3BUP

Golgi alpha-mannosidase II D341N acid-base catalyst mutant with bound mannose

3BUP の概要

• エントリーDOI: 10.2210/pdb3bup/pdb
• 関連するPDBエントリー: 1HTY 1HWW 1HXK 1PS2 1QWN 1QWU 1QX1 1R33 1R34 1TQS 1TQT 1TQU 1TQV 1TQW 2ALW 2F18 2F1A 2F1B 2F7O 2F7P 2F7Q 2F7R 3BUB 3BUD 3BUI 3BUQ
• 分子名称: Alpha-mannosidase 2, 2-acetamido-2-deoxy-beta-D-glucopyranose, alpha-D-mannopyranose, ... (6 entities in total)
• 機能のキーワード: glycosyl hydrolase family 38, glycosidase, golgi apparatus, membrane, signal-anchor, transmembrane, hydrolase
• 由来する生物種: Drosophila melanogaster (Fruit fly)
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 120285.58

構造登録者

Kuntz, D.A.,Rose, D.R. (登録日: 2008-01-03, 公開日: 2008-07-01, 最終更新日: 2024-11-13)

主引用文献

Zhong, W.,Kuntz, D.A.,Ember, B.,Singh, H.,Moremen, K.W.,Rose, D.R.,Boons, G.J.
Probing the substrate specificity of Golgi alpha-mannosidase II by use of synthetic oligosaccharides and a catalytic nucleophile mutant.
J.Am.Chem.Soc., 130:8975-8983, 2008

PubMed Abstract: Inhibition of Golgi alpha-mannosidase II (GMII), which acts late in the N-glycan processing pathway, provides a route to blocking cancer-induced changes in cell surface oligosaccharide structures. To probe the substrate requirements of GMII, oligosaccharides were synthesized that contained an alpha(1,3)- or alpha(1,6)-linked 1-thiomannoside. Surprisingly, these oligosaccharides were not observed in X-ray crystal structures of native Drosophila GMII (dGMII). However, a mutant enzyme in which the catalytic nucleophilic aspartate was changed to alanine (D204A) allowed visualization of soaked oligosaccharides and led to the identification of the binding site for the alpha(1,3)-linked mannoside of the natural substrate. These studies also indicate that the conformational change of the bound mannoside to a high-energy B 2,5 conformation is facilitated by steric hindrance from, and the formation of strong hydrogen bonds to, Asp204. The observation that 1-thio-linked mannosides are not well tolerated by the catalytic site of dGMII led to the synthesis of a pentasaccharide containing the alpha(1,6)-linked Man of the natural substrate and the beta(1,2)-linked GlcNAc moiety proposed to be accommodated by the extended binding site of the enzyme. A cocrystal structure of this compound with the D204A enzyme revealed the molecular interactions with the beta(1,2)-linked GlcNAc. The structure is consistent with the approximately 80-fold preference of dGMII for the cleavage of substrates containing a nonreducing beta(1,2)-linked GlcNAc. By contrast, the lysosomal mannosidase lacks an equivalent GlcNAc binding site and kinetic analysis indicates oligomannoside substrates without non-reducing-terminal GlcNAc modifications are preferred, suggesting that selective inhibitors for GMII could exploit the additional binding specificity of the GlcNAc binding site.

PubMed: 18558690
DOI: 10.1021/ja711248y

実験手法

X-RAY DIFFRACTION (2.03 Å)