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Exploring the evolution of novel enzyme functions within structurally defined protein superfamilies

Furnham, N; Sillitoe, I; Holliday, GL; Cuff, AL; Laskowski, RA; Orengo, CA; Thornton, JM; (2012) Exploring the evolution of novel enzyme functions within structurally defined protein superfamilies. PLoS Comput Biol , 8 (3) e1002403+-e1002403+. 10.1371/journal.pcbi.1002403%20%5Bdoi%5D.

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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.

Type: Article
Title: Exploring the evolution of novel enzyme functions within structurally defined protein superfamilies
DOI: 10.1371/journal.pcbi.1002403%20%5Bdoi%5D
Publisher version: http://dx.doi.org/10.1371/journal.pcbi.1002403%20%...
Additional information: citeulike-article-id: 12411842 citeulike-linkout-0: http://dx.doi.org/10.1371/journal.pcbi.1002403%20%5Bdoi%5D comment: eng —=note-separator=— Nlm —=note-separator=— Furnham, Nicholas Sillitoe, Ian Holliday, Gemma L Cuff, Alison L Laskowski, Roman A Orengo, Christine A Thornton, Janet M 081989/Z/07/A/Wellcome Trust/United Kingdom Biotechnology and Biological Sciences Research Council/United Kingdom Research Support, Non-U.S. Gov’t Research Support, U.S. Gov’t, Non-P.H.S. United States PLoS computational biology PLoS Comput Biol. 2012;8(3):e1002403. doi: 10.1371/journal.pcbi.1002403. Epub 2012 Mar 1. —=note-separator=— Exploring the evolution of novel enzyme functions within structurally defined protein superfamilies keywords: acid, amino, analysis, chemistry-, data, enzymes-, evolution, methods, molecular, physiology, protein-, relationship, sequence, structure-activity, *file-import-13-06-12 posted-at: 2013-06-12 22:01:27 priority: 2 bdsk-url-1: http://dx.doi.org/10.1371/journal.pcbi.1002403%5C%20%5C%5Bdoi%5C%5D bdsk-url-2: http://dx.doi.org/10.1371/journal.pcbi.1002403%5C%2520%5C%255Bdoi%5C%255D
UCL classification: UCL > Provost and Vice Provost Offices
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences > Structural and Molecular Biology
URI: http://discovery.ucl.ac.uk/id/eprint/1396626
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