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Chapter 12 : Kinetics of β-Lactamases and Penicillin-Binding Proteins

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Abstract:

The discovery of novel β-lactamases and penicillin-binding proteins (PBPs) often requires kinetic characterization. As such, the rate at which a β-lactamase hydrolyzes a β-lactam is influenced by several factors. The first is concentration of β-lactam, which is designated [S] and is expressed in units of molarity. The second is temperature. As the temperature rises, molecular motion, and hence collisions between β-lactamase and β-lactam, and the rates of interconversion of intermediates increase. The third factor is the presence of inhibitors. β-lactamase inhibitors are clinically used to hinder the activity of the β-lactamase. The last is pH: the charge of active-site groups and the conformation of a protein are influenced by pH, and enzyme activity is crucially dependent on both these factors. The equations of enzyme kinetics are conceptual tools that allow us to interpret quantitative measurements of enzyme activity. Nitrocefin is the most practical reference compound, since the accumulation of ER* can be monitored at 480 to 490 nm and no interference is expected with most other β-lactams which do not yield acyl enzymes absorbing in this wavelength range. Several class D β-lactamases also exhibit substrate-induced inactivation (or biphasic kinetics) with a significant number of substrates. Indeed, in some but not all cases, the substrate-induced inactivation disappeared in the presence of a saturating concentration of bicarbonate which was assumed to completely maintain the Lys in the carboxylated form.

Citation: Galleni M, Frère J. 2007. Kinetics of β-Lactamases and Penicillin-Binding Proteins, p 195-213. In Bonomo R, Tolmasky M (ed), Enzyme-Mediated Resistance to Antibiotics. ASM Press, Washington, DC. doi: 10.1128/9781555815615.ch12

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Citation: Galleni M, Frère J. 2007. Kinetics of β-Lactamases and Penicillin-Binding Proteins, p 195-213. In Bonomo R, Tolmasky M (ed), Enzyme-Mediated Resistance to Antibiotics. ASM Press, Washington, DC. doi: 10.1128/9781555815615.ch12
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Citation: Galleni M, Frère J. 2007. Kinetics of β-Lactamases and Penicillin-Binding Proteins, p 195-213. In Bonomo R, Tolmasky M (ed), Enzyme-Mediated Resistance to Antibiotics. ASM Press, Washington, DC. doi: 10.1128/9781555815615.ch12
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Citation: Galleni M, Frère J. 2007. Kinetics of β-Lactamases and Penicillin-Binding Proteins, p 195-213. In Bonomo R, Tolmasky M (ed), Enzyme-Mediated Resistance to Antibiotics. ASM Press, Washington, DC. doi: 10.1128/9781555815615.ch12
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Figure 12.1

(A) Dependence of the initial rate on substrate concentration in the Henri-Michaelis-Menten model. (B) Hanes-Woolf plot for the determination of the kinetic parameters and V.

Citation: Galleni M, Frère J. 2007. Kinetics of β-Lactamases and Penicillin-Binding Proteins, p 195-213. In Bonomo R, Tolmasky M (ed), Enzyme-Mediated Resistance to Antibiotics. ASM Press, Washington, DC. doi: 10.1128/9781555815615.ch12
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Citation: Galleni M, Frère J. 2007. Kinetics of β-Lactamases and Penicillin-Binding Proteins, p 195-213. In Bonomo R, Tolmasky M (ed), Enzyme-Mediated Resistance to Antibiotics. ASM Press, Washington, DC. doi: 10.1128/9781555815615.ch12
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Figure 12.2

Complete time course of the hydrolysis of a substrate. (A) Decrease of the substrate concentration versus time. (B) Plot of 1/ (ln S/S - P) versus P/.

Citation: Galleni M, Frère J. 2007. Kinetics of β-Lactamases and Penicillin-Binding Proteins, p 195-213. In Bonomo R, Tolmasky M (ed), Enzyme-Mediated Resistance to Antibiotics. ASM Press, Washington, DC. doi: 10.1128/9781555815615.ch12
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Citation: Galleni M, Frère J. 2007. Kinetics of β-Lactamases and Penicillin-Binding Proteins, p 195-213. In Bonomo R, Tolmasky M (ed), Enzyme-Mediated Resistance to Antibiotics. ASM Press, Washington, DC. doi: 10.1128/9781555815615.ch12
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Figure 12.3

Dependence of the rate constant for acyl enzyme accumulation () on substrate concentration. (A) >> . (B) General case.

Citation: Galleni M, Frère J. 2007. Kinetics of β-Lactamases and Penicillin-Binding Proteins, p 195-213. In Bonomo R, Tolmasky M (ed), Enzyme-Mediated Resistance to Antibiotics. ASM Press, Washington, DC. doi: 10.1128/9781555815615.ch12
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Figure 12.4

Structures of two chromogenic substrates.

Citation: Galleni M, Frère J. 2007. Kinetics of β-Lactamases and Penicillin-Binding Proteins, p 195-213. In Bonomo R, Tolmasky M (ed), Enzyme-Mediated Resistance to Antibiotics. ASM Press, Washington, DC. doi: 10.1128/9781555815615.ch12
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Figure 12.5

Titration of the R39 -carboxypeptidase with nitrocefin, based on the inhibition of the enzyme activity and on alteration of the antibiotic molecule. Symbols:○, residual activity; •, concentration of hydrolyzed nitrocefin; and Δ, concentration of intact nitrocefin. Adapted from reference .

Citation: Galleni M, Frère J. 2007. Kinetics of β-Lactamases and Penicillin-Binding Proteins, p 195-213. In Bonomo R, Tolmasky M (ed), Enzyme-Mediated Resistance to Antibiotics. ASM Press, Washington, DC. doi: 10.1128/9781555815615.ch12
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Figure 12.6

The reporter substrate method. Disappearance of the reporter substrate (R) in the absence ( ) and in the presence (curves 1 and 2) of an inactivator or an alternative substrate for which is 0 or negligible compared to S/(’ + S) (curve 1, = 0) or not (curve 2, > 0).

Citation: Galleni M, Frère J. 2007. Kinetics of β-Lactamases and Penicillin-Binding Proteins, p 195-213. In Bonomo R, Tolmasky M (ed), Enzyme-Mediated Resistance to Antibiotics. ASM Press, Washington, DC. doi: 10.1128/9781555815615.ch12
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Citation: Galleni M, Frère J. 2007. Kinetics of β-Lactamases and Penicillin-Binding Proteins, p 195-213. In Bonomo R, Tolmasky M (ed), Enzyme-Mediated Resistance to Antibiotics. ASM Press, Washington, DC. doi: 10.1128/9781555815615.ch12
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Citation: Galleni M, Frère J. 2007. Kinetics of β-Lactamases and Penicillin-Binding Proteins, p 195-213. In Bonomo R, Tolmasky M (ed), Enzyme-Mediated Resistance to Antibiotics. ASM Press, Washington, DC. doi: 10.1128/9781555815615.ch12
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Figure 12.7

Product inhibition of CphA by hydrolyzed biapenem. Curve 1 represents the complete hydrolysis time course of 200 μM biapenem. Curves 2, 3, and 4 are the complete hydrolysis time courses of 200 μM biapenem recorded in the presence of 200, 400, and 600 μM hydrolyzed biapenem, respectively (reference and Bebrone and Galleni, unpublished data).

Citation: Galleni M, Frère J. 2007. Kinetics of β-Lactamases and Penicillin-Binding Proteins, p 195-213. In Bonomo R, Tolmasky M (ed), Enzyme-Mediated Resistance to Antibiotics. ASM Press, Washington, DC. doi: 10.1128/9781555815615.ch12
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Citation: Galleni M, Frère J. 2007. Kinetics of β-Lactamases and Penicillin-Binding Proteins, p 195-213. In Bonomo R, Tolmasky M (ed), Enzyme-Mediated Resistance to Antibiotics. ASM Press, Washington, DC. doi: 10.1128/9781555815615.ch12
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Figure 12.8

Inhibition by excess substrate. Inhibition of the CMY-1 β-lactamase by excess nitrocefin. The activities of CMY-1 (○) and of the chromosomal P99 β-lactamase (□) were determined as the initial rates of hydrolysis of nitrocefin solutions prepared in 50 mM MOPS (morpholinepropanesulfonic acid) buffer pH 7.0, containing 50 mM NaCl. The dotted and continuous lines were obtained by fitting the data to the Henri-Michaelis (for P99) and to the substrate inhibition equations (for CMY-1), respectively. Both enzymes are class C β-lactamases. The equation for substrate inhibition is : = /( + + /), where is the dissociation constant of the inactive ES complex (2a).

Citation: Galleni M, Frère J. 2007. Kinetics of β-Lactamases and Penicillin-Binding Proteins, p 195-213. In Bonomo R, Tolmasky M (ed), Enzyme-Mediated Resistance to Antibiotics. ASM Press, Washington, DC. doi: 10.1128/9781555815615.ch12
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Figure 12.9

Titration curve of the ACT-1 β-lactamase by aztreonam. The residual activity of ACT-1 versus the [aztreonam]/[ACT-1] ratio is shown. The linear regression allows one to determine the actual concentrations of active enzyme (2a).

Citation: Galleni M, Frère J. 2007. Kinetics of β-Lactamases and Penicillin-Binding Proteins, p 195-213. In Bonomo R, Tolmasky M (ed), Enzyme-Mediated Resistance to Antibiotics. ASM Press, Washington, DC. doi: 10.1128/9781555815615.ch12
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Citation: Galleni M, Frère J. 2007. Kinetics of β-Lactamases and Penicillin-Binding Proteins, p 195-213. In Bonomo R, Tolmasky M (ed), Enzyme-Mediated Resistance to Antibiotics. ASM Press, Washington, DC. doi: 10.1128/9781555815615.ch12
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Citation: Galleni M, Frère J. 2007. Kinetics of β-Lactamases and Penicillin-Binding Proteins, p 195-213. In Bonomo R, Tolmasky M (ed), Enzyme-Mediated Resistance to Antibiotics. ASM Press, Washington, DC. doi: 10.1128/9781555815615.ch12
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Figure 12.10

Structure of good linear substrates of β-lactamases. The peptides CH-CO- and CH-CO-O--Ala--Ala are very poor substrates.

Citation: Galleni M, Frère J. 2007. Kinetics of β-Lactamases and Penicillin-Binding Proteins, p 195-213. In Bonomo R, Tolmasky M (ed), Enzyme-Mediated Resistance to Antibiotics. ASM Press, Washington, DC. doi: 10.1128/9781555815615.ch12
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Citation: Galleni M, Frère J. 2007. Kinetics of β-Lactamases and Penicillin-Binding Proteins, p 195-213. In Bonomo R, Tolmasky M (ed), Enzyme-Mediated Resistance to Antibiotics. ASM Press, Washington, DC. doi: 10.1128/9781555815615.ch12
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Citation: Galleni M, Frère J. 2007. Kinetics of β-Lactamases and Penicillin-Binding Proteins, p 195-213. In Bonomo R, Tolmasky M (ed), Enzyme-Mediated Resistance to Antibiotics. ASM Press, Washington, DC. doi: 10.1128/9781555815615.ch12
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Figure 12.11

Expulsion of the C-3′ leaving group during (right) and after (left) hydrolysis of cephalosporins. The reaction is described by the scheme shown in the text (adapted from reference ).

Citation: Galleni M, Frère J. 2007. Kinetics of β-Lactamases and Penicillin-Binding Proteins, p 195-213. In Bonomo R, Tolmasky M (ed), Enzyme-Mediated Resistance to Antibiotics. ASM Press, Washington, DC. doi: 10.1128/9781555815615.ch12
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Citation: Galleni M, Frère J. 2007. Kinetics of β-Lactamases and Penicillin-Binding Proteins, p 195-213. In Bonomo R, Tolmasky M (ed), Enzyme-Mediated Resistance to Antibiotics. ASM Press, Washington, DC. doi: 10.1128/9781555815615.ch12
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Citation: Galleni M, Frère J. 2007. Kinetics of β-Lactamases and Penicillin-Binding Proteins, p 195-213. In Bonomo R, Tolmasky M (ed), Enzyme-Mediated Resistance to Antibiotics. ASM Press, Washington, DC. doi: 10.1128/9781555815615.ch12
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Citation: Galleni M, Frère J. 2007. Kinetics of β-Lactamases and Penicillin-Binding Proteins, p 195-213. In Bonomo R, Tolmasky M (ed), Enzyme-Mediated Resistance to Antibiotics. ASM Press, Washington, DC. doi: 10.1128/9781555815615.ch12
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Figure 12.12

The time dependence of TEM-1 β-lactamase activity in the presence of clavulanic acid. C/E represents the molar ratio of the concentration of clavulanic acid (C) and the enzyme (E) (adapted from reference ).

Citation: Galleni M, Frère J. 2007. Kinetics of β-Lactamases and Penicillin-Binding Proteins, p 195-213. In Bonomo R, Tolmasky M (ed), Enzyme-Mediated Resistance to Antibiotics. ASM Press, Washington, DC. doi: 10.1128/9781555815615.ch12
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Figure 12.13

Structures of the different β-lactam families.

Citation: Galleni M, Frère J. 2007. Kinetics of β-Lactamases and Penicillin-Binding Proteins, p 195-213. In Bonomo R, Tolmasky M (ed), Enzyme-Mediated Resistance to Antibiotics. ASM Press, Washington, DC. doi: 10.1128/9781555815615.ch12
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Figure 12.14

Structure of the intermediate postulated on the hydrolysis pathway of nitrocefin by metallo-β-lactamases.

Citation: Galleni M, Frère J. 2007. Kinetics of β-Lactamases and Penicillin-Binding Proteins, p 195-213. In Bonomo R, Tolmasky M (ed), Enzyme-Mediated Resistance to Antibiotics. ASM Press, Washington, DC. doi: 10.1128/9781555815615.ch12
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Figure 12.15

(A) Dependence of values versus [Zn] for the hydrolysis of benzylpenicillin by the subclass B1 569H β-lactamase BcII. (B) Dependence of the residual activity on [Zn] for the subclass B2 CphA zinc β-lactamase. In both cases, N represents the number of Zn ions bound per molecule of enzyme.

Citation: Galleni M, Frère J. 2007. Kinetics of β-Lactamases and Penicillin-Binding Proteins, p 195-213. In Bonomo R, Tolmasky M (ed), Enzyme-Mediated Resistance to Antibiotics. ASM Press, Washington, DC. doi: 10.1128/9781555815615.ch12
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References

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Tables

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Table 12.1

Kinetic parameters for the hydrolysis of biapenem by the metallo-β-lactamase CphA

Citation: Galleni M, Frère J. 2007. Kinetics of β-Lactamases and Penicillin-Binding Proteins, p 195-213. In Bonomo R, Tolmasky M (ed), Enzyme-Mediated Resistance to Antibiotics. ASM Press, Washington, DC. doi: 10.1128/9781555815615.ch12

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