Evidence for coupled motion and hydrogen tunneling of the reaction catalyzed by glutamate mutase

Glutamate mutase is one of a group of adenosylcobalamin-dependent enzymes that catalyze unusual isomerizations that proceed through organic radical intermediates generated by homolytic fission of the coenzyme's unique cobalt-carbon bond. These enzymes are part of a larger family of enzymes that catalyze radical chemistry in which a key step is the abstraction of a hydrogen atom from an otherwise inert substrate. To gain insight into the mechanism of hydrogen transfer, we previously used pre-steady-state, rapid-quench techniques to measure the alpha-secondary tritium kinetic and equilibrium isotope effects associated with the formation of 5'-deoxyadenosine when glutamate mutase was reacted with [5'-(3)H]adenosylcobalamin and L-glutamate. We showed that both the kinetic and equilibrium isotope effects are large and inverse, 0.76 and 0.72, respectively. We have now repeated these measurements using glutamate deuterated in the position of hydrogen abstraction. The effect of introducing a primary deuterium kinetic isotope effect on the hydrogen transfer step is to reduce the magnitude of the secondary kinetic isotope effect to a value close to unity, 1.05 +/- 0.08, whereas the equilibrium isotope effect is unchanged. The significant reduction in the secondary kinetic isotope effect is consistent with motions of the 5'-hydrogen atoms being coupled in the transition state to the motion of the hydrogen undergoing transfer, in a reaction that involves a large degree of quantum tunneling.     

Isotope effects for deuterium transfer between substrate and coenzyme in adenosylcobalamin-dependent glutamate mutase

A key step in the mechanism of all adenosylcobalamin-dependent enzymes is the abstraction of a hydrogen atom from the substrate by a 5'-deoxyadenosyl radical generated by homolytic fission of the coenzyme cobalt-carbon bond. We have investigated the isotope effects associated with this process for glutamate mutase reacting with deuterated glutamate. The kinetics of deuterium incorporation into 5'-deoxyadenosine (5'-dA) during the reaction were followed by rapid chemical quench, using HPLC and electrospray mass spectrometry to analyze the 5'-dA formed. The kinetics of 5'-dA formation are biphasic, comprising a rapid phase k(app) = 37 +/- 3 s(-)(1) and a slower phase k(app) = 0.9 +/- 0.4 s(-)(1). The mass spectral data clearly show that the faster phase is associated with the formation of monodeuterated 5'-dA whereas the slower phase is associated with the incorporation of a second and then a third deuterium into 5'-dA. This observation implies that a large inverse equilibrium secondary isotope effect is associated with the formation of 5'-dA from adenosylcobalamin. The primary deuterium kinetic isotope effects on V and V/K for the formation of 5'-dA were determined from time-based and competition experiments. (D)V = 2.4 +/-0.4 whereas (D)(V/K) = 10 +/- 0.4, implying that an isotopically insensitive step is partially rate-determining. The additional data provided by these experiments cause us to revise our interpretation of earlier UV-visible stopped-flow kinetic measurements of AdoCbl homolysis obtained with deuterated substrates.     

Alpha-secondary isotope effects in the lipoxygenase reaction

Isotope effects for the oxidation of [5,6,8,9,11,12,14,15-3H]arachidonic acid catalyzed by soybean lipoxygenase and by 5-lipoxygenase were measured. This labeling pattern represents substitution at each of the vinylic hydrogens of the substrate. The observed isotope effect for soybean lipoxygenase was 1.16 +/- 0.02 and for 5-lipoxygenase was 1.11 +/- 0.05. These isotope effects are inconsistent with any change in hybridization (sp2 to sp3) at the vinylic carbons prior to or during the rate-determining step and are concluded to be most consistent with the formation of a carbanion-like intermediate or transition state. In contrast, the oxidation of arachidonic acid by Ce(IV), which is thought to proceed via a cation radical intermediate, exhibited at most a small isotope effect (1.02 +/- 0.01). The reduction potential for the cation radical formed from arachidonic acid in this reaction is estimated to be 2.7 V vs NHE by comparison of the rates of oxidation of arachidonic acid and cyclohexene by Ce(IV). This is similar to the potential for the cation radical of 2-butene. No isotope effect (1.00 +/- 0.03) was observed in the 5-lipoxygenase reaction for conversion of the initially formed product 5-hydroperoxyeicosatetraenoic acid to the epoxide leukotriene A4. From this it is concluded that there is little carbon-oxygen bond formation prior to or during the rate-determining step for epoxide formation.     

Radical SAM activation of the B12-independent glycerol dehydratase results in formation of 5'-deoxy-5'-(methylthio)adenosine and not 5'-deoxyadenosine

Activation of glycyl radical enzymes (GREs) by S-adenosylmethonine (AdoMet or SAM)-dependent enzymes has long been shown to proceed via the reductive cleavage of SAM. The AdoMet-dependent (or radical SAM) enzymes catalyze this reaction by using a [4Fe-4S] cluster to reductively cleave AdoMet to form a transient 5'-deoxyadenosyl radical and methionine. This radical is then transferred to the GRE, and methionine and 5'-deoxyadenosine are also formed. In contrast to this paradigm, we demonstrate that generation of a glycyl radical on the B(12)-independent glycerol dehydratase by the glycerol dehydratase activating enzyme results in formation of 5'-deoxy-5'-(methylthio)adenosine and not 5'-deoxyadenosine. This demonstrates for the first time that radical SAM activases are also capable of an alternative cleavage pathway for SAM.     

The photochemistry of 8-bromo-2'-deoxyadenosine. A direct entry to cyclopurine lesions.

The UV photolysis of 8-bromo-2'-deoxyadenosine has been investigated in different solvents and in the presence of additives like halide anions. Photolytic cleavage of the C-Br bond leads to formation of the C8 radical. In methanol, subsequent hydrogen abstraction from the solvent is the main radical reaction; however, in water or acetonitrile intramolecular hydrogen abstraction from the sugar moiety, to give the C5' radical, is the major path. This C5' radical undergoes a cyclization reaction on the adenine and gives the aminyl radical. A rate constant of 1.8 x 10(5) s(-1) has been measured by laser flash photolysis in CH(3)CN for this unimolecular process. Product studies from steady-state photolysis in acetonitrile have shown the conversion of 8-bromo-2'-deoxyadenosine to 5',8-cyclo-2'-deoxyadenosine in 65% yield and in a diastereoisomeric ratio (5' R):(5' S)= 1.7. Evidence supporting that the equilibrium Br*+ Br(-)[right left harpoons] Br(2)*(-) plays an important role in this synthetically useful radical cascade is obtained by regulating the relative concentrations of the two reactive oxidizing species.     

Tritium partitioning and isotope effects in adenosylcobalamin-dependent glutamate mutase.

Tritiated adenosylcobalamin, labeled at the exchangeable position, has been used to investigate the partitioning of tritium between substrate and product in the reaction catalyzed by glutamate mutase. The isotope partitions between glutamate and methylaspartate in nearly 1:1 ratio, regardless of the direction in which the overall reaction is proceeding. This is consistent with a free-energy profile in which the interconversion of the intermediate glutamyl and methylaspartyl radicals is rapid relative to the transfer of tritium from 5'-deoxyadenosine to either substrate or product. Initial velocity measurements have been used to measure the tritium isotope effects for the transfer of tritium from adenosylcobalamin to product in each direction. The isotope effect is 21 for the formation of glutamate and 19 for the formation of methylasparate. The large magnitude of these isotope effects makes it likely that the rate-determining step may be altered by the substitution of tritium for hydrogen in the reaction. The results of these experiments are compared with previous isotope effect measurements made on other adenosylcobalamin-dependent enzymes.     

Hydrogen atom exchange between 5'-deoxyadenosine and hydroxyethylhydrazine during the single turnover inactivation of ethanolamine ammonia-lyase.

The early steps in the single turnover inactivation of ethanolamine ammonia-lyase (EAL) from Salmonella typhimurium by hydroxyethylhydrazine (HEH) have been probed by rapid-mixing sampling techniques, and the destiny of deuterium atoms, present initially in HEH, has been investigated by mass spectrometry. The inactivation reaction produces acetaldehyde, the hydrazine cation radical, 5'-deoxyadenosine, and cob(II)alamin (B(12r)) in amounts stoichiometric with active sites. Rapid-mix freeze-quench EPR spectroscopy and stopped-flow rapid-scan spectrophotometry revealed that the hydrazine cation radical and B(12r) appeared at a rate of approximately 3 s(-)(1) at 21 degrees C. Analysis of 5'-deoxyadenosine isolated from a reaction mixture prepared in (2)H(2)O did not contain deuterium-a result which demonstrates that solvent-exchangeable sites are not involved in the hydrogen-transfer processes. In contrast, all of the 5'-deoxyadenosine, isolated from inactivation reactions with [1,1,2,2-(2)H(4)]HEH, had acquired at least one (2)H from the labeled inactivator. Significant fractions of the 5'-deoxyadenosine acquired two and three deuteriums. These results indicate that hydrogen abstraction from HEH by a radical derived from the cofactor is reversible. The distribution of 5'-deoxyadenosine with one, two, and three deuteriums incorporated and the absence of unlabeled 5'-deoxyadenosine in the product are consistent with a model in which there is direct transfer of hydrogens between the inactivator and the 5'-methyl of 5'-deoxyadenosine. These results reinforce the concept that the 5'-deoxyadenosyl radical is the species that abstracts hydrogen atoms from the substrate in EAL.     

Carbon isotope effects on the pyruvate dehydrogenase reaction and their importance for relative carbon-13 depletion in lipids

A method has been developed for the positional 13C isotope analysis of pyruvate and acetate by stepwise quantitative degradation. On its base, the kinetic isotope effects on the pyruvate dehydrogenase reaction (enzymes from Escherichia coli and Saccharomyces cerevisiae) for both of the carbon atoms involved in the bond scission (double isotope effect determination) and on C-3 of pyruvate have been determined. The experimental k12/k13 values with the enzyme from E. coli on C-1 and C-2 of pyruvate are 1.0093 +/- 0.0007 and 1.0213 +/- 0.0017, respectively, and, with the enzyme from S. cerevisiae, the values are 1.0238 +/- 0.0013 and 1.0254 +/- 0.0016, respectively. A secondary isotope effect of 1.0031 +/- 0.0009 on C-3 (CH3-group) was found with both enzymes. The size of the isotope on C-1 indicates that decarboxylation is more rate-determining with the yeast enzyme than with the enzyme from E. coli, although it is not the entirely rate-limiting step in the overall reaction sequence. Assuming appropriate values for the intrinsic isotope effect on the decarboxylation step (k3) and the equilibrium isotope effect on the reversible substrate binding (k1, k2), one can calculate values for the partitioning factor R (k3/k2: E. coli enzyme 4.67, S. cerevisiae enzyme 1.14) and the intrinsic isotope effects related to the carbonyl-C (k1/k'1 = 1.019; k3/k'3 = 1.033). The isotope fractionation at C-2 of pyruvate gives strong evidence that the well known relative carbon-13 depletion in lipids from biological material is mainly caused by the isotope effect on the pyruvate dehydrogenase reaction. In addition, our results indicate an alternating 13C abundance in fatty acids, that has already been verified in some cases.     

Identification of cis-ethanesemidione as the organic radical derived from glycolaldehyde in the suicide inactivation of dioldehydrase and of ethanolamine ammonia-lyase

The hydrate of glycolaldehyde is a substrate analogue that induces the formation of cob(II)alamin and 5'-deoxyadenosine from adenosylcobalamin at the active site of dioldehydrase, and the resulting complex is inactive. The carbon atoms of glycolaldehyde hydrate remain bound to this complex, and it has been postulated that the first step or steps of the catalytic process on glycolaldehyde hydrate generate an intermediate that undergoes a destructive side reaction leading to inactivation of the enzyme [Wagner, O. W., Lee, H. A., Jr., Frey, P. A., and Abeles, R. H. (1966) J. Biol. Chem. 249, 1751-1762]. All evidence suggests that dioldehydrase reaction proceeds by a radical mechanism, and the glycolaldehyde hydrate is expected to be converted initially into a radical. Electron paramagnetic resonance (EPR) spectroscopic analysis of the inactivated complex shows that glycolaldehyde is transformed into a cis-ethanesemidione radical that is weakly spin-coupled to the cob(II)alamin in the active site of the enzyme. This radical has been identified by analysis of EPR spectra obtained from samples with (13)C- and (2)H-labeled forms of glycolaldehyde. The analysis shows that the stable radical associated with the inactive complex is symmetrical and that it contains a single solvent-exchangeable proton, consistent with a cis-ethanesemidione. Glycolaldehyde also inactivates ethanolamine ammonia-lyase (EAL). EPR studies of ethanolamine ammonia-lyase reveal that treatment with glycolaldehyde also results in formation of an ethanesemidione radical bound in the active site. The suicide inactivation in both enzymatic reactions is postulated to result from formation of this stable radical, which cannot react further to abstract a hydrogen atom from 5'-deoxyadenosine. Analysis of the electron spin-spin coupling between the semidione radicals and cob(II)alamin in both enzymes indicates that the distance between the radical and Co(2+) is approximately 11 A in each case.     

A Secondary beta Deuterium Kinetic Isotope Effect in the Chorismate Synthase Reaction

Chorismate synthase (EC 4.6.1.4) is the shikimate pathway enzyme that catalyzes the conversion of 5-enolpyruvylshikimate 3-phosphate (EPSP) to chorismate. The enzyme reaction is unusual because it involves a trans-1,4 elimination of the C-3 phosphate and the C-6 proR hydrogen and it has an absolute requirement for reduced flavin. Several mechanisms have been proposed to account for the cofactor requirement and stereochemistry of the reaction, including a radical mechanism. This paper describes the synthesis of [4-(2)H]EPSP and the observation of kinetic isotope effects using this substrate with both Neurospora crassa and Escherichia coli chorismate synthases. The magnitude of the effects were (D)(V) = 1.08 +/- 0.01 for the N. crassa enzyme and 1.10 +/- 0.02 on phosphate release under single-turnover conditions for the E. coli enzyme. The effects are best rationalised as substantial secondary beta isotope effects. It is most likely that the C(3)-O bond is cleaved first in a nonconcerted E1 or radical reaction mechanism. Although this study alone cannot rule out a concerted E2-type mechanism, the C(3)-O bond would have to be substantially more broken than the proR C(6)-H bond in a transition state of such a mechanism. Importantly, although the E. coli and N. crassa enzymes have different rate limiting steps, their catalytic mechanisms are most likely to be chemically identical. Copyright 2000 Academic Press.     

Radical mechanisms in adenosylmethionine- and adenosylcobalamin-dependent enzymatic reactions

A class of enzymatic reactions of S-adenosylmethionine (AdoMet) has recently been recognized, in which AdoMet plays a novel role by initiating free radical formation through the intermediate formation of 5'-deoxyadenosine-5'-yl, the 5'-deoxyadenosyl radical. The reactions are in this way related to adenosylcobalamin-dependent processes, which also depend on the formation of the 5'-deoxyadenosyl radical as an intermediate. The mechanisms by which the 5'-deoxyadenosyl radical is generated by the AdoMet- and adenosylcobalamin-dependent enzymes are very different. However, the functions of the 5'-deoxyadenosyl radical are similar in that in all cases it abstracts hydrogen from a substrate to form 5'-deoxyadenosine and a substrate-derived free radical. In this paper, the role of the 5'-deoxyadenosyl radical in the reaction of the adenosylcobalamin-dependent reactions will be compared with its role in the AdoMet-dependent reaction of lysine 2,3-aminomutase. The mechanism by which AdoMet is cleaved to the 5'-deoxyadenosyl radical at enzymatic sites will also be discussed.     

A kinetic isotope effect study and transition state analysis of the S-adenosylmethionine synthetase reaction

The biosynthesis of S-adenosylmethionine occurs in a unique enzymatic reaction in which the synthesis of the sulfonium center results from displacement of the entire polyphosphate chain from MgATP. The mechanism of S-adenosylmethionine synthetase (ATP:L-methionine s-adenosyltransferase) from Escherichia coli has been characterized by kinetic isotope effect and substrate trapping measurements. Replacement of 12C by 14C at the 5' carbon of ATP yields a primary Vmax/Km isotope effect (12C/14C) of 1.128 +/- 0.003 in the absence of added monovalent cation activator (K+). At saturating K+ concentrations (10 mM) the primary isotope effect diminishes slightly to 1.108 +/- 0.003, indicating that the step in the mechanism involving bond breaking at the 5' carbon of MgATP has a small commitment to catalysis at conditions near Vmax. No alpha-secondary 3H isotope effect from [5'-3H]ATP was detected, (1H/3H) = 1.000 +/- 0.002, even in the absence of KCl. There was no significant primary sulfur isotope effect from [35S]methionine at KCl concentrations from 0 to 10 mM. Substitution of the methyl group of methionine with tritium yielded a beta-secondary isotope effect (CH3/C3H3) = 1.009 +/- 0.008 independent of KCl concentration. The reaction of selenomethionine and [5'-14C]ATP gave a primary isotope effect of 1.097 +/- 0.006, independent of KCl concentration. Substrate trapping experiments demonstrated that the step in the mechanism involving bond making to sulfur of methionine does not have a significant commitment to catalysis at 0.25 mM KCl, therefore intrinsic isotope effects were observed. Substrate trapping experiments indicated that the step involving bond breaking at carbon 5' of MgATP has a 10% commitment to catalysis at 0.25 mM KCl. The isotope effects are interpreted in terms of an Sn2-like transition state structure in which bonding of the C5' is symmetric with respect to the departing tripolyphosphate group and the incoming sulfur of methionine. With selenomethionine as substrate an earlier transition state is implicated.     

Radical oxidation of the adenine moiety of nucleoside and DNA: 2-hydroxy-2'-deoxyadenosine is a minor decomposition product

A method involving high performance liquid chromatography (HPLC) separation associated with tandem mass spectrometry (MS/MS) detection in the multiple reaction monitoring mode was set-up for the measurement of 2-hydroxy-2'-deoxyadenosine (2-OHdAdo). This modified nucleoside, arising from the radical oxidation of 2'-deoxyadenosine (dAdo), has been described in the literature as a potential biological marker of the Fenton reaction. Using the specific and sensitive HPLC-MS/MS assay, 8-oxo-7,8-dihydro-2'-deoxyadenosine, 4,6-diamino-5-formamidopyrimidine and 2-hydroxy-2'-deoxyadenosine (2-OHdAdo) were measured within 2'-deoxyadenosine and DNA solutions either exposed to γ-rays or treated under Fenton reaction conditions. It was found that the yield of 2-OHdAdo was low compared to that of 8-oxodAdo under most of the oxidative conditions studied. In particular and in contrast to previous works, the formation of 2-OHdAdo was shown to be a minor process both upon gamma irradiation and under Fenton reaction conditions. However, a significant yield of formation of 2-OHdAdo was observed either upon incubation with high concentrations of Fe 2+ ions in the absence of hydrogen peroxide or upon γ-radiolysis of a nucleoside solution in the presence of the copper/ ( o )-phenanthroline complex.     

Cofactor dependence of reduction potentials for [4Fe-4S]2+/1+ in lysine 2,3-aminomutase

Lysine 2,3-aminomutase (LAM) catalyzes the interconversion of l-lysine and l-beta-lysine by a free radical mechanism. The 5'-deoxyadenosyl radical derived from the reductive cleavage of S-adenosyl-l-methionine (SAM) initiates substrate-radical formation. The [4Fe-4S](1+) cluster in LAM is the one-electron source in the reductive cleavage of SAM, which is directly ligated to the unique iron site in the cluster. We here report the midpoint reduction potentials of the [4Fe-4S](2+/1+) couple in the presence of SAM, S-adenosyl-l-homocysteine (SAH), or 5'-{N-[(3S)-3-aminocarboxypropyl]-N-methylamino}-5'-deoxyadenosine (azaSAM) as measured by spectroelectrochemistry. The reduction potentials are -430 +/- 2 mV in the presence of SAM, -460 +/- 3 mV in the presence of SAH, and -497 +/- 10 mV in the presence of azaSAM. In the absence of SAM or an analogue and the presence of dithiothreitol, dihydrolipoate, or cysteine as ligands to the unique iron, the midpoint potentials are -479 +/- 5, -516 +/- 5, and -484 +/- 3 mV, respectively. LAM is a member of the radical SAM superfamily of enzymes, in which the CxxxCxxC motif donates three thiolate ligands to iron in the [4Fe-4S] cluster and SAM donates the alpha-amino and alpha-carboxylate groups of the methionyl moiety as ligands to the fourth iron. The results show the reduction potentials in the midrange for ferredoxin-like [4Fe-4S] clusters. They show that SAM elevates the reduction potential by 86 mV relative to that of dihydrolipoate as the cluster ligand. This difference accounts for the SAM-dependent reduction of the [4Fe-4S](2+) cluster by dithionite reported earlier. Analogues of SAM have a weakened capacity to raise the potential. We conclude that the midpoint reduction potential of the cluster ligated to SAM is 1.2 V less negative than the half-wave potential for the one-electron reductive cleavage of simple alkylsulfonium ions in aqueous solution. The energetic barrier in the reductive cleavage of SAM may be overcome through the use of binding energy.     

Transition state analysis for human and Plasmodium falciparum purine nucleoside phosphorylases

Recent studies have shown that Plasmodium falciparum is sensitive to a purine salvage block at purine nucleoside phosphorylase (PNP) and that human PNP is a target for T-cell proliferative diseases. Specific tight-binding inhibitors might be designed on the basis of specific PNP transition state structures. Kinetic isotope effects (KIEs) were measured for arsenolysis of inosine catalyzed by P. falciparum and human purine nucleoside phosphorylases. Intrinsic KIEs from [1'-(3)H]-, [2'-(3)H]-, [1'-(14)C]-, [9-(15)N]-, and [5'-(3)H]inosines were 1.184 +/- 0.004, 1.031 +/- 0.004, 1.002 +/- 0.006, 1.029 +/- 0.006, and 1.062 +/- 0.002 for the human enzyme and 1.116 +/- 0.007, 1.036 +/- 0.003, 0.996 +/- 0.006, 1.019 +/- 0.005, and 1.064 +/- 0.003 for P. falciparum PNPs, respectively. Analysis of KIEs indicated a highly dissociative D(N)A(N) (S(N)1) stepwise mechanism with very little leaving group involvement. The near-unity 1'-(14)C KIEs for both human and P. falciparum PNP agree with the theoretical value for a 1'-(14)C equilibrium isotope effect for oxacarbenium ion formation when computed at the B1LYP/6-31G(d) level of theory. The 9-(15)N KIE for human PNP is also in agreement with theory for equilibrium formation of hypoxanthine and oxacarbenium ion at this level of theory. The 9-(15)N KIE for P. falciparum PNP shows a constrained vibrational environment around N9 at the transition state. A relatively small beta-secondary 2'-(3)H KIE for both enzymes indicates a 3'-endo conformation for ribose and relatively weak hyperconjugation at the transition state. The large 5'-(3)H KIE reveals substantial distortion at the 5'-hydroxymethyl group which causes loosening of the C5'-H5' bonds during the reaction coordinate.     

Carbon isotope effects on the decarboxylation of carboxylic acids. Comparison of the lactate oxidase reaction and the degradation of pyruvate by H2O2.

The isotope effect at C-1 on the H2O2-catalysed decarboxylation of pyruvate (used as a model reaction for the enzymic reaction) increases between pH 3 and 10 from 1.0007 +/- 0.0004 to 1.0283 +/- 0.0014 (25 degrees C). This result indicates a change in the rate-determining step from formation of the tetrahedral intermediate to decarboxylation of this intermediate. Practically no isotope fractionation at C-1 (1.0011 +/- 0.0002, pH 6.0, 25 degrees C) is found in the lactate oxidase-catalysed decarboxylation of lactate, which is indicative for the existence of an irreversible O2-dependent step prior to the enzyme-catalysed decarboxylation. In addition, the result provides further evidence that dissociation of pyruvate and H2O2 from the enzyme can be excluded. The isotope effect at C-2 of lactate in the enzymic reaction (1.0048 +/- 0.0004) is attributed to the hydrogen transfer step from lactate to the coenzyme.     

Malate synthase: proof of a stepwise Claisen condensation using the double-isotope fractionation test

Although aldolase-catalyzed condensations proceed by stepwise mechanisms via the intermediacy of nucleophilic enol(ate)s or enamines, the mechanisms of those enzymes that catalyze Claisen-type condensations are unclear. The reaction pathway followed by an enzyme from this second group, malate synthase, has been studied by the double-isotope fractionation method to determine whether the reaction is stepwise or concerted. In agreement with earlier work, a deuterium kinetic isotope effect D(V/K) of 1.3 +/- 0.1 has been found when [2H3]acetyl-CoA is the substrate. The 13C isotope effect at the aldehydic carbon of glyoxylate has also been measured. For this determination, the malate product (containing the carbon of interest at C-2) was quantitatively transformed into a new sample of malate having the carbon of interest at C-4. This material was decarboxylated by malic enzyme to produce the appropriate CO2 for isotope ratio mass spectrometric analysis. The 13C isotope effect with [1H3]acetyl-CoA [that is, 13(V/K)H] is 1.0037 +/- 0.0004. By use of the known values of the intermolecular and intramolecular deuterium effects and of 13(V/K)H, the value of the 13C isotope effect when deuteriated [2H3]acetyl-CoA is the substrate [that is, 13(V/K)D] can be predicted for three possible mechanisms. If 13(V/K)H is a kinetic isotope effect and the reaction is concerted, the value of the 13C effect on deuteriation of acetyl-CoA will rise to 1.011; if 13(V/K)H is a kinetic isotope effect and the reaction is stepwise, the value of the 13C effect will fall to 1.0025; and if the 13C effect is an equilibrium isotope effect deriving from glyoxylate dehydration, the reaction is necessarily stepwise, and the value of 13(V/K)D will be 1.0037, unchanged from that of 13(V/K)H. Experimentally, the value of 13(V/K)D is 1.0037 +/- 0.0007, which requires that malate synthase follow a stepwise path. It is therefore clear that the two salient characteristics of enzymes that catalyze Claisen-like condensations, namely, the absence of enzyme-catalyzed proton exchange with solvent and the inversion of the configuration at the nucleophilic center, which had been suggestive of a concerted pathway, are not mechanistically diagnostic.     

Mechanistic study on the reaction of a radical SAM dehydrogenase BtrN by electron paramagnetic resonance spectroscopy

BtrN is a radical SAM ( S-adenosyl- l-methionine) enzyme that catalyzes the oxidation of 2-deoxy- scyllo-inosamine (DOIA) into 3-amino-2,3-dideoxy- scyllo-inosose (amino-DOI) during the biosynthesis of 2-deoxystreptamine (DOS) in the butirosin producer Bacillus circulans. Recently, we have shown that BtrN catalyzes the transfer of a hydrogen atom at C-3 of DOIA to 5'-deoxyadenosine, and thus, the reaction was proposed to proceed through the hydrogen atom abstraction by the 5'-deoxyadenosyl radical. In this work, the BtrN reaction was analyzed by EPR spectroscopy. A sharp double triplet EPR signal was observed when the EPR spectrum of the enzyme reaction mixture was recorded at 50 K. The spin coupling with protons partially disappeared by reaction with [2,2- (2)H 2]DOIA, which unambiguously proved the observed signal to be a radical on C-3 of DOIA. On the other hand, the EPR spectrum of the [4Fe-4S] cluster of BtrN during the reaction showed a complex signal due to the presence of several species. Comparison of signals derived from a [4Fe-4S] center of BtrN incubated with various combinations of products (5'-deoxyadenosine, l-methionine, and amino-DOI) and substrates (SAM and DOIA) indicated that the EPR signals observed during the reaction were derived from free BtrN, a BtrN-SAM complex, and a BtrN-SAM-DOIA complex. Significant changes in the EPR signals upon binding of SAM and DOIA suggest the close interaction of both substrates with the [4Fe-4S] cluster.     

Binding of carbon dioxide to phosphoenolpyruvate carboxykinase deduced from carbon kinetic isotope effects.

Phosphoenolpyruvate carboxykinase [ATP:oxaloacetate carboxy-lyase (transphosphorylating), EC 4.1.1.49] from Chloris gayana Kunth has been purified by a combination of ammonium sulfate fractionation, ion exchange, gel filtration, and affinity chromatography on agarose-hexane-ATP. In the direction of OAA formation, the specific activity of the enzyme was 33 mumol/(min.mg of protein). The carbon isotope effect on carboxylation was measured by successive analysis of remaining CO2 over the course of the reaction. At 22 mM PEP and 1.3 mM MgADP, pH 7.5, the isotope effect is 1.024 +/- 0.001. When the concentration of PEP was reduced to 1 mM, the isotope effect rose to 1.034 +/- 0.004; when the concentration of MgADP was reduced to 60 microM, the value rose to 1.040 +/- 0.006. The variation of the carbon isotope effect on carboxylation with both substrate concentrations indicates that the enzyme operates by a random kinetic mechanism. This in turn requires that the enzyme have a binding site for substrate CO2; this is one of the first enzymes for which such a site has been demonstrated.     

Isotopic probes of the argininosuccinate lyase reaction

The mechanism of the argininosuccinate lyase reaction has been probed by the measurement of the effects of isotopic substitution at the reaction centers. A primary deuterium isotope effect of 1.0 on both V and V/K is obtained with (2S,3R)-argininosuccinate-3-d, while a primary 15N isotope effect on V/K of 0.9964 +/- 0.0003 is observed. The 15N isotope effect on the equilibrium constant is 1.018 +/- 0.001. The proton that is abstracted from C-3 of argininosuccinate is unable to exchange with the solvent from the enzyme-intermediate complex but is rapidly exchanged with solvent from the enzyme-fumarate-arginine complex. A deuterium solvent isotope effect of 2.0 is observed on the Vmax of the forward reaction. These and other data have been interpreted to suggest that argininosuccinate lyase catalyzes the cleavage of argininosuccinate via a carbanion intermediate. The proton abstraction step is not rate limiting, but the inverse 15N primary isotope effect and the solvent deuterium isotope effect suggest that protonation of the guanidino group and carbon-nitrogen bond cleavage of argininosuccinate are kinetically significant.