3WBA
Rice Os3BGlu6 E178Q with Covalent Glucosyl Moiety from p-nitrophenyl glucopyranoside.
Summary for 3WBA
| Entry DOI | 10.2210/pdb3wba/pdb |
| Related | 3GNO 3GNP 3GNR |
| Descriptor | Beta-glucosidase 6, alpha-D-glucopyranose, GLYCEROL, ... (4 entities in total) |
| Functional Keywords | tim barrel, beta-glucosidase, covalently bound to glucose, secreted, hydrolase |
| Biological source | Oryza sativa Japonica Group (Japonica rice) |
| Cellular location | Secreted (Potential): Q8L7J2 |
| Total number of polymer chains | 1 |
| Total formula weight | 56013.63 |
| Authors | Sansenya, S.,Hua, Y.,Cairns, J.R.K. (deposition date: 2013-05-14, release date: 2013-09-04, Last modification date: 2024-10-09) |
| Primary citation | Hua, Y.,Sansenya, S.,Saetang, C.,Wakuta, S.,Cairns, J.R.K. Enzymatic and structural characterization of hydrolysis of gibberellin A4 glucosyl ester by a rice beta-d-glucosidase Arch.Biochem.Biophys., 537:39-48, 2013 Cited by PubMed Abstract: 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. PubMed: 23811195DOI: 10.1016/j.abb.2013.06.005 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.9 Å) |
Structure validation
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