cofactor complex is two-a finding consistent with the hydrogens in the C5' methylene of coenzyme B(12).     

Novel l-specific cleavage of the urethane bond of t -butoxycarbonylamino acids by whole cells of Corynebacterium aquaticum

Microorganisms capable of cleaving the urethane bond of t-butoxycarbonyl (Boc) amino acids in a whole-cell reaction were screened among stock cultures, and Corynebacterium aquaticum IFO12154 was the most promising. The conversion of Boc-Ala to Ala was stimulated by CoSO₄ in the medium and reaction mixture. The optimum whole-cell concentration was 25 mg lyophilized cells/ml. Boc-l-Met was the best substrate for this reaction, and other Boc-L-amino acids, as well as benzyloxycarbonyl-l-amino acids with hydrophobic residues, were also good substrates. Boc-d- and Z-d-amino acids were inert. When the reactions had proceeded for 24 h with each substrate at 10 mM, the molar conversion rates from Boc-l-, dl- and d-Met were 100%, 50%, and 0% respectively. From 150 mM Boc-l-Met, 143 mM l-Met was formed at a molar yield of 95.3%. Received: 3 September 1996 / Received last revision: 7 April 1997 / Accepted: 19 April 1997     

Initial step of B12-dependent enzymatic catalysis: energetic implications regarding involvement of the one-electron-reduced form of adenosylcobalamin cofactor

Density functional theory analysis was performed to elucidate the impact of one-electron reduction upon the initial step of adenosylcobalamin-dependent enzymatic catalysis. The transition state (TS) corresponding to the Co–C bond cleavage and subsequent hydrogen abstraction from the substrate was located. The intrinsic reaction coordinate calculations predicted that the reaction consisting of Co–C5′ bond cleavage in [Co^III(corrin^•)]–Rib (where Rib is ribosyl) and hydrogen-atom abstraction from the CH₃–CH₂–CHO substrate occurs in a concerted fashion. The computed activation energy barrier of the reaction (15.0 kcal/mol) was lowered by approximately 54.5% in comparison with the reaction involving the positively charged cofactor model (Im–[Co^III(corrin)]–Rib⁺, where Im is imidazole; energy barrier = 33.0 kcal/mol). The Im base was detached during the TS search in the reaction involving the one-electron-reduced analogue. Thus, to compare the energetics of the two reactions, the axial Im ligand detachment energy for the Im–[Co^III(corrin^•)]–Rib model was computed [7.6 kcal/mol (gas phase); 4.6 kcal/mol (water)]. Consequently, the effective activation energy barrier for the reaction mediated by the Im-off [Co^III(corrin^•)]–Rib was estimated to be 22.6 kcal/mol, which implied an overall 31.5% reduction in the energetic demands of the reaction. Considering that the lengthened Co–N_axial bond has been observed in X-ray crystal structure studies of B₁₂-dependent mutases, the catalytic impact induced by one-electron reduction of the cofactor is expected to be higher in the presence of the enzymatic environment.     

Modification of the active site of isocitrate lyase from Pseudomonas indigofera

Kinetic analysis of inactivation of isocitrate lyase from Pseudomonas indigofera by 3-bromopyruvate established that enzyme binds this compound prior to alkylation and that substrate, D_s-isocitrate, competes for the same site on the enzyme. The rate of inactivation was increased by EDTA which is a promoter of catalysis in the presence of activated (reduced) enzyme and substrate. The combination of products, glyoxylate plus succinate, also protected against inactivation. Glyoxylate plus itaconate, phosphoenolpyruvate, or maleate also protected. However, each of the latter three compounds or glyoxylate or succinate alone provided little or no protection. Pyruvate, a competitive inhibitor with respect to glyoxylate in the condensation reaction, also failed to protect. However, two dicarboxylates, meso-tartrate and oxalate, that are also competitive inhibitors with respect to glyoxylate provide some protection against inactivation by BrP perhaps by bridging across cationic sites that facilitate glyoxylate and succinate binding. These and other results imply that alkylation by 3-bromopyruvate occurs at the succinate part of the active site. A mechanism which includes a catalytic role for the cysteine residue at the active site is presented and discussed.     

Methyl transfer from methylcobalamin to thiols. A reinvestigation

The methyl transfer from methylcobalamin to thiols has been reinvestigated. By use of methylcobalamin selectively enriched with 13C in the methyl moiety, the methyl transfer to thiols was followed by 13C NMR. The methyl transfer occurs in aqueous mildly alkaline (pH 8-12) solution, even in the complete absence of oxygen. 31P NMR and EPR studies demonstrate that cob(II)alamin is the final corrinoid product. However, the pH dependence of the methyl-transfer reaction from methylcobalamin to beta-mercaptoethanol is consistent only with a nucleophilic displacement of the methyl group by a thiolate anion, resulting in the heterolytic cleavage of the carbon-cobalt bond. Difference visible spectroscopic measurements of the reaction mixture suggest that cob(I)alamin is formed as an intermediate.     

Protection of radical intermediates at the active site of adenosylcobalamin-dependent methylmalonyl-CoA mutase

Adenosylcobalamin-dependent methylmalonyl-CoA mutase catalyzes the interconversion of methylmalonyl-CoA and succinyl-CoA via radical intermediates generated by substrate-induced homolysis of the coenzyme carbon-cobalt bond. From the structure of methylmalonyl-CoA mutase it is evident that the deeply buried active site is completely shielded from solvent with only a few polar contacts made between the protein and the substrate. Site-directed mutants of amino acid His244, a residue close to the inferred site of radical chemistry, were engineered to investigate its role in catalysis. Two mutants, His244Ala and His244Gln, were characterized using kinetic and spectroscopic techniques. These results confirmed that His244 is not an essential residue. However, compared with that of the wild type, k(cat) was lowered by 10(2)- and 10(3)-fold for the His244Gln and His244Ala mutants, respectively, while the K(m) for succinyl-CoA was essentially unchanged in both cases. The primary kinetic tritium isotope effect (k(H)/k(T)) for the His244Gln mutant was 1.5 +/- 0.3, and tritium partitioning was now found to be dependent on the substrate used to initiate the reaction, indicating that the rearrangement of the substrate radical to the product radical was extremely slow. The His244Ala mutant underwent inactivation under aerobic conditions at a rate between 1 and 10% of the initial rate of turnover. The crystal structure of the His244Ala mutant, determined at 2.6 A resolution, indicated that the mutant enzyme is unaltered except for a cavity in the active site which is occupied by an ordered water molecule. Molecular oxygen reaching this cavity may lead directly to inactivation. These results indicate that His244 assists directly in the unusual carbon skeleton rearrangement and that alterations in this residue substantially lower the protection of reactive radical intermediates during catalysis.