title: Theory and computation show that Asp463 is the catalytic proton donor in human endoplasmic reticulum alpha-(1-->2)-mannosidase I.
abstract: It has been difficult to identify the proton donor and nucleophilic assistant/base of endoplasmic reticulum alpha-(1-->2)-mannosidase I, a member of glycoside hydrolase Family 47, which cleaves the glycosidic bond between two alpha-(1-->2)-linked mannosyl residues by the inverting mechanism, trimming Man(9)GlcNAc(2) to Man(8)GlcNAc(2) isomer B. Part of the difficulty is caused by the enzyme's use of a water molecule to transmit the proton that attacks the glycosidic oxygen atom. We earlier used automated docking to conclusively determine that Glu435 in the yeast enzyme (Glu599 in the corresponding human enzyme) is the nucleophilic assistant. The commonly accepted proton donor has been Glu330 in the human enzyme (Glu132 in the yeast enzyme). However, for theoretical reasons this conclusion is untenable. Theory, automated docking of alpha-d-(3)S(1)-mannopyranosyl-(1-->2)-alpha-d-(4)C(1)-mannopyranose and water molecules associated with candidate proton donors, and estimation of dissociation constants of the latter have shown that the true proton donor is Asp463 in the human enzyme (Asp275 in the yeast enzyme).
authors.affiliation: Department of Chemical and Biological Engineering, Iowa State University, Ames, IA 50011, USA.
authors.forename: David
authors.initials: D
authors.lastname: Cantú
authors.forename: Wim
authors.initials: W
authors.lastname: Nerinckx
authors.forename: Peter J
authors.initials: PJ
authors.lastname: Reilly
mesh_terms: D001224:Aspartic Acid / Q000737:chemistry*; D001665:Binding Sites; D002241:Carbohydrates / Q000737:chemistry; D002384:Catalysis; D018360:Crystallography, X-Ray / Q000379:methods; D004721:Endoplasmic Reticulum / Q000201:enzymology*; D006801:Humans; D006863:Hydrogen-Ion Concentration; D008361:Mannosidases / Q000737:chemistry*; D008956:Models, Chemical; D008968:Molecular Conformation; D010100:Oxygen / Q000737:chemistry; D011522:Protons; D055672:Static Electricity; D014867:Water / Q000737:chemistry
chemical_list: D002241:Carbohydrates; D011522:Protons; D014867:Water; D001224:Aspartic Acid; D008361:Mannosidases; C046090:mannosyl-oligosaccharide 1,2-alpha-mannosidase; D010100:Oxygen