title: Crystal structure of the branching enzyme I (BEI) from Oryza sativa L with implications for catalysis and substrate binding.
abstract: Starch-branching enzyme catalyzes the cleavage of α-1, 4-linkages and the subsequent transfer of α-1,4 glucan to form an α-1,6 branch point in amylopectin. Sequence analysis of the rice-branching enzyme I (BEI) indicated a modular structure in which the central α-amylase domain is flanked on each side by the N-terminal carbohydrate-binding module 48 and the α-amylase C-domain. We determined the crystal structure of BEI at a resolution of 1.9 Å by molecular replacement using the Escherichia coli glycogen BE as a search model. Despite three modular structures, BEI is roughly ellipsoidal in shape with two globular domains that form a prominent groove which is proposed to serve as the α-polyglucan-binding site. Amino acid residues Asp344 and Glu399, which are postulated to play an essential role in catalysis as a nucleophile and a general acid/base, respectively, are located at a central cleft in the groove. Moreover, structural comparison revealed that in BEI, extended loop structures cause a narrowing of the substrate-binding site, whereas shortened loop structures make a larger space at the corresponding subsite in the Klebsiella pneumoniae pullulanase. This structural difference might be attributed to distinct catalytic reactions, transglycosylation and hydrolysis, respectively, by BEI and pullulanase.
authors.affiliation: Laboratory of Structural Biology, Graduate School of Systems Life Sciences, Faculty of Agriculture, Kyushu University, Hakozaki 6-10-1, Fukuoka 812-8581, Japan.
authors.forename: Junji
authors.initials: J
authors.lastname: Noguchi
authors.forename: Kimiko
authors.initials: K
authors.lastname: Chaen
authors.forename: Nhuan Thi
authors.initials: NT
authors.lastname: Vu
authors.forename: Taiki
authors.initials: T
authors.lastname: Akasaka
authors.forename: Hiroaki
authors.initials: H
authors.lastname: Shimada
authors.forename: Takashi
authors.initials: T
authors.lastname: Nakashima
authors.forename: Aiko
authors.initials: A
authors.lastname: Nishi
authors.forename: Hikaru
authors.initials: H
authors.lastname: Satoh
authors.forename: Toshiro
authors.initials: T
authors.lastname: Omori
authors.forename: Yoshimitsu
authors.initials: Y
authors.lastname: Kakuta
authors.forename: Makoto
authors.initials: M
authors.lastname: Kimura
mesh_terms: D015061:1,4-alpha-Glucan Branching Enzyme / Q000737:chemistry* / Q000378:metabolism; D001665:Binding Sites; D055162:Biocatalysis; D018360:Crystallography, X-Ray; D004789:Enzyme Activation; D008958:Models, Molecular; D012275:Oryza / Q000201:enzymology*; D013379:Substrate Specificity
chemical_list: D015061:1,4-alpha-Glucan Branching Enzyme