title: Structural insights into the catalytic reaction that is involved in the reorientation of Trp238 at the substrate-binding site in GH13 dextran glucosidase.
abstract: Streptococcus mutans dextran glucosidase (SmDG) belongs to glycoside hydrolase family 13, and catalyzes both the hydrolysis of substrates such as isomaltooligosaccharides and subsequent transglucosylation to form α-(1→6)-glucosidic linkage at the substrate non-reducing ends. Here, we report the 2.4Å resolution crystal structure of glucosyl-enzyme intermediate of SmDG. In the obtained structure, the Trp238 side-chain that constitutes the substrate-binding site turned away from the active pocket, concurrently with conformational changes of the nucleophile and the acid/base residues. Different conformations of Trp238 in each reaction stage indicated its flexibility. Considering the results of kinetic analyses, such flexibility may reflect a requirement for the reaction mechanism of SmDG.
authors.affiliation: Graduate School of Life Science, Hokkaido University, Kita-10, Nishi-8, Kita-ku, Sapporo 060-0810, Japan.
authors.forename: Momoko
authors.initials: M
authors.lastname: Kobayashi
authors.affiliation: Research Faculty of Agriculture, Hokkaido University, Kita-9, Nishi-9, Kita-ku, Sapporo 060-8589, Japan.
authors.forename: Wataru
authors.initials: W
authors.lastname: Saburi
authors.affiliation: Research Faculty of Agriculture, Hokkaido University, Kita-9, Nishi-9, Kita-ku, Sapporo 060-8589, Japan.
authors.forename: Daichi
authors.initials: D
authors.lastname: Nakatsuka
authors.affiliation: Research Faculty of Agriculture, Hokkaido University, Kita-9, Nishi-9, Kita-ku, Sapporo 060-8589, Japan.
authors.forename: Hironori
authors.initials: H
authors.lastname: Hondoh
authors.affiliation: Graduate School of Life Science, Hokkaido University, Kita-10, Nishi-8, Kita-ku, Sapporo 060-0810, Japan; Faculty of Advanced Life Science, Hokkaido University, Kita-10, Nishi-8, Kita-ku, Sapporo 060-0810, Japan.
authors.forename: Koji
authors.initials: K
authors.lastname: Kato
authors.affiliation: Research Faculty of Agriculture, Hokkaido University, Kita-9, Nishi-9, Kita-ku, Sapporo 060-8589, Japan.
authors.forename: Masayuki
authors.initials: M
authors.lastname: Okuyama
authors.affiliation: Research Faculty of Agriculture, Hokkaido University, Kita-9, Nishi-9, Kita-ku, Sapporo 060-8589, Japan.
authors.forename: Haruhide
authors.initials: H
authors.lastname: Mori
authors.affiliation: Research Faculty of Agriculture, Hokkaido University, Kita-9, Nishi-9, Kita-ku, Sapporo 060-8589, Japan.
authors.forename: Atsuo
authors.initials: A
authors.lastname: Kimura
authors.affiliation: Graduate School of Life Science, Hokkaido University, Kita-10, Nishi-8, Kita-ku, Sapporo 060-0810, Japan; Faculty of Advanced Life Science, Hokkaido University, Kita-10, Nishi-8, Kita-ku, Sapporo 060-0810, Japan.
authors.forename: Min
authors.initials: M
authors.lastname: Yao
mesh_terms: D001426:Bacterial Proteins / Q000737:chemistry*; D020134:Catalytic Domain; D018360:Crystallography, X-Ray; D003911:Dextrans / Q000737:chemistry*; D005959:Glucosidases / Q000737:chemistry*; D006860:Hydrogen Bonding; D008958:Models, Molecular; D011485:Protein Binding; D013295:Streptococcus mutans / Q000201:enzymology; D014364:Tryptophan / Q000737:chemistry
chemical_list: D001426:Bacterial Proteins; D003911:Dextrans; D014364:Tryptophan; D005959:Glucosidases
keywords: Acceptor specificity; Dextran glucosidase; Glucosyl-enzyme intermediate; Glycoside hydrolase family 13; Retaining glycosidase; transglucosylation