Merck
  • Início
  • Resultados da busca
  • Crystal structure of glycoside hydrolase family 127 β-l-arabinofuranosidase from Bifidobacterium longum.

Crystal structure of glycoside hydrolase family 127 β-l-arabinofuranosidase from Bifidobacterium longum.

Biochemical and biophysical research communications (2014-04-01)
Tasuku Ito, Kyo Saikawa, Seonah Kim, Kiyotaka Fujita, Akihiro Ishiwata, Sophon Kaeothip, Takatoshi Arakawa, Takayoshi Wakagi, Gregg T Beckham, Yukishige Ito, Shinya Fushinobu
RESUMO

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.

MATERIAIS
Número do produto
Marca
Descrição do produto

Sigma-Aldrich
L-Cysteine, ≥97%, FG
Sigma-Aldrich
L-Cysteine, 97%
Sigma-Aldrich
Zinc, foil, thickness 0.25 mm, 99.9% trace metals basis
Sigma-Aldrich
Zinc, wire, diam. 1.0 mm, 99.995% trace metals basis
Sigma-Aldrich
L-Glutamic acid, FCC
Sigma-Aldrich
Zinc, powder, <150 μm, 99.995% trace metals basis
Sigma-Aldrich
Zinc, purum, powder
SAFC
L-Cysteine
Sigma-Aldrich
Zinc, granular, 30-100 mesh, 99%
Sigma-Aldrich
L-Glutamic acid, BioUltra, ≥99.5% (NT)
Sigma-Aldrich
L-Cysteine, BioUltra, ≥98.5% (RT)
Sigma-Aldrich
D-Glutamic acid, ≥99% (TLC)
Sigma-Aldrich
L-Glutamic acid, ReagentPlus®, ≥99% (HPLC)
Sigma-Aldrich
L-Glutamic acid, from non-animal source, meets EP testing specifications, suitable for cell culture, 98.5-100.5%
Sigma-Aldrich
L-Cysteine, from non-animal source, BioReagent, suitable for cell culture, ≥98%
Supelco
L-Cysteine, certified reference material, TraceCERT®
Supelco
L-Glutamic acid, certified reference material, TraceCERT®
Supelco
L-Glutamic acid, Pharmaceutical Secondary Standard; Certified Reference Material
Sigma-Aldrich
Zinc, mossy, ≥99%
Zinc, foil, 0.5m coil, thickness 0.025mm, as rolled, 99.95+%
Zinc, foil, 0.5m coil, thickness 0.25mm, as rolled, 99.95+%
Zinc, foil, 25x25mm, thickness 0.175mm, as rolled, 99.95+%
Zinc, foil, 50x50mm, thickness 3mm, as rolled, 99.99+%
Zinc, foil, 0.5m coil, thickness 0.35mm, as rolled, 99.95+%
Zinc, foil, 50x50mm, thickness 0.25mm, as rolled, 99.95+%
Zinc, foil, 15mm disks, thickness 0.175mm, as rolled, 99.95+%
Zinc, foil, 0.3m coil, thickness 0.075mm, as rolled, 99.95+%
Zinc, foil, 25x25mm, thickness 0.5mm, as rolled, 99.99+%
Zinc, foil, 50x50mm, thickness 0.175mm, as rolled, 99.95+%
Zinc, foil, 50x50mm, thickness 6mm, as rolled, polished on both sides, 99.99+%