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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

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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
Subjects: Q Science > QH Natural history
Q Science > QP Physiology
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:
DateEvent
27 November 2020Published
23 September 2020Available
23 September 2020Accepted
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:
Project/Grant IDRIOXX Funder NameFunder ID
2018YFC1406700National Key Research and Development Program of China Stem Cell and Translational Researchhttp://dx.doi.org/10.13039/501100013290
91851205[NSFC] National Natural Science Foundation of Chinahttp://dx.doi.org/10.13039/501100001809
31870052[NSFC] National Natural Science Foundation of Chinahttp://dx.doi.org/10.13039/501100001809
31800107[NSFC] National Natural Science Foundation of Chinahttp://dx.doi.org/10.13039/501100001809
U1706207[NSFC] National Natural Science Foundation of Chinahttp://dx.doi.org/10.13039/501100001809
91751101 [NSFC] National Natural Science Foundation of Chinahttp://dx.doi.org/10.13039/501100001809
41706152[NSFC] National Natural Science Foundation of Chinahttp://dx.doi.org/10.13039/501100001809
41676180[NSFC] National Natural Science Foundation of Chinahttp://dx.doi.org/10.13039/501100001809
2019JZZY010817Department of Science and Technology of Shandong Provincehttp://dx.doi.org/10.13039/100012905
tspd20181203Taishan Scholar Project of Shandong Provincehttp://dx.doi.org/10.13039/501100010040
2017ASTCP-OS14Qingdao National Laboratory for Marine Science and Technologyhttp://dx.doi.org/10.13039/501100010954
QNLM2016ORP0310Qingdao National Laboratory for Marine Science and Technologyhttp://dx.doi.org/10.13039/501100010954
2017WLJH57Shandong Universityhttp://dx.doi.org/10.13039/100009108

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