7RKA | pdb_00007rka

Crystal structure analysis of Colorado potato beetle glutathione-S transferase LdGSTu1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 
    0.182 (Depositor), 0.184 (DCC) 
  • R-Value Work: 
    0.159 (Depositor) 
  • R-Value Observed: 
    0.160 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

Structural and Functional Characterization of One Unclassified Glutathione S-Transferase in Xenobiotic Adaptation of Leptinotarsa decemlineata.

Liu, Y.Moural, T.Koirala B K, S.Hernandez, J.Shen, Z.Alyokhin, A.Zhu, F.

(2021) Int J Mol Sci 22

  • DOI: https://doi.org/10.3390/ijms222111921
  • Primary Citation Related Structures: 
    7RKA

  • PubMed Abstract: 

    Arthropod Glutathione S-transferases (GSTs) constitute a large family of multifunctional enzymes that are mainly associated with xenobiotic or stress adaptation. GST-mediated xenobiotic adaptation takes place through direct metabolism or sequestration of xenobiotics, and/or indirectly by providing protection against oxidative stress induced by xenobiotic exposure. To date, the roles of GSTs in xenobiotic adaptation in the Colorado potato beetle (CPB), a notorious agricultural pest of plants within Solanaceae, have not been well studied. Here, we functionally expressed and characterized an unclassified-class GST, LdGSTu1. The three-dimensional structure of the LdGSTu1 was solved with a resolution up to 1.8 Å by X-ray crystallography. The signature motif VSDGPPSL was identified in the "G-site", and it contains the catalytically active residue Ser14. Recombinant LdGSTu1 was used to determine enzyme activity and kinetic parameters using 1-chloro-2, 4-dinitrobenzene (CDNB), GSH, p-nitrophenyl acetate (PNA) as substrates. The enzyme kinetic parameters and enzyme-substrate interaction studies demonstrated that LdGSTu1 could catalyze the conjugation of GSH to both CDNB and PNA, with a higher turnover number for CDNB than PNA. The LdGSTu1 enzyme inhibition assays demonstrated that the enzymatic conjugation of GSH to CDNB was inhibited by multiple pesticides, suggesting a potential function of LdGSTu1 in xenobiotic adaptation.


  • Organizational Affiliation
    • Department of Entomology, Pennsylvania State University, University Park, PA 16802, USA.

Macromolecule Content 

  • Total Structure Weight: 53.21 kDa 
  • Atom Count: 3,753 
  • Modeled Residue Count: 422 
  • Deposited Residue Count: 460 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
glutathione S-transferase u1
A, B
230Leptinotarsa decemlineataMutation(s): 0 
EC: 2.5.1.18
UniProt
Find proteins for A0A1P8PEY0 (Leptinotarsa decemlineata)
Explore A0A1P8PEY0 
Go to UniProtKB:  A0A1P8PEY0
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1P8PEY0
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GSH
(Subject of Investigation/LOI)

Query on GSH



Download:Ideal Coordinates CCD File
C [auth A]Glutathione
C10 H17 N3 O6 S
RWSXRVCMGQZWBV-WDSKDSINSA-N

Biologically Interesting Molecules (External Reference) 

1 Unique

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free:  0.182 (Depositor), 0.184 (DCC) 
  • R-Value Work:  0.159 (Depositor) 
  • R-Value Observed: 0.160 (Depositor) 
Space Group: P 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.452α = 90
b = 46.44β = 91.35
c = 87.192γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
United States Department of Agriculture (USDA)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2022-07-06
    Type: Initial release
  • Version 1.1: 2023-10-18
    Changes: Data collection, Refinement description