PDBsum entry 2rgl

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Hydrolase PDB id
Protein chains
471 a.a. *
MES ×2
GOL ×2
SO4 ×2
Waters ×1187
* Residue conservation analysis
PDB id:
Name: Hydrolase
Title: Rice bglu1 beta-glucosidase, a plant exoglucanase/beta-gluco
Structure: Beta-glucosidase. Chain: a, b. Fragment: residues unp 29-504. Engineered: yes
Source: Oryza sativa japonica group. Organism_taxid: 39947. Strain: orion. Gene: os3bglu7. Expressed in: escherichia coli. Expression_system_taxid: 562.
2.20Å     R-factor:   0.164     R-free:   0.205
Authors: W.Chuenchor,J.R.Ketudat Cairns,S.Pengthaisong,R.C.Robinson, J.Yuvaniyama,C.-J.Chen
Key ref:
W.Chuenchor et al. (2008). Structural insights into rice BGlu1 beta-glucosidase oligosaccharide hydrolysis and transglycosylation. J Mol Biol, 377, 1200-1215. PubMed id: 18308333 DOI: 10.1016/j.jmb.2008.01.076
04-Oct-07     Release date:   12-Feb-08    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
Q75I93  (BGL07_ORYSJ) -  Beta-glucosidase 7
504 a.a.
471 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.  - Beta-glucosidase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Hydrolysis of terminal, non-reducing beta-D-glucose residues with release of beta-D-glucose.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular region   4 terms 
  Biological process     metabolic process   2 terms 
  Biochemical function     hydrolase activity     18 terms  


DOI no: 10.1016/j.jmb.2008.01.076 J Mol Biol 377:1200-1215 (2008)
PubMed id: 18308333  
Structural insights into rice BGlu1 beta-glucosidase oligosaccharide hydrolysis and transglycosylation.
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.
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.
  Selected figure(s)  
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.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21345211 S.Khan, T.Pozzo, M.Megyeri, S.Lindahl, A.Sundin, C.Turner, and E.N.Karlsson (2011).
Aglycone specificity of Thermotoga neapolitana β-glucosidase 1A modified by mutagenesis, leading to increased catalytic efficiency in quercetin-3-glucoside hydrolysis.
  BMC Biochem, 12, 11.  
20490603 J.R.Ketudat Cairns, and A.Esen (2010).
  Cell Mol Life Sci, 67, 3389-3405.  
19955176 M.Behrendt, J.Polaina, and H.Y.Naim (2010).
Structural hierarchy of regulatory elements in the folding and transport of an intestinal multidomain protein.
  J Biol Chem, 285, 4143-4152.  
19682295 R.Sánchez-Pérez, K.Jørgensen, M.S.Motawia, F.Dicenta, and B.L.Møller (2009).
Tissue and cellular localization of individual beta-glycosidases using a substrate-specific sugar reducing assay.
  Plant J, 60, 894-906.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time.