Catalytic sites convergence

Evolution of protein function Catalytic site convergence versus divergence... 

This catalytic site resembles that of DNA polymerase (Secion 27.2.2) in that it includes two metal ions in its active form (Figure 28.2). One metal ion remains bound to the enzyme, whereas the other appears to come in with the nucleoside triphosphate and leave with the pyrophosphate. Three conserved aspartate residues of the enzyme participate in binding these metal ions. Note that the overall structures of DNA polymerase and RNA polymerase are quite different their similar active sites are the products of convergent evolution. 

Convergence of catalytic site in nonhomologous structures. Serine... 

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. 

A third family, the -carbonic anhydrases, also has been identified, initially in the archaeon Methanosarcina thermophila. The crystal structure of this enzyme reveals three zinc sites extremely similar to those in the a-carbonic anhydrases. In this case, however, the three zinc sites lie at the interfaces between the three subunits of a trimeric enzyme (Figure 9.31). The very striking left-handed P-helix (a P strand twisted into a left-handed helix) structure present in this enzyme has also been found in enzymes that catalyze reactions unrelated to those of carbonic anhydrase. Thus, convergent evolution has generated carbonic anhydrases that rely on coordinated zinc ions at least three times. In each case, the catalytic activity appears to be associated with zinc-bound water molecules. 

Other proteases employ the same catalytic strategy. Some of these proteases, such as trypsin and elastase, are homologs of chymotrypsin. In other proteases, such as subtilisin, a very similar catalytic triad has arisen by convergent evolution. Active-site structures that differ from the catalytic triad are present in a number of other classes of proteases. These classes employ a range of catalytic strategies but, in each case, a nucleophile is generated that is sufficiently powerful to attack the peptide carbonyl group. In some enzymes, the nucleophile is derived from a side chain whereas, in others, an activated water molecule attacks the peptide carbonyl directly. 

Other enzymes that are not homologs of chymotrypsin have been found to contain very similar active sites. As noted in Chapter 6, the presence of very active sites in these different protein families is a consequence of convergent evolution. Subtilisin, a protease in bacteria such as Bacillus amyloliq-uejadens, is a particularly well characterized example. The active site of this enzyme includes both the catalytic triad and thcoxyanion hole. However, one NH groups that forms the oxyanion hole comes from the side chain of an asparagine residue rather than from the peptide backbone (Figure 9.14). 

Convergence may also occur when the sequence and structure of molecules are very different, but the mechanisms by which they act are similar. Serine proteases have evolved independently in bacteria (e.g. subtilisin) and vertebrates (e.g. trypsin). Despite their very different sequences and three-dimensional structures, in each the same set of three amino acids form the active site. The catalytic triads are His57, Aspl02, and Serl95 (trypsin) and Asp32, His64, and Ser221 (subtilisin) (Doolittle, 1994 A. Tramontano, personal communication). 

Construction of such active sites with small synthetic molecules would be very difficult. Several catalytic elements are to be placed on the molecular framework. Furthermore, those catalytic elements should take productive positions and the conformational freedom of the molecular framework should be controlled to maintain the productive conformation. Thus, a large amount of laborious computational and skillful synthetic work is needed to synthesize such active sites. Instead, synthetic as well as natural macromolecules have been frequently chosen as the backbone of artificial enzymes. Nature has adopted polypeptide as the backbone of the catalysts for fine tuning of the positions and the reactivity of the convergent catalytic elements. 

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