3GNR

Crystal Structure of a Rice Os3BGlu6 Beta-Glucosidase with covalently bound 2-deoxy-2-fluoroglucoside to the catalytic nucleophile E396

Summary for 3GNR

• Entry DOI: 10.2210/pdb3gnr/pdb
• Related: 3GNO 3GNP
• Descriptor: Os03g0212800 protein, 2-deoxy-2-fluoro-alpha-D-glucopyranose, GLYCEROL, ... (4 entities in total)
• Functional Keywords: beta-alpha barrel, glycosidase, hydrolase
• Biological source: Oryza sativa subsp. japonica (Rice)
• Cellular location: Secreted (Potential): Q8L7J2
• Total number of polymer chains: 1
• Total formula weight: 55683.27

Authors

Seshadri, S.,Akiyama, T.,Opassiri, R.,Kuaprasert, B.,Cairns, J.R.K. (deposition date: 2009-03-17, release date: 2009-07-21, Last modification date: 2024-10-16)

Primary citation

Seshadri, S.,Akiyama, T.,Opassiri, R.,Kuaprasert, B.,Cairns, J.R.K.
Structural and enzymatic characterization of Os3BGlu6, a rice beta-glucosidase hydrolyzing hydrophobic glycosides and (1->3)- and (1->2)-linked disaccharides.
Plant Physiol., 151:47-58, 2009

PubMed Abstract: Glycoside hydrolase family 1 (GH1) beta-glucosidases play roles in many processes in plants, such as chemical defense, alkaloid metabolism, hydrolysis of cell wall-derived oligosaccharides, phytohormone regulation, and lignification. However, the functions of most of the 34 GH1 gene products in rice (Oryza sativa) are unknown. Os3BGlu6, a rice beta-glucosidase representing a previously uncharacterized phylogenetic cluster of GH1, was produced in recombinant Escherichia coli. Os3BGlu6 hydrolyzed p-nitrophenyl (pNP)-beta-d-fucoside (k(cat)/K(m) = 67 mm(-1) s(-1)), pNP-beta-d-glucoside (k(cat)/K(m) = 6.2 mm(-1) s(-1)), and pNP-beta-d-galactoside (k(cat)/K(m) = 1.6 mm(-1)s(-1)) efficiently but had little activity toward other pNP glycosides. It also had high activity toward n-octyl-beta-d-glucoside and beta-(1-->3)- and beta-(1-->2)-linked disaccharides and was able to hydrolyze apigenin beta-glucoside and several other natural glycosides. Crystal structures of Os3BGlu6 and its complexes with a covalent intermediate, 2-deoxy-2-fluoroglucoside, and a nonhydrolyzable substrate analog, n-octyl-beta-d-thioglucopyranoside, were solved at 1.83, 1.81, and 1.80 A resolution, respectively. The position of the covalently trapped 2-F-glucosyl residue in the enzyme was similar to that in a 2-F-glucosyl intermediate complex of Os3BGlu7 (rice BGlu1). The side chain of methionine-251 in the mouth of the active site appeared to block the binding of extended beta-(1-->4)-linked oligosaccharides and interact with the hydrophobic aglycone of n-octyl-beta-d-thioglucopyranoside. This correlates with the preference of Os3BGlu6 for short oligosaccharides and hydrophobic glycosides.

PubMed: 19587102
DOI: 10.1104/pp.109.139436

Experimental method

X-RAY DIFFRACTION (1.81 Å)