Structural and molecular basis for the substrate positioning mechanism of a new PL7 subfamily alginate lyase from the Arctic
Alginate lyases play important roles in alginate degradation in the ocean. Although a large number of alginate lyases have been characterized, little is yet known about those in extremely cold polar environments, which may have unique mechanisms for environmental adaptation and for alginate degradat...
Published in: | Journal of Biological Chemistry |
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American Society for Biochemistry & Molecular Biology (ASBMB)
2020
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Online Access: | http://wrap.warwick.ac.uk/142441/ http://wrap.warwick.ac.uk/142441/7/WRAP-Structural-molecular-basis-substrate-positioning-mechanism-PL7-Chen-2020.pdf http://wrap.warwick.ac.uk/142441/1/WRAP-Structural-molecular-basis-substrate-positioning-mechanism-PL7-Chen-2020.pdf https://doi.org/10.1074/jbc.ra120.015106 |
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ftuwarwick:oai:wrap.warwick.ac.uk:142441 2023-05-15T14:27:46+02:00 Structural and molecular basis for the substrate positioning mechanism of a new PL7 subfamily alginate lyase from the Arctic Xu, Fei Chen, Xiu-Lan Sun, Xiao-Hui Dong, Fang Li, Chun-Yang Li, Ping-Yi Ding, Haitao Chen, Yin Zhang, Yu-Zhong Wang, Peng 2020-11-27 application/pdf http://wrap.warwick.ac.uk/142441/ http://wrap.warwick.ac.uk/142441/7/WRAP-Structural-molecular-basis-substrate-positioning-mechanism-PL7-Chen-2020.pdf http://wrap.warwick.ac.uk/142441/1/WRAP-Structural-molecular-basis-substrate-positioning-mechanism-PL7-Chen-2020.pdf https://doi.org/10.1074/jbc.ra120.015106 unknown American Society for Biochemistry & Molecular Biology (ASBMB) http://wrap.warwick.ac.uk/142441/7/WRAP-Structural-molecular-basis-substrate-positioning-mechanism-PL7-Chen-2020.pdf http://wrap.warwick.ac.uk/142441/1/WRAP-Structural-molecular-basis-substrate-positioning-mechanism-PL7-Chen-2020.pdf Xu, Fei, Chen, Xiu-Lan, Sun, Xiao-Hui, Dong, Fang, Li, Chun-Yang, Li, Ping-Yi, Ding, Haitao, Chen, Yin, Zhang, Yu-Zhong and Wang, Peng (2020) Structural and molecular basis for the substrate positioning mechanism of a new PL7 subfamily alginate lyase from the Arctic. Journal of Biological Chemistry, 295 (48). pp. 16380-16392. doi:10.1074/jbc.ra120.015106 <http://dx.doi.org/10.1074/jbc.ra120.015106> ISSN 1083-351X. QH Natural history QP Physiology Journal Article NonPeerReviewed 2020 ftuwarwick https://doi.org/10.1074/jbc.ra120.015106 2023-03-16T23:42:08Z Alginate lyases play important roles in alginate degradation in the ocean. Although a large number of alginate lyases have been characterized, little is yet known about those in extremely cold polar environments, which may have unique mechanisms for environmental adaptation and for alginate degradation. Here, we report the characterization of a novel PL7 alginate lyase AlyC3 from Psychromonas sp. C-3 isolated from the Arctic brown alga Laminaria, including its phylogenetic classification, catalytic properties and structure. We propose the establishment of a new PM-specific subfamily of PL7 (subfamily 6) represented by AlyC3 based on phylogenetic analysis and enzymatic properties. Structural and biochemical analyses showed that AlyC3 is a dimer, representing the first dimeric endo-alginate lyase structure. AlyC3 is activated by NaCl and adopts a novel salt-activated mechanism, that is, salinity adjusts the enzymatic activity by affecting its aggregation states. We further solved the structure of an inactive mutant H127A/Y244A in complex with a dimannuronate molecule, and proposed the catalytic process of AlyC3 based on structural and biochemical analyses. We show that Arg82 and Tyr190 at the two ends of the catalytic canyon help the positioning of the repeated units of the substrate, and that His127, Tyr244, Arg78, and Gln125 mediate the catalytic reaction. Our study uncovers, for the first time, the amino acid residues for alginate positioning in an alginate lyase, and demonstrate that such residues involved in alginate positioning are conserved in other alginate lyases. This study provides a better understanding of the mechanisms of alginate degradation by alginate lyases. Article in Journal/Newspaper Arctic Arctic The University of Warwick: WRAP - Warwick Research Archive Portal Arctic Journal of Biological Chemistry 295 48 16380 16392 |
institution |
Open Polar |
collection |
The University of Warwick: WRAP - Warwick Research Archive Portal |
op_collection_id |
ftuwarwick |
language |
unknown |
topic |
QH Natural history QP Physiology |
spellingShingle |
QH Natural history QP Physiology Xu, Fei Chen, Xiu-Lan Sun, Xiao-Hui Dong, Fang Li, Chun-Yang Li, Ping-Yi Ding, Haitao Chen, Yin Zhang, Yu-Zhong Wang, Peng Structural and molecular basis for the substrate positioning mechanism of a new PL7 subfamily alginate lyase from the Arctic |
topic_facet |
QH Natural history QP Physiology |
description |
Alginate lyases play important roles in alginate degradation in the ocean. Although a large number of alginate lyases have been characterized, little is yet known about those in extremely cold polar environments, which may have unique mechanisms for environmental adaptation and for alginate degradation. Here, we report the characterization of a novel PL7 alginate lyase AlyC3 from Psychromonas sp. C-3 isolated from the Arctic brown alga Laminaria, including its phylogenetic classification, catalytic properties and structure. We propose the establishment of a new PM-specific subfamily of PL7 (subfamily 6) represented by AlyC3 based on phylogenetic analysis and enzymatic properties. Structural and biochemical analyses showed that AlyC3 is a dimer, representing the first dimeric endo-alginate lyase structure. AlyC3 is activated by NaCl and adopts a novel salt-activated mechanism, that is, salinity adjusts the enzymatic activity by affecting its aggregation states. We further solved the structure of an inactive mutant H127A/Y244A in complex with a dimannuronate molecule, and proposed the catalytic process of AlyC3 based on structural and biochemical analyses. We show that Arg82 and Tyr190 at the two ends of the catalytic canyon help the positioning of the repeated units of the substrate, and that His127, Tyr244, Arg78, and Gln125 mediate the catalytic reaction. Our study uncovers, for the first time, the amino acid residues for alginate positioning in an alginate lyase, and demonstrate that such residues involved in alginate positioning are conserved in other alginate lyases. This study provides a better understanding of the mechanisms of alginate degradation by alginate lyases. |
format |
Article in Journal/Newspaper |
author |
Xu, Fei Chen, Xiu-Lan Sun, Xiao-Hui Dong, Fang Li, Chun-Yang Li, Ping-Yi Ding, Haitao Chen, Yin Zhang, Yu-Zhong Wang, Peng |
author_facet |
Xu, Fei Chen, Xiu-Lan Sun, Xiao-Hui Dong, Fang Li, Chun-Yang Li, Ping-Yi Ding, Haitao Chen, Yin Zhang, Yu-Zhong Wang, Peng |
author_sort |
Xu, Fei |
title |
Structural and molecular basis for the substrate positioning mechanism of a new PL7 subfamily alginate lyase from the Arctic |
title_short |
Structural and molecular basis for the substrate positioning mechanism of a new PL7 subfamily alginate lyase from the Arctic |
title_full |
Structural and molecular basis for the substrate positioning mechanism of a new PL7 subfamily alginate lyase from the Arctic |
title_fullStr |
Structural and molecular basis for the substrate positioning mechanism of a new PL7 subfamily alginate lyase from the Arctic |
title_full_unstemmed |
Structural and molecular basis for the substrate positioning mechanism of a new PL7 subfamily alginate lyase from the Arctic |
title_sort |
structural and molecular basis for the substrate positioning mechanism of a new pl7 subfamily alginate lyase from the arctic |
publisher |
American Society for Biochemistry & Molecular Biology (ASBMB) |
publishDate |
2020 |
url |
http://wrap.warwick.ac.uk/142441/ http://wrap.warwick.ac.uk/142441/7/WRAP-Structural-molecular-basis-substrate-positioning-mechanism-PL7-Chen-2020.pdf http://wrap.warwick.ac.uk/142441/1/WRAP-Structural-molecular-basis-substrate-positioning-mechanism-PL7-Chen-2020.pdf https://doi.org/10.1074/jbc.ra120.015106 |
geographic |
Arctic |
geographic_facet |
Arctic |
genre |
Arctic Arctic |
genre_facet |
Arctic Arctic |
op_relation |
http://wrap.warwick.ac.uk/142441/7/WRAP-Structural-molecular-basis-substrate-positioning-mechanism-PL7-Chen-2020.pdf http://wrap.warwick.ac.uk/142441/1/WRAP-Structural-molecular-basis-substrate-positioning-mechanism-PL7-Chen-2020.pdf Xu, Fei, Chen, Xiu-Lan, Sun, Xiao-Hui, Dong, Fang, Li, Chun-Yang, Li, Ping-Yi, Ding, Haitao, Chen, Yin, Zhang, Yu-Zhong and Wang, Peng (2020) Structural and molecular basis for the substrate positioning mechanism of a new PL7 subfamily alginate lyase from the Arctic. Journal of Biological Chemistry, 295 (48). pp. 16380-16392. doi:10.1074/jbc.ra120.015106 <http://dx.doi.org/10.1074/jbc.ra120.015106> ISSN 1083-351X. |
op_doi |
https://doi.org/10.1074/jbc.ra120.015106 |
container_title |
Journal of Biological Chemistry |
container_volume |
295 |
container_issue |
48 |
container_start_page |
16380 |
op_container_end_page |
16392 |
_version_ |
1766301661619290112 |