title: Structural elucidation of the cyclization mechanism of α-1,6-glucan by Bacillus circulans T-3040 cycloisomaltooligosaccharide glucanotransferase.
abstract: Bacillus circulans T-3040 cycloisomaltooligosaccharide glucanotransferase belongs to the glycoside hydrolase family 66 and catalyzes an intramolecular transglucosylation reaction that produces cycloisomaltooligosaccharides from dextran. The crystal structure of the core fragment from Ser-39 to Met-738 of B. circulans T-3040 cycloisomaltooligosaccharide glucanotransferase, devoid of its N-terminal signal peptide and C-terminal nonconserved regions, was determined. The structural model contained one catalytic (β/α)8-barrel domain and three β-domains. Domain N with an immunoglobulin-like β-sandwich fold was attached to the N terminus; domain C with a Greek key β-sandwich fold was located at the C terminus, and a carbohydrate-binding module family 35 (CBM35) β-jellyroll domain B was inserted between the 7th β-strand and the 7th α-helix of the catalytic domain A. The structures of the inactive catalytic nucleophile mutant enzyme complexed with isomaltohexaose, isomaltoheptaose, isomaltooctaose, and cycloisomaltooctaose revealed that the ligands bound in the catalytic cleft and the sugar-binding site of CBM35. Of these, isomaltooctaose bound in the catalytic site extended to the second sugar-binding site of CBM35, which acted as subsite -8, representing the enzyme·substrate complex when the enzyme produces cycloisomaltooctaose. The isomaltoheptaose and cycloisomaltooctaose bound in the catalytic cleft with a circular structure around Met-310, representing the enzyme·product complex. These structures collectively indicated that CBM35 functions in determining the size of the product, causing the predominant production of cycloisomaltooctaose by the enzyme. The canonical sugar-binding site of CBM35 bound the mid-part of isomaltooligosaccharides, indicating that the original function involved substrate binding required for efficient catalysis.
authors.affiliation: Biomolecular Research Unit, National Institute of Agrobiological Sciences, Tsukuba 305-8602.
authors.forename: Nobuhiro
authors.initials: N
authors.lastname: Suzuki
authors.affiliation: Biomolecular Research Unit, National Institute of Agrobiological Sciences, Tsukuba 305-8602. Electronic address: zui@affrc.go.jp.
authors.forename: Zui
authors.initials: Z
authors.lastname: Fujimoto
authors.affiliation: Biomolecular Research Unit, National Institute of Agrobiological Sciences, Tsukuba 305-8602; Division of Applied Bioscience, Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589.
authors.forename: Young-Min
authors.initials: YM
authors.lastname: Kim
authors.affiliation: Biomolecular Research Unit, National Institute of Agrobiological Sciences, Tsukuba 305-8602.
authors.forename: Mitsuru
authors.initials: M
authors.lastname: Momma
authors.affiliation: Biomolecular Research Unit, National Institute of Agrobiological Sciences, Tsukuba 305-8602.
authors.forename: Naomi
authors.initials: N
authors.lastname: Kishine
authors.affiliation: Applied Microbiology Division, National Food Research Institute, National Agriculture and Food Research Organization, Tsukuba 305-8642.
authors.forename: Ryuichiro
authors.initials: R
authors.lastname: Suzuki
authors.affiliation: College of Life, Environment, and Advanced Sciences, Osaka Prefecture University, Sakai 599-8531.
authors.forename: Shiho
authors.initials: S
authors.lastname: Suzuki
authors.affiliation: College of Life, Environment, and Advanced Sciences, Osaka Prefecture University, Sakai 599-8531.
authors.forename: Shinichi
authors.initials: S
authors.lastname: Kitamura
authors.affiliation: Biomolecular Research Unit, National Institute of Agrobiological Sciences, Tsukuba 305-8602; Applied Microbiology Division, National Food Research Institute, National Agriculture and Food Research Organization, Tsukuba 305-8642; Department of Food and Health Science, Jissen Women's University, Hino 191-8510, Japan.
authors.forename: Mikihiko
authors.initials: M
authors.lastname: Kobayashi
authors.affiliation: Division of Applied Bioscience, Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589.
authors.forename: Atsuo
authors.initials: A
authors.lastname: Kimura
authors.affiliation: Applied Microbiology Division, National Food Research Institute, National Agriculture and Food Research Organization, Tsukuba 305-8642. Electronic address: funane@affrc.go.jp.
authors.forename: Kazumi
authors.initials: K
authors.lastname: Funane
mesh_terms: D001407:Bacillus / Q000201:enzymology*; D002236:Carbohydrate Conformation; D003500:Cyclization; D005936:Glucans / Q000737:chemistry* / Q000378:metabolism; D005964:Glucosyltransferases / Q000378:metabolism*; D008024:Ligands; D008958:Models, Molecular; D013379:Substrate Specificity
chemical_list: D005936:Glucans; D008024:Ligands; C504992:alpha-1-6-glucan; D005964:Glucosyltransferases; C087517:cycloisomaltooligosaccharide glucanotransferase
keywords: Carbohydrate Structure; Carbohydrate-binding Protein; Crystal Structure; Cycloisomaltooligosaccharide Glucanotransferase; Dextran; Enzyme Catalysis; Enzyme Structure; Glycoside Hydrolases; X-ray Crystallography