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J F Kirsch

Publications and source records attributed to J F Kirsch.

At least 73 records · Page 4Linked to original sources
PubMed1989

Site-directed mutagenesis of the catalytic residues Asp-52 and Glu-35 of chicken egg white lysozyme.

The roles of the catalytic active-site residues aspartic acid-52 and glutamic acid-35 of chicken lysozyme (EC 3.2.1.17) have been investigated by separate in vitro mutagenesis of each residue to its corresponding amide (denoted as D52N and E35Q, respectively). The mutant enzyme D52N exhibits approximately 5% of the wild-type lytic activity against Micrococcus luteus cell walls, while there is no measurable activity associated with E35Q (0.1% +/- 0.1%). The measured dissociation constants for the chitotriose-enzyme complexes were 4.1 microM (D52N) and 13.4 microM (E35Q) vs. 8.6 microM for wild type, indicating that the alterations in catalytic properties may be due in part to binding effects as well as to direct catalytic participation of these residues. The mutant lysozymes have been expressed in and secreted from yeast and obtained at a level of approximately 5 mg per liter of culture by high-salt elution from the cell walls.

Animals↗
PubMed1988

Role of arginine-292 in the substrate specificity of aspartate aminotransferase as examined by site-directed mutagenesis.

X-ray crystallographic data have implicated Arg-292 as the residue responsible for the preferred side-chain substrate specificity of aspartate aminotransferase. It forms a salt bridge with the beta or gamma carboxylate group of the substrate [Kirsch, J. F., Eichele, G., Ford, G. C., Vincent, M. G., Jansonius, J. N., Gehring, H., & Christen, P. (1984) J. Mol. Biol. 174, 497-525]. In order to test this proposal and, in addition, to attempt to reverse the substrate charge specificity of this enzyme, Arg-292 has been converted to Asp-292 by site-directed mutagenesis. The activity (kcat/KM) of the mutant enzyme, R292D, toward the natural anionic substrates L-aspartate, L-glutamate, and alpha-ketoglutarate is depressed by over 5 orders of magnitude, whereas the activity toward the keto acid pyruvate and a number of aromatic and other neutral amino acids is reduced by only 2-9 fold. These results confirm the proposal that Arg-292 is critical for the rapid turnover of substrates bearing anionic side chains and show further that, apart from the desired alteration, no major perturbations of the remainder of the molecule have been made. The activity of R292D toward the cationic amino acids L-arginine, L-lysine, and L-ornithine is increased by 9-16-fold over that of wild type and the ratio (kcat/KM)cationic/(kcat/KM)anionic is in the range 2-40-fold for R292D, whereas this ratio has a range of [(0.3-6) x 10(-6)]-fold for wild type. Thus, the mutation has produced an inversion of the substrate charge specificity.(ABSTRACT TRUNCATED AT 250 WORDS)

Arginine↗
PubMed1987

Tyrosine 70 increases the coenzyme affinity of aspartate aminotransferase. A site-directed mutagenesis study.

The crucial step in enzymatic transamination is the tautomerization of aldimine/ketimine intermediates, formed between the pyridoxyl coenzyme and the amino/keto acid substrate, which is catalyzed primarily by the active site residue Lys-258 (Malcolm, B. A., and Kirsch, J. F. (1985) Biochem. Biophys. Res. Commun. 132, 915-921; W. L. Finlayson and J. F. Kirsch, in preparation). Tyr-70 is localized in close proximity to Lys-258 and, in addition, forms a hydrogen bond with the coenzyme phosphate. Tyr-70 has been postulated to have an important role in the tautomerization (Kirsch, J. F., Eichele, G., Ford, G. C., Vincent, M. G., Jansonius, J. N., Gehring, H., and Christen, P. (1984) J. Mol. Biol. 174, 497-525). This hypothesis has now been tested by the construction and analysis of a mutant Escherichia coli aspartate aminotransferase in which Tyr-70 has been changed to Phe (Y70F). Y70F retains at least 15% of the maximal activity of the wild type enzyme (WT) (kcat = 170 +/- 15 s-1 for WT versus greater than or equal to 26 +/- 3 s-1 for Y70F and shows increased Michaelis constants for both substrates (KmAsp = 2.5 +/- 0.4 mM; Km alpha Kg = 0.59 +/- 0.08 mM for WT versus KmAsp = 3.9 +/- 0.3 mM; Km alpha Kg = 2.70 +/- 0.02 mM for Y70F (where alpha Kg is alpha-ketoglutarate) ). The spectrophotometrically determined pK a values of the internal aldimines formed between pyridoxal 5'-phosphate (PLP) and Lys-258 are identical for WT and Y70F. In assays where excess L-aspartate and excess PLP are incubated with either WT or Y70F, the mutant enzyme converts the free PLP to free pyridoxamine 5'-phosphate 80-fold faster than WT (k = (3.75 +/- 0.23) X 10(-2)s-1 for Y70F versus (4.90 +/- 0.02) X 10(-4)s-1 for WT). Y70F also converts free pyridoxamine 5'-phosphate to free PLP faster than WT. Thus, Y70F dissociates coenzyme more readily than does WT. It therefore appears that the role of Tyr-70 is mainly in preventing the dissociation of the coenzyme from the enzyme. Tyr-70 does not function in an essential chemical step.

Aspartate Aminotransferases↗
PubMed1987

The stereospecific labilization of the C-4' pro-S hydrogen of pyridoxamine 5'-phosphate is abolished in (Lys258----Ala) aspartate aminotransferase.

Reconstitution of wild-type apoaspartate aminotransferase from Escherichia coli with [4'-3H]pyridoxamine 5'-phosphate results in stereospecific release of the pro-S C-4' 3H to the solvent. The reaction follows first-order kinetics (t1/2 = 15 min at pH 7.5 and 25 degrees C), its rate constant being similar to that found previously with mitochondrial aspartate aminotransferase from chicken (Tobler, H.P., Christen, P., and Gehring, H. (1986) J. Biol. Chem. 261, 7105-7108). Substituting the active site residue Lys258 by alanine via site-directed mutagenesis yields a catalytically inactive enzyme (Malcolm, B. A., and Kirsch, J. F. (1985) Biochem. Biophys. Res. Commun. 132, 915-921). This mutant enzyme fails to release any measurable 3H from bound [4'-3H]pyridoxamine 5'-phosphate. The data are consistent with earlier proposals that Lys258 is indispensable for the ketimine/aldimine tautomerization, and corroborate the previous conclusion that 3H exchange from enzyme-bound pyridoxamine 5'-phosphate mechanistically corresponds to the deprotonation at C-4' of the ketimine intermediate during the transamination reaction.

Alanine↗
PubMed1986

Preliminary X-ray data for aspartate aminotransferase from Escherichia coli.

Crystals of the aspartate aminotransferase from Escherichia coli (aspC gene product) have been examined by X-ray analysis. The crystals grow as elongated rectangular prisms, with the symmetry of space group C2221. Unit cell dimensions are a = 156 A, b = 87.6 A, c = 80.6 A and alpha = beta = gamma = 90 degrees. There is one protein subunit of molecular weight 43,600 per asymmetric unit.

Aspartate Aminotransferases↗
PubMed1986

Fractional diffusion-limited component of reactions catalyzed by acetylcholinesterase.

The values of kcat/Km for the reactions of four substrates, p-nitrophenyl acetate (PNPA), propionyl-beta-methylthiocholine (PrMSCh), 3,3-dimethylbutyl thioacetate (DBTA), and acetylthiocholine (AcSCh), with acetylcholinesterase were determined as a function of increasing viscosity (eta rel) in sucrose-containing and in glycerol-containing buffers. Glycerol, or possibly some contaminant of it, was found to be a nonspecific inhibitor and sucrose a nonspecific activator of the enzyme as reflected in the dependence of kcat/Km values measured for PNPA and PrMSCh upon the concentration of these reagents. The rates of reactions of these two substrates, the first neutral and the second cationic, are chemically limited rather than diffusion limited, and they thus serve as quantitative controls or internal standards to monitor the effects of the viscosogens on the enzyme, which are not related to diffusion. The additional effect on kcat/Km over the controls observed for the rapidly reacting substrates AcSCh (cationic) and DBTA (neutral) serves as a measure of the extent to which these values of kcat/Km measure diffusion-controlled processes. The reaction rate of DBTA with the enzyme is 24% diffusion controlled as measured in glycerol-containing buffers and 16-20% as determined in sucrose-containing buffers, while that for AcSCh is 100% (in glycerol) and 24-40% (in sucrose) diffusion controlled.

Acetylcholinesterase↗
PubMed1985

Site-directed mutagenesis of aspartate aminotransferase from E. coli.

The gene for aspartate aminotransferase from E. coli (aspC) was subcloned into M13 phage and sequenced using the Sanger dideoxy method with synthetic oligonucleotide primers. A mutant gene was constructed using site-directed mutagenesis techniques in which the codon for the lysine that forms the Schiffs base with pyridoxal phosphate was replaced with one coding for alanine. The mutant gene was expressed under control of the Tac promoter to overproduce a mutant protein lacking enzymatic activity.

Aspartate Aminotransferases↗
PubMed1984

Mechanism of action of aspartate aminotransferase proposed on the basis of its spatial structure.

Aspartate aminotransferase is a pyridoxal phosphate-dependent enzyme that catalyses the transamination reaction: L-aspartate + 2-oxoglutarate----oxaloacetate + L-glutamate. The enzyme shuttles between its pyridoxal and pyridoxamine forms in a double-displacement process. This paper proposes a mechanism of action that delineates the dynamic role of the protein moiety of this enzyme. It is based on crystallographically determined spatial structures (at 2.8 A resolution) of the mitochondrial isoenzyme in its unliganded forms and in complexes with substrate analogues, as well as on model building studies. The enzyme is composed of two identical subunits, which consist of two domains. The coenzyme is bound to the larger domain and is situated in a pocket near the subunit interface. The proximal and distal carboxylate group of dicarboxylic substrates are bound to Arg386 and Arg292 , respectively, the latter residue belonging to the adjacent subunit. These interactions largely determine the substrate specificity of the enzyme. They not only position the substrate efficient catalysis but also bring about a bulk movement of the small domain that closes the active site crevice and moves Arg386 about 3 A closer to the coenzyme. The replacement of the epsilon-amino group of Lys258 by the alpha-amino group of the substrate in the aldimine bond to pyridoxal phosphate is accompanied by a tilting of the coenzyme by approximately 30 degrees. The released epsilon-amino group of Lys258 serves as a proton acceptor/donor in the 1,3- prototropic shift producing the ketimine intermediate. At this stage, or after hydrolysis of the ketimine bond, the coenzyme rotates back to an orientation between that in the "external" aldimine intermediate and that in the pyridoxal form. Throughout this process, the protonated pyridine nitrogen atom maintains a hydrogen bond to the beta-carboxylate group of Asp222 . Upon formation of the pyridoxamine form, the small domain moves back to its original position. The proposed mechanism is compatible with the known kinetic and stereochemical features of enzymic transamination.

Aspartate Aminotransferases↗
PubMed1984

pH dependence and solvent deuterium oxide kinetic isotope effects on Bacillus cereus beta-lactamase I catalyzed reactions.

The solvent kinetic isotope effects (SKIE's) on k(cat) (D(V)) and on k(cat/Km[D(V/K)] were determined for the Bacillus cereus beta-lactamase I catalyzed hydrolysis of five substrates that have values of k(cat)/K(m) varying over the range (0.014-46.3) X 10(6)M(-1) s(-1) and of k(cat) between 0.5 and 2019 s(-1). The variation of D(V/K) was only from 1.06 to 1.25 among these compounds and that in D(V) was from 1.50 to 2.16. These results require that Dk(1), the SKIE on the enzyme-substrate association rate constant, and D(k-1/k2), that on the partition ratio of the ES complex, both be near 1. The larger SKIE observed on D(V) requires that an exchangeable proton be in flight for either or both the acylation and the deacylation reaction. The pH dependence of the values k(cat)/K(m) for three substrates shows identical pK(a)s of 5.5. and 8.4. This identity combined with the fact that only one of these three substrates is kinetically "sticky" proves that the substrates can combine productively with only one protonic form of the enzyme. There is considerable substrate variation in the pK(a) values of k(cat) observed vs. pH profiles; the inflection points for all substrates studied are at pH values more extreme than are observed in the pH profiles for k(cat)/K(m).

Bacillus cereus↗
PubMed1984

Anomalous pH dependence of the reactions of carbenicillin and sulbenicillin with Bacillus cereus beta-lactamase I. Influence of the alpha-substituent charge on the kinetic parameters.

The pH dependence of k(cat) for the Bacillus cereus beta-lactamase I catalyzed hydrolysis of carbenicillin(VI), which differs from benzylpenicillin (I) in having a carboxylic moiety alpha to the phenyl ring, exhibits a profile consistent with a model in which the alpha-COOH and alpha-COO forms of the ES complex turn over with respective rate constants of 2152 s(-1) and 384 s(-1). The pK(a)(app) for the alpha-COOH is shifted from 3.2 in solution to 6.1 in the ES complex. The normalized k(cat)/K(m) vs. pH profile for VI is not superimposable on that of I, indicating that both the neutral and anionic forms of the carboxyl moiety of VI combine with the enzyme to give the first irreversibly formed complex, presumably the acyl-enzyme. Quantitative accord with the kinetic data is achieved only through fitting to a model where kinetically significant proton transfer in the ES complex is permitted. The second-order rate constants for the reaction of the enzyme with the alpha-COOH and alpha-COO forms of VI are 2.2 x 10(8) M(-1) s(-1) and 3.8 x 10(6) M(-1) s(-1), respectively. The high value for the alpha-COOH form suggests that this reaction may be in part diffusion controlled. This conjecture is borne out by the observation that the sensitivity of k(cat)/K(m) to eta(rel) decreases with increasing pH for VI, whereas this sensitivity is pH independent for I. These conclusions are further supported by the results of a kinetic investigation of the pH dependence of sulbenicillin (VII) where an alpha-SO3H replaces the alpha-COOH of VI. The strongly acidic sulfonic acid moiety of VII is fully ionized throughout nearly the entire pH range of interest, and its kinetics, as a function of pH, are very similar to those observed and calculated for the alpha-COO form of VI. Solvent deuterium kinetic isotope effects are reported for k(cat) and k(cat)/K(m) for both VI and VII.

Bacillus cereus↗
PubMed1984

Diffusion-limited component of reactions catalyzed by Bacillus cereus beta-lactamase I.

The Bacillus cereus beta-lactamase I catalyzes the hydrolysis of a wide variety of penicillins and cephalosporins with values of k(cat)/K(m) varying over several orders of magnitude. The values of this parameter for the most reactive of these compounds, benzylpenicillin, I, and furylacryloyl-penicillin, II (k(cat)/K(m) = 2.43 x 10(7) M(-1) s(-1) and 2.35 x 10(7) M(-1) s(-1), respectively, at pH 7.0 in potassium phosphate buffer containing 0.17 M KCl, I(c) = 0.63, 25 degrees C) are decreased markedly by increasing viscosity in sucrose- or glycerol-containing buffers. The relative sensitivities to viscosity of k(cat)/K(m) values for I and for cephaloridine, III, were found to be virtually unchanged at pH 3.8 from those observed at pH 7.0. The differential effects of viscosity on the reactive vs. the sluggish [e.g., cephalothin (IV), k(cat)/K(m) = 1 x 10(4) M(-1) s(-1)] substrates support the contention that the rates of reaction of the former with the enzyme are in part diffusion controlled. Quantitative analysis gives values for the association rate constants, k(1), of 7.6 x 10(7) M(-1) s(-1), 4 x 10(7) M(-1) s(-1), and 1.1 x 10(7) M(-1) s(-1) for I, II, and III, respectively. As both reactive and sluggish substrates associate with the active site of the enzyme with relatively similar rate constants, the variation in k(cat)/K(m) values is primarily due to the variation in the partition ratios k(-1)/k(2), for the ES complex, which are 2.3, 0.77, and 30 for I, II, and III, respectively. The preceding analysis is based on direct application of the Stokes-Einstein diffusion law to enzyme kinetics. The range of applicability of this law to the diffusion of substrate size molecules and the mechanics of diffusion of ionic species through viscous solutions of sucrose vs. polymers are explored.

Bacillus cereus↗
PubMed1982

Investigation of diffusion-limited rates of chymotrypsin reactions by viscosity variation.

The possibility that the rates of acylation of chymotrypsin by certain highly reactive substrates approach the diffusion-controlled limits was investigated by measuring the values of kcat/Km for three substrates as a function of increasing viscosity with sucrose and ficoll as the viscosogenic reagents. The values of Kcat/Km (pH 8.0, 25 degrees C) representing the acylation rate constants are the following: N-(methoxycarbonyl)-L-tryptophan p-nitrophenyl ester, 3.5 x 10(7) M-1 s-1; N-acetyl-L-tryptophan methyl ester, 8 x 10(5) M-1 s-1; N-acetyl-L-tryptophan p-nitroanilide, 300 M-1 s-1. The rate constants decrease significantly with increasing viscosity for the first compound, decrease slightly for the second, and are insensitive to this perturbation for the third. The p-nitroanilide results taken together with the observation that the high concentrations of sucrose or ficoll used produce insignificant changes in kcat for the ester substrates argue against a general nonspecific perturbation in the enzyme structure effected by these reagents. The values of the association rate constants calculated from these results are 9 x 10(7) and 1 x 10(7) M-1 s-1 for the p-nitrophenyl and methyl esters, respectively. The values of kcat/Km divided by the association rate constants show that the rates of acylation by the p-nitrophenyl ester occur at ca. 40% and by the methyl ester at ca. 10% of the diffusion limits. Possibilities involving reorientation of a nonproductively bound substrate within the ES complex or desolvation of part of the active site of the enzyme are considered to account for the lower association rate constant for the methyl as compared to the p-nitrophenyl ester.

Chemical Phenomena↗
PubMed1981

Oxygen-18 leaving group kinetic isotope effects on the hydrolysis of nitrophenyl glycosides. 1. beta-galactosidease-catalyzed hydrolysis.

Oxygen-18 leaving group kinetic isotope effects (KIEs) have been determined on both Vmax (V) and Vmax/Km (V/K) for the beta-galactosidase-catalyzed hydrolysis of p-nitrophenyl beta-D-galactoside (I) and 2,4-dinitrophenyl beta-D-galactoside (II). The former substrate exhibits KIEs of 1.022 +/- 0.002 and 1.014 +/- 0.003 on V and V/K, respectively, while corresponding KIEs for the latter are 1.002 +/- 0.0009 and 1.030 +/- 0.003. These results indicate that bond scission is largely rate determining for I but not for II at substrate saturation. The first irreversible step for both substrates must involve cleavage of the bond to the nitrophenyl leaving group. The mechanism proposed for this reaction is characterized by two parallel pathways for substrate hydrolysis. The predominant route for all but the most reactive substrates involves a SN2 nucleophilic displacement of aglycon by the enzyme to yield a covalent galactosyl-enzyme which in turn is hydrolyzed via a nucleophilic attach by water. The most reactive substrates (e.g., II) from transiently an enzyme-bound galactosyl oxo-carbonium ion which partitions between enzyme to give the covalent galactosyl-enzyme and H2O to yield galactose.

Galactosidases↗
PubMed1981

Oxygen-18 leaving group kinetic isotope effects on the hydrolysis of nitrophenyl glycosides. 2. Lysozyme and beta-glucosidase: acid and alkaline hydrolysis.

Oxygen-18 leaving group kinetic isotope effects (KIEs) have been measured for a set of glycosyl transfer reactions with p-nitrophenyl beta-D-glycosides as substrates. Acid-catalyzed hydrolysis and alkaline hydrolysis exhibit KIEs of K16/k18 = 1.0355 +/- 0.0015 and 1.0386 +/- 0.0032, respectively. Lysozyme and beta-glucosidase A show KIEs on Vmax/Km (V/K) of (V/KI)16/(V/K)18 = 1.0467 +/- 0.0015 and 1.0377 +/0 0.0061, respectively. The large magnitude of these KIEs requires that carbon-oxygen bond scission be far advanced in the transition states for these reactions; therefore in the transition states for the first irreversible steps in these reaction sequences, scission of the glycosidic bond must be essentially complete for the reactions catalyzed by lysozyme and beta-glucosidase A, which are thought to proceed via SN1 and SN2 mechanisms, respectively. Acid-catalyzed hydrolysis is shown to proceed through a transition state involving at least 80% C-O bond cleavage and only partially proton transfer to the leaving p-nitrophenyl oxygen atom.

Glucosidases↗