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PDBsum entry 2rgl

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Hydrolase PDB id
2rgl
Jmol
Contents
Protein chains
471 a.a.
Ligands
MES ×2
GOL ×2
SO4 ×2
Metals
_ZN
Waters ×1187

References listed in PDB file
Key reference
Title Structural insights into rice bglu1 beta-Glucosidase oligosaccharide hydrolysis and transglycosylation.
Authors W.Chuenchor, S.Pengthaisong, R.C.Robinson, J.Yuvaniyama, W.Oonanant, D.R.Bevan, A.Esen, C.J.Chen, R.Opassiri, J.Svasti, J.R.Cairns.
Ref. J Mol Biol, 2008, 377, 1200-1215. [DOI no: 10.1016/j.jmb.2008.01.076]
PubMed id 18308333
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.
Figure 2.
Fig. 2. Asymmetric unit of the rice BGlu1/G2F complex structure. (a) A ribbon diagram representing the overall structure of the BGlu1/G2F inhibitor complex asymmetric unit. The β-strands are colored green, α-helices red and loops cyan. The nucleophilc catalytic residue E386, which is covalently bound to the G2F inhibitor is shown as ball and stick and colored by atoms with carbon in yellow. Hetero atoms found in the crystal structure: GOL (glycerol), MES, and SO[4], are drawn as ball and stick (colored by atoms) and a yellow sphere represents Zn^2+. (b) Crystallographic contacts mediated by Zn^2+. The two protein molecules in the asymmetric unit are linked by D65 and H68 (ball and stick, with nitrogen blue and oxygen red ) from molecule A and B via Zn^2+ (yellow sphere). Broken lines represent the chelating interactions with their distances given in ångström units.
Figure 3.
Fig. 3. Superimposition of the structures of rice BGlu1 (green), linamarase from Trifolium repens (1CBG, yellow), Zea mays β-glucosidase isozyme I (1E1E, blue), and Paenibacillus polymyxa β-glucosidase BglB (2JIE, pink). Loops A–D, which constitute the doorway to the active site are expanded to the side, as indicated by the arrows, to show the differences in loop structures. Sorghum bicolor dhurrinase isozyme I (1V02) and Synapis alba myrosinase (1MYR) were similarly superimposed, but are not shown for the sake of clarity.
The above figures are reprinted by permission from Elsevier: J Mol Biol (2008, 377, 1200-1215) copyright 2008.
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