Docking studies on glycoside hydrolase Family 47 endoplasmic reticulum α-(1→2)-mannosidase I to elucidate the pathway to the substrate transition state
Docking studies on glycoside hydrolase Family 47 endoplasmic reticulum α-(1→2)-mannosidase I to elucidate the pathway to the substrate transition state
复制标题
DOI：
10.1016/j.carres.2006.05.011
复制
发表时间：
2006-09-25
影响因子：
3.1
通讯作者：
Reilly, Peter J.
中科院分区：
文献类型：
--
作者：
Mulakala, Chandrika;Nerinckx, Wim;Reilly, Peter J.
来自内质网的α-（1 -> 2）-甘露糖苷酶I（ERManI）是家族47糖苷水解酶，是N-聚糖合成途径中的关键酶。酵母和人ERMan 1的催化结构域的晶体结构已经确定，前者与水解产物和后者没有配体，与抑制剂1-脱氧mannojirimycin和kifunensine，并与硫代二糖底物类似物。这两种抑制剂结合在漏斗形活性位点的底部，作为不寻常的C-1（4）构象异构体，而底物类似物糖基是S-3（1）构象异构体。在本研究中，AutoDock用于将α-D-吡喃甘露糖基-（1-2）-α-D-吡喃甘露糖与其糖基在椅子（C-1（4），C-4（1）），半椅子（H-3（2），H-3（4），H-4（3）），斜船（S-O（2），S-3（1），S-5（1）），船（B-2、B-5、B-3、B-O、B-1、B-4、B-2、B-5）和包膜（E-3、E-4、E-3、E-4）构象进入酵母ERManI活性位点。对接的能量和对接配体原子上的力进行了计算，以确定如何配体扭曲的过渡态。由此我们可以得出结论：（1）C-1（4）和S-O（2）都可以作为起始构象;（2）最可能的结合途径是C-1（4）-> H-3（2）-> S-O（2）-> B-3，B-O -> S-3（1）-> E-3;（3）过渡态可能接近3 E构象。(c)2006爱思唯尔有限公司保留所有权利。
alpha-(1 -> 2)-Mannosidase I from the endoplasmic reticulum (ERManI), a Family 47 glycoside hydrolase, is a key enzyme in the N-glycan synthesis pathway. Catalytic-domain crystal structures of yeast and human ERMan1s have been determined, the former with a hydrolytic product and the latter without ligands, with the inhibitors 1-deoxymannojirimycin and kifunensine, and with a thiodisaccharide substrate analog. Both inhibitors were bound at the base of the funnel-shaped active site as the unusual C-1(4) conformer, while the substrate analog glycon is a S-3(1) conformer. In the current study, AutoDock was used to dock alpha-D-mannopyranosyl-(1-2)-alpha-D-mannopyranose with its glycon in chair (C-1(4),C-4(1)), half-chair (H-3(2),H-3(4),H-4(3)), skew-boat (S-O(2),S-3(1),S-5(1)), boat (B-2,B-5, B-3,B-O, B-1,B-4, B-2,B-5), and envelope (E-3, E-4, E-3, E-4) conformations into the yeast ERManI active site. Both docked energies and forces on docked ligand atoms were calculated to determine how the ligand distorts to the transition state. From these, we can conclude that (1) both C-1(4) and S-O(2) can be the starting conformers; (2) the most likely binding pathway is C-1(4)-> H-3(2)-> S-O(2)-> B-3,B-O -> S-3(1)-> E-3; (3) the transition state is likely to be close to a 3 E conformation. (c) 2006 Elsevier Ltd. All rights reserved.