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Structural and molecular basis for the substrate positioning mechanism of a new PL7 subfamily alginate lyase from the Arctic
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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
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Official URL: https://doi.org/10.1074/jbc.ra120.015106
Abstract
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.
| Item Type: | Journal Article | ||||||||||||||||||||||||||||||||||||||||||
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| Subjects: | Q Science > QH Natural history Q Science > QP Physiology |
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| Divisions: | Faculty of Science > Life Sciences (2010- ) | ||||||||||||||||||||||||||||||||||||||||||
| SWORD Depositor: | Library Publications Router | ||||||||||||||||||||||||||||||||||||||||||
| Library of Congress Subject Headings (LCSH): | Lyases, Alginates, Molecular biology | ||||||||||||||||||||||||||||||||||||||||||
| Journal or Publication Title: | Journal of Biological Chemistry | ||||||||||||||||||||||||||||||||||||||||||
| Publisher: | American Society for Biochemistry & Molecular Biology (ASBMB) | ||||||||||||||||||||||||||||||||||||||||||
| ISSN: | 1083-351X | ||||||||||||||||||||||||||||||||||||||||||
| Official Date: | 27 November 2020 | ||||||||||||||||||||||||||||||||||||||||||
| Dates: |
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| Date of first compliant deposit: | 2 October 2020 | ||||||||||||||||||||||||||||||||||||||||||
| Volume: | 295 | ||||||||||||||||||||||||||||||||||||||||||
| Number: | 48 | ||||||||||||||||||||||||||||||||||||||||||
| Page Range: | pp. 16380-16392 | ||||||||||||||||||||||||||||||||||||||||||
| DOI: | 10.1074/jbc.ra120.015106 | ||||||||||||||||||||||||||||||||||||||||||
| Status: | Peer Reviewed | ||||||||||||||||||||||||||||||||||||||||||
| Publication Status: | Published | ||||||||||||||||||||||||||||||||||||||||||
| Publisher Statement: | This research was originally published in the Journal of Biological Chemistry. Author(s). Title. J Biol Chem. Year; Vol:pp-pp. © the American Society for Biochemistry and Molecular Biology or © the Author(s). | ||||||||||||||||||||||||||||||||||||||||||
| Access rights to Published version: | Open Access | ||||||||||||||||||||||||||||||||||||||||||
| Copyright Holders: | © the American Society for Biochemistry and Molecular Biology | ||||||||||||||||||||||||||||||||||||||||||
| RIOXX Funder/Project Grant: |
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