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Structure- and context-based analysis of the GxGYxYP family reveals a new putative class of Glycoside Hydrolase
BACKGROUND: Gut microbiome metagenomics has revealed many protein families and domains found largely or exclusively in that environment. Proteins containing the GxGYxYP domain are over-represented in the gut microbiota, and are found in Polysaccharide Utilization Loci in the gut symbiont Bacteroides...
Autores principales: | , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2014
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4071793/ https://www.ncbi.nlm.nih.gov/pubmed/24938123 http://dx.doi.org/10.1186/1471-2105-15-196 |
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author | Rigden, Daniel J Eberhardt, Ruth Y Gilbert, Harry J Xu, Qingping Chang, Yuanyuan Godzik, Adam |
author_facet | Rigden, Daniel J Eberhardt, Ruth Y Gilbert, Harry J Xu, Qingping Chang, Yuanyuan Godzik, Adam |
author_sort | Rigden, Daniel J |
collection | PubMed |
description | BACKGROUND: Gut microbiome metagenomics has revealed many protein families and domains found largely or exclusively in that environment. Proteins containing the GxGYxYP domain are over-represented in the gut microbiota, and are found in Polysaccharide Utilization Loci in the gut symbiont Bacteroides thetaiotaomicron, suggesting their involvement in polysaccharide metabolism, but little else is known of the function of this domain. RESULTS: Genomic context and domain architecture analyses support a role for the GxGYxYP domain in carbohydrate metabolism. Sparse occurrences in eukaryotes are the result of lateral gene transfer. The structure of the GxGYxYP domain-containing protein encoded by the BT2193 locus reveals two structural domains, the first composed of three divergent repeats with no recognisable homology to previously solved structures, the second a more familiar seven-stranded β/α barrel. Structure-based analyses including conservation mapping localise a presumed functional site to a cleft between the two domains of BT2193. Matching to a catalytic site template from a GH9 cellulase and other analyses point to a putative catalytic triad composed of Glu272, Asp331 and Asp333. CONCLUSIONS: We suggest that GxGYxYP-containing proteins constitute a novel glycoside hydrolase family of as yet unknown specificity. |
format | Online Article Text |
id | pubmed-4071793 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2014 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-40717932014-06-27 Structure- and context-based analysis of the GxGYxYP family reveals a new putative class of Glycoside Hydrolase Rigden, Daniel J Eberhardt, Ruth Y Gilbert, Harry J Xu, Qingping Chang, Yuanyuan Godzik, Adam BMC Bioinformatics Research Article BACKGROUND: Gut microbiome metagenomics has revealed many protein families and domains found largely or exclusively in that environment. Proteins containing the GxGYxYP domain are over-represented in the gut microbiota, and are found in Polysaccharide Utilization Loci in the gut symbiont Bacteroides thetaiotaomicron, suggesting their involvement in polysaccharide metabolism, but little else is known of the function of this domain. RESULTS: Genomic context and domain architecture analyses support a role for the GxGYxYP domain in carbohydrate metabolism. Sparse occurrences in eukaryotes are the result of lateral gene transfer. The structure of the GxGYxYP domain-containing protein encoded by the BT2193 locus reveals two structural domains, the first composed of three divergent repeats with no recognisable homology to previously solved structures, the second a more familiar seven-stranded β/α barrel. Structure-based analyses including conservation mapping localise a presumed functional site to a cleft between the two domains of BT2193. Matching to a catalytic site template from a GH9 cellulase and other analyses point to a putative catalytic triad composed of Glu272, Asp331 and Asp333. CONCLUSIONS: We suggest that GxGYxYP-containing proteins constitute a novel glycoside hydrolase family of as yet unknown specificity. BioMed Central 2014-06-17 /pmc/articles/PMC4071793/ /pubmed/24938123 http://dx.doi.org/10.1186/1471-2105-15-196 Text en Copyright © 2014 Rigden et al.; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/4.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. |
spellingShingle | Research Article Rigden, Daniel J Eberhardt, Ruth Y Gilbert, Harry J Xu, Qingping Chang, Yuanyuan Godzik, Adam Structure- and context-based analysis of the GxGYxYP family reveals a new putative class of Glycoside Hydrolase |
title | Structure- and context-based analysis of the GxGYxYP family reveals a new putative class of Glycoside Hydrolase |
title_full | Structure- and context-based analysis of the GxGYxYP family reveals a new putative class of Glycoside Hydrolase |
title_fullStr | Structure- and context-based analysis of the GxGYxYP family reveals a new putative class of Glycoside Hydrolase |
title_full_unstemmed | Structure- and context-based analysis of the GxGYxYP family reveals a new putative class of Glycoside Hydrolase |
title_short | Structure- and context-based analysis of the GxGYxYP family reveals a new putative class of Glycoside Hydrolase |
title_sort | structure- and context-based analysis of the gxgyxyp family reveals a new putative class of glycoside hydrolase |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4071793/ https://www.ncbi.nlm.nih.gov/pubmed/24938123 http://dx.doi.org/10.1186/1471-2105-15-196 |
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