Structural classification by the Lipase Engineering Database: a case study of Candida antarctica lipase A
Abstract Background The Lipase Engineering Database (LED) integrates information on sequence, structure and function of lipases, esterases and related proteins with the α/β hydrolase fold. A new superfamily for Candida antarctica lipase A (CALA) was introduced including the recently published crysta...
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ftdoajarticles:oai:doaj.org/article:f1168d69c05242ffb5e091777ff2935c 2023-05-15T13:55:45+02:00 Structural classification by the Lipase Engineering Database: a case study of Candida antarctica lipase A Juhl P Benjamin Widmann Michael Pleiss Jürgen 2010-02-01T00:00:00Z https://doi.org/10.1186/1471-2164-11-123 https://doaj.org/article/f1168d69c05242ffb5e091777ff2935c EN eng BMC http://www.biomedcentral.com/1471-2164/11/123 https://doaj.org/toc/1471-2164 doi:10.1186/1471-2164-11-123 1471-2164 https://doaj.org/article/f1168d69c05242ffb5e091777ff2935c BMC Genomics, Vol 11, Iss 1, p 123 (2010) Biotechnology TP248.13-248.65 Genetics QH426-470 article 2010 ftdoajarticles https://doi.org/10.1186/1471-2164-11-123 2022-12-31T09:15:25Z Abstract Background The Lipase Engineering Database (LED) integrates information on sequence, structure and function of lipases, esterases and related proteins with the α/β hydrolase fold. A new superfamily for Candida antarctica lipase A (CALA) was introduced including the recently published crystal structure of CALA. Since CALA has a highly divergent sequence in comparison to other α/β hydrolases, the Lipase Engineering Database was used to classify CALA in the frame of the already established classification system. This involved the comparison of CALA to similar structures as well as sequence-based comparisons against the content of the LED. Results The new release 3.0 (December 2009) of the Lipase Engineering Database contains 24783 sequence entries for 18585 proteins as well as 656 experimentally determined protein structures, including the structure of CALA. In comparison to the previous release 1 with 4322 protein and 167 structure entries this update represents a significant increase in data volume. By comparing CALA to representative structures from all superfamilies, a structure from the deacetylase superfamily was found to be most similar to the structure of CALA. While the α/β hydrolase fold is conserved in both proteins, the major difference is found in the cap region. Sequence alignments between both proteins show a sequence similarity of only 15%. A multisequence alignment of both protein families was used to create hidden Markov models for the cap region of CALA and showed that the cap region of CALA is unique among all other proteins of the α/β hydrolase fold. By specifically comparing the substrate binding pocket of CALA to other binding pockets of α/β hydrolases, the binding pocket of Candida rugosa lipase was identified as being highly similar. This similarity also applied to the lid of Candida rugosa lipase in comparison to the potential lid of CALA. Conclusion The LED serves as a valuable tool for the systematic analysis of single proteins or protein families. The updated release 3.0 was ... Article in Journal/Newspaper Antarc* Antarctica Directory of Open Access Journals: DOAJ Articles Rugosa ENVELOPE(-61.250,-61.250,-62.633,-62.633) BMC Genomics 11 1 123 |
institution |
Open Polar |
collection |
Directory of Open Access Journals: DOAJ Articles |
op_collection_id |
ftdoajarticles |
language |
English |
topic |
Biotechnology TP248.13-248.65 Genetics QH426-470 |
spellingShingle |
Biotechnology TP248.13-248.65 Genetics QH426-470 Juhl P Benjamin Widmann Michael Pleiss Jürgen Structural classification by the Lipase Engineering Database: a case study of Candida antarctica lipase A |
topic_facet |
Biotechnology TP248.13-248.65 Genetics QH426-470 |
description |
Abstract Background The Lipase Engineering Database (LED) integrates information on sequence, structure and function of lipases, esterases and related proteins with the α/β hydrolase fold. A new superfamily for Candida antarctica lipase A (CALA) was introduced including the recently published crystal structure of CALA. Since CALA has a highly divergent sequence in comparison to other α/β hydrolases, the Lipase Engineering Database was used to classify CALA in the frame of the already established classification system. This involved the comparison of CALA to similar structures as well as sequence-based comparisons against the content of the LED. Results The new release 3.0 (December 2009) of the Lipase Engineering Database contains 24783 sequence entries for 18585 proteins as well as 656 experimentally determined protein structures, including the structure of CALA. In comparison to the previous release 1 with 4322 protein and 167 structure entries this update represents a significant increase in data volume. By comparing CALA to representative structures from all superfamilies, a structure from the deacetylase superfamily was found to be most similar to the structure of CALA. While the α/β hydrolase fold is conserved in both proteins, the major difference is found in the cap region. Sequence alignments between both proteins show a sequence similarity of only 15%. A multisequence alignment of both protein families was used to create hidden Markov models for the cap region of CALA and showed that the cap region of CALA is unique among all other proteins of the α/β hydrolase fold. By specifically comparing the substrate binding pocket of CALA to other binding pockets of α/β hydrolases, the binding pocket of Candida rugosa lipase was identified as being highly similar. This similarity also applied to the lid of Candida rugosa lipase in comparison to the potential lid of CALA. Conclusion The LED serves as a valuable tool for the systematic analysis of single proteins or protein families. The updated release 3.0 was ... |
format |
Article in Journal/Newspaper |
author |
Juhl P Benjamin Widmann Michael Pleiss Jürgen |
author_facet |
Juhl P Benjamin Widmann Michael Pleiss Jürgen |
author_sort |
Juhl P Benjamin |
title |
Structural classification by the Lipase Engineering Database: a case study of Candida antarctica lipase A |
title_short |
Structural classification by the Lipase Engineering Database: a case study of Candida antarctica lipase A |
title_full |
Structural classification by the Lipase Engineering Database: a case study of Candida antarctica lipase A |
title_fullStr |
Structural classification by the Lipase Engineering Database: a case study of Candida antarctica lipase A |
title_full_unstemmed |
Structural classification by the Lipase Engineering Database: a case study of Candida antarctica lipase A |
title_sort |
structural classification by the lipase engineering database: a case study of candida antarctica lipase a |
publisher |
BMC |
publishDate |
2010 |
url |
https://doi.org/10.1186/1471-2164-11-123 https://doaj.org/article/f1168d69c05242ffb5e091777ff2935c |
long_lat |
ENVELOPE(-61.250,-61.250,-62.633,-62.633) |
geographic |
Rugosa |
geographic_facet |
Rugosa |
genre |
Antarc* Antarctica |
genre_facet |
Antarc* Antarctica |
op_source |
BMC Genomics, Vol 11, Iss 1, p 123 (2010) |
op_relation |
http://www.biomedcentral.com/1471-2164/11/123 https://doaj.org/toc/1471-2164 doi:10.1186/1471-2164-11-123 1471-2164 https://doaj.org/article/f1168d69c05242ffb5e091777ff2935c |
op_doi |
https://doi.org/10.1186/1471-2164-11-123 |
container_title |
BMC Genomics |
container_volume |
11 |
container_issue |
1 |
container_start_page |
123 |
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1766262591334645760 |