Structure and function of a β-1,2-galactosidase from Bacteroides xylanisolvens, an intestinal bacterium
Abstract Galactosides are major carbohydrates that are found in plant cell walls and various prebiotic oligosaccharides. Studying the detailed biochemical functions of β-galactosidases in degrading these carbohydrates is important. In particular, identifying β-galactosidases with new substrate speci...
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2025-01-01
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| Series: | Communications Biology |
| Online Access: | https://doi.org/10.1038/s42003-025-07494-1 |
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| author | Yutaka Nakazawa Masumi Kageyama Tomohiko Matsuzawa Ziqin Liang Kaito Kobayashi Hisaka Shimizu Kazuki Maeda Miho Masuhiro Sei Motouchi Saika Kumano Nobukiyo Tanaka Kouji Kuramochi Hiroyuki Nakai Hayao Taguchi Masahiro Nakajima |
| author_facet | Yutaka Nakazawa Masumi Kageyama Tomohiko Matsuzawa Ziqin Liang Kaito Kobayashi Hisaka Shimizu Kazuki Maeda Miho Masuhiro Sei Motouchi Saika Kumano Nobukiyo Tanaka Kouji Kuramochi Hiroyuki Nakai Hayao Taguchi Masahiro Nakajima |
| author_sort | Yutaka Nakazawa |
| collection | DOAJ |
| description | Abstract Galactosides are major carbohydrates that are found in plant cell walls and various prebiotic oligosaccharides. Studying the detailed biochemical functions of β-galactosidases in degrading these carbohydrates is important. In particular, identifying β-galactosidases with new substrate specificities could help in the production of potentially beneficial oligosaccharides. In this study, we identify a β-galactosidase with novel substrate specificity from Bacteroides xylanisolvens, an intestinal bacterium. The enzyme do not show hydrolytic activity toward natural β-galactosides during the first screening. However, when α-d-galactosyl fluoride (α-GalF) as a donor substrate and galactose or d-fucose as an acceptor substrate are incubated with a nucleophile mutant, reaction products are detected. The galactobiose produced from the α-GalF and galactose is identified as β-1,2-galactobiose using NMR. Kinetic analysis reveals that this enzyme effectively hydrolyzes β-1,2-galactobiose and β-1,2-galactotriose. In the complex structure with methyl β-galactopyranose as a ligand, the ligand is only located at subsite +1. The 2-hydroxy group and the anomeric methyl group of methyl β-galactopyranose faces in the direction of subsite −1 and the solvent, respectively. This observation is consistent with the substrate specificity of the enzyme regarding linkage position and chain length. Overall, we conclude that the enzyme is a β-galactosidase acting on β-1,2-galactooligosaccharides. |
| format | Article |
| id | doaj-art-d2cb4ea01ca848a29633a457075074bb |
| institution | Kabale University |
| issn | 2399-3642 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Communications Biology |
| spelling | doaj-art-d2cb4ea01ca848a29633a457075074bb2025-02-09T12:50:25ZengNature PortfolioCommunications Biology2399-36422025-01-018111210.1038/s42003-025-07494-1Structure and function of a β-1,2-galactosidase from Bacteroides xylanisolvens, an intestinal bacteriumYutaka Nakazawa0Masumi Kageyama1Tomohiko Matsuzawa2Ziqin Liang3Kaito Kobayashi4Hisaka Shimizu5Kazuki Maeda6Miho Masuhiro7Sei Motouchi8Saika Kumano9Nobukiyo Tanaka10Kouji Kuramochi11Hiroyuki Nakai12Hayao Taguchi13Masahiro Nakajima14Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of ScienceDepartment of Applied Biological Science, Faculty of Science and Technology, Tokyo University of ScienceDepartment of Applied Biological Science, Faculty of Agriculture, Kagawa UniversityDepartment of Applied Biological Science, Faculty of Science and Technology, Tokyo University of ScienceDepartment of Applied Biological Science, Faculty of Science and Technology, Tokyo University of ScienceDepartment of Applied Biological Science, Faculty of Science and Technology, Tokyo University of ScienceDepartment of Applied Biological Science, Faculty of Science and Technology, Tokyo University of ScienceDepartment of Applied Biological Science, Faculty of Science and Technology, Tokyo University of ScienceDepartment of Applied Biological Science, Faculty of Science and Technology, Tokyo University of ScienceDepartment of Applied Biological Science, Faculty of Science and Technology, Tokyo University of ScienceDepartment of Applied Biological Science, Faculty of Science and Technology, Tokyo University of ScienceDepartment of Applied Biological Science, Faculty of Science and Technology, Tokyo University of ScienceFaculty of Agriculture, Niigata UniversityDepartment of Applied Biological Science, Faculty of Science and Technology, Tokyo University of ScienceDepartment of Applied Biological Science, Faculty of Science and Technology, Tokyo University of ScienceAbstract Galactosides are major carbohydrates that are found in plant cell walls and various prebiotic oligosaccharides. Studying the detailed biochemical functions of β-galactosidases in degrading these carbohydrates is important. In particular, identifying β-galactosidases with new substrate specificities could help in the production of potentially beneficial oligosaccharides. In this study, we identify a β-galactosidase with novel substrate specificity from Bacteroides xylanisolvens, an intestinal bacterium. The enzyme do not show hydrolytic activity toward natural β-galactosides during the first screening. However, when α-d-galactosyl fluoride (α-GalF) as a donor substrate and galactose or d-fucose as an acceptor substrate are incubated with a nucleophile mutant, reaction products are detected. The galactobiose produced from the α-GalF and galactose is identified as β-1,2-galactobiose using NMR. Kinetic analysis reveals that this enzyme effectively hydrolyzes β-1,2-galactobiose and β-1,2-galactotriose. In the complex structure with methyl β-galactopyranose as a ligand, the ligand is only located at subsite +1. The 2-hydroxy group and the anomeric methyl group of methyl β-galactopyranose faces in the direction of subsite −1 and the solvent, respectively. This observation is consistent with the substrate specificity of the enzyme regarding linkage position and chain length. Overall, we conclude that the enzyme is a β-galactosidase acting on β-1,2-galactooligosaccharides.https://doi.org/10.1038/s42003-025-07494-1 |
| spellingShingle | Yutaka Nakazawa Masumi Kageyama Tomohiko Matsuzawa Ziqin Liang Kaito Kobayashi Hisaka Shimizu Kazuki Maeda Miho Masuhiro Sei Motouchi Saika Kumano Nobukiyo Tanaka Kouji Kuramochi Hiroyuki Nakai Hayao Taguchi Masahiro Nakajima Structure and function of a β-1,2-galactosidase from Bacteroides xylanisolvens, an intestinal bacterium Communications Biology |
| title | Structure and function of a β-1,2-galactosidase from Bacteroides xylanisolvens, an intestinal bacterium |
| title_full | Structure and function of a β-1,2-galactosidase from Bacteroides xylanisolvens, an intestinal bacterium |
| title_fullStr | Structure and function of a β-1,2-galactosidase from Bacteroides xylanisolvens, an intestinal bacterium |
| title_full_unstemmed | Structure and function of a β-1,2-galactosidase from Bacteroides xylanisolvens, an intestinal bacterium |
| title_short | Structure and function of a β-1,2-galactosidase from Bacteroides xylanisolvens, an intestinal bacterium |
| title_sort | structure and function of a β 1 2 galactosidase from bacteroides xylanisolvens an intestinal bacterium |
| url | https://doi.org/10.1038/s42003-025-07494-1 |
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