4H04

Lacto-N-biosidase from Bifidobacterium bifidum

4H04 の概要

• エントリーDOI: 10.2210/pdb4h04/pdb
• 分子名称: Lacto-N-biosidase, beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose, SULFATE ION, ... (4 entities in total)
• 機能のキーワード: tim barrel, hydrolase, extracellular
• 由来する生物種: Bifidobacterium bifidum
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 145319.66

構造登録者

Ito, T.,Katayama, T.,Wada, J.,Suzuki, R.,Ashida, H.,Wakagi, T.,Yamamoto, K.,Fushinobu, S. (登録日: 2012-09-07, 公開日: 2013-03-20, 最終更新日: 2024-10-09)

主引用文献

Ito, T.,Katayama, T.,Hattie, M.,Sakurama, H.,Wada, J.,Suzuki, R.,Ashida, H.,Wakagi, T.,Yamamoto, K.,Stubbs, K.A.,Fushinobu, S.
Crystal structures of a glycoside hydrolase family 20 lacto-N-biosidase from Bifidobacterium bifidum
J.Biol.Chem., 288:11795-11806, 2013

PubMed Abstract: Human milk oligosaccharides contain a large variety of oligosaccharides, of which lacto-N-biose I (Gal-β1,3-GlcNAc; LNB) predominates as a major core structure. A unique metabolic pathway specific for LNB has recently been identified in the human commensal bifidobacteria. Several strains of infant gut-associated bifidobacteria possess lacto-N-biosidase, a membrane-anchored extracellular enzyme, that liberates LNB from the nonreducing end of human milk oligosaccharides and plays a key role in the metabolic pathway of these compounds. Lacto-N-biosidase belongs to the glycoside hydrolase family 20, and its reaction proceeds via a substrate-assisted catalytic mechanism. Several crystal structures of GH20 β-N-acetylhexosaminidases, which release monosaccharide GlcNAc from its substrate, have been determined, but to date, a structure of lacto-N-biosidase is unknown. Here, we have determined the first three-dimensional structures of lacto-N-biosidase from Bifidobacterium bifidum JCM1254 in complex with LNB and LNB-thiazoline (Gal-β1,3-GlcNAc-thiazoline) at 1.8-Å resolution. Lacto-N-biosidase consists of three domains, and the C-terminal domain has a unique β-trefoil-like fold. Compared with other β-N-acetylhexosaminidases, lacto-N-biosidase has a wide substrate-binding pocket with a -2 subsite specific for β-1,3-linked Gal, and the residues responsible for Gal recognition were identified. The bound ligands are recognized by extensive hydrogen bonds at all of their hydroxyls consistent with the enzyme's strict substrate specificity for the LNB moiety. The GlcNAc sugar ring of LNB is in a distorted conformation near (4)E, whereas that of LNB-thiazoline is in a (4)C1 conformation. A possible conformational pathway for the lacto-N-biosidase reaction is discussed.

PubMed: 23479733
DOI: 10.1074/jbc.M112.420109

実験手法

X-RAY DIFFRACTION (1.8 Å)