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

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 evo...

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Autores principales:	Nicholas Furnham, Ian Sillitoe, Gemma L Holliday, Alison L Cuff, Roman A Laskowski, Christine A Orengo, Janet M Thornton
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2012
Materias:	Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/3f40aaa07cb648a8bc60cdf2ba6ec48b
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spelling	oai:doaj.org-article:3f40aaa07cb648a8bc60cdf2ba6ec48b2021-11-18T05:51:32ZExploring the evolution of novel enzyme functions within structurally defined protein superfamilies.1553-734X1553-735810.1371/journal.pcbi.1002403https://doaj.org/article/3f40aaa07cb648a8bc60cdf2ba6ec48b2012-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/22396634/?tool=EBIhttps://doaj.org/toc/1553-734Xhttps://doaj.org/toc/1553-7358In 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.Nicholas FurnhamIan SillitoeGemma L HollidayAlison L CuffRoman A LaskowskiChristine A OrengoJanet M ThorntonPublic Library of Science (PLoS)articleBiology (General)QH301-705.5ENPLoS Computational Biology, Vol 8, Iss 3, p e1002403 (2012)
institution	DOAJ
collection	DOAJ
language	EN
topic	Biology (General) QH301-705.5
spellingShingle	Biology (General) QH301-705.5 Nicholas Furnham Ian Sillitoe Gemma L Holliday Alison L Cuff Roman A Laskowski Christine A Orengo Janet M Thornton Exploring the evolution of novel enzyme functions within structurally defined protein superfamilies.
description	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.
format	article
author	Nicholas Furnham Ian Sillitoe Gemma L Holliday Alison L Cuff Roman A Laskowski Christine A Orengo Janet M Thornton
author_facet	Nicholas Furnham Ian Sillitoe Gemma L Holliday Alison L Cuff Roman A Laskowski Christine A Orengo Janet M Thornton
author_sort	Nicholas Furnham
title	Exploring the evolution of novel enzyme functions within structurally defined protein superfamilies.
title_short	Exploring the evolution of novel enzyme functions within structurally defined protein superfamilies.
title_full	Exploring the evolution of novel enzyme functions within structurally defined protein superfamilies.
title_fullStr	Exploring the evolution of novel enzyme functions within structurally defined protein superfamilies.
title_full_unstemmed	Exploring the evolution of novel enzyme functions within structurally defined protein superfamilies.
title_sort	exploring the evolution of novel enzyme functions within structurally defined protein superfamilies.
publisher	Public Library of Science (PLoS)
publishDate	2012
url	https://doaj.org/article/3f40aaa07cb648a8bc60cdf2ba6ec48b
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Exploring the evolution of novel enzyme functions within structurally defined protein superfamilies.

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