Tetrahydropteroylpolyglutamate derivatives as substrates of two multifunctional proteins with folate-dependent enzyme activities

Several of the folate-mediated reactions in eucaryotic cells are carried out by multifunctional proteins using the naturally occurring pteroylpolyglutamate derivatives. The compounds tetrahydropteroyl(glutamate)_n where n = 1, 3, 5, or 7 were used to determine whether the additional glutamyl residues on the substrates provide kinetic advantages with two folate-dependent multifunctional protein. Methylenetetrahydrofolate dehydrogenase(EC 1.5.1.5)-methenyltetrahydrofolate cyclohydrolase (EC 3.5.4.9)-formyltetrahydrofolate synthetase (EC 6.3.4.3) activities comprise a trifunctional protein, and formiminoglutamate:tetrahydrofolate formiminotransferase(EC 2.1.2.5)-formiminotetrahydrofolate cyclodeaminase (EC 4.3.1.40 for a bifunctional one. The dehydrogenase, transferase and synthetase were found to have 10–40-fold lower K_m values for the tetrahydropteroylpolyglutamate derivatives with essentially unchanged values of V. Specificities with cyclodeaminase and cyclo-activities; hydrolase were determined by using pteroylglutamates as inhibitors of the activities; pteroylpentaglutamate is a 70-fold better inhibitor than folate with cyclodeaminase, but is only 10-fold better with cyclohydrolase. Because of the sequential nature of the enzymic activities in these multifunctional proteins, the tetrahydropteroylpolyglutamate substrates were examined to see if they provide a kinetic advantage by promoting transfer of folate intermediates between active sites on a single enzyme molecule. With the sequential transferase-deaminase activities, it was observed that the product of the transferase accumulates in the medium with tetrahydropteroylmonoglutamate as the substrate, but does not when the pentaglutamate is used. Chemical modification to selectively inactive the transferase and deaminase, followed by recombination, demonstrated that this kinetic property is observed because the intermediate formiminotetrahydropteroylpentaglutamate is transferred preferentially to the daminase site rather than equilibrating with the medium.     

Steady-state kinetic mechanism of Ras farnesyl:protein transferase.

The steady-state kinetic mechanism of bovine brain farnesyl:protein transferase (FPTase) has been determined using a series of initial velocity studies, including both dead-end substrate and product inhibitor experiments. Reciprocal plots of the initial velocity data intersected on the 1/[s] axis, indicating that a ternary complex forms (sequential mechanism) and suggesting that the binding of one substrate does not affect the binding of the other. The order of substrate addition was probed by determining the patterns of dead-end substrate and product inhibition. Two nonhydrolyzable analogues of farnesyl diphosphate, (alpha-hydroxyfarnesyl)phosphonic acid (1) and [[(farnesylmethyl)hydroxyphosphinyl]methyl]phosphonic acid (2), were both shown to be competitive inhibitors of farnesyl diphosphate and noncompetitive inhibitors of Ras-CVLS. Four nonsubstrate tetrapeptides, CV[D-L]S, CVLS-NH2, N-acetyl-L-penicillamine-VIM, and CIFM, were all shown to be noncompetitive inhibitors of farnesyl diphosphate and competitive inhibitors of Ras-CVLS. These data are consistent with random order of substrate addition. Product inhibition patterns corroborated the results found with the dead-end substrate inhibitors. We conclude that bovine brain FPTase proceeds through a random order sequential mechanism. Determination of steady-state parameters for several physiological Ras-CaaX variants showed that amino acid changes affected the values of KM, but not those of kcat, suggesting that the catalytic efficiencies (kcat/KM) of Ras-CaaX substrates depend largely upon their relative binding affinity for FPTase.     

Glucose-6-phosphate dehydrogenase from rabbit erythrocytes

Glucose-6-phosphate dehydrogenase (d-glucose-6-phosphate:NADP⁺ 1-oxidoreductase, EC 1.1.1.49) was purified from rabbit erythrocytes. Initial velocity studies and product and dead-end inhibitor studies with this enzyme are consistent with a rapid equilibrium random mechanism with an enzyme-NADPH-glucose 6-phosphate dead-end complex.     

The kinetic mechanism of pyruvate reduction by lactate dehydrogenase from Phycomyces blakesleeanus

The kinetics of pyruvate reduction by lactate dehydrogenase from Phycomyces blakesleeanus NRRL 1555 (-) have been determined at pH 6.0. Initial rate studies performed in the pyruvate reduction direction suggest that a sequential mechanism is operating. Product inhibition studies with NAD+ and L(+)-lactate are consistent with an ordered sequential mechanism if we considered that NAD+ mimics the NADH that binds cooperatively on the enzyme and also the existence of dead-end complex responsible for substrate inhibition by pyruvate at this pH value.     

Formiminotransferase-cyclodeaminase from porcine liver. A sulfhydryl essential for the deaminase activity of the bifunctional enzyme

Reaction of the bifunctional enzyme formiminoglutamate:tetrahydrofolate formiminotransferase (EC 2.1.2.5) - formiminotetrahydrofolate cyclodeaminase (EC 4.3.1.4) with the sulfhydryl reagent 5,5'-dithiobis (2-nitrobenzoic acid) selectively inactivates the cyclodeaminase. Loss of activity correlates with the modification of two sulfhydryl groups per subunit. The inhibitor folic acid reduces the rates of inactivation and sulfhydryl modification, and protection experiments demonstrate that only one of the two sulfhydryls modified is important for enzyme activity. The results indicate the presence of a cyclodeaminase site on each polypeptide, assuming one sulfhydryl per site, in agreement with a quaternary structure containing identical polypeptides. Modification does not cause dissociation of the enzyme and is reversible with dithiothreitol.     

Regulation of smooth-muscle myosin-light-chain kinase. Steady-state kinetic studies of the reaction mechanism

The kinetic mechanism of turkey gizzard smooth muscle myosin-light-chain kinase was investigated using the isolated 20-kDa light chain of myosin as substrate. The kinetic and product inhibition patterns of the forward reaction indicated an ordered sequential mechanism in which MgATP bound first, ADP was released last. The order of substrate binding and product release was confirmed independently by competitive, dead-end inhibition patterns obtained using the non-hydrolizable ATP analog adenosine 5'-[beta,gamma-imido]triphosphate. The mechanism was also characterized by a relatively strong product inhibition by ADP and a weak one by phosphorylated 20-kDa light-chain myosin, in addition to a significant inhibition by the latter product via a formation of a dead-end complex. [gamma-32P]ATP in equilibrium with [32P]phosphorylated light chain isotope-exchange data were consistent with the deduced mechanism and with the presence of the latter dead-end complex.     

Substrate inhibition in a human variant of hypoxanthine-guanine phosphoribosyltransferase

Hypoxanthine-guanine phosphoribosyltransferase from a young man with purine overproduction and decreased purine salvage in fibroblast cultures was found to have low activity at concentrations of purine substrates at which the enzyme from normal individuals showed near maximal activity. The low enzyme activity was not associated with changes in the values of the Km(app) and Vmax(app) for any of the enzyme substrates. However, the enzyme activity was susceptible to substrate inhibition by hypoxanthine and guanine. The values obtained for the true Km, true Vmax, and true Ki for hypoxanthine were 26 +/- 10 microM, 1761 +/- 382 microunits/mg of protein, and 80 +/- 20 microM, respectively. The pattern of the substrate inhibition, as seen on a plot of 1/v versus hypoxanthine concentration, was characteristic of that associated with the formation of a dead-end complex between the inhibitory substrate and an enzyme form with which it normally does not react. The nature of this enzyme form and that of the dead-end complex was determined from double inhibition experiments, which indicated that hypoxanthine interacted with an enzyme-PPi intermediate to form an enzyme-hypoxanthine-PPi dead-end complex. The trapping of the enzyme in this inactive form explains the low activity at high purine base concentrations. Further information as to the nature of the reaction mechanism was obtained from plots of the reciprocal of enzyme activity versus the reciprocal of PP-ribose-P concentration at different fixed hypoxanthine concentrations. A pattern characteristic of uncompetitive substrate inhibition was obtained. This is indicative of an ordered sequential binding of substrates on the enzyme; PP-ribose-P binding before hypoxanthine. Thus, the variant enzyme showed an ordered sequential reaction mechanism, with the inhibitory substrate forming a dead-end complex with an enzyme-PPi intermediate.     

Anabolic ornithine carbamolytransferase of Pseudomonas. The bases of its functional specialization.

The anabolic ornithine carbamoyltransferase of Pseudomonas appears to be extremely specialized. Unlike the other carbamoyltransferases studied, this enzyme catalyzes the phosphorolytic cleavage of citrulline with a very poor efficiency. The main goal of this paper is to understand what, in the catalytic process, causes this directed functional specialization. On the basis of kinetic data and thermodynamic properties of the reaction, it appears that the reaction mechanism is the same as for ornithine carbamoyltransferases from other sources, that is, of the sequential ordered type, where carbamoylphosphate is the first substrate to be bound and phosphate the last product to be released. In addition to this, and here lies the difference with other ornithine carbamoyltransferases, the anabolic transferase of Pseudomonas forms a binary dead-end complex with citrulline, leading to inefficient binding of phosphate and citrulline to the enzyme. Therefore the phosphorolytic cleavage of citrulline is equally inefficient. It should be mentioned that the affinity of the enzyme for citrulline at its catalytic site is low as compared to other transferases.     

Random-order ternary complex reaction mechanism of serine acetyltransferase from Escherichia coli

Although serine acetyltransferase (SAT) from Escherichia coli is homologous with a number of bacterial enzymes that catalyze O-acetyl transfer by a sequential (ternary complex) mechanism, it has been suggested, from experiments with the nearly identical enzyme from Salmonella typhimurium, that the reaction could proceed via an acetyl-enzyme intermediate. To resolve the matter, the E. coli gene for SAT was overexpressed and the enzyme purified 13-fold to homogeneity. The results of a steady-state kinetic analysis of the forward reaction are diagnostic for a ternary complex mechanism, and the response of SAT to dead-end inhibitors indicates a random order for the addition of substrates. The linearity of primary double-reciprocal plots, in the presence and absence of dead-end inhibitors, argues that interconversion of ternary complexes is not significantly faster than kcat, whereas substrate inhibition by serine suggests that breakdown of the SAT.CoA binary complex is rate-determining. The results of equilibrium isotope exchange experiments, for both half-reactions, rule out a "ping-pong" mechanism involving an acetyl-enzyme intermediate, and a pre-steady-state kinetic analysis of the turnover of AcCoA supports such a conclusion. Kinetic data for the reverse reaction (acetylation of CoA by O-acetylserine) are also consistent with a steady-state random-order mechanism, wherein both the breakdown of the SAT*serine complex and the interconversion of ternary complexes are partially rate-determining.     

The substrate specificity, kinetics, and mechanism of glycerate-3-kinase from spinach leaves

Glycerate-3-kinase (EC 2.7.1.31) from spinach leaves shows absolute specificity for D-glycerate as phosphate acceptor, yielding 3-phosphoglycerate as a product. ATP complexed with either Mg2+ or Mn2+ is the preferred phosphate donor. The enzyme has Km (D-glycerate) = 0.25 mM, Km (Mg-ATP) = 0.21 mM, Vmax = 300 mumol min-1 mg protein-1, and a turnover number = 12,000 X min-1. The equilibrium constant for the reaction is approximately 300 at pH 7.8. Pyrophosphate, 3-phosphoglycerate and ribulose 1,5-bisphosphate are the strongest inhibitors among the phosphorylated and nonphosphorylated metabolites tested; however, their regulatory role in vivo is questioned. Substrate kinetics, as well as product and analog inhibition data, are consistent with a sequential random mechanism. The distinct characteristic of the glycerate kinase-catalyzed reaction is the formation of a dead-end complex between the enzyme, D-glycerate, and 3-phosphoglycerate.     

The enzymatic mechanism of glucuronidation catalyzed by two purified rat liver steroid UDP-glucuronosyltransferases

A kinetic analysis of two homogeneous rat liver steroid (3 alpha-hydroxysteroid and 17 beta-hydroxysteroid) UDP-glucuronosyltransferases was conducted using bisubstrate kinetic analysis, product inhibition studies, and dead-end competitive inhibition studies. Double reciprocal plots of initial velocity versus substrate concentration, using bisubstrate kinetic analysis, gave a sequential mechanism. Product inhibition studies were compatible with either a rapid equilibrium, random-order kinetic mechanism or an ordered Theorell-Chance mechanism. Results of dead-end competitive inhibition studies excluded an ordered Theorell-Chance mechanism. The cumulative results are consistent with a rapid equilibrium random-order sequential kinetic mechanism for the glucuronidation of testosterone by purified 17 beta-hydroxysteroid UDP-glucuronosyltransferase and of androsterone by purified 3 alpha-hydroxysteroid UDP-glucuronosyltransferase.     

Accumulation and depletion of trans octadecenoic acid in rat peripheral nerve phospholipid

Crude extracts from cells of a Streptomyces strain isolated from a palm-grove soil and grown on different carbon sources showed a constitutive glucokinase. Specifically inducible kinase activity for mannose was found in cells grown on mannose or beta-D-mannan. The activity on mannose was due to a highly specific mannokinase (ATP:D-mannose 6-phosphotransferase, EC 2.7.1.7) which has been separated from the glucokinase by Ultrogel AcA 54 gel filtration chromatography. Initial velocity and inhibition product studies were carried out to investigate the reaction pathway. In the absence of products, reciprocal plots intersecting on the abscissas were observed when either mannose or ATP concentration was varied in the presence of several fixed concentrations of the non-varied substrate. Km values for mannose and Mg-ATP complex are 0.33 and 1.1 mM, respectively. In the product inhibition studies, mannose-6-P was observed to be competitive with mannose and non-competitive with Mg-ATP. The reverse was observed when ADP was used as inhibitor. These data are consistent with a random sequential Bi-Bi mechanism with two dead-end ternary complexes.     

Kinetic mechanism of histidine-tagged homocitrate synthase from Saccharomyces cerevisiae

Kinetic data have been collected suggesting a preferred sequential ordered kinetic mechanism for the histidine-tagged homocitrate synthase (HCS) from Saccharomyces cerevisiae with alpha-ketoglutarate binding before AcCoA and CoA released before homocitrate. Oxaloacetate is also a substrate for HCS, but with lower affinity than alpha-ketoglutarate. In agreement with the ordered kinetic mechanism desulfo-CoA is uncompetitive and citrate is competitive vs alpha-ketoglutarate. Varying AcCoA, citrate is a noncompetitive inhibitor as predicted, but CoA is noncompetitive vs AcCoA suggesting binding of CoA to E:homocitrate and E:alpha-ketoglutarate. The product CoA behaves in a manner identical to the dead-end analogue desulfo-CoA, suggesting an E:alpha-ketoglutarate:CoA dead-end complex. Data further suggest an irreversible reaction overall, in agreement with the downhill nature of the reaction as a result of homocitryl-CoA hydrolysis. Fluorescence titration data generally agree with the steady state data, but show finite binding of CoA and AcCoA to free enzyme, suggesting that the mechanism may be random with a high degree of synergism of binding between the reactants.     

Kinetics of human erythrocyte glucose-6-phosphate dehydrogenase dimers

The steady-state kinetics of human erythrocyte glucose-6-phosphate dehydrogenase (D-glucose-6-phosphate: NADP+ 1-oxidoreductase, EC 1.1.1.49) dimers were studied by initial rate measurement. These experiments gave intersecting double-reciprocal plots suggesting a ternary complex mechanism with a Km for NADP and glucose 6-phosphate of 11 microM and 43 microM, respectively. These studies were combined with rate measurements in the presence of one product (NADPH), dead-end inhibitors, as well as alternative substrates. The inhibition by NADPH was found to be competitive with respect to both substrates. Alternate substrates experiments gave linear double-reciprocal plots over a wide range of substrate concentrations. The results suggest that the dimeric enzyme follows either a random or a Theorell-Chance mechanism.     

Kinetic studies on the enzyme (S)-hydroxynitrile lyase from hevea brasiliensis using initial rate methods and progress curve analysis

(S)-Hydroxynitrile lyase (EC 4.1.2.39) from Hevea brasiliensis(rubber tree) catalyzes the reversible cleavage of cyanohydrins to aldehydes or ketones and prussic acid (HCN). Enzyme kinetics in both directions was studied on a model system with mandelonitrile, benzaldehyde, and HCN using two different methods-initial rate measurements and progress curve analysis. To discriminate between possible mechanisms with the initial rate method, product inhibition was studied. Benzaldehyde acts as a linear competitive inhibitor against mandelonitrile whereas HCN shows S-linear I-parabolic mixed-type inhibition. These results indicate an Ordered Uni Bi mechanism with the formation of a dead-end complex of enzyme, (S)-mandelonitrile and HCN. Prussic acid is the first product released from the enzyme followed by benzaldehyde. For progress curve analysis, a kinetic model of an Ordered Uni Bi mechanism including a dead-end complex, enzyme inactivation, and the chemical parallel reaction was set up, which described the experimental values very well. From the reaction rates obtained the kinetic constants were calculated and compared with the ones obtained from the initial rate method. Good agreement could be achieved between the two methods supporting the suggested mechanism. Copyright 1999 John Wiley & Sons, Inc.     

Methanococcus jannaschii generates L-proline by cyclization of L-ornithine

Cell extracts of Methanococcus jannaschii have been shown to readily convert L-ornithine to L-proline. This cyclization reaction proceeds with the loss of only the C-2 nitrogen, as has been documented for ornithine cyclodeaminase (EC 4.3.1.12). Since no gene homologous to that coding for ornithine cyclodeaminase is present in the genome of M. jannaschii, these results indicate that proline biosynthesis in M. jannaschii is accomplished by a previously unrecognized enzyme.     

3-Deoxy-D-arabino-heptulosonate 7-phosphate synthase. Purification, properties, and kinetics of the tyrosine-sensitive isoenzyme from Escherichia coli.

The tyrosine-sensitive 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase (7-phospho-2-keto-3-deoxy-D-arabino-heptonate D-erythrose-4-phosphate lyase (pyruvate-phosphorylating), EC 4.2.1.15) was purified to homogeneity from extracts of Escherichia coli K12. A spectrophotometric assay of the enzyme activity, based on the absorption difference of substrates and products at 232 nm, was developed. The enzyme has a molecular weight of 66,000 as judged by gel filtration on Sephadex G-200, and a subunit molecular weight of 39,000 as determined by polyacrylamide gel electrophoresis in the presence of sodium dodecyl sulfate. This suggests either a rapid monomer-dimer equilibrium, or a very asymmetric shape for the native enzyme. The enzyme shows a narrow pH optimum around pH 7.0. The enzyme is stable for several months when stored at -20 degrees in phosphate buffer containing phosphoenol-pyruvate. Intersecting lines in double reciprocal plots of initial velocity data at substrate concentrations in the micromolar range suggest a sequential mechanism with-catalyzed reaction. Product inhibition studies specify an ordered sequential BiBi mechanism with a dead-end E-P complex. The feedback inhibitor tyrosine at concentrations above 10 muM exhibits noncompetitive inhibition with respect to erythrose-4-P, and competitive inhibition with respect to the other substrate, P-enolpyruvate. In addition, tyrosine at concentrations of at least 10 muM causes an alteration of one or more than one kinetic parameter of the enzyme.     

A study of the kinetic mechanism followed by glutathione reductase from mycelium of Phycomyces blakesleeanus

An investigation of the reaction mechanism of glutathione reductase isolated from the mycelium of Phycomyces blakesleeanus NRRL 1555(-) was conducted. The enzyme showed GSSG concentration-dependent substrate inhibition by NADPH and pH-dependent substrate inhibition by GSSG. At pH 7.5, the kinetic data were consistent with a basic scheme corresponding to the branching mechanism, involving a ping-pong with formation of a dead-end F.NADPH complex and an ordered sequential mechanism. Both pathways have in common the step in which NADPH binds to the free oxidized form (E) of the glutathione reductase. At low concentrations of GSSG the ping-pong mechanism prevails, whereas at high concentrations the ordered mechanism appears to dominate. The data were analyzed on the basis of the limiting ping-pong mechanism with F.NADPH complex formation and of the hybrid mechanism, and the kinetic constants of the model were calculated. The data obtained at acidic pH values do not rule out the possibility that the kinetic model may be more complicated than the basic scheme studied.     

Partial purification, properties, and kinetic studies of UDP-glucose:p-hydroxybenzoate glucosyltransferase from cell cultures of Lithospermum erythrorhizon.

A glucosyltransferase, which catalyzed the transfer of glucose from UDP-glucose (UDPG) to p-hydroxybenzoate (PHB) in cell cultures of Lithospermum erythrorhizon Sieb. et Zucc., Boraginaceae, was purified 219-fold by ammonium sulfate fractionation and chromatography on DEAE-Sephacel, Sephadex G-150, and phenyl-Sepharose Cl-4B. p-Hydroxybenzoic acid O-beta-D-glucoside (PHB-glc) was identified as a product of the enzymatic reaction. This glucosyltransferase has a molecular weight of 47,500 Da, an isoelectric point at pH 5.0, and a pH optimum of 7.8. The enzyme does not sediment at 100,000g. Enzyme activity did not require metal cofactors. The enzyme was highly specific for p-hydroxybenzoate (Km 0.264 mM) and UDP-glucose (Km 0.268 mM). Initial velocity studies suggest that the enzyme reaction mechanism is a sequential rather than a ping-pong mechanism. Product inhibition patterns are consistent with an ordered sequential bi-bi mechanism, where UDPG is the first substrate to bind to the enzyme and UDP the final product released. The data indicate the formation of a dead-end complex between PHB-glc and the enzyme. Uncompetitive inhibition by the substrate PHB can be put down to the formation of an abortive complex between E-UDP and PHB.     

The nature of the substrate inhibition of cytoplasmic malate dehydrogenase from Phycomyces blakesleeanus

The mechanism that leads to substrate inhibition of cytoplasmic malate dehydrogenase (l-malate:NAD oxidoreductase, EC 1.1.1.37) from mycelium of Phycomyces blakesleeanus was investigated. A dead-end complex between enzyme and the enol-oxalacetate form appears to be responsible for this inhibition. The formation of the complex occurs more readily at acidic pH values. Results of this study suggest that the binding of oxalacetate as inhibitor prevent the NADH binding, with an estimated K_i for oxalacetate of 1.8 ± 0.1 mM. Such a competitive inhibition implies that the binding site for oxalacetate is the same both as inhibitor as well as substrate.