Docking studies on glycoside hydrolase Family 47 endoplasmic reticulum α-(1→2)-mannosidase I to elucidate the pathway to the substrate transition state

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2012-09-25
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Mulakala, Chandrika
Nerinckx, Wim
Reilly, Peter
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Chemical and Biological Engineering
Abstract

α-(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 1C4 conformer, while the substrate analog glycon is a 3S1 conformer. In the current study, AutoDock was used to dock α-d-mannopyranosyl-(1→2)-α-d-mannopyranose with its glycon in chair (1C4, 4C1), half-chair (3H2, 3H4, 4H3), skew-boat (OS2, 3S1, 5S1), boat (2,5B, 3,OB, B1,4, B2,5), and envelope (3E, 4E, E3, E4) 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 1C4 andOS2 can be the starting conformers; (2) the most likely binding pathway is1C43H2OS23,OB3S13E; (3) the transition state is likely to be close to a 3E conformation.

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This is a post-print of an article from Carbohydrate Research, 341, no. 15 (25 September 2007): 2233–2245, doi: 10.1016/j.carres.2006.05.011.

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Sun Jan 01 00:00:00 UTC 2006
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