title: Structural and thermodynamic analyses of solute-binding Protein from Bifidobacterium longum specific for core 1 disaccharide and lacto-N-biose I.
abstract: Recently, a gene cluster involving a phosphorylase specific for lacto-N-biose I (LNB; Galbeta1-3GlcNAc) and galacto-N-biose (GNB; Galbeta1-3GalNAc) has been found in Bifidobacterium longum. We showed that the solute-binding protein of a putative ATP-binding cassette-type transporter encoded in the cluster crystallizes only in the presence of LNB or GNB, and therefore we named it GNB/LNB-binding protein (GL-BP). Isothermal titration calorimetry measurements revealed that GL-BP specifically binds LNB and GNB with K(d) values of 0.087 and 0.010 microm, respectively, and the binding process is enthalpy-driven. The crystal structures of GL-BP complexed with LNB, GNB, and lacto-N-tetraose (Galbeta1-3GlcNAcbeta1-3Galbeta1-4Glc) were determined. The interactions between GL-BP and the disaccharide ligands mainly occurred through water-mediated hydrogen bonds. In comparison with the LNB complex, one additional hydrogen bond was found in the GNB complex. These structural characteristics of ligand binding are in agreement with the thermodynamic properties. The overall structure of GL-BP was similar to that of maltose-binding protein; however, the mode of ligand binding and the thermodynamic properties of these proteins were significantly different.
authors.affiliation: Department of Biotechnology, the University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan.
authors.forename: Ryuichiro
authors.initials: R
authors.lastname: Suzuki
authors.forename: Jun
authors.initials: J
authors.lastname: Wada
authors.forename: Takane
authors.initials: T
authors.lastname: Katayama
authors.forename: Shinya
authors.initials: S
authors.lastname: Fushinobu
authors.forename: Takayoshi
authors.initials: T
authors.lastname: Wakagi
authors.forename: Hirofumi
authors.initials: H
authors.lastname: Shoun
authors.forename: Hayuki
authors.initials: H
authors.lastname: Sugimoto
authors.forename: Akiyoshi
authors.initials: A
authors.lastname: Tanaka
authors.forename: Hidehiko
authors.initials: H
authors.lastname: Kumagai
authors.forename: Hisashi
authors.initials: H
authors.lastname: Ashida
authors.forename: Motomitsu
authors.initials: M
authors.lastname: Kitaoka
authors.forename: Kenji
authors.initials: K
authors.lastname: Yamamoto
mesh_terms: D000117:Acetylglucosamine / Q000031:analogs & derivatives* / Q000737:chemistry / Q000378:metabolism; D001426:Bacterial Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D001644:Bifidobacterium / Q000235:genetics / Q000378:metabolism*; D002151:Calorimetry; D002236:Carbohydrate Conformation; D018360:Crystallography, X-Ray; D004187:Disaccharides / Q000737:chemistry* / Q000378:metabolism*; D037102:Lectins / Q000737:chemistry / Q000378:metabolism; D008024:Ligands; D008958:Models, Molecular; D011485:Protein Binding; D020836:Protein Structure, Quaternary; D017434:Protein Structure, Tertiary; D013379:Substrate Specificity; D013816:Thermodynamics
chemical_list: D001426:Bacterial Proteins; D004187:Disaccharides; D037102:Lectins; D008024:Ligands; C033398:galactosyl-1,3-N-acetylglucosamine; D000117:Acetylglucosamine