title: Crystal structure of glycoside hydrolase family 127 β-l-arabinofuranosidase from Bifidobacterium longum.
abstract: Enzymes acting on β-linked arabinofuranosides have been unknown until recently, in spite of wide distribution of β-l-arabinofuranosyl oligosaccharides in plant cells. Recently, a β-l-arabinofuranosidase from the glycoside hydrolase family 127 (HypBA1) was discovered in the newly characterized degradation system of hydroxyproline-linked β-l-arabinooligosaccharides in the bacterium Bifidobacterium longum. Here, we report the crystal structure of HypBA1 in the ligand-free and β-l-arabinofuranose complex forms. The structure of HypBA1 consists of a catalytic barrel domain and two additional β-sandwich domains, with one β-sandwich domain involved in the formation of a dimer. Interestingly, there is an unprecedented metal-binding motif with Zn(2+) coordinated by glutamate and three cysteines in the active site. The glutamate residue is located far from the anomeric carbon of the β-l-arabinofuranose ligand, but one cysteine residue is appropriately located for nucleophilic attack for glycosidic bond cleavage. The residues around the active site are highly conserved among GH127 members. Based on biochemical experiments and quantum mechanical calculations, a possible reaction mechanism involving cysteine as the nucleophile is proposed.
authors.affiliation: Department of Biotechnology, The University of Tokyo, Tokyo, Japan.
authors.forename: Tasuku
authors.initials: T
authors.lastname: Ito
authors.affiliation: Department of Biotechnology, The University of Tokyo, Tokyo, Japan.
authors.forename: Kyo
authors.initials: K
authors.lastname: Saikawa
authors.affiliation: National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO, USA.
authors.forename: Seonah
authors.initials: S
authors.lastname: Kim
authors.affiliation: Faculty of Agriculture, Kagoshima University, Korimoto, Kagoshima, Japan.
authors.forename: Kiyotaka
authors.initials: K
authors.lastname: Fujita
authors.affiliation: Synthetic Cellular Chemistry Laboratory, RIKEN, Japan.
authors.forename: Akihiro
authors.initials: A
authors.lastname: Ishiwata
authors.affiliation: ERATO Glycotrilogy Project, JST, Wako, Saitama, Japan.
authors.forename: Sophon
authors.initials: S
authors.lastname: Kaeothip
authors.affiliation: Department of Biotechnology, The University of Tokyo, Tokyo, Japan.
authors.forename: Takatoshi
authors.initials: T
authors.lastname: Arakawa
authors.affiliation: Department of Biotechnology, The University of Tokyo, Tokyo, Japan.
authors.forename: Takayoshi
authors.initials: T
authors.lastname: Wakagi
authors.affiliation: National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO, USA. Electronic address: Gregg.Beckham@nrel.gov.
authors.forename: Gregg T
authors.initials: GT
authors.lastname: Beckham
authors.affiliation: Synthetic Cellular Chemistry Laboratory, RIKEN, Japan; ERATO Glycotrilogy Project, JST, Wako, Saitama, Japan.
authors.forename: Yukishige
authors.initials: Y
authors.lastname: Ito
authors.affiliation: Department of Biotechnology, The University of Tokyo, Tokyo, Japan. Electronic address: asfushi@mail.ecc.u-tokyo.ac.jp.
authors.forename: Shinya
authors.initials: S
authors.lastname: Fushinobu
mesh_terms: D000595:Amino Acid Sequence; D001089:Arabinose / Q000031:analogs & derivatives / Q000378:metabolism; D001644:Bifidobacterium / Q000201:enzymology; D020134:Catalytic Domain; D003545:Cysteine / Q000737:chemistry; D018698:Glutamic Acid / Q000737:chemistry; D006026:Glycoside Hydrolases / Q000737:chemistry* / Q000378:metabolism; D008958:Models, Molecular; D008969:Molecular Sequence Data; D017434:Protein Structure, Tertiary; D011789:Quantum Theory; D016415:Sequence Alignment; D013379:Substrate Specificity; D015032:Zinc / Q000737:chemistry
chemical_list: C431714:arabinofuranose; D018698:Glutamic Acid; D001089:Arabinose; D006026:Glycoside Hydrolases; D015032:Zinc; D003545:Cysteine
keywords: Crystal structure; DUF1680; Human gut bacteria; Plant polysaccharide; Quantum mechanical calculations; Retaining glycoside hydrolase