ArticlePLoS computational biology2012
Exploring the evolution of novel enzyme functions within structurally defined protein superfamilies.
Article in PLoS computational biology, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 48 papers.
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Who cites it
48 citing papers in PubMed.
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- Noncanonical Amino Acids: Bringing New-to-Nature Functionalities to Biocatalysis.Chemical reviews · 2024Review
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- Biochemical and molecular characterization of a novel glycerol dehydratase from Klebsiella pneumoniae 2e with high tolerance against crude glycerol impurities.Biotechnology for biofuels and bioproducts · 2023Article
- Using mechanism similarity to understand enzyme evolution.Biophysical reviews · 2022Review
- Uniform binding and negative catalysis at the origin of enzymes.Protein science : a publication of the Protein Society · 2022Article
- The Role of Gene Duplication in the Divergence of Enzyme Function: A Comparative Approach.Frontiers in genetics · 2021Article
- Evolutionary aspects and enzymology of metazoan carotenoid cleavage oxygenases.Biochimica et biophysica acta. Molecular and cell biology of lipids · 2020Review
- A flavin-dependent monooxygenase catalyzes the initial step in cyanogenic glycoside synthesis in ferns.Communications biology · 2020Article
- Effect of sequence padding on the performance of deep learning models in archaeal protein functional prediction.Scientific reports · 2020Article
- Selective Modulation of Dynamic Protein Complexes.Cell chemical biology · 2020Review
- Emerging Frontiers in the Study of Molecular Evolution.Journal of molecular evolution · 2020Article
- A global analysis of function and conservation of catalytic residues in enzymes.The Journal of biological chemistry · 2020Review
- Computational classification of MocR transcriptional regulators into subgroups as a support for experimental and functional characterization.Bioinformation · 2019Article
- Evolutionary repurposing of a sulfatase: A new Michaelis complex leads to efficient transition state charge offset.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
- Highly active enzymes by automated combinatorial backbone assembly and sequence design.Nature communications · 2018Article
- Evolution of enzymes with new specificity by high-throughput screening using DmpR-based genetic circuits and multiple flow cytometry rounds.Scientific reports · 2018Article
- To what extent do structural changes in catalytic metal sites affect enzyme function?Journal of inorganic biochemistry · 2018Article
- Atlas of the Radical SAM Superfamily: Divergent Evolution of Function Using a "Plug and Play" Domain.Methods in enzymology · 2018Article
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7 authors.
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Abstract
In order to understand the evolution of enzyme reactions and to gain an overview of biological catalysis we have combined sequence and structural data to generate phylogenetic trees in an analysis of 276 structurally defined enzyme superfamilies, and used these to study how enzyme functions have evolved. We describe in detail the analysis of two superfamilies to illustrate different paradigms of enzyme evolution. Gathering together data from all the superfamilies supports and develops the observation that they have all evolved to act on a diverse set of substrates, whilst the evolution of new chemistry is much less common. Despite that, by bringing together so much data, we can provide a comprehensive overview of the most common and rare types of changes in function. Our analysis demonstrates on a larger scale than previously studied, that modifications in overall chemistry still occur, with all possible changes at the primary level of the Enzyme Commission (E.C.) classification observed to a greater or lesser extent. The phylogenetic trees map out the evolutionary route taken within a superfamily, as well as all the possible changes within a superfamily. This has been used to generate a matrix of observed exchanges from one enzyme function to another, revealing the scale and nature of enzyme evolution and that some types of exchanges between and within E.C. classes are more prevalent than others. Surprisingly a large proportion (71%) of all known enzyme functions are performed by this relatively small set of 276 superfamilies. This reinforces the hypothesis that relatively few ancient enzymatic domain superfamilies were progenitors for most of the chemistry required for life.
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