Oxyanion catalysis

As judged from our ecological model compound sea water, the bioavailability of molybdenum (104 nM) is higher than that of chromium (962pM) (see Table 1.1). While chromium is insoluble as Cr(III) in the Earth s crust, the reduction of molybdate is not as easy as chromate reduction, which leads to a factor of 10 000 when the release of chromium and molybdenum from the Earth s crust into sea water is compared. Together with its low toxicity (Nies 1999), this makes molybdate the prime choice for biochemical reactions requiring oxyanion catalysis (Williams and da Silva 2002). 

Serine proteinases such as chymotrypsin and subtilisin catalyze the cleavage of peptide bonds. Four features essential for catalysis are present in the three-dimensional structures of all serine proteinases a catalytic triad, an oxyanion binding site, a substrate specificity pocket, and a nonspecific binding site for polypeptide substrates. These four features, in a very similar arrangement, are present in both chymotrypsin and subtilisin even though they are achieved in the two enzymes in completely different ways by quite different three-dimensional structures. Chymotrypsin is built up from two p-barrel domains, whereas the subtilisin structure is of the a/p type. These two enzymes provide an example of convergent evolution where completely different loop regions, attached to different framework structures, form similar active sites. 

For many serine and cysteine peptidases catalysis first involves formation of a complex known as an acyl intermediate. An essential residue is required to stabilize this intermediate by helping to form the oxyanion hole. In cathepsin B a glutamine performs this role and sometimes a catalytic tetrad (Gin, Cys, His, Asn) is referred too. In chymotrypsin, a glycine is essential for stabilizing the oxyanion hole. 

The mechanism for the lipase-catalyzed reaction of an acid derivative with a nucleophile (alcohol, amine, or thiol) is known as a serine hydrolase mechanism (Scheme 7.2). The active site of the enzyme is constituted by a catalytic triad (serine, aspartic, and histidine residues). The serine residue accepts the acyl group of the ester, leading to an acyl-enzyme activated intermediate. This acyl-enzyme intermediate reacts with the nucleophile, an amine or ammonia in this case, to yield the final amide product and leading to the free biocatalyst, which can enter again into the catalytic cycle. A histidine residue, activated by an aspartate side chain, is responsible for the proton transference necessary for the catalysis. Another important factor is that the oxyanion hole, formed by different residues, is able to stabilize the negatively charged oxygen present in both the transition state and the tetrahedral intermediate. 

Tosylate is displaced by weak oxyanions with little elimination in aprotic solvents, providing alternative routes to polymer-bound esters and aryl ethers. Alkoxides, unfortunately, give significant functional yields of (vinyl)polystyrene under the same conditions. Phosphines and sulfides can also be prepared from the appropriate anions (57), the latter lipophilic enough for phase-transfer catalysis free from poisonning by released tosylate. 

Zhang Y, Kua J, McCammon JA (2002) Role of the catalytic triad and oxyanion hole in acetylcholinesterase catalysis an ab initio QM/MM study. J Am Chem Soc 124 10572—10577... 

Clearly, the oxyanion hole is now as significant a feature of the binding site of such acyl transfer abzymes as it is already for esterases and peptidases — and not without good reason. Knossow has analysed the structures of three esterase-like catalytic antibodies, each elicited in response to the same phosphonate TSA hapten (Charbonnier et al., 1997). Catalysis for all three is accounted for by transition state stabilization and in each case there is an... 

This reaction encompasses a number of interesting features (general Brpnsted acid/ Brpnsted base catalysis, bifunctional catalysis, enantioselective organocatalysis, very short hydrogen bonds, similarity to serine protease mechanism, oxyanion hole), and we were able to obtain a complete set of DFT based data for the entire reaction path, from the starting catalyst-substrate complex to the product complex. 

In this chapter, we review the key properties of a central structural feature in hydrogen bonding powered enzymatic catalysis-the oxyanion hole. 

The contributions of hydrogen bond donors to catalysis can be estimated by site-directed mutagenesis studies in cases where the hydrogen bond donor is located in the amino acid side chain. Deletion of the main chain NH is only possible by substituting the amino acid with a proUne. In all cases, the effects of the substitution to key enzyme kinetic parameters, and K, should be checked. Typically, the oxyanion hole residues contribute only Uttle to the binding of substrate [19-21]. This is reflected in the values, which typically remain very similar... 

Table 4.2 Contributions of different oxyanion hole residues to catalysis. AACf calculated from the kinetic data, is the increase in the free energy of the transition state barrier, due to the mutation. 

Scheme 4.13 (a) Two different types of xanthone-based oxyanion hole receptors developed by Simon and co-workers and (b) possible mode of catalysis of a conjugate addition reaction between pyrrolidine and a, 5-unsaturated valerolactam by one of the receptors. 

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