5I9K

The structure of microsomal glutathione transferase 1


Experimental Data Snapshot

  • Method: ELECTRON CRYSTALLOGRAPHY
  • Resolution: 3.50 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.270 
  • R-Value Observed: 0.271 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Dead-end complex, lipid interactions and catalytic mechanism of microsomal glutathione transferase 1, an electron crystallography and mutagenesis investigation.

Kuang, Q.Purhonen, P.Alander, J.Svensson, R.Hoogland, V.Winerdal, J.Spahiu, L.Ottosson-Wadlund, A.Jegerschold, C.Morgenstern, R.Hebert, H.

(2017) Sci Rep 7: 7897-7897

  • DOI: 10.1038/s41598-017-07912-3
  • Primary Citation of Related Structures:  
    5I9K, 5IA9

  • PubMed Abstract: 
  • Microsomal glutathione transferase 1 (MGST1) is a detoxification enzyme belonging to the Membrane Associated Proteins in Eicosanoid and Glutathione Metabolism (MAPEG) superfamily. Here we have used electron crystallography of two-dimensional crystals in order to determine an atomic model of rat MGST1 in a lipid environment ...

    Microsomal glutathione transferase 1 (MGST1) is a detoxification enzyme belonging to the Membrane Associated Proteins in Eicosanoid and Glutathione Metabolism (MAPEG) superfamily. Here we have used electron crystallography of two-dimensional crystals in order to determine an atomic model of rat MGST1 in a lipid environment. The model comprises 123 of the 155 amino acid residues, two structured phospholipid molecules, two aliphatic chains and one glutathione (GSH) molecule. The functional unit is a homotrimer centered on the crystallographic three-fold axes of the unit cell. The GSH substrate binds in an extended conformation at the interface between two subunits of the trimer supported by new in vitro mutagenesis data. Mutation of Arginine 130 to alanine resulted in complete loss of activity consistent with a role for Arginine 130 in stabilizing the strongly nucleophilic GSH thiolate required for catalysis. Based on the new model and an electron diffraction data set from crystals soaked with trinitrobenzene, that forms a dead-end Meisenheimer complex with GSH, a difference map was calculated. The map reveals side chain movements opening a cavity that defines the second substrate site.


    Organizational Affiliation

    Department of Biosciences and Nutrition, Karolinska Institutet and School of Technology and Health, Royal Institute of Technology, SE-141 83, Huddinge, Sweden. Hans.Hebert@ki.se.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Microsomal glutathione S-transferase 1A155Rattus norvegicusMutation(s): 0 
Gene Names: Mgst1Gst12
EC: 2.5.1.18
Membrane Entity: Yes 
UniProt
Find proteins for P08011 (Rattus norvegicus)
Explore P08011 
Go to UniProtKB:  P08011
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PC1 (Subject of Investigation/LOI)
Query on PC1

Download Ideal Coordinates CCD File 
C [auth A], D [auth A]1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
C44 H88 N O8 P
NRJAVPSFFCBXDT-HUESYALOSA-N
 Ligand Interaction
GSH (Subject of Investigation/LOI)
Query on GSH

Download Ideal Coordinates CCD File 
B [auth A]GLUTATHIONE
C10 H17 N3 O6 S
RWSXRVCMGQZWBV-WDSKDSINSA-N
 Ligand Interaction
PLM (Subject of Investigation/LOI)
Query on PLM

Download Ideal Coordinates CCD File 
E [auth A], F [auth A]PALMITIC ACID
C16 H32 O2
IPCSVZSSVZVIGE-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON CRYSTALLOGRAPHY
  • Resolution: 3.50 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.270 
  • R-Value Observed: 0.271 
  • Space Group: P 6
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.8α = 90
b = 81.8β = 90
c = 100γ = 120
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
VRSweden--
CIMEDSweden--

Revision History  (Full details and data files)

  • Version 1.0: 2017-07-12
    Type: Initial release
  • Version 1.1: 2017-08-23
    Changes: Data collection, Database references