Biological Assembly 1  

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 56013.63 
• Atom Count: 3964 
• Residue Count: 489 
• Unique protein chains: 1

3WBA

Rice Os3BGlu6 E178Q with Covalent Glucosyl Moiety from p-nitrophenyl glucopyranoside.

• DOI: 10.2210/pdb3WBA/pdb

• Classification: HYDROLASE
• Organism(s): Oryza sativa subsp. japonica
• Expression System: Escherichia coli
• Mutation(s): 1 


• Deposited: 2013-05-14 Released: 2013-09-04 
• Deposition Author(s): Sansenya, S., Hua, Y., Cairns, J.R.K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.9 Å
• R-Value Free: 0.179 
• R-Value Work: 0.146 

Literature

Enzymatic and structural characterization of hydrolysis of gibberellin A4 glucosyl ester by a rice beta-d-glucosidase

Hua, Y., Sansenya, S., Saetang, C., Wakuta, S., Cairns, J.R.K.

(2013) Arch.Biochem.Biophys. 537: 39-48

• PubMed: 23811195 
• DOI: 10.1016/j.abb.2013.06.005
• Primary Citation of Related Structures:  
  3WBE


• PubMed Abstract: 
  

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 (200-400 mM) 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.

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Organizational Affiliation: 

School of Biochemistry and Chemistry, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima, Thailand.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Beta-glucosidase 6	A	489	Oryza sativa subsp. japonica	Mutation(s): 1  Gene Names: BGLU6 EC: 3.2.1.21
Find proteins for Q8L7J2 (Oryza sativa subsp. japonica) Go to UniProtKB:  Q8L7J2

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
GOL	A	GLYCEROL GLYCERIN; PROPANE-1,2,3-TRIOL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
GLC	A	ALPHA-D-GLUCOSE C6 H12 O6 WQZGKKKJIJFFOK-DVKNGEFBSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.9 Å
• R-Value Free: 0.179 
• R-Value Work: 0.146 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 56.986	α = 90.00
b = 91.127	β = 90.00
c = 111.221	γ = 90.00

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data scaling
HKL-2000	data reduction
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-05-14 
• Released Date: 2013-09-04 
• Deposition Author(s): Sansenya, S., Hua, Y., Cairns, J.R.K.

Revision History 

• Version 1.0: 2013-09-04
  Type: Initial release