Quantitative comparison of catalytic mechanisms and overall reactions in convergently evolved enzymes: implications for classification of enzyme function.

Daniel E Almonacid,Emmanuel R Yera,John B O Mitchell,Patricia C Babbitt,Christine A Orengo

doi:10.1371/journal.pcbi.1000700

Daniel E Almonacid, Emmanuel R Yera + Show 3 more

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https://doi.org/10.1371/journal.pcbi.1000700

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Abstract

Functionally analogous enzymes are those that catalyze similar reactions on similar substrates but do not share common ancestry, providing a window on the different structural strategies nature has used to evolve required catalysts. Identification and use of this information to improve reaction classification and computational annotation of enzymes newly discovered in the genome projects would benefit from systematic determination of reaction similarities. Here, we quantified similarity in bond changes for overall reactions and catalytic mechanisms for 95 pairs of functionally analogous enzymes (non-homologous enzymes with identical first three numbers of their EC codes) from the MACiE database. Similarity of overall reactions was computed by comparing the sets of bond changes in the transformations from substrates to products. For similarity of mechanisms, sets of bond changes occurring in each mechanistic step were compared; these similarities were then used to guide global and local alignments of mechanistic steps. Using this metric, only 44% of pairs of functionally analogous enzymes in the dataset had significantly similar overall reactions. For these enzymes, convergence to the same mechanism occurred in 33% of cases, with most pairs having at least one identical mechanistic step. Using our metric, overall reaction similarity serves as an upper bound for mechanistic similarity in functional analogs. For example, the four carbon-oxygen lyases acting on phosphates (EC 4.2.3) show neither significant overall reaction similarity nor significant mechanistic similarity. By contrast, the three carboxylic-ester hydrolases (EC 3.1.1) catalyze overall reactions with identical bond changes and have converged to almost identical mechanisms. The large proportion of enzyme pairs that do not show significant overall reaction similarity (56%) suggests that at least for the functionally analogous enzymes studied here, more stringent criteria could be used to refine definitions of EC sub-subclasses for improved discrimination in their classification of enzyme reactions. The results also indicate that mechanistic convergence of reaction steps is widespread, suggesting that quantitative measurement of mechanistic similarity can inform approaches for functional annotation.

Highlights

IntroductionUsing the Enzyme Commission (EC) classification to describe function [1] and the structure and sequence similarity between proteins as a measure of homology, numerous works have reported cases of divergence and convergence of function in enzymes [2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17]
We investigated the relationship between functional similarity in enzymes according to the Enzyme Commission (EC) classification and similarity of overall reactions based on the bond changes that occur in the transformations from substrates to products
Less than half of the pairs of enzymes in our dataset showed significant overall reaction similarity, leading us to conclude that the EC classification, and by extension catalytic activities in the Gene Ontology, may not accurately reflect functional similarities among a large subset of the reactions catalyzed by enzymes

Summary

Introduction

Using the Enzyme Commission (EC) classification to describe function [1] and the structure and sequence similarity between proteins as a measure of homology, numerous works have reported cases of divergence and convergence of function in enzymes [2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17]. As a note in proof, it was observed that the three hydrogen-bonded catalytic residues in the active site of subtilisin were present in the functionally similar serine protease chymotrypsin [23], leading them to hypothesize the involvement of the triad in the enzymatic mechanism of both proteases. This first example of convergence of active site and catalytic mechanism presaged subsequent findings that convergence of function in enzymes is widespread. Could it be that unrelated enzymes bind similar substrates carrying the same functional groups, but the reaction mechanisms vary significantly

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