Bioinformatic analysis of alpha/beta-hydrolase fold enzymes reveals subfamily-specific positions responsible for discrimination of amidase and lipase activities
Superfamily of alpha-beta hydrolases is one of the largest groups of structurally related enzymes with diverse catalytic functions. Bioinformatic analysis was used to study how lipase and amidase catalytic activities are implemented into the same structural framework. Subfamily-specific positions—co...
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fthighwire:oai:open-archive.highwire.org:proeng:25/11/689 2023-05-15T14:04:25+02:00 Bioinformatic analysis of alpha/beta-hydrolase fold enzymes reveals subfamily-specific positions responsible for discrimination of amidase and lipase activities Suplatov, D.A. Besenmatter, W. Svedas, V.K. Svendsen, A. 2012-11-01 00:00:00.0 text/html http://peds.oxfordjournals.org/cgi/content/short/25/11/689 https://doi.org/10.1093/protein/gzs068 en eng Oxford University Press http://peds.oxfordjournals.org/cgi/content/short/25/11/689 http://dx.doi.org/10.1093/protein/gzs068 Copyright (C) 2012, Oxford University Press Original articles TEXT 2012 fthighwire https://doi.org/10.1093/protein/gzs068 2015-02-28T22:33:30Z Superfamily of alpha-beta hydrolases is one of the largest groups of structurally related enzymes with diverse catalytic functions. Bioinformatic analysis was used to study how lipase and amidase catalytic activities are implemented into the same structural framework. Subfamily-specific positions—conserved within lipases and peptidases but different between them—that were supposed to be responsible for functional discrimination have been identified. Mutations at subfamily-specific positions were used to introduce amidase activity into Candida antarctica lipase B (CALB). Molecular modeling was implemented to evaluate influence of selected residues on binding and catalytic conversion of amide substrate by corresponding library of mutants. In silico screening was applied to select reactive enzyme-substrate complexes that satisfy knowledge-based criteria of amidase catalytic activity. Selected CALB variants with substitutions at subfamily-specific positions Gly39, Thr103, Trp104, and Leu278 were produced and showed significant improvement of experimentally measured amidase activity. Based on these results, we suggest that value of subfamily-specific positions should be further explored in order to develop a systematic tool to study structure-function relationship in enzymes and to use this information for rational enzyme engineering. Text Antarc* Antarctica HighWire Press (Stanford University) Protein Engineering Design and Selection 25 11 689 697 |
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Original articles Suplatov, D.A. Besenmatter, W. Svedas, V.K. Svendsen, A. Bioinformatic analysis of alpha/beta-hydrolase fold enzymes reveals subfamily-specific positions responsible for discrimination of amidase and lipase activities |
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Original articles |
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Superfamily of alpha-beta hydrolases is one of the largest groups of structurally related enzymes with diverse catalytic functions. Bioinformatic analysis was used to study how lipase and amidase catalytic activities are implemented into the same structural framework. Subfamily-specific positions—conserved within lipases and peptidases but different between them—that were supposed to be responsible for functional discrimination have been identified. Mutations at subfamily-specific positions were used to introduce amidase activity into Candida antarctica lipase B (CALB). Molecular modeling was implemented to evaluate influence of selected residues on binding and catalytic conversion of amide substrate by corresponding library of mutants. In silico screening was applied to select reactive enzyme-substrate complexes that satisfy knowledge-based criteria of amidase catalytic activity. Selected CALB variants with substitutions at subfamily-specific positions Gly39, Thr103, Trp104, and Leu278 were produced and showed significant improvement of experimentally measured amidase activity. Based on these results, we suggest that value of subfamily-specific positions should be further explored in order to develop a systematic tool to study structure-function relationship in enzymes and to use this information for rational enzyme engineering. |
format |
Text |
author |
Suplatov, D.A. Besenmatter, W. Svedas, V.K. Svendsen, A. |
author_facet |
Suplatov, D.A. Besenmatter, W. Svedas, V.K. Svendsen, A. |
author_sort |
Suplatov, D.A. |
title |
Bioinformatic analysis of alpha/beta-hydrolase fold enzymes reveals subfamily-specific positions responsible for discrimination of amidase and lipase activities |
title_short |
Bioinformatic analysis of alpha/beta-hydrolase fold enzymes reveals subfamily-specific positions responsible for discrimination of amidase and lipase activities |
title_full |
Bioinformatic analysis of alpha/beta-hydrolase fold enzymes reveals subfamily-specific positions responsible for discrimination of amidase and lipase activities |
title_fullStr |
Bioinformatic analysis of alpha/beta-hydrolase fold enzymes reveals subfamily-specific positions responsible for discrimination of amidase and lipase activities |
title_full_unstemmed |
Bioinformatic analysis of alpha/beta-hydrolase fold enzymes reveals subfamily-specific positions responsible for discrimination of amidase and lipase activities |
title_sort |
bioinformatic analysis of alpha/beta-hydrolase fold enzymes reveals subfamily-specific positions responsible for discrimination of amidase and lipase activities |
publisher |
Oxford University Press |
publishDate |
2012 |
url |
http://peds.oxfordjournals.org/cgi/content/short/25/11/689 https://doi.org/10.1093/protein/gzs068 |
genre |
Antarc* Antarctica |
genre_facet |
Antarc* Antarctica |
op_relation |
http://peds.oxfordjournals.org/cgi/content/short/25/11/689 http://dx.doi.org/10.1093/protein/gzs068 |
op_rights |
Copyright (C) 2012, Oxford University Press |
op_doi |
https://doi.org/10.1093/protein/gzs068 |
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Protein Engineering Design and Selection |
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25 |
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11 |
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689 |
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1766275507624607744 |