8HVD

Crystal structure of lacto-N-biosidase StrLNBase from Streptomyces sp. strain 142, galacto-N-biose complex 2

Summary for 8HVD

• Entry DOI: 10.2210/pdb8hvd/pdb
• Descriptor: Lacto-N-biosidase, beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-alpha-D-galactopyranose (3 entities in total)
• Functional Keywords: glycoside hydrolase, lacto-n-biosidase, galacto-n-biose complex 2, hydrolase
• Biological source: Streptomyces sp.
• Total number of polymer chains: 1
• Total formula weight: 66618.32

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

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: 40502377
DOI: 10.5458/jag.7202101

Experimental method

X-RAY DIFFRACTION (1.41 Å)