(426m) Toward the Transition State: Further Docking Studies on Family 47 Alpha-1,2-Mannosidases

Alpha-1,2-Mannosidase
from the endoplasmic reticulum (ERMan), a Family 47 glycosyl hydrolase, is a
key enzyme in the N-glycan
synthesis pathway. Catalytic-domain crystal structures of human and yeast
ERMans have been determined, the former 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 glycone is a ³S₁ conformer. In the current
study, AutoDock was used to dock alpha-D-mannopyranosyl-(1,2)-alpha-D-mannopyranose with its glycone in chair
(¹C₄,
⁴C₁),
half-chair (³H₂,³H₄,⁴H₃),
skew-boat (^OS₂,³S₁,⁵S₁),
boat (^2,5B,
^3,OB, B_1,4, B_2,5), and envelope (³E, ⁴E, E₃,E₄) conformations into the
yeast ERMan 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 and ^OS₂ can be the starting
conformers; 2) the most likely binding pathways are ¹C₄ to³H₂ to^OS₂ to^3,OB to ³S₁ to ³E and ^OS₂ to^3,OB to ³S₁
to³E
with ¹C₄
and ^OS₂
as starting conformers, respectively; 3) the transition state is likely
to be close to a ³E conformation.