1YZX

Crystal structure of human kappa class glutathione transferase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.182 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Thioredoxin-like domain of human kappa class glutathione transferase reveals sequence homology and structure similarity to the theta class enzyme

Li, J.Xia, Z.Ding, J.

(2005) Protein Sci 14: 2361-2369

  • DOI: 10.1110/ps.051463905
  • Primary Citation of Related Structures:  
    1YZX

  • PubMed Abstract: 
  • Glutathione transferases (GSTs) are a superfamily of enzymes that play a vital functional role in the cellular detoxification process. They catalyze the conjugation of the thiol group of glutathione (GSH) to the electrophilic groups of a wide range o ...

    Glutathione transferases (GSTs) are a superfamily of enzymes that play a vital functional role in the cellular detoxification process. They catalyze the conjugation of the thiol group of glutathione (GSH) to the electrophilic groups of a wide range of hydrophobic substrates, leading to an easier removal of the latter from the cells. The kappa class is the least studied one among various classes within the superfamily. We report here the expression, purification, and crystal structure of human kappa class GST (hGSTK), which has been determined by the multiple-isomorphous replacement method and refined to 1.93 A resolution. The overall structure of hGSTK is similar to the recently reported structure of kappa class GST from rat mitochondrion. Each subunit of the dimeric hGSTK contains a thioredoxin (TRX)-like domain and a helical domain. A molecule of glutathione sulfinate, an oxidized product of GSH, is found to bind at the G site of each monomer. One oxygen atom of the sulfino group of GSF forms a hydrogen bond with the hydroxyl group of the catalytic residue Ser16. The TRX-like domain of hGSTK shares 19% sequence identity and structure similarity with human theta class GST, suggesting that the kappa class of GST is more closely related to the theta class enzyme within the GST superfamily. The structure of the TRX-like domain of hGSTK is also similar to that of glutathione peroxidase (GPx), implying an evolutionary relationship between GST and GPx.


    Organizational Affiliation

    State Key Laboratory of Bio-organic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 354 Fenglin Road, Shanghai 200032, PR China.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Glutathione S-transferase kappa 1AB226Homo sapiensMutation(s): 0 
Gene Names: GSTK1HDCMD47P
EC: 2.5.1.18
Find proteins for Q9Y2Q3 (Homo sapiens)
Explore Q9Y2Q3 
Go to UniProtKB:  Q9Y2Q3
NIH Common Fund Data Resources
PHAROS  Q9Y2Q3
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GSF
Query on GSF

Download CCD File 
A, B
L-GAMMA-GLUTAMYL-3-SULFINO-L-ALANYLGLYCINE
C10 H17 N3 O8 S
DMAPAHUEYHXRFI-WDSKDSINSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.182 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.275α = 90
b = 118.274β = 102.67
c = 52.591γ = 90
Software Package:
Software NamePurpose
CNSrefinement
MAR345data collection
AUTOMARdata reduction
SOLVEphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2005-02-28 
  • Released Date: 2005-11-15 
  • Deposition Author(s): Li, J., Xia, Z., Ding, J.

Revision History 

  • Version 1.0: 2005-11-15
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Refinement description
  • Version 1.4: 2017-12-20
    Changes: Database references