Acid–Base Catalysis by Enzymes

Abstract

Proton transfer is the commonest reaction that enzymes perform. Most enzyme reactions go by ionic mechanisms, involving the creation or disappearance of charge. Such reactions are typically acid or base catalysed, but acid and base concentrations are minimal under physiological conditions near pH 7. Enzymes have evolved subtle and highly effective solutions to this problem, involving general acid and general base catalysis by the functional groups available on the side‐chains of amino acids strategically placed in their active sites. General acid and general base catalysis by the same functional groups can be observed, and the relevant mechanisms elucidated, by studying simple systems. But this work typically involves the use of properly designed activated substrates. The extraordinary efficiency of such catalysis in enzyme active sites has not so far been reproduced in model systems, and this remains an active area of investigation.

Key Concepts:

  • The enzyme active site provides a highly sophisticated reaction vessel, tailored to the needs of the specific reaction and the specific substrate.

  • General acid and general base catalysis are first‐line support services for the making and breaking of covalent bonds that define the chemistry of metabolic processes.

  • The unexceptional functional groups available on the side‐chains of amino acids acquire exceptional catalytic proficiency when strategically placed in enzyme active sites.

Keywords: general acid; general base; proton transfer; effective molarity; enzyme mechanism

Figure 1.

Specific acid–base catalysis and enzyme catalysis compared. Shown are pH–rate profiles (plots of log kobs versus pH) for acid‐ and base‐catalysed reactions of an unreactive (I) and an activated substrate (II) in vitro, and (III) for a typical enzyme‐catalysed reaction. The slopes of the lines in curves I and II are either zero or (±)unity, and denote the order with respect to aH. (The rate law for curves I and II is kobs=k0+kHaH+kOHaOH: the k0 term is negligible in the case of curve I.)

Figure 8.

Dependence on pH of the fractions of the three ionic forms for a system () with two different ionizing groups with pKa values of 6.0 and 8.0.

Figure 10.

Schematic energy profile diagram for the transfer of a proton from an acid HA to a base B. Any bimolecular reaction involves at least three steps: diffusion together of the reactants, bond‐making and breaking and diffusion apart of the products. When the activation energy for the chemical step (here the proton transfer) is lower than the effective ΔG for the diffusion apart of the reactants from the encounter complex (or in an enzyme‐catalysed reaction, the Michaelis complex) the diffusion step may become rate limiting. This happens for the transfer of a proton in the thermodynamically favourable direction. (Note that by the principle of microscopic reversibility the same step (kdiffusion, now for the diffusion apart of the products) must also be rate determining in the reverse – thermodynamically unfavourable – direction.)

Figure 15.

The balance between general acid and general base catalysis in enzyme catalysis depends on the type of reaction involved, but both can usually be identified in any enzyme reaction (see the text). (The picture is more complicated when one or more metal cations are involved in the catalytic process.)

Figure 16.

Transition state‐binding interactions (red) in the initial step of a serine protease reaction (the peptide substrate is green and the enzyme is blue). The smaller arrows represent the dynamic binding derived from general acid–base catalysis. The fat arrow indicates a partial covalent bond between heavy atoms, corresponding to nucleophilic catalysis.

Figure 2.

Mechanism for specific acid catalysis.

Figure 3.

Specific base‐catalysed H/D exchange.

Figure 4.

Mechanism for specific acid catalysis of amide hydrolysis.

Figure 5.

Mechanism for the pH‐independent water reaction: gb, general base; ga, general acid and nuc, nucleophile.

Figure 6.

Mechanism for general base catalysis of ester hydrolysis.

Figure 7.

Mechanism for general acid–base catalysis of enolization.

Figure 9.

Ionization equilibria of an amino acid, etc. (see text).

Figure 11.

General acid‐catalysed hydrolysis of enol ethers. Kresge AJ, Chen HL, Chiang Y et al. (1971) Vinyl ether hydrolysis. Journal of the American Chemical Society93: 413–423.

Figure 12.

General base catalysis of the hydrolysis of ethyl formate.

Figure 13.

Efficient intramolecular catalysis of amide hydrolysis. Aldersley MF, Kirby AJ, Lancaster PW, McDonald RS and Smith CR (1974) Intramolecular catalysis of amide hydrolysis by the carboxy‐group. Rate determining proton transfer from external general acids in the hydrolysis of substituted maleamic acids. Journal of the Chemical Society, Perkin Transactions2: 1487–1495.

Figure 14.

Intramolecular general acid catalysis of glucoside hydrolysis. Capon B (1963) Intramolecular catalysis in glucoside hydrolysis. Tetrahedron Letters 911–912.

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References

Cleland WW, Frey PA and Gerlt JA (1998) The low barrier hydrogen bond in enzymatic catalysis. Journal of Biological Chemistry 273: 25529–25532.

Kirby AJ (1980) Effective molarities for intramolecular reactions. Advances in Physical Organic Chemistry 17: 183–278.

Kirby AJ (1996) Enzyme mechanisms, models and mimics. Angewandte Chemie, International Edition in English 35: 707–724.

Kirby AJ (1997) Efficiency of proton transfer catalysis in models and enzymes. Accounts of Chemical Research 30: 290–296.

Lairson LL, Henrissat B, Davies GJ and Withers SG (2008) Glycosyltransferases: structures, functions, and mechanisms. Annual Reviews of Biochemistry 77: 521–525.

Stefanidis D and Jencks WP (1993) General base catalysis of ester hydrolysis. Journal of the American Chemical Society 115: 6045–6050.

Further Reading

Fersht AR (1999) Structure and Mechanism in Protein Science. New York: Freeman.

Frey PA and Hegeman AD (2007) Enzymatic Reaction Mechanisms. New York: Oxford.

Jencks WP (1969) Catalysis in Chemistry and Enzymology. New York: McGraw‐Hill.

Kirby AJ and Hollfelder F (2009) From Enzyme Models to Model Enzymes. Cambridge: Royal Society of Chemistry.

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How to Cite close
Kirby, Anthony John(Mar 2010) Acid–Base Catalysis by Enzymes. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0000602.pub2]