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Hoffmann, R. A wiki for the life sciences where authorship matters. Nature Genetics (2008)

The fate of beta-d-mannopyranose after its formation by endoplasmic reticulum alpha-(1-->2)-mannosidase I catalysis.

The automated docking program AutoDock was used to dock all 38 characteristic beta-d-mannopyranose ring conformers into the active site of the yeast endoplasmic reticulum alpha-(1-->2)-mannosidase I, a Family 47 glycoside hydrolase that converts Man(9)GlcNAc(2) to Man(8)GlcNAc(2). The subject of this work is to establish the conformational pathway that allows the cleaved glycon product to leave the enzyme active site and eventually reach the ground-state conformation. Twelve of the 38 conformers optimally dock in the active site where the inhibitors 1-deoxymannonojirimycin and kifunensine are found in enzyme crystal structures. A further 23 optimally dock in a second site on the side of the active-site well, while three dock outside the active-site cavity. It appears, through analysis of the internal energies of different ring conformations, of intermolecular energies between the ligands and enzyme, and of forces exerted on the ligands by the enzyme, that beta-d-mannopyranose follows the path (3)E-->(1)C(4)-->(1)H(2)-->B(2,5) before being expelled by the enzyme. The highly conserved second site that strongly binds beta-d-mannopyranose-(4)C(1) may exist to prevent competitive inhibition by the product, and is worthy of further investigation.[1]


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