Crystal Structure of β- d-Xylosidase from Thermoanaerobacterium saccharolyticum, a Family 39 Glycoside Hydrolase

1,4-β- d-Xylan is the major component of plant cell-wall hemicelluloses. β- d-Xylosidases are involved in the breakdown of xylans into xylose and belong to families 3, 39, 43, 52, and 54 of glycoside hydrolases. Here, we report the first crystal structure of a member of family 39 glycoside hydrolase...

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Published in:Journal of molecular biology 2004-01, Vol.335 (1), p.155-165
Main Authors: Yang, Jin Kuk, Yoon, Hye-Jin, Ahn, Hyung Jun, Il Lee, Byung, Pedelacq, Jean-Denis, Liong, Elaine C., Berendzen, Joel, Laivenieks, Maris, Vieille, Claire, Zeikus, Gregory J., Vocadlo, David J., Withers, Stephen G., Suh, Se Won
Format: Article
Language:English
Subjects:
Catalysis
Catalytic Domain
Clostridium - enzymology
covalent glycosyl-enzyme intermediate
Crystallography, X-Ray
family 39 glycoside hydrolase
Glycoside Hydrolases - chemistry
Molecular Structure
Protein Binding
Protein Structure, Secondary
Protein Structure, Tertiary
Substrate Specificity
Thermoanaerobacterium saccharolyticum
xylan
xylose
Xylose - chemistry
xylosidase
Xylosidases - chemistry
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Summary:1,4-β- d-Xylan is the major component of plant cell-wall hemicelluloses. β- d-Xylosidases are involved in the breakdown of xylans into xylose and belong to families 3, 39, 43, 52, and 54 of glycoside hydrolases. Here, we report the first crystal structure of a member of family 39 glycoside hydrolase, i.e. β- d-xylosidase from Thermoanaerobacterium saccharolyticum strain B6A-RI. This study also represents the first structure of any β-xylosidase of the above five glycoside hydrolase families. Each monomer of T. saccharolyticum β-xylosidase comprises three distinct domains; a catalytic domain of the canonical (β/α) 8-barrel fold, a β-sandwich domain, and a small α-helical domain. We have determined the structure in two forms: d-xylose-bound enzyme and a covalent 2-deoxy-2-fluoro-α- d-xylosyl-enzyme intermediate complex, thus providing two snapshots in the reaction pathway. This study provides structural evidence for the proposed double displacement mechanism that involves a covalent intermediate. Furthermore, it reveals possible functional roles for His228 as the auxiliary acid/base and Glu323 as a key residue in substrate recognition.
ISSN:0022-2836
1089-8638
DOI:10.1016/j.jmb.2003.10.026