Carbonic anhydrase substrate activation

Urease catalyzes the hydrolysis of mea to NH3 and CO2 and incorporates nF in an octahedral environment. The function of the Ni center(s) in these enzymes is thought to be analogous to that of in carbonic anhydrase, to activate the mea substrate electrostatically to nucleophilic attack. The binuclear nF complex (108) displays mease activity, firstly via conversion of mea to ammonia and cyanate, followed by a second step involving the hydrolysis of the cyanate. " In addition, a related asymmetric complex reacts with mea and allows the structmal characterization of the isocyanate product. 

Several model systems related to metalloenzymes such as carboxypeptidase and carbonic anhydrase have been reviewed. Breslow contributed a great deal to this field. He showed how to design precise geometries of bis- or trisimidazole derivatives as in natural enzymes. He was able to synthesize a modified cyclodextrin having both a catalytic metal ion moiety and a substrate binding cavity (26). Murakami prepared a novel macrocyclic bisimidazole compound which has also a substrate binding cavity and imidazole ligands for metal ion complexation. Yet the catalytic activities of these model systems are by no means enzymic. 

The interaction of carbon disulfide as a substrate in carbonic anhydrase model systems has been studied using density functional theory methods. A higher activation energy of CS2 compared to C02 in the reaction with [L3ZnOH]+ was due to the reduced electrophilicity of CS2. The reversibility of the reaction on the basis of these calculations is questionable with [L3ZnSC(0)SH]+ as intermediate.572... 

Different enzymes exhibit different specific activities and turnover numbers. The specific activity is a measure of enzyme purity and is defined as the number of enzyme units per milligram of protein. During the purification of an enzyme, the specific activity increases, and it reaches its maximum when the enzyme is in the pure state. The turnover number of an enzyme is the maximal number of moles of substrate hydrolyzed per mole of enzyme per unit time [63], For example, carbonic anhydrase, found in red blood cells, is a very active enzyme with a turnover number of 36 X 106/min per enzyme molecule. It catalyzes a very important reaction of reversible hydration of dissolved carbon dioxide in blood to form carbonic acid [57, p. 220],... 

In the other subdivision, water activation occurs in the first step of the enzymatic cycle. This activation is achieved by a carboxylate group in aspartic hydrolases (Fig. 3.10), Zn2+ and a carboxy group in metallopep-tidases (Fig. 3.12 ), a histidine side chain in calcium-dependent hydrolases (Fig. 3.14), or a Zn2+ in carbonic anhydrase (Fig. 3.15). The substrate, on the other hand, is polarized (activated) by a carboxy group in aspartic hydrolases or by a cation in metallopeptidases and calcium-dependent hydrolases. In this manner, the reactivity of both the water molecule and the substrate is enhanced and fine-tuned to drive formation of a tetrahedral intermediate that will break down to form the hydrolysis products. 

Chronic in vivo hemolysis produces serum lactic dehydrogenase elevations in patients with mitral or atrial valve cardiac prosthesis (J2). In a series of 11 such patients these increases ranged from 1.1 to 1.6 times the upper limit of normal (S29). Blood pH is altered in hemolyzcd specimens because carbonic anhydrase is liberated from the erythrocytes and presumably alters the distribution of H2CO3 and NaHCOs (B2). Hemolysis will effect acid phosphatase activity if the substrate is hydrolyzed by erythrocyte acid phosphatase. Thus, hemolysis would be of concern if phenyl phosphate was the substrate, but would have a negligible effect if )8-glycerophosphate, which is not hydrolyzed by red cell acid phosphatase, was used (Bl). 

The catalysis of CO2 hydration by carbonic anhydrase II occurs via the two chemically independent steps outlined in Scheme 2 a general mechanistic profile is found in Fig. 23. The first step involves the association of substrate with enzyme and the chemical conversion of substrate into product. The second step is product dissociation and the regeneration of the catalytically active nucleophile zinc hydroxide (Coleman, 1967). Below, we address the structural aspects of zinc coordination in each of these steps. 

The results of kinetic and X-ray crystallographic experiments on mutant carbonic anhydrases II, in which side-chain alterations have been made at the residue comprising the base of the hydrophobic pocket (Val-143), illuminate the role of this pocket in enzyme-substrate association. Site-specific mutants in which smaller hydrophobic amino acids such as glycine, or slightly larger hydrophobic residues such as leucine or isoleucine, are substituted for Val-143 do not exhibit an appreciable change in CO2 hydrase activity relative to the wild-type enzyme however, a substitution to the bulky aromatic side chain of phenylalanine diminishes activity by a factor of about 10 , and a substitution to tyrosine results in a protein which displays activity diminished by a factor of about 10 (Fierke et o/., 1991). 

It is interesting that although the Val-143— His mutation leads to a bulky side chain at the base of the hydrophobic pocket, the mutant enzyme exhibits only a 10 -fold loss of CO2 hydrase activity relative to the wild-type enzyme (Fierke et ai, 1991). In this mutant the Val-I43- His side chain packs differently in the pocket relative to the side chains of the Val-143—>Phe and Val-143- Tyr mutants (Alexander et ai, 1991). It is likely that differences in side-chain packing, as well as differences involving active-site solvent structure, are responsible for differences in enzyme-substrate association behavior among the residue-143 mutants of carbonic anhydrase II. 

Subsequent to CO2 association in the hydrophobic pocket, the chemistry of turnover requires the intimate participation of zinc. The role of zinc is to promote a water molecule as a potent nucleophile, and this is a role which the zinc of carbonic anhydrase II shares with the metal ion of the zinc proteases (discussed in the next section). In fact, the zinc of carbonic anhydrase II promotes the ionization of its bound water so that the active enzyme is in the zinc-hydroxide form (Coleman, 1967 Lindskog and Coleman, 1973 Silverman and Lindskog, 1988). Studies of small-molecule complexes yield effective models of the carbonic anhydrase active site which are catalytically active in zinc-hydroxide forms (Woolley, 1975). In addition to its role in promoting a nucleophilic water molecule, the zinc of carbonic anhydrase II is a classical electrophilic catalyst that is, it stabilizes the developing negative charge of the transition state and product bicarbonate anion. This role does not require the inner-sphere interaction of zinc with the substrate C=0 in a precatalytic complex. 

The most important chemical function of Zn2+ in enzymes is probably that of a Lewis acid providing a concentrated center of positive charge at a nucleophilic site on the substrate/ This role for Zn2+ is discussed for carboxypeptidases (Fig.12-16) and thermolysin, alkaline phosphatase (Fig. 12-23),h RNA polymerases, DNA polymerases, carbonic anhydrase (Fig. 13-1),1 class II aldolases (Fig. 13-7), some alcohol dehydrogenases (Fig. 15-5), and superoxide dismutases (Fig.16-22). Zinc ions in enzymes can often be replaced by Mn2+, Co2+, and other ions with substantial retention of catalytic activity/ ... 

The catalytic activity of an enzyme is measured by its turnover number, which is defined as the number of substrate molecules acted on by one molecule of enzyme per second. As indicated in Table 24.2, enzymes vary greatly in their turnover number. Most enzymes have values in the 1-20,000 range, but carbonic anhydrase, which catalyzes the reaction of C02 with water to yield bicarbonate ion, acts on 600,000 substrate molecules per second. 

Until more concrete structural information is obtained, the discussion on the catalytic mechanism of carbonic anhydrase must remain rather speculative. The experimental evidence requires the presence in the active site of a basic group being in some manner linked to the metal ion. This group is generally thought to play a critical role either as a nucleophile in a direct reaction with the substrate, or through general base catlysis. Several schemes for the function of carbonic anhydrase have been proposed (16, 41, 50, 78, 79) ... 

The catalytic mechanism for C02 hydration-dehydration by carbonic anhydrase represents the focal issue of the present discussion. We have to consider two aspects (1) the mode of binding of the C02 substrate at the active site, and (2) the physical-chemical state of ligands on the zinc ion. 

We have already seen a number of models for the zinc(II) containing enzymes such as carbonic anhydrase in Section 11.3.2. Zinc is an essential component in biochemistry, and forms part of the active site of more then 100 enzymes, of which hydrolases (such as alkaline phosphatase and carboxypeptidase A), transferases (e.g. DNA and RNA polymerase), oxidoreductases (e.g. alcohol dehydrogenase and superoxide dismutase) and lysases (carbonic anhydrase) are the most common. In addition, the non-enzyme zinc finger proteins have an important regulatory function. In many of these systems, the non-redox-active Zn2+ ion is present as a Fewis acidic centre at which substrates are coordinated, polarised and hence activated. Other roles of zinc include acting as a template and playing a structural or regulatory role. 

Metal ions are vital to the function of many enzymes that catalyze hydrolytic reactions. Coordination of a water molecule to a metal ion alters its acid-base properties, usually making it easier to deprotonate, which can offer a ready means for catalyzing a hydrolytic reaction. Also, the placement of a metal center in the active site of a hydrolytic enzyme could permit efficient delivery of a catalytic water molecule to the hydrolyzable substrate. In fact, the first enzyme discovered, carbonic an-hydrase, is a metalloenzyme that requires a Zn2+ center for its catalytic activity (32). The function of carbonic anhydrase is to catalyze the hydrolysis of carbon dioxide to bicarbonate ... 

Tapia and Eklund (1986) carried out a Monte Carlo simulation of the substrate channel of liver alcohol dehydrogenase, based on the X-ray diffraction structure for this enzyme. The addition of substrate and the associated conformation change induce an order—disorder transition for the solvent in the channel. A solvent network, connecting the active-site zinc ion and the protein surface, may provide the basis for a proton relay system. A molecular dynamics simulation of carbonic anhydrase showed two proton relay networks connecting the active-site zinc atom to the surrounding solvent (Vedani et ai, 1989). They remain intact when the substrate, HCOf, is bound. 

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