8Z47
Beta-galactosidase from Bacteroides xylanisolvens (ligand-free)
Summary for 8Z47
| Entry DOI | 10.2210/pdb8z47/pdb |
| Related | 8Z43 |
| Descriptor | Beta-galactosidase, alpha-D-galactopyranose (3 entities in total) |
| Functional Keywords | glycoside hydrolase, hydrolase |
| Biological source | Bacteroides xylanisolvens XB1A |
| Total number of polymer chains | 1 |
| Total formula weight | 62776.64 |
| Authors | Nakajima, M.,Motouchi, S.,Kobayashi, K. (deposition date: 2024-04-16, release date: 2025-01-01, Last modification date: 2025-03-19) |
| Primary citation | Nakazawa, Y.,Kageyama, M.,Matsuzawa, T.,Liang, Z.,Kobayashi, K.,Shimizu, H.,Maeda, K.,Masuhiro, M.,Motouchi, S.,Kumano, S.,Tanaka, N.,Kuramochi, K.,Nakai, H.,Taguchi, H.,Nakajima, M. Structure and function of a beta-1,2-galactosidase from Bacteroides xylanisolvens, an intestinal bacterium. Commun Biol, 8:66-66, 2025 Cited by PubMed 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. PubMed: 39820076DOI: 10.1038/s42003-025-07494-1 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.86 Å) |
Structure validation
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