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Mechanistic insight into the substrate specificity of 1,2-β-oligoglucan phosphorylase from Lachnoclostridium phytofermentans

Glycoside phosphorylases catalyze the phosphorolysis of oligosaccharides into sugar phosphates. Recently, we found a novel phosphorylase acting on β-1,2-glucooligosaccharides with degrees of polymerization of 3 or more (1,2-β-oligoglucan phosphorylase, SOGP) in glycoside hydrolase family (GH) 94. He...

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Autores principales: Nakajima, Masahiro, Tanaka, Nobukiyo, Furukawa, Nayuta, Nihira, Takanori, Kodutsumi, Yuki, Takahashi, Yuta, Sugimoto, Naohisa, Miyanaga, Akimasa, Fushinobu, Shinya, Taguchi, Hayao, Nakai, Hiroyuki
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5309861/
https://www.ncbi.nlm.nih.gov/pubmed/28198470
http://dx.doi.org/10.1038/srep42671
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author Nakajima, Masahiro
Tanaka, Nobukiyo
Furukawa, Nayuta
Nihira, Takanori
Kodutsumi, Yuki
Takahashi, Yuta
Sugimoto, Naohisa
Miyanaga, Akimasa
Fushinobu, Shinya
Taguchi, Hayao
Nakai, Hiroyuki
author_facet Nakajima, Masahiro
Tanaka, Nobukiyo
Furukawa, Nayuta
Nihira, Takanori
Kodutsumi, Yuki
Takahashi, Yuta
Sugimoto, Naohisa
Miyanaga, Akimasa
Fushinobu, Shinya
Taguchi, Hayao
Nakai, Hiroyuki
author_sort Nakajima, Masahiro
collection PubMed
description Glycoside phosphorylases catalyze the phosphorolysis of oligosaccharides into sugar phosphates. Recently, we found a novel phosphorylase acting on β-1,2-glucooligosaccharides with degrees of polymerization of 3 or more (1,2-β-oligoglucan phosphorylase, SOGP) in glycoside hydrolase family (GH) 94. Here, we characterized SOGP from Lachnoclostridium phytofermentans (LpSOGP) and determined its crystal structure. LpSOGP is a monomeric enzyme that contains a unique β-sandwich domain (Ndom1) at its N-terminus. Unlike the dimeric GH94 enzymes possessing catalytic pockets at their dimer interface, LpSOGP has a catalytic pocket between Ndom1 and the catalytic domain. In the complex structure of LpSOGP with sophorose, sophorose binds at subsites +1 to +2. Notably, the Glc moiety at subsite +1 is flipped compared with the corresponding ligands in other GH94 enzymes. This inversion suggests the great distortion of the glycosidic bond between subsites −1 and +1, which is likely unfavorable for substrate binding. Compensation for this disadvantage at subsite +2 can be accounted for by the small distortion of the glycosidic bond in the sophorose molecule. Therefore, the binding mode at subsites +1 and +2 defines the substrate specificity of LpSOGP, which provides mechanistic insights into the substrate specificity of a phosphorylase acting on β-1,2-glucooligosaccharides.
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spelling pubmed-53098612017-02-22 Mechanistic insight into the substrate specificity of 1,2-β-oligoglucan phosphorylase from Lachnoclostridium phytofermentans Nakajima, Masahiro Tanaka, Nobukiyo Furukawa, Nayuta Nihira, Takanori Kodutsumi, Yuki Takahashi, Yuta Sugimoto, Naohisa Miyanaga, Akimasa Fushinobu, Shinya Taguchi, Hayao Nakai, Hiroyuki Sci Rep Article Glycoside phosphorylases catalyze the phosphorolysis of oligosaccharides into sugar phosphates. Recently, we found a novel phosphorylase acting on β-1,2-glucooligosaccharides with degrees of polymerization of 3 or more (1,2-β-oligoglucan phosphorylase, SOGP) in glycoside hydrolase family (GH) 94. Here, we characterized SOGP from Lachnoclostridium phytofermentans (LpSOGP) and determined its crystal structure. LpSOGP is a monomeric enzyme that contains a unique β-sandwich domain (Ndom1) at its N-terminus. Unlike the dimeric GH94 enzymes possessing catalytic pockets at their dimer interface, LpSOGP has a catalytic pocket between Ndom1 and the catalytic domain. In the complex structure of LpSOGP with sophorose, sophorose binds at subsites +1 to +2. Notably, the Glc moiety at subsite +1 is flipped compared with the corresponding ligands in other GH94 enzymes. This inversion suggests the great distortion of the glycosidic bond between subsites −1 and +1, which is likely unfavorable for substrate binding. Compensation for this disadvantage at subsite +2 can be accounted for by the small distortion of the glycosidic bond in the sophorose molecule. Therefore, the binding mode at subsites +1 and +2 defines the substrate specificity of LpSOGP, which provides mechanistic insights into the substrate specificity of a phosphorylase acting on β-1,2-glucooligosaccharides. Nature Publishing Group 2017-02-15 /pmc/articles/PMC5309861/ /pubmed/28198470 http://dx.doi.org/10.1038/srep42671 Text en Copyright © 2017, The Author(s) http://creativecommons.org/licenses/by/4.0/ This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/
spellingShingle Article
Nakajima, Masahiro
Tanaka, Nobukiyo
Furukawa, Nayuta
Nihira, Takanori
Kodutsumi, Yuki
Takahashi, Yuta
Sugimoto, Naohisa
Miyanaga, Akimasa
Fushinobu, Shinya
Taguchi, Hayao
Nakai, Hiroyuki
Mechanistic insight into the substrate specificity of 1,2-β-oligoglucan phosphorylase from Lachnoclostridium phytofermentans
title Mechanistic insight into the substrate specificity of 1,2-β-oligoglucan phosphorylase from Lachnoclostridium phytofermentans
title_full Mechanistic insight into the substrate specificity of 1,2-β-oligoglucan phosphorylase from Lachnoclostridium phytofermentans
title_fullStr Mechanistic insight into the substrate specificity of 1,2-β-oligoglucan phosphorylase from Lachnoclostridium phytofermentans
title_full_unstemmed Mechanistic insight into the substrate specificity of 1,2-β-oligoglucan phosphorylase from Lachnoclostridium phytofermentans
title_short Mechanistic insight into the substrate specificity of 1,2-β-oligoglucan phosphorylase from Lachnoclostridium phytofermentans
title_sort mechanistic insight into the substrate specificity of 1,2-β-oligoglucan phosphorylase from lachnoclostridium phytofermentans
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5309861/
https://www.ncbi.nlm.nih.gov/pubmed/28198470
http://dx.doi.org/10.1038/srep42671
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