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Title: Crystal structure of glycoside hydrolase family 127 β-L-arabinofuranosidase from Bifidobacterium longum

Abstract

Graphical abstract: - Highlights: • HypBA1 β-L-arabinofuranosidase belongs to glycoside hydrolase family 127. • Crystal structure of HypBA1 was determined. • HypBA1 consists of a catalytic barrel and two additional β-sandwich domains. • The active site contains a Zn{sup 2+} coordinated by glutamate and three cysteines. • A possible reaction mechanism involving cysteine as the nucleophile is proposed. - 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{sup 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 themore » 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.« less

Authors:
;  [1];  [2];  [3];  [4];  [5]; ;  [1];  [4];  [1]
  1. Department of Biotechnology, The University of Tokyo, Tokyo (Japan)
  2. National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO (United States)
  3. Faculty of Agriculture, Kagoshima University, Korimoto, Kagoshima (Japan)
  4. Synthetic Cellular Chemistry Laboratory, RIKEN (Japan)
  5. ERATO Glycotrilogy Project, JST, Wako, Saitama (Japan)
Publication Date:
OSTI Identifier:
22416398
Resource Type:
Journal Article
Journal Name:
Biochemical and Biophysical Research Communications
Additional Journal Information:
Journal Volume: 447; Journal Issue: 1; Other Information: Copyright (c) 2014 Elsevier Science B.V., Amsterdam, The Netherlands, All rights reserved.; Country of input: International Atomic Energy Agency (IAEA); Journal ID: ISSN 0006-291X
Country of Publication:
United States
Language:
English
Subject:
60 APPLIED LIFE SCIENCES; BACTERIA; CARBON; CRYSTAL STRUCTURE; CYSTEINE; DIMERS; ENZYMES; GLYCOSIDES; HUMAN POPULATIONS; HYDROXYPROLINE; LIGANDS; OLIGOSACCHARIDES; POLYSACCHARIDES; QUANTUM MECHANICS; REACTION KINETICS; ZINC IONS

Citation Formats

Ito, Tasuku, Saikawa, Kyo, Kim, Seonah, Fujita, Kiyotaka, Ishiwata, Akihiro, Kaeothip, Sophon, Arakawa, Takatoshi, Wakagi, Takayoshi, Beckham, Gregg T., E-mail: Gregg.Beckham@nrel.gov, Ito, Yukishige, ERATO Glycotrilogy Project, JST, Wako, Saitama, and Fushinobu, Shinya. Crystal structure of glycoside hydrolase family 127 β-L-arabinofuranosidase from Bifidobacterium longum. United States: N. p., 2014. Web. doi:10.1016/J.BBRC.2014.03.096.
Ito, Tasuku, Saikawa, Kyo, Kim, Seonah, Fujita, Kiyotaka, Ishiwata, Akihiro, Kaeothip, Sophon, Arakawa, Takatoshi, Wakagi, Takayoshi, Beckham, Gregg T., E-mail: Gregg.Beckham@nrel.gov, Ito, Yukishige, ERATO Glycotrilogy Project, JST, Wako, Saitama, & Fushinobu, Shinya. Crystal structure of glycoside hydrolase family 127 β-L-arabinofuranosidase from Bifidobacterium longum. United States. doi:10.1016/J.BBRC.2014.03.096.
Ito, Tasuku, Saikawa, Kyo, Kim, Seonah, Fujita, Kiyotaka, Ishiwata, Akihiro, Kaeothip, Sophon, Arakawa, Takatoshi, Wakagi, Takayoshi, Beckham, Gregg T., E-mail: Gregg.Beckham@nrel.gov, Ito, Yukishige, ERATO Glycotrilogy Project, JST, Wako, Saitama, and Fushinobu, Shinya. Fri . "Crystal structure of glycoside hydrolase family 127 β-L-arabinofuranosidase from Bifidobacterium longum". United States. doi:10.1016/J.BBRC.2014.03.096.
@article{osti_22416398,
title = {Crystal structure of glycoside hydrolase family 127 β-L-arabinofuranosidase from Bifidobacterium longum},
author = {Ito, Tasuku and Saikawa, Kyo and Kim, Seonah and Fujita, Kiyotaka and Ishiwata, Akihiro and Kaeothip, Sophon and Arakawa, Takatoshi and Wakagi, Takayoshi and Beckham, Gregg T., E-mail: Gregg.Beckham@nrel.gov and Ito, Yukishige and ERATO Glycotrilogy Project, JST, Wako, Saitama and Fushinobu, Shinya},
abstractNote = {Graphical abstract: - Highlights: • HypBA1 β-L-arabinofuranosidase belongs to glycoside hydrolase family 127. • Crystal structure of HypBA1 was determined. • HypBA1 consists of a catalytic barrel and two additional β-sandwich domains. • The active site contains a Zn{sup 2+} coordinated by glutamate and three cysteines. • A possible reaction mechanism involving cysteine as the nucleophile is proposed. - 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{sup 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.},
doi = {10.1016/J.BBRC.2014.03.096},
journal = {Biochemical and Biophysical Research Communications},
issn = {0006-291X},
number = 1,
volume = 447,
place = {United States},
year = {2014},
month = {4}
}