8HVB
Crystal structure of lacto-N-biosidase StrLNBase from Streptomyces sp. strain 142, lacto-N-biose complex
Summary for 8HVB
| Entry DOI | 10.2210/pdb8hvb/pdb |
| Descriptor | Lacto-N-biosidase, beta-D-galactopyranose, 2-acetamido-2-deoxy-alpha-D-glucopyranose, ... (4 entities in total) |
| Functional Keywords | glycoside hydrolase, lacto-n-biosidase, lacto-n-biose complex, hydrolase |
| Biological source | Streptomyces sp. |
| Total number of polymer chains | 1 |
| Total formula weight | 66636.33 |
| Authors | Fushinobu, S.,Yamada, C.,Fujio, N. (deposition date: 2022-12-26, release date: 2023-12-27, Last modification date: 2025-07-09) |
| Primary citation | Fujio, N.,Fushinobu, S.,Yamada, C. Crystal Structure of Glycoside Hydrolase Family 20 Lacto- N -biosidase from Soil Bacterium Streptomyces sp. Strain 142. J Appl Glycosci (1999), 72:7202101-7202101, 2025 Cited by PubMed Abstract: Lacto--biosidase hydrolyzes the β-GlcNAc or β-GalNAc bond of sugar chains to release lacto--biose I (Gal-β1,3-GlcNAc) or galacto--biose (Gal-β1,3-GalNAc) from the non-reducing end. Typical substrates for lacto--biosidase include type I oligosaccharides contained in human breast milk, such as lacto--tetraose. Lacto--biosidases have recently received significant attention because of their potential to synthesize milk oligosaccharides. Bifidobacterial lacto--biosidases belonging to glycoside hydrolase families 20 and 136 have been studied. The GH20 lacto--biosidases utilize a substrate-associated hydrolysis mechanism. LnbB from is the only lacto--biosidase with reported crystal structures in GH20. In this study, the crystal structure of the lacto--biosidase from sp. strain 142 (LNBase) was solved in a complex with lacto--biose and galacto--biose. The stabilizing residue, which recognizes the nitrogen atom of the -acetyl group of the -1 subsite, and the catalytic acid/base residue, were determined to be D304 and E305, respectively. The structure of LNBase is similar to that of LnbB; however, in the complex with galacto--biose, there were two structures exhibiting different sugar conformations. A phylogenetic analysis revealed that lacto--biosidases discovered in the soil bacteria spp. and human gut bacteria spp. may be divided into two separate groups, which suggests that they evolved divergently. PubMed: 40502377DOI: 10.5458/jag.7202101 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.6 Å) |
Structure validation
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