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

Abstract

Lacto-N-biosidase hydrolyzes the β-GlcNAc or β-GalNAc bond of sugar chains to release lacto-N-biose I (Gal-β1,3-GlcNAc) or galacto-N-biose (Gal-β1,3-GalNAc) from the non-reducing end. Typical substrates for lacto-N-biosidase include type I oligosaccharides contained in human breast milk, such as lacto-N-tetraose. Lacto-N-biosidases have recently received significant attention because of their potential to synthesize milk oligosaccharides. Bifidobacterial lacto-N-biosidases belonging to glycoside hydrolase families 20 and 136 have been studied. The GH20 lacto-N-biosidases utilize a substrate-associated hydrolysis mechanism. LnbB from Bifidobacterium bifidum is the only lacto-N-biosidase with reported crystal structures in GH20. In this study, the crystal structure of the lacto-N-biosidase from Streptomyces sp. strain 142 (StrLNBase) was solved in a complex with lacto-N-biose and galacto-N-biose. The stabilizing residue, which recognizes the nitrogen atom of the N-acetyl group of the −1 subsite, and the catalytic acid/base residue, were determined to be D304 and E305, respectively. The structure of StrLNBase is similar to that of LnbB; however, in the complex with galacto-N-biose, there were two structures exhibiting different sugar conformations. A phylogenetic analysis revealed that lacto-N-biosidases discovered in the soil bacteria Streptomyces spp. and human gut bacteria Bifidobacterium spp. may be divided into two separate groups, which suggests that they evolved divergently.