3RBT

Crystal structure of glutathione S-transferase Omega 3 from the silkworm Bombyx mori

• PDB DOI:  https://doi.org/10.2210/pdb3RBT/pdb

• Classification: TRANSFERASE
• Organism(s): Bombyx mori
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-03-29 Released: 2011-08-10 
• Deposition Author(s): Chen, B.-Y., Ma, X.-X., Tan, X., Yang, J.-P., Zhang, N.-N., Li, W.-F., Chen, Y., Xia, Q., Zhou, C.-Z.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.263 
• R-Value Work: 0.215 
• R-Value Observed: 0.217 

Literature

Structure-guided activity restoration of the silkworm glutathione transferase Omega GSTO3-3

Chen, B.-Y., Ma, X.-X., Guo, P.-C., Tan, X., Li, W.-F., Yang, J.-P., Zhang, N.-N., Chen, Y., Xia, Q., Zhou, C.-Z.

(2011) J Mol Biol 412: 204-211

• PubMed: 21816159 
• DOI: https://doi.org/10.1016/j.jmb.2011.07.019
• Primary Citation of Related Structures:  
  3RBT


• PubMed Abstract: 
  

Glutathione transferases (GSTs) are ubiquitous detoxification enzymes that conjugate hydrophobic xenobiotics with reduced glutathione. The silkworm Bombyx mori encodes four isoforms of GST Omega (GSTO), featured with a catalytic cysteine, except that bmGSTO3-3 has an asparagine substitution of this catalytic residue. Here, we determined the 2.20-Å crystal structure of bmGSTO3-3, which shares a typical GST overall structure. However, the extended C-terminal segment that exists in all the four bmGSTOs occupies the G-site of bmGSTO3-3 and makes it unworkable, as shown by the activity assays. Upon mutation of Asn29 to Cys and truncation of the C-terminal segment, the in vitro GST activity of bmGSTO3-3 could be restored. These findings provided structural insights into the activity regulation of GSTOs.

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Organizational Affiliation: 

School of Life Sciences and Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, Anhui 230027, People's Republic of China.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 assigned by authors.

Biological Assembly 4  

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 4 assigned by authors.

Macromolecule Content

• Total Structure Weight: 117.99 kDa 
• Atom Count: 8,238 
• Modelled Residue Count: 932 
• Deposited Residue Count: 984 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutathione transferase o1	A, B, C, D	246	Bombyx mori	Mutation(s): 0  EC: 2.5.1.18
UniProt
Find proteins for Q1HPV9 (Bombyx mori) Explore Q1HPV9  Go to UniProtKB:  Q1HPV9

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	E [auth A], F [auth B], G [auth C], H [auth D]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.263 
• R-Value Work: 0.215 
• R-Value Observed: 0.217 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 108.537	α = 90
b = 139.03	β = 90
c = 128.816	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-08-10 
Deposition Author(s): Chen, B.-Y., Ma, X.-X., Tan, X., Yang, J.-P., Zhang, N.-N., Li, W.-F., Chen, Y., Xia, Q., Zhou, C.-Z.

Revision History  

• Version 1.0: 2011-08-10
  Type: Initial release
  
• Version 1.1: 2012-09-19
  Changes: Database references, Derived calculations