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

Almonacid DE, Yera ER, Mitchell JB, Babbitt PC - PLoS Comput. Biol. (2010)

Bottom Line: For example, the four carbon-oxygen lyases acting on phosphates (EC 4.2.3) show neither significant overall reaction similarity nor significant mechanistic similarity.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.

View Article: PubMed Central - PubMed

Affiliation: Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California, United States of America.

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.

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Mechanistic vs. overall reaction similarity.All 95 pairs in the dataset of functional analogs and 3570 pairs in the background dataset are included. Sizes of shapes are not proportional to the number of pairs they contain.
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pcbi-1000700-g004: Mechanistic vs. overall reaction similarity.All 95 pairs in the dataset of functional analogs and 3570 pairs in the background dataset are included. Sizes of shapes are not proportional to the number of pairs they contain.

Mentions: Figure 4 plots mechanistic similarity against overall reaction similarity for all 95 pairs of functionally analogous enzymes and for all 3570 pairs in the background dataset. Pairs in the background dataset populated all areas of the plot, whereas pairs in the functionally analogous dataset almost exclusively populated the area below the diagonal. Only one pair from the dataset appeared above the diagonal in Figure 4: phosphoenolpyruvate carboxykinase (ATP) (MACiE M0051, EC 4.1.1.49, PDB 1aq2) [57] and methylmalonyl-CoA decarboxylase (MACiE M0070, EC 4.1.1.41, PDB 1ef8) [58]. These enzymes share an identical step and highly similar mechanisms, yet the extra phosphorylation catalyzed by the former enzyme makes the overall reactions non-similar (Table S3). Thus, for functionally analogous pairs of enzymes, overall reaction similarity serves as an upper bound on mechanistic similarity. This is expected since functionally analogous enzymes are proteins without a common ancestor that have converged to catalyze a similar overall reaction. In contrast, in homologous superfamilies of enzymes, conserved active site residues, organic cofactors or metal ions catalyze at least one identical catalytic step, even in very different overall reactions [4]–[7], [19]–[21]. Thus, homologous superfamilies exhibit significant mechanistic similarity, but not necessarily significant overall reaction similarity [59]. This notwithstanding, the higher the overall reaction similarity attained by a pair of functionally analogous enzymes, the higher the chances are that the pair also shows mechanistic similarity. Considering both functionally analogous and homologous enzymes, it seems that overall reaction similarity can vary greatly after sequence divergence, with mechanistic similarity being much more conserved in homologous superfamilies. A companion study to this one is currently under way to compare in detail overall reaction and mechanistic similarities in homologous superfamilies.


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

Almonacid DE, Yera ER, Mitchell JB, Babbitt PC - PLoS Comput. Biol. (2010)

Mechanistic vs. overall reaction similarity.All 95 pairs in the dataset of functional analogs and 3570 pairs in the background dataset are included. Sizes of shapes are not proportional to the number of pairs they contain.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2837397&req=5

pcbi-1000700-g004: Mechanistic vs. overall reaction similarity.All 95 pairs in the dataset of functional analogs and 3570 pairs in the background dataset are included. Sizes of shapes are not proportional to the number of pairs they contain.
Mentions: Figure 4 plots mechanistic similarity against overall reaction similarity for all 95 pairs of functionally analogous enzymes and for all 3570 pairs in the background dataset. Pairs in the background dataset populated all areas of the plot, whereas pairs in the functionally analogous dataset almost exclusively populated the area below the diagonal. Only one pair from the dataset appeared above the diagonal in Figure 4: phosphoenolpyruvate carboxykinase (ATP) (MACiE M0051, EC 4.1.1.49, PDB 1aq2) [57] and methylmalonyl-CoA decarboxylase (MACiE M0070, EC 4.1.1.41, PDB 1ef8) [58]. These enzymes share an identical step and highly similar mechanisms, yet the extra phosphorylation catalyzed by the former enzyme makes the overall reactions non-similar (Table S3). Thus, for functionally analogous pairs of enzymes, overall reaction similarity serves as an upper bound on mechanistic similarity. This is expected since functionally analogous enzymes are proteins without a common ancestor that have converged to catalyze a similar overall reaction. In contrast, in homologous superfamilies of enzymes, conserved active site residues, organic cofactors or metal ions catalyze at least one identical catalytic step, even in very different overall reactions [4]–[7], [19]–[21]. Thus, homologous superfamilies exhibit significant mechanistic similarity, but not necessarily significant overall reaction similarity [59]. This notwithstanding, the higher the overall reaction similarity attained by a pair of functionally analogous enzymes, the higher the chances are that the pair also shows mechanistic similarity. Considering both functionally analogous and homologous enzymes, it seems that overall reaction similarity can vary greatly after sequence divergence, with mechanistic similarity being much more conserved in homologous superfamilies. A companion study to this one is currently under way to compare in detail overall reaction and mechanistic similarities in homologous superfamilies.

Bottom Line: For example, the four carbon-oxygen lyases acting on phosphates (EC 4.2.3) show neither significant overall reaction similarity nor significant mechanistic similarity.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.

View Article: PubMed Central - PubMed

Affiliation: Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California, United States of America.

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.

Show MeSH
Related in: MedlinePlus