The topology of a domain yields information about its evolutionary history. Extensive studies on the sequence variation among a family of similar enzymes found in differing organisms reveal that for a given biological function the protein fold is more conserved than the sequence, except for catalytically vital residues. Remarkably the same protein fold is found in proteins that share no significant sequence similarity.Together these observations suggest that a given fold can accept a wide range of sequences and that evolution preserves the core three-dimensional structure. There are two explanations for these observations. The first explanation suggests that evolution of proteins occurs primarily through point mutations which requires that the evolutionary intermediates must be functional and stable. Clearly this is required if the changes involve an essential enzyme. The same requirement applies to more drastic genetic rearrangements which must also proceed through useful, stable intermediates to survive selective pressure and again this will preserve the protein fold. An alternative explanation is that there are a limited number of stable folds and that enzymes have evolved to reach these conformers. In all likelihood both of these arguments contain elements of truth.
There is no doubt that nature has frequently adapted successful protein architectures to carry out new biological functions. This can be seen clearly in the repeated use of common ligand binding domains (such as the dinucleotide binding motif) that occur repeatedly in proteins that require the same ligand even it is used in differing chemical reactions. Such use of common building blocks can be rationalized as a consequence of genetic rearrangement. It would appear that some folds, such as the TIM barrel, are particularly well suited for the evolution of new functionalities. The TIM barrel is one of the most abundant enzyme folds and appears to have arisen at least twice during evolution on the basis of the hydrogen bonding pattern observed within the barrel. There are a wide number of enzymes that utilize this fold as the foundation of their active sites which suggests that enzymes may evolve by retooling of existing functional folds.
The enolase superfamily, which contains a variant of the TIM barrel, is a good example of retooling of a functional fold since these enzymes share a common catalytic step of abstraction of the α-proton of a carboxylate anion. This group of enzymes catalyzes a remarkable range of chemical reactions including racemization, β- elimination of water, β-elimination of ammonia, and cycloisomerization. Each enzyme contains similar catalytic bases and acids and each appears to have evolved by reusing a structural framework that facilitates a difficult chemical task. This is consistent with the observation that the protein fold is the component of the structure that changes most slowly during evolution. Fundamentally this is the result of the marginal thermodynamic stablity of proteins.
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