Crystal Structure of Glycoside Hydrolase Family 20 Lacto--biosidase from Soil Bacterium sp. Strain 142.

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.