3WBA: Rice Os3bglu6 E178q With Covalent Glucosyl Moiety From P-nitrophenyl Glucopyranoside

In order to identify a rice gibberellin ester beta-d-glucosidase, gibberellin A4 beta-d-glucosyl ester (GA4-GE) was synthesized and used to screen rice beta-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 beta-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 beta-d-glucopyranosyl azide, in a pH-dependent manner, while acetate also rescued Os3BGlu6 E178A at low pH. High concentrations of sodium azide (200-400mM) inhibited Os3BGlu6 E178Q but not Os3BGlu6 E178A. The structures of Os3BGlu6 E178Q crystallized with either GA4-GE or pNPGlc had a native alpha-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 beta-glucosidase uses the same retaining catalytic mechanism to hydrolyze 1-O-acyl glucose ester and glucoside.
PDB ID: 3WBADownload
MMDB ID: 113129
PDB Deposition Date: 2013/5/14
Updated in MMDB: 2013/09
Experimental Method:
x-ray diffraction
Resolution: 1.9  Å
Source Organism:
Similar Structures:
Biological Unit for 3WBA: monomeric; determined by author and by software (PISA)
Molecular Components in 3WBA
Label Count Molecule
Protein (1 molecule)
Beta-glucosidase 6(Gene symbol: LOC4332041)
Molecule annotation
Chemicals (6 molecules)
* Click molecule labels to explore molecular sequence information.

Citing MMDB