title: Structural insights into substrate specificity and function of glucodextranase.
abstract: A glucodextranase (iGDase) from Arthrobacter globiformis I42 hydrolyzes alpha-1,6-glucosidic linkages of dextran from the non-reducing end to produce beta-D-glucose via an inverting reaction mechanism and classified into the glycoside hydrolase family 15 (GH15). Here we cloned the iGDase gene and determined the crystal structures of iGDase of the unliganded form and the complex with acarbose at 2.42-A resolution. The structure of iGDase is composed of four domains N, A, B, and C. Domain A forms an (alpha/alpha)(6)-barrel structure and domain N consists of 17 antiparallel beta-strands, and both domains are conserved in bacterial glucoamylases (GAs) and appear to be mainly concerned with catalytic activity. The structure of iGDase complexed with acarbose revealed that the positions and orientations of the residues at subsites -1 and +1 are nearly identical between iGDase and GA; however, the residues corresponding to subsite 3, which form the entrance of the substrate binding pocket, and the position of the open space and constriction of iGDase are different from those of GAs. On the other hand, domains B and C are not found in the bacterial GAs. The primary structure of domain C is homologous with a surface layer homology domain of pullulanases, and the three-dimensional structure of domain C resembles the carbohydrate-binding domain of some glycohydrolases.
authors.affiliation: Department of Applied Biological Science, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan.
authors.forename: Masahiro
authors.initials: M
authors.lastname: Mizuno
authors.forename: Takashi
authors.initials: T
authors.lastname: Tonozuka
authors.forename: Saori
authors.initials: S
authors.lastname: Suzuki
authors.forename: Rie
authors.initials: R
authors.lastname: Uotsu-Tomita
authors.forename: Shigehiro
authors.initials: S
authors.lastname: Kamitori
authors.forename: Atsushi
authors.initials: A
authors.lastname: Nishikawa
authors.forename: Yoshiyuki
authors.initials: Y
authors.lastname: Sakano
mesh_terms: D000595:Amino Acid Sequence; D001173:Arthrobacter / Q000201:enzymology; D001665:Binding Sites; D002241:Carbohydrates / Q000737:chemistry; D020134:Catalytic Domain; D003001:Cloning, Molecular; D018360:Crystallography, X-Ray; D004247:DNA / Q000737:chemistry; D005959:Glucosidases / Q000737:chemistry* / Q000502:physiology*; D008954:Models, Biological; D008958:Models, Molecular; D008969:Molecular Sequence Data; D011485:Protein Binding; D011487:Protein Conformation; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D017386:Sequence Homology, Amino Acid; D013379:Substrate Specificity
chemical_list: D002241:Carbohydrates; D004247:DNA; D005959:Glucosidases; C023149:exo-1,6-alpha-glucosidase