scholarly journals The mechanism of catalysis and the inhibition of the Bacillus cereus zinc-dependent β-lactamase

1998 ◽  
Vol 331 (3) ◽  
pp. 703-711 ◽  
Author(s):  
Sakina BOUNAGA ◽  
Andrew P. LAWS ◽  
Moreno GALLENI ◽  
Michael I. PAGE

The plot of kcat/Km against pH for the Bacillus cereus569/H β-lactamase class B catalysed hydrolysis of benzylpenicillin and cephalosporin indicates that there are three catalytically important groups, two of pKa 5.6±0.2 and one of pKa 9.5±0.2. Below pH 5 there is an inverse second-order dependence of reactivity upon hydrogen ion concentration, indicative of the requirement of two basic residues for catalysis. These are assigned to zinc(II)-bound water and Asp-90, both with a pKa of 5.6±0.2. A thiol, N-(2´-mercaptoethyl)-2-phenylacetamide, is an inhibitor of the class B enzyme with a Ki of 70 µM. The pH-dependence of Ki shows similar pH inflections to those observed in the catalysed hydrolysis of substrates. The pH-independence of Ki between pH 6 and 9 indicates that the pKa of zinc(II)-bound water must be 5.6 and not the higher pKa of 9.5. The kinetic solvent isotope effect on kcat/Km is 1.3±0.5 and that on kcat is 1.5. There is no effect on reactivity by either added zinc(II) or methanol. The possible mechanisms of action for the class B β-lactamase are discussed, and it is concluded that zinc(II) acts as a Lewis acid to stabilize the dianionic form of the tetrahedral intermediate and to provide a hydroxide-ion bound nucleophile, whereas the carboxylate anion of Asp-90 acts as a general base to form the dianion and also, presumably, as a general acid catalyst facilitating C–N bond fission.

2020 ◽  
Author(s):  
Shreya Ghosh ◽  
Anam Ejaz ◽  
Lucas Repeta ◽  
Stewart Shuman

Abstract Pseudomonas putida MPE exemplifies a novel clade of manganese-dependent single-strand DNA endonuclease within the binuclear metallophosphoesterase superfamily. MPE is encoded within a widely conserved DNA repair operon. Via structure-guided mutagenesis, we identify His113 and His81 as essential for DNA nuclease activity, albeit inessential for hydrolysis of bis-p-nitrophenylphosphate. We propose that His113 contacts the scissile phosphodiester and serves as a general acid catalyst to expel the OH leaving group of the product strand. We find that MPE cleaves the 3′ and 5′ single-strands of tailed duplex DNAs and that MPE can sense and incise duplexes at sites of short mismatch bulges and opposite a nick. We show that MPE is an ambidextrous phosphodiesterase capable of hydrolyzing the ssDNA backbone in either orientation to generate a mixture of 3′-OH and 3′-PO4 cleavage products. The directionality of phosphodiester hydrolysis is dictated by the orientation of the water nucleophile vis-à-vis the OH leaving group, which must be near apical for the reaction to proceed. We propose that the MPE active site and metal-bound water nucleophile are invariant and the enzyme can bind the ssDNA productively in opposite orientations.


1975 ◽  
Vol 53 (24) ◽  
pp. 3697-3701 ◽  
Author(s):  
Milton Cornelius Weekes ◽  
Thomas Wilson Swaddle

The rate of hydrolysis of iodopentaaquochromium(III) ion has been measured as a function of pressure (0.1 to 250 MPa) and hydrogen ion concentration (0.1 to 1.0 mol kg−1) at 298.2 K and ionic strength 1.0 mol kg−1 (aqueous HClO4–LiClO4). The volumes of activation for the acid independent and inversely acid dependent hydrolysis pathways are −5.4 ± 0.5 and −1.6 ± 0.3 cm3 mol−1 respectively, and are not detectably pressure-dependent. Consideration of these values, together with the molar volume change of −3.3 ± 0.3 cm3 mol−1 determined dilatometrically for the completed hydrolysis reaction, indicates that the mechanisms of the two pathways are associative interchange (Ia) and dissociative conjugate base (Dcb) respectively.


1973 ◽  
Vol 51 (4) ◽  
pp. 588-596 ◽  
Author(s):  
R. Roman ◽  
H. B. Dunford

The kinetics of the oxidation of sulfite and nitrite by horseradish peroxidase compounds I and II have been studied as a function of pH at 25° and ionic strength 0.11. The pH dependence of the rate of the reaction between compound I and sulfite over the pH range 2–7 is interpreted in terms of two ground state enzyme dissociations with pka values of 5.1 and 3.3, and that for the compound II reaction with sulfite in terms of a single ground state enzyme dissociation with a pKa value of 3.9. Whereas the reaction between compound I and sulfite produces the native enzyme without the intermediate formation of compound II, the reaction of compound I with nitrite yields compound II. The second-order rate constants for the reactions of compounds I and II with nitrite increase linearly with increasing hydrogen ion concentration over the pH range 6–8.


1989 ◽  
Vol 68 (2) ◽  
pp. 124-129 ◽  
Author(s):  
E.C. Reynolds ◽  
P.F. Riley

Proteins of known composition and structural characteristics were incubated (1.0 mglmL) with re-suspended salivary sediment (2.5% vl v) in a lactate-salt medium with an initial pH of 5.2 for two hr at 37°C. Hydrolysis of the proteins was monitored by sodium dodecyl sulfate polyacrylamide gel electrophoresis. Hydrogen ion, amines, and ammonia were measured by use of a combined pH electrode, high performance liquid chromatography, and glutamate dehydrogenase, respectively. Of the proteins studied, the caseins αs1, β, and K and the histones H1 and H3 were extensively hydrolyzed by the salivary-sediment bacteria. The hydrolysis of these proteins was attributed to their relative lack of tertiary (folded) structure. The only amine detected was the polyamine putrescine arising from the catabolism of arginine following the hydrolysis of the arginine-rich histone H3. None of the other proteins extensively hydrolyzed by salivary sediment, although containing arginyl and lysyl residues, served as substrates for putrescine or cadaverine production. Pre-hydrolysis of the arginine-rich histone H3 and poly-L-arginine with trypsin resulted in a marked increase in putrescine produced, suggesting that the salivary-sediment proteolytic activity was not "trypsin-like". Incubation of salivary-sediment bacteria with the caseins and the histone H3 resulted in an increase in ammonium ion concentration and an associated decrease in hydrogen ion concentration. The increase in ammonium ion concentration not attributed to arginine hydrolysis was correlated with the content of glutaminyl plus asparaginyl residues of the proteins. The results suggest that amido nitrogen, in the form of glutaminyl and asparaginyl residues of salivary and dietary proteins, is a potential source of nitrogen for oral bacteria and may also play a role in plaque pH homeostasis.


1920 ◽  
Vol 3 (2) ◽  
pp. 211-227 ◽  
Author(s):  
John H. Northrop

The experiments described above show that the rate of digestion and the conductivity of protein solutions are very closely parallel. If the isoelectric point of a protein is at a lower hydrogen ion concentration than that of another, the conductivity and also the rate of digestion of the first protein extends further to the alkaline side. The optimum hydrogen ion concentration for the rate of digestion and the degree of ionization (conductivity) of gelatin solutions is the same, and the curves for the ionization and rate of digestion as plotted against the pH are nearly parallel throughout. The addition of a salt with the same anion as the acid to a solution of protein already containing the optimum amount of the acid has the same depressing effect on the digestion as has the addition of the equivalent amount of acid. These facts are in quantitative agreement with the hypothesis that the determining factor in the digestion of proteins by pepsin is the amount of ionized protein present in the solution. It was shown in a previous paper that this would also account for the peculiar relation between the rate of digestion and the concentration of protein. The amount of ionized protein in the solution depends on the amount of salt formed between the protein (a weak base) and the acid. This quantity, in turn, according to the hydrolysis theory of the salts of weak bases and strong acids, is a function of the hydrogen ion concentration, up to the point at which all the protein is combined with the acid as a salt. This point is the optimum hydrogen ion concentration for digestion, since the solution now contains the maximum concentration of protein ions. The hydrogen ion concentration in this range therefore is merely a convenient indicator of the amount of ionized protein present in the solution and takes no active part in the hydrolysis. After sufficient acid has been added to combine with all the protein, i.e. at pH of about 2.0, the further addition of acid serves to depress the ionization of the protein salt by increasing the concentration of the common anion. The hydrogen ion concentration is, therefore, no longer an indicator of the amount of ionized protein present, since this quantity is now determined by the anion concentration. Hence on the acid side of the optimum the addition of the same concentration of anion should have the same influence on the rate of digestion irrespective of whether it is combined with hydrogen or some other ion (provided, of course, that there is no other secondary effect of the other ion). The proposed mechanism is very similar to that suggested by Stieglitz and his coworkers for the hydrolysis of the imido esters. Pekelharing and Ringer have shown that pure pepsin in acid solution is always negatively charged; i.e., it is an anion. The experiments described above show further that it behaves just as would be expected of any anion in the presence of a salt containing the protein ion as the cation and as has been shown by Loeb to be the case with inorganic anions. Nothing has been said in regard to the quantitative agreement between the increasing amounts of ionized protein found in the solution (as shown by the conductivity values) and the amount predicted by the hydrolysis theory of the formation of salts of weak bases and strong acids. There is little doubt that the values are in qualitative agreement with such a theory. In order to make a quantitative comparison, however, it would be necessary to know the ionization constant of the protein and of the protein salt and also the number of hydroxyl (or amino) groups in the protein molecule as well as the molecular weight of the protein. Since these values are not known with any degree of certainty there appears to be no value at present in attempting to apply the hydrolysis equations to the data obtained. It it clear that the hypothesis as outlined above for the hydrolysis of proteins by pepsin cannot be extended directly to enzymes in general, since in many cases the substrate is not known to exist in an ionized condition at all. It is possible, however, that ionization is really present or that the equilibrium instead of being ionic is between two tautomeric forms of the substrate, only one of which is attacked by the enzyme. Furthermore, it is clear that even in the case of proteins there are difficulties in the way since the pepsin obtained from young animals, or a similar enzyme preparation from yeast or other microorganisms, is said to have a different optimum hydrogen ion concentration than that found for the pepsin used in these experiments. The activity of these enzyme preparations therefore would not be found to depend on the ionization of the protein. It is possible of course that the enzyme preparations mentioned may contain several proteolytic enzymes and that the action observed is a combination of the action of several enzymes. Dernby has shown that this is a very probable explanation of the action of the autolytic enzymes. The optimum hydrogen ion concentration for the activity of the pepsin used in these experiments agrees very closely with that found by Ringer for pepsin prepared by him directly from gastric juice and very carefully purified. Ringer's pepsin probably represents as pure an enzyme preparation as it is possible to prepare. There is every reason to suppose therefore that the enzyme used in this work was not a mixture of several enzymes.


1983 ◽  
Vol 213 (1) ◽  
pp. 61-66 ◽  
Author(s):  
R Bicknell ◽  
V Knott-Hunziker ◽  
S G Waley

The classification by structure allots beta-lactamases to (at present) three classes, A, B and C. The pH-dependence of the kinetic parameters for class B and class C have been determined. They differ from each other and from class A beta-lactamases. The class B enzyme was beta-lactamase II from Bacillus cereus 569/H/9. The plots of kcat against pH for the hydrolysis of benzylpenicillin by Zn(II)-requiring beta-lactamase II and Co(II)-requiring beta-lactamase II were not symmetrical, but those of kcat/Km were. A similar feature was observed for the hydrolysis of both benzylpenicillin and cephalosporin C by a class C beta-lactamase from Pseudomonas aeruginosa. The results have been interpreted by a scheme in which two ionic forms of an intermediate can give product, but do so at differing rates.


1994 ◽  
Vol 179 (1) ◽  
pp. 229-234 ◽  
Author(s):  
M A Sherman ◽  
H A Runnels ◽  
J C Moore ◽  
L J Stern ◽  
P E Jensen

We analyzed the binding of an influenza matrix protein-derived peptide, MAT(17-31), to cell surface and purified DR1. The pH dependence of peptide binding was dramatically influenced by the membrane environment. Cell surface binding was enhanced at low pH, with little or no binding detected at neutral pH and optimal binding at pH 4. By contrast, hydrogen ion concentration had minimal effect on peptide binding to purified DR1. Exposure to low pH in the absence of peptide did not affect the peptide binding capacity of cell-associated DR1. Purified DR1 was stable at low pH, excluding the possibility that enhanced binding was offset by a competing denaturation event at low pH. The striking effect of pH on peptide binding characteristic of cell surface DR1 was recovered after reconstitution of purified DR1 in B cell membranes by detergent dialysis. This behavior was partially recovered by reconstitution of full-length, but not truncated DR1 in vesicles containing purified lipid. Our results demonstrate that interactions involving membrane components influence the peptide-binding behavior of DR1.


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