2ZXQ

Crystal structure of endo-alpha-N-acetylgalactosaminidase from Bifidobacterium longum (EngBF)

2ZXQ の概要

• エントリーDOI: 10.2210/pdb2zxq/pdb
• 分子名称: Endo-alpha-N-acetylgalactosaminidase, MANGANESE (II) ION, (4S)-2-METHYL-2,4-PENTANEDIOL, ... (4 entities in total)
• 機能のキーワード: broken tim barrel, glycosidase, hydrolase
• 由来する生物種: Bifidobacterium longum
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 150369.07

構造登録者

Suzuki, R.,Katayama, T.,Ashida, H.,Yamamoto, K.,Kitaoka, M.,Fushinobu, S. (登録日: 2009-01-05, 公開日: 2009-06-16, 最終更新日: 2024-03-13)

主引用文献

Suzuki, R.,Katayama, T.,Kitaoka, M.,Kumagai, H.,Wakagi, T.,Shoun, H.,Ashida, H.,Yamamoto, K.,Fushinobu, S.
Crystallographic and mutational analyses of substrate recognition of endo-{alpha}-N-acetylgalactosaminidase from Bifidobacterium longum.
J.Biochem., 2009

PubMed Abstract: Endo-alpha-N-acetylgalactosaminidase (endo-alpha-GalNAc-ase), a member of the glycoside hydrolase (GH) family 101, hydrolyses the O-glycosidic bonds in mucin-type O-glycan between alpha-GalNAc and Ser/Thr. Endo-alpha-GalNAc-ase from Bifidobacterium longum JCM1217 (EngBF) is highly specific for the core 1-type O-glycan to release the disaccharide Galbeta1-3GalNAc (GNB), whereas endo-alpha-GalNAc-ase from Clostridium perfringens (EngCP) exhibits broader substrate specificity. We determined the crystal structure of EngBF at 2.0 A resolution and performed automated docking analysis to investigate possible binding modes of GNB. Mutational analysis revealed important residues for substrate binding, and two Trp residues (Trp748 and Trp750) appeared to form stacking interactions with the beta-faces of sugar rings of GNB by substrate-induced fit. The difference in substrate specificities between EngBF and EngCP is attributed to the variations in amino acid sequences in the regions forming the substrate-binding pocket. Our results provide a structural basis for substrate recognition by GH101 endo-alpha-GalNAc-ases and will help structure-based engineering of these enzymes to produce various kinds of neo-glycoconjugates.

PubMed: 19502354
DOI: 10.1093/jb/mvp086

実験手法

X-RAY DIFFRACTION (2 Å)