Cargando…
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...
Autores principales: | , , , , , , , , , , |
---|---|
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 |
_version_ | 1782507783008026624 |
---|---|
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. |
format | Online Article Text |
id | pubmed-5309861 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2017 |
publisher | Nature Publishing Group |
record_format | MEDLINE/PubMed |
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 |
work_keys_str_mv | AT nakajimamasahiro mechanisticinsightintothesubstratespecificityof12boligoglucanphosphorylasefromlachnoclostridiumphytofermentans AT tanakanobukiyo mechanisticinsightintothesubstratespecificityof12boligoglucanphosphorylasefromlachnoclostridiumphytofermentans AT furukawanayuta mechanisticinsightintothesubstratespecificityof12boligoglucanphosphorylasefromlachnoclostridiumphytofermentans AT nihiratakanori mechanisticinsightintothesubstratespecificityof12boligoglucanphosphorylasefromlachnoclostridiumphytofermentans AT kodutsumiyuki mechanisticinsightintothesubstratespecificityof12boligoglucanphosphorylasefromlachnoclostridiumphytofermentans AT takahashiyuta mechanisticinsightintothesubstratespecificityof12boligoglucanphosphorylasefromlachnoclostridiumphytofermentans AT sugimotonaohisa mechanisticinsightintothesubstratespecificityof12boligoglucanphosphorylasefromlachnoclostridiumphytofermentans AT miyanagaakimasa mechanisticinsightintothesubstratespecificityof12boligoglucanphosphorylasefromlachnoclostridiumphytofermentans AT fushinobushinya mechanisticinsightintothesubstratespecificityof12boligoglucanphosphorylasefromlachnoclostridiumphytofermentans AT taguchihayao mechanisticinsightintothesubstratespecificityof12boligoglucanphosphorylasefromlachnoclostridiumphytofermentans AT nakaihiroyuki mechanisticinsightintothesubstratespecificityof12boligoglucanphosphorylasefromlachnoclostridiumphytofermentans |