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

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