title: Understanding protein structure-function relationships in Family 47 alpha-1,2-mannosidases through computational docking of ligands.
abstract: Family 47 alpha-1,2-mannosidases are crucial enzymes involved in N-glycan maturation in the endoplasmic reticula and Golgi apparati of eukaryotic cells. High-resolution crystal structures of the human and yeast endoplasmic reticulum alpha-1,2-mannosidases have been recently determined, the former complexed with the inhibitors 1-deoxymannojirimycin and kifunensine, both of which bind in its active site in the unusual 1C4 conformation. However, unambiguous identification of the catalytic proton donor and nucleophile involved in glycoside bond hydrolysis was not possible from this structural information. In this work, alpha-D-galactose, alpha-D-glucose, and alpha-D-mannose were computationally docked in the active site in the energetically stable 4C1 conformation as well as in the 1C4 conformation to compare their interaction energetics. From these docked structures, a model for substrate and conformer selectivity based on the dimensions of the active site was proposed. Alpha-D-galactopyranosyl-(1-->2)-alpha-D-mannopyranose, alpha-D-glucopyranosyl-(1-->2)-alpha-D-mannopyranose, and alpha-D-mannopyranosyl-(1-->2)-alpha-D-mannopyranose were also docked into the active site with their nonreducing-end residues in the 1C4 and E4 (representing the transition state) conformations. Based on the docked structure of alpha-D-mannopyranosyl-E4-(1-->2)-alpha-D-mannopyranose, the catalytic acid and base are Glu132 and Glu435, respectively.
authors.affiliation: Department of Chemical Engineering, Iowa State University, Ames, Iowa 50011-2230, USA.
authors.forename: Chandrika
authors.initials: C
authors.lastname: Mulakala
authors.forename: Peter J
authors.initials: PJ
authors.lastname: Reilly
mesh_terms: D017485:1-Deoxynojirimycin / Q000737:chemistry / Q000378:metabolism; D000470:Alkaloids / Q000737:chemistry / Q000378:metabolism; D001665:Binding Sites; D002384:Catalysis; D019295:Computational Biology; D003198:Computer Simulation; D004187:Disaccharides / Q000737:chemistry / Q000378:metabolism; D004791:Enzyme Inhibitors / Q000737:chemistry / Q000378:metabolism; D006801:Humans; D008024:Ligands; D008361:Mannosidases / Q000737:chemistry* / Q000378:metabolism / Q000502:physiology*; D008958:Models, Molecular; D009005:Monosaccharides / Q000737:chemistry / Q000378:metabolism; D011487:Protein Conformation; D017433:Protein Structure, Secondary; D015203:Reproducibility of Results; D012441:Saccharomyces cerevisiae / Q000201:enzymology; D016415:Sequence Alignment; D013329:Structure-Activity Relationship
chemical_list: D000470:Alkaloids; D004187:Disaccharides; D004791:Enzyme Inhibitors; D008024:Ligands; D009005:Monosaccharides; C065629:kifunensine; D017485:1-Deoxynojirimycin; D008361:Mannosidases; C046090:mannosyl-oligosaccharide 1,2-alpha-mannosidase