ArticleJournal of molecular biology2016
Large-Scale Analysis Exploring Evolution of Catalytic Machineries and Mechanisms in Enzyme Superfamilies.
Article in Journal of molecular biology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed.
- Investigating enzyme function by geometric matching of catalytic motifs.Protein science : a publication of the Protein Society · 2026Article
- Paradigms of convergent evolution in enzymes.The FEBS journal · 2025Article
- Enzyme function and evolution through the lens of bioinformatics.The Biochemical journal · 2023Review
- MAHOMES II: A webserver for predicting if a metal binding site is enzymatic.Protein science : a publication of the Protein Society · 2023Article
- MAHOMES II: A webserver for predicting if a metal binding site is enzymatic.bioRxiv : the preprint server for biology · 2023Article
- Cold-Active Lipases and Esterases: A Review on Recombinant Overexpression and Other Essential Issues.International journal of molecular sciences · 2022Review
- Evolution of Enzyme Function and the Development of Catalytic Efficiency: Triosephosphate Isomerase, Jeremy R. Knowles, and W. John Albery.Biochemistry · 2021Article
- CATH functional families predict functional sites in proteins.Bioinformatics (Oxford, England) · 2021Article
- The Role of Gene Duplication in the Divergence of Enzyme Function: A Comparative Approach.Frontiers in genetics · 2021Article
- Differential Evolution of α-Glucan Water Dikinase (GWD) in Plants.Plants (Basel, Switzerland) · 2020Article
- Harnessing Conformational Plasticity to Generate Designer Enzymes.Journal of the American Chemical Society · 2020Review
- A strategy for large-scale comparison of evolutionary- and reaction-based classifications of enzyme function.Database : the journal of biological databases and curation · 2020Article
- Structural Studies based on two Lysine Dioxygenases with Distinct Regioselectivity Brings Insights Into Enzyme Specificity within the Clavaminate Synthase-Like Family.Scientific reports · 2018Article
- Insights into a dual function amide oxidase/macrocyclase from lankacidin biosynthesis.Nature communications · 2018Article
- Evolution of cyclohexadienyl dehydratase from an ancestral solute-binding protein.Nature chemical biology · 2018Article
- Ligand Binding Site Structure Influences the Evolution of Protein Complex Function and Topology.Cell reports · 2018Article
- Differential catalytic promiscuity of the alkaline phosphatase superfamily bimetallo core reveals mechanistic features underlying enzyme evolution.The Journal of biological chemistry · 2017Article
- Genomic Enzymology: Web Tools for Leveraging Protein Family Sequence-Function Space and Genome Context to Discover Novel Functions.Biochemistry · 2017Review
- Parallel evolution of non-homologous isofunctional enzymes in methionine biosynthesis.Nature chemical biology · 2017Article
- De novo active sites for resurrected Precambrian enzymes.Nature communications · 2017Article
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
Enzymes, as biological catalysts, form the basis of all forms of life. How these proteins have evolved their functions remains a fundamental question in biology. Over 100 years of detailed biochemistry studies, combined with the large volumes of sequence and protein structural data now available, means that we are able to perform large-scale analyses to address this question. Using a range of computational tools and resources, we have compiled information on all experimentally annotated changes in enzyme function within 379 structurally defined protein domain superfamilies, linking the changes observed in functions during evolution to changes in reaction chemistry. Many superfamilies show changes in function at some level, although one function often dominates one superfamily. We use quantitative measures of changes in reaction chemistry to reveal the various types of chemical changes occurring during evolution and to exemplify these by detailed examples. Additionally, we use structural information of the enzymes active site to examine how different superfamilies have changed their catalytic machinery during evolution. Some superfamilies have changed the reactions they perform without changing catalytic machinery. In others, large changes of enzyme function, in terms of both overall chemistry and substrate specificity, have been brought about by significant changes in catalytic machinery. Interestingly, in some superfamilies, relatives perform similar functions but with different catalytic machineries. This analysis highlights characteristics of functional evolution across a wide range of superfamilies, providing insights that will be useful in predicting the function of uncharacterised sequences and the design of new synthetic enzymes.
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