title: Complex structures of Thermoactinomyces vulgaris R-47 alpha-amylase 1 with malto-oligosaccharides demonstrate the role of domain N acting as a starch-binding domain.
abstract: The X-ray structures of complexes of Thermoactinomyces vulgaris R-47 alpha-amylase 1 (TVAI) with an inhibitor acarbose and an inactive mutant TVAI with malto-hexaose and malto-tridecaose have been determined at 2.6, 2.0 and 1.8A resolution, and the structures have been refined to R-factors of 0.185 (R(free)=0.225), 0.184 (0.217) and 0.164 (0.200), respectively, with good chemical geometries. Acarbose binds to the catalytic site of TVAI, and interactions between acarbose and the enzyme are very similar to those found in other structure-solved alpha-amylase/acarbose complexes, supporting the proposed catalytic mechanism. Based on the structure of the TVAI/acarbose complex, the binding mode of pullulan containing alpha-(1,6) glucoside linkages could be deduced. Due to the structural difference caused by the replaced amino acid residue (Gln396 for Glu) in the catalytic site, malto-hexaose and malto-tridecaose partially bind to the catalytic site, giving a mimic of the enzyme/product complex. Besides the catalytic site, four sugar-binding sites on the molecular surface are found in these X-ray structures. Two sugar-binding sites in domain N hold the oligosaccharides with a regular helical structure of amylose, which suggests that the domain N is a starch-binding domain acting as an anchor to starch in the catalytic reaction of the enzyme. An assay of hydrolyzing activity for the raw starches confirmed that TVAI can efficiently hydrolyze raw starch.
authors.affiliation: Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan.
authors.forename: Akemi
authors.initials: A
authors.lastname: Abe
authors.forename: Takashi
authors.initials: T
authors.lastname: Tonozuka
authors.forename: Yoshiyuki
authors.initials: Y
authors.lastname: Sakano
authors.forename: Shigehiro
authors.initials: S
authors.lastname: Kamitori
mesh_terms: D001665:Binding Sites; D018360:Crystallography, X-Ray; D004791:Enzyme Inhibitors / Q000737:chemistry; D008320:Maltose; D008848:Micromonosporaceae / Q000201:enzymology*; D008958:Models, Molecular; D009154:Mutation; D009844:Oligosaccharides / Q000737:chemistry*; D017434:Protein Structure, Tertiary; D013213:Starch / Q000737:chemistry / Q000378:metabolism; D000516:alpha-Amylases / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism
chemical_list: D004791:Enzyme Inhibitors; D009844:Oligosaccharides; D008320:Maltose; D013213:Starch; D000516:alpha-Amylases