3WBA image
Entry Detail
PDB ID:
3WBA
Keywords:
Title:
Rice Os3BGlu6 E178Q with Covalent Glucosyl Moiety from p-nitrophenyl glucopyranoside.
Biological Source:
Host Organism:
PDB Version:
Deposition Date:
2013-05-14
Release Date:
2013-09-04
Method Details:
Experimental Method:
Resolution:
1.90 Å
R-Value Free:
0.17
R-Value Work:
0.14
R-Value Observed:
0.14
Space Group:
P 21 21 21
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:Beta-glucosidase 6
Mutations:E178Q
Chain IDs:A
Chain Length:489
Number of Molecules:1
Biological Source:Oryza sativa Japonica Group
Primary Citation
Enzymatic and structural characterization of hydrolysis of gibberellin A4 glucosyl ester by a rice beta-d-glucosidase
Arch.Biochem.Biophys. 537 39 48 (2013)
PMID: 23811195 DOI: 10.1016/j.abb.2013.06.005

Abstact

In order to identify a rice gibberellin ester β-D-glucosidase, gibberellin A4 β-D-glucosyl ester (GA4-GE) was synthesized and used to screen rice β-glucosidases. Os3BGlu6 was found to have the highest hydrolysis activity to GA4-GE among five recombinantly expressed rice glycoside hydrolase family GH1 enzymes from different phylogenic clusters. The kinetic parameters of Os3BGlu6 and its mutants E178Q, E178A, E394D, E394Q and M251N for hydrolysis of p-nitrophenyl β-D-glucopyranoside (pNPGlc) and GA4-GE confirmed the roles of the catalytic acid/base and nucleophile for hydrolysis of both substrates and suggested M251 contributes to binding hydrophobic aglycones. The activities of the Os3BGlu6 E178Q and E178A acid/base mutants were rescued by azide, which they transglucosylate to produce β-D-glucopyranosyl azide, in a pH-dependent manner, while acetate also rescued Os3BGlu6 E178A at low pH. High concentrations of sodium azide (200-400 mM) inhibited Os3BGlu6 E178Q but not Os3BGlu6 E178A. The structures of Os3BGlu6 E178Q crystallized with either GA4-GE or pNPGlc had a native α-D-glucosyl moiety covalently linked to the catalytic nucleophile, E394, which showed the hydrogen bonding to the 2-hydroxyl in the covalent intermediate. These data suggest that a GH1 β-glucosidase uses the same retaining catalytic mechanism to hydrolyze 1-O-acyl glucose ester and glucoside.

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