3VK9

Crystal structure of delta-class glutathione transferase from silkmoth


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.191 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural basis for catalytic activity of a silkworm Delta-class glutathione transferase

Yamamoto, K.Usuda, K.Kakuta, Y.Kimura, M.Higashiura, A.Nakagawa, A.Aso, Y.Suzuki, M.

(2012) Biochim Biophys Acta 1820: 1469-1474

  • DOI: https://doi.org/10.1016/j.bbagen.2012.04.022
  • Primary Citation of Related Structures:  
    3VK9

  • PubMed Abstract: 

    Glutathione transferase (GST) catalyzes glutathione conjugation, a major detoxification pathway for xenobiotics and endogenous substances. Here, we determined the crystal structure of a Delta-class GST from Bombyx mori (bmGSTD) to examine its catalytic residues. The three-dimensional structure of bmGSTD was resolved by the molecular replacement method and refined to a resolution of 2.0Å. Structural alignment with a Delta-class GST of Anopheles gambiae indicated that bmGSTD contains 2 distinct domains (an N-terminal domain and a C-terminal domain) connected by a linker. The bound glutathione localized at the N-terminal domain. Putative catalytic residues were changed to alanine by site-directed mutagenesis, and the resulting mutants were characterized in terms of catalytic activity using glutathione and 1-chloro-2,4-dinitrobenzene, a synthetic substrate of GST. Kinetic analysis of bmGSTD mutants indicated that Ser11, Gln51, His52, Ser67, and Arg68 are important for enzyme function. These results provide structural insights into the catalysis of glutathione conjugation in B. mori by bmGSTD.


  • Organizational Affiliation

    Faculty of Agriculture, Kyushu University Graduate School, 6-10-1 Hakozaki, Higashi-ku, Fukuoka 812-8581, Japan. yamamok@agr.kyushu-u.ac.jp


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glutathione S-transferase delta
A, B, C, D
216Bombyx moriMutation(s): 0 
Gene Names: GST delta
EC: 2.5.1.18
UniProt
Find proteins for Q60GK5 (Bombyx mori)
Explore Q60GK5 
Go to UniProtKB:  Q60GK5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ60GK5
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.191 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 128.393α = 90
b = 162.184β = 90
c = 86.791γ = 90
Software Package:
Software NamePurpose
BSSdata collection
MOLREPphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-10-03
    Type: Initial release
  • Version 1.1: 2024-03-20
    Changes: Data collection, Database references, Derived calculations