PDBsum entry 3wba

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protein ligands links
Hydrolase PDB id
Protein chain
478 a.a.
GOL ×5
Waters ×534
PDB id:
Name: Hydrolase
Title: Rice os3bglu6 e178q with covalent glucosyl moiety from p-nit glucopyranoside.
Structure: Beta-glucosidase 6. Chain: a. Fragment: unp residues 38-521. Synonym: os3bglu6. Engineered: yes. Mutation: yes
Source: Oryza sativa japonica group. Japonica rice. Organism_taxid: 39947. Strain: yukihikari (japonica). Gene: bglu6, loc_os03g11420, os03g0212800. Expressed in: escherichia coli. Expression_system_taxid: 562.
1.90Å     R-factor:   0.148     R-free:   0.179
Authors: S.Sansenya,Y.Hua,J.R.K.Cairns
Key ref: Y.Hua et al. (2013). Enzymatic and structural characterization of hydrolysis of gibberellin A4 glucosyl ester by a rice β-D-glucosidase. Arch Biochem Biophys, 537, 39-48. PubMed id: 23811195 DOI: 10.1016/
14-May-13     Release date:   04-Sep-13    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
Q8L7J2  (BGL06_ORYSJ) -  Beta-glucosidase 6
521 a.a.
478 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   1 term 
  Biological process     metabolic process   2 terms 
  Biochemical function     hydrolase activity     10 terms  


DOI no: 10.1016/ Arch Biochem Biophys 537:39-48 (2013)
PubMed id: 23811195  
Enzymatic and structural characterization of hydrolysis of gibberellin A4 glucosyl ester by a rice β-D-glucosidase.
Y.Hua, S.Sansenya, C.Saetang, S.Wakuta, J.R.Ketudat Cairns.
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 (200-400mM) 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.