2RGM

Rice BGlu1 beta-glucosidase, a plant exoglucanase/beta-glucosidase

Summary for 2RGM

• Entry DOI: 10.2210/pdb2rgm/pdb
• Related: 2RGL
• Descriptor: Beta-glucosidase, 2-deoxy-2-fluoro-alpha-D-glucopyranose, ZINC ION, ... (7 entities in total)
• Functional Keywords: beta-alpha-barrels, glycosidase, hydrolase
• Biological source: Oryza sativa Japonica Group
• Total number of polymer chains: 2
• Total formula weight: 110653.42

Authors

Chuenchor, W.,Ketudat Cairns, J.R.,Pengthaisong, S.,Robinson, R.C.,Yuvaniyama, J.,Chen, C.-J. (deposition date: 2007-10-04, release date: 2008-02-12, Last modification date: 2024-10-09)

Primary citation

Chuenchor, W.,Pengthaisong, S.,Robinson, R.C.,Yuvaniyama, J.,Oonanant, W.,Bevan, D.R.,Esen, A.,Chen, C.J.,Opassiri, R.,Svasti, J.,Cairns, J.R.K.
Structural Insights into Rice BGlu1 beta-Glucosidase Oligosaccharide Hydrolysis and Transglycosylation
J.Mol.Biol., 377:1200-1215, 2008

PubMed Abstract: The structures of rice BGlu1 beta-glucosidase, a plant beta-glucosidase active in hydrolyzing cell wall-derived oligosaccharides, and its covalent intermediate with 2-deoxy-2-fluoroglucoside have been solved at 2.2 A and 1.55 A resolution, respectively. The structures were similar to the known structures of other glycosyl hydrolase family 1 (GH1) beta-glucosidases, but showed several differences in the loops around the active site, which lead to an open active site with a narrow slot at the bottom, compatible with the hydrolysis of long beta-1,4-linked oligosaccharides. Though this active site structure is somewhat similar to that of the Paenibacillus polymyxa beta-glucosidase B, which hydrolyzes similar oligosaccharides, molecular docking studies indicate that the residues interacting with the substrate beyond the conserved -1 site are completely different, reflecting the independent evolution of plant and microbial GH1 exo-beta-glucanase/beta-glucosidases. The complex with the 2-fluoroglucoside included a glycerol molecule, which appears to be in a position to make a nucleophilic attack on the anomeric carbon in a transglycosylation reaction. The coordination of the hydroxyl groups suggests that sugars are positioned as acceptors for transglycosylation by their interactions with E176, the catalytic acid/base, and Y131, which is conserved in barley BGQ60/beta-II beta-glucosidase, that has oligosaccharide hydrolysis and transglycosylation activity similar to rice BGlu1. As the rice and barley enzymes have different preferences for cellobiose and cellotriose, residues that appeared to interact with docked oligosaccharides were mutated to those of the barley enzyme to see if the relative activities of rice BGlu1 toward these substrates could be changed to those of BGQ60. Although no single residue appeared to be responsible for these differences, I179, N190 and N245 did appear to interact with the substrates.

PubMed: 18308333
DOI: 10.1016/j.jmb.2008.01.076

Experimental method

X-RAY DIFFRACTION (1.55 Å)