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The Laccase Engineering Database: a classification and analysis system for laccases and related multicopper oxidases
Laccases and their homologues form the protein superfamily of multicopper oxidases (MCO). They catalyze the oxidation of many, particularly phenolic substances, and, besides playing an important role in many cellular activities, are of interest in biotechnological applications. The Laccase Engineeri...
Autores principales: | , , , , |
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Formato: | Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2011
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3077825/ https://www.ncbi.nlm.nih.gov/pubmed/21498547 http://dx.doi.org/10.1093/database/bar006 |
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author | Sirim, Demet Wagner, Florian Wang, Lei Schmid, Rolf D Pleiss, Jürgen |
author_facet | Sirim, Demet Wagner, Florian Wang, Lei Schmid, Rolf D Pleiss, Jürgen |
author_sort | Sirim, Demet |
collection | PubMed |
description | Laccases and their homologues form the protein superfamily of multicopper oxidases (MCO). They catalyze the oxidation of many, particularly phenolic substances, and, besides playing an important role in many cellular activities, are of interest in biotechnological applications. The Laccase Engineering Database (LccED, http://www.lcced.uni-stuttgart.de) was designed to serve as a tool for a systematic sequence-based classification and analysis of the diverse multicopper oxidase protein family. More than 2200 proteins were classified into 11 superfamilies and 56 homologous families. For each family, the LccED provides multiple sequence alignments, phylogenetic trees and family-specific HMM profiles. The integration of structures for 14 different proteins allows a comprehensive comparison of sequences and structures to derive biochemical properties. Among the families, the distribution of the proteins regarding different kingdoms was investigated. The database was applied to perform a comprehensive analysis by MCO- and laccase-specific patterns. The LccED combines information of sequences and structures of MCOs. It serves as a classification tool to assign new proteins to a homologous family and can be applied to investigate sequence–structure–function relationship and to guide protein engineering. Database URL: http://www.lcced.uni-stuttgart.de |
format | Text |
id | pubmed-3077825 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2011 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-30778252011-04-15 The Laccase Engineering Database: a classification and analysis system for laccases and related multicopper oxidases Sirim, Demet Wagner, Florian Wang, Lei Schmid, Rolf D Pleiss, Jürgen Database (Oxford) Original Article Laccases and their homologues form the protein superfamily of multicopper oxidases (MCO). They catalyze the oxidation of many, particularly phenolic substances, and, besides playing an important role in many cellular activities, are of interest in biotechnological applications. The Laccase Engineering Database (LccED, http://www.lcced.uni-stuttgart.de) was designed to serve as a tool for a systematic sequence-based classification and analysis of the diverse multicopper oxidase protein family. More than 2200 proteins were classified into 11 superfamilies and 56 homologous families. For each family, the LccED provides multiple sequence alignments, phylogenetic trees and family-specific HMM profiles. The integration of structures for 14 different proteins allows a comprehensive comparison of sequences and structures to derive biochemical properties. Among the families, the distribution of the proteins regarding different kingdoms was investigated. The database was applied to perform a comprehensive analysis by MCO- and laccase-specific patterns. The LccED combines information of sequences and structures of MCOs. It serves as a classification tool to assign new proteins to a homologous family and can be applied to investigate sequence–structure–function relationship and to guide protein engineering. Database URL: http://www.lcced.uni-stuttgart.de Oxford University Press 2011-04-15 /pmc/articles/PMC3077825/ /pubmed/21498547 http://dx.doi.org/10.1093/database/bar006 Text en © The Author(s) 2011. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/2.5 This is Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.5), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Original Article Sirim, Demet Wagner, Florian Wang, Lei Schmid, Rolf D Pleiss, Jürgen The Laccase Engineering Database: a classification and analysis system for laccases and related multicopper oxidases |
title | The Laccase Engineering Database: a classification and analysis system for laccases and related multicopper oxidases |
title_full | The Laccase Engineering Database: a classification and analysis system for laccases and related multicopper oxidases |
title_fullStr | The Laccase Engineering Database: a classification and analysis system for laccases and related multicopper oxidases |
title_full_unstemmed | The Laccase Engineering Database: a classification and analysis system for laccases and related multicopper oxidases |
title_short | The Laccase Engineering Database: a classification and analysis system for laccases and related multicopper oxidases |
title_sort | laccase engineering database: a classification and analysis system for laccases and related multicopper oxidases |
topic | Original Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3077825/ https://www.ncbi.nlm.nih.gov/pubmed/21498547 http://dx.doi.org/10.1093/database/bar006 |
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