Crystal structure of beta-D-xylosidase from Thermoanaerobacterium saccharolyticum, a family 39 glycoside hydrolase.
1,4-beta-D-Xylan is the major component of plant cell-wall hemicelluloses. beta-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. beta-D-xylosidase from Thermoanaerobacterium saccharolyticum strain B6A-RI. This study also represents the first structure of any beta-xylosidase of the above five glycoside hydrolase families. Each monomer of T. saccharolyticum beta-xylosidase comprises three distinct domains; a catalytic domain of the canonical (beta/alpha)(8)-barrel fold, a beta-sandwich domain, and a small alpha-helical domain. We have determined the structure in two forms: D-xylose-bound enzyme and a covalent 2-deoxy-2-fluoro-alpha-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.
Yang
Jin Kuk
JK
Structural Proteomics Laboratory, Department of Chemistry, College of Natural Sciences, Seoul National University, 151-742, Seoul, South Korea.
Yoon
Hye Jin
HJ
Ahn
Hyung Jun
HJ
Lee
Byung Il
BI
Pedelacq
Jean-Denis
JD
Liong
Elaine C
EC
Berendzen
Joel
J
Laivenieks
Maris
M
Vieille
Claire
C
Zeikus
Gregory J
GJ
Vocadlo
David J
DJ
Withers
Stephen G
SG
Suh
Se Won
SW
D002384:Catalysis; D020134:Catalytic Domain; D003013:Clostridium / Q000201:enzymology*; D018360:Crystallography, X-Ray; D006026:Glycoside Hydrolases / Q000737:chemistry; D015394:Molecular Structure; D011485:Protein Binding; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D013379:Substrate Specificity; D014994:Xylose / Q000737:chemistry; D014995:Xylosidases / Q000737:chemistry*
D014994:Xylose; D006026:Glycoside Hydrolases; D014995:Xylosidases; C026579:exo-1,4-beta-D-xylosidase