7OPY

Camel GSTM1-1 in complex with S-(p-nitrobenzyl)glutathione


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.195 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

Structural and Functional Characterization of Camelus dromedarius Glutathione Transferase M1-1.

Perperopoulou, F.Poudel, N.Papageorgiou, A.C.Ataya, F.S.Labrou, N.E.

(2022) Life (Basel) 12

  • DOI: https://doi.org/10.3390/life12010106
  • Primary Citation of Related Structures:  
    7OPY, 7OPZ

  • PubMed Abstract: 

    Glutathione transferases (GSTs; EC. 2.5.1.18) are a large family of multifunctional enzymes that play crucial roles in the metabolism and inactivation of a broad range of xenobiotic compounds. In the present work, we report the kinetic and structural characterization of the isoenzyme GSTM1-1 from Camelus dromedarius ( Cd GSTM1-1). The Cd GSΤM1-1 was expressed in E. coli BL21 (DE3) and was purified by affinity chromatography. Kinetics analysis showed that the enzyme displays a relative narrow substrate specificity and restricted ability to bind xenobiotic compounds. The crystal structures of Cd GSΤM1-1 were determined by X-ray crystallography in complex with the substrate (GSH) or the reaction product (S-p-nitrobenzyl-GSH), providing snapshots of the induced-fit catalytic mechanism. The thermodynamic stability of Cd GSTM1-1 was investigated using differential scanning fluorimetry (DSF) in the absence and in presence of GSH and S-p-nitrobenzyl-GSH and revealed that the enzyme's structure is significantly stabilized by its ligands. The results of the present study advance the understanding of camelid GST detoxification mechanisms and their contribution to abiotic stress adaptation in harsh desert conditions.


  • Organizational Affiliation

    Laboratory of Enzyme Technology, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, 75 Iera Odos Street, GR-11855 Athens, Greece.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glutathione transferaseA [auth F],
B [auth A],
C [auth B],
D [auth C]
218Camelus dromedariusMutation(s): 0 
Gene Names: Cadr_000010866
EC: 2.5.1.18
UniProt
Find proteins for G9B5E4 (Camelus dromedarius)
Explore G9B5E4 
Go to UniProtKB:  G9B5E4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG9B5E4
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GTB (Subject of Investigation/LOI)
Query on GTB

Download Ideal Coordinates CCD File 
E [auth F],
I [auth A],
K [auth B],
M [auth C]
S-(P-NITROBENZYL)GLUTATHIONE
C17 H22 N4 O8 S
OAWORKDPTSAMBZ-STQMWFEESA-N
FMT
Query on FMT

Download Ideal Coordinates CCD File 
H [auth F]FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
F,
G [auth F],
J [auth A],
L [auth B]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
CSO
Query on CSO
A [auth F],
B [auth A],
C [auth B],
D [auth C]
L-PEPTIDE LINKINGC3 H7 N O3 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.195 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.388α = 90
b = 177.376β = 115.002
c = 59.42γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
MrBUMPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2022-02-16
    Type: Initial release
  • Version 1.1: 2024-01-31
    Changes: Data collection, Refinement description
  • Version 1.2: 2024-10-23
    Changes: Structure summary