How enzymes came to be

Consider the decarboxylation of orotidine 5′-phosphate reaction. This reaction is essential for the synthesis of DNA. Without the corresponding enzyme, the uncatalyzed reaction would take millions of years to complete. With the enzyme, the reaction happens in milliseconds. The Journal of Biological Chemistry’s recent thematic minireview series focuses on how enzymes acquire and optimize their traits for such efficiency.

If the reactions necessary for life occur so slowly, how could an enzyme even begin to evolve from its ancestral form? In the first review of the series, Richard Wolfenden of the University of North Carolina at Chapel Hill discusses how temperature changes as the Earth developed encouraged the evolutionary process. Recent studies demonstrated that very slow reactions, like some in the body, are sensitive to temperature, supporting the idea that the very warm temperatures of primordial Earth would have accelerated their rates dramatically. Other studies have shown that the extent to which artificial catalysts enhance the reaction rate increases as temperature decreases. If early enzymes behaved like this, Wolfenden contends, as the Earth cooled, the rate enhancement from the enzymes would have increased, compensating for the decrease in the reaction rate itself. Studies also have reported that the rate of genetic mutations is sensitive to temperature. The generation of genetic variants might have been extremely prolific at the early stages of the evolutionary process.

What interactions change as an enzyme evolves? In the second review, Judith P. Klinman of the University of California, Berkeley, and Amnon Kohen of the University of Iowa present examples of how protein dynamics and the chemical reaction being catalyzed influence enzyme evolution. For dihydrofolate reductase, residues directly affecting the reaction step were shown to evolve together, although the functions of residues that coevolved were not necessarily part of the chemical reaction coordinate. The chronological order of mutations also is important, as some mutations in higher organisms can support the chemical step only if earlier mutations have occurred. Studies in two highly related alcohol dehydrogenases that function at extremely different temperatures showed how protein dynamics can increase the efficiency of the catalyzed reaction by creating active site configurations with highly specific internuclear distance and charge, illustrating one way proteins can adapt to different environmental conditions.

What structures and functions did an enzyme acquire at each evolutionary step? In the third review, Charles W. Carter Jr. of the University of North Carolina at Chapel Hill describes how Urzymes can be used to find these evolutionary intermediates. The Urzyme of an enzyme is created by cutting away portions of the enzyme that are not conserved in all members of its superfamily. What remains is the part that provides the catalytic activity, the core of the enzyme. While the Urzyme has somewhat reduced catalytic activity, it has lost much of its specificity. Carter references studies that demonstrate that adding protein domains can confer specificity  and that these domains influence specificity through their synergy, or epistasis, suggesting how specificity and function developed as enzymes evolved.

Enzymes in the same superfamily share a common partial reaction or chemical capability. However, the reactions that enzymes within the same superfamily catalyze can vary widely. In the fourth review, Shoshana D. Brown and Patricia C. Babbitt of the University of California, San Francisco, explore how this divergent evolution occurs. Variations in the active site and other features can generate diversity while conserving common traits. The specific variation differs by superfamily. In the two dinucleotide binding domains flavoprotein, or tDBDF, superfamily, the organization of cofactors within the active site are physically and chemically constrained to limit how they are used, while changing the protein-protein interactions allows different reactions to occur. In the nucleophilic attack, 6-bladed beta-propeller, or N6P superfamily, the active sites and the reactions catalyzed vary dramatically between the subgroups. However, all the subgroups initiate their reactions by the same strategy.

Many enzymes accept a number of substrates to catalyze a chemical reaction. In the final review, Debra Dunaway-Mariano of the University of New Mexico and Karen N. Allen and colleagues of Boston University discuss how a cell capitalizes on this promiscuity and how substrate ambiguity can occur. Substrate-ambiguous enzymes carry out other cellular functions, such as removing toxic metabolites and balancing metabolite pools. Substrate ambiguity can be promoted by varying the size of the active site and increasing the number of locations that can contribute binding energy through domain insertion.

Maggie Kuo Maggie Kuo (mkuo@asbmb.org) is an intern at ASBMB Today and a Ph.D. candidate in biomedical engineering at Johns Hopkins University.