5ZQX

Crystal structure of beta-xylosidase mutant (E186Q) from Bacillus pumilus

Summary for 5ZQX

• Entry DOI: 10.2210/pdb5zqx/pdb
• Related: 5ZQJ
• Related PRD ID: PRD_900116
• Descriptor: Beta-xylosidase, beta-D-xylopyranose-(1-4)-beta-D-xylopyranose (3 entities in total)
• Functional Keywords: xylobiose hydrolysis, hydrolase
• Biological source: Bacillus pumilus (Bacillus mesentericus)
• Total number of polymer chains: 4
• Total formula weight: 249486.93

Authors

Ha, N.C.,Hong, S.,Jo, I. (deposition date: 2018-04-20, release date: 2018-05-30, Last modification date: 2023-11-22)

Primary citation

Hong, S.,Kyung, M.,Jo, I.,Kim, Y.R.,Ha, N.C.
Structure-based protein engineering of bacterial beta-xylosidase to increase the production yield of xylobiose from xylose
Biochem. Biophys. Res. Commun., 501:703-710, 2018

PubMed Abstract: Xylobiose consists of two molecules of xylose and has been highly recognized as a food supplement because it possesses high prebiotic functions. β-xylosidase exhibits enzymatic activity to hydrolyze xylobiose, and the enzyme can also catalyze the reverse reaction in the presence of high concentrations of xylose. Previously, β-xylosidase from Bacillus pumilus IPO (BpXynB), belonging to GH family 43, was employed to produce xylobiose from xylose. To improve the enzymatic efficiency, this study determined the high-resolution structure of BpXynB in a complex with xylobiose and engineered BpXynB based on the structures. The structure of BpXynB deciphered the residues involved in the recognition of the xylobiose. A site-directed mutation at the residue for xylobiose recognition increased the yield of xylobiose by 20% compared to a similar activity of the wild type enzyme. The complex structure of the mutant enzyme and xylobiose provided the structural basis for a higher yield of the engineered protein. This engineered enzyme would enable a higher economic production of xylobiose, and a similar engineering strategy could be applied within the same family of enzymes.

PubMed: 29752942
DOI: 10.1016/j.bbrc.2018.05.051

Experimental method

X-RAY DIFFRACTION (2 Å)