6SSS

Crystal structure of Human Microsomal Glutathione S-Transferase 2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.221 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 3.1 of the entry. See complete history


Literature

Crystal structures of human MGST2 reveal synchronized conformational changes regulating catalysis.

Thulasingam, M.Orellana, L.Nji, E.Ahmad, S.Rinaldo-Matthis, A.Haeggstrom, J.Z.

(2021) Nat Commun 12: 1728-1728

  • DOI: https://doi.org/10.1038/s41467-021-21924-8
  • Primary Citation of Related Structures:  
    6SSR, 6SSS, 6SSU, 6SSW

  • PubMed Abstract: 

    Microsomal glutathione S-transferase 2 (MGST2) produces leukotriene C 4 , key for intracrine signaling of endoplasmic reticulum (ER) stress, oxidative DNA damage and cell death. MGST2 trimer restricts catalysis to only one out of three active sites at a time, but the molecular basis is unknown. Here, we present crystal structures of human MGST2 combined with biochemical and computational evidence for a concerted mechanism, involving local unfolding coupled to global conformational changes that regulate catalysis. Furthermore, synchronized changes in the biconical central pore modulate the hydrophobicity and control solvent influx to optimize reaction conditions at the active site. These unique mechanistic insights pertain to other, structurally related, drug targets.


  • Organizational Affiliation

    Department of Medical Biochemistry and Biophysics, Division of Chemistry II, Karolinska Institutet, Solnavägen 9, 171 65 Stockholm, Sweden. madhuranayaki.thulasingam@ki.se.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Microsomal glutathione S-transferase 2
A, B, C, D, E
A, B, C, D, E, F
153Homo sapiensMutation(s): 0 
Gene Names: MGST2GST2
EC: 2.5.1.18
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q99735 (Homo sapiens)
Explore Q99735 
Go to UniProtKB:  Q99735
PHAROS:  Q99735
GTEx:  ENSG00000085871 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ99735
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
M88
Query on M88

Download Ideal Coordinates CCD File 
J [auth B],
K [auth B],
L [auth B],
M [auth B],
Y [auth F]
1-(8Z-hexadecenoyl)-sn-glycerol
C19 H36 O4
CRXZGWVXXGFOLB-GIFJBRJJSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
G [auth A]
I [auth B]
N [auth C]
Q [auth D]
S [auth E]
G [auth A],
I [auth B],
N [auth C],
Q [auth D],
S [auth E],
X [auth F]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
P [auth C],
U [auth E]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
SCN
Query on SCN

Download Ideal Coordinates CCD File 
V [auth E]THIOCYANATE ION
C N S
ZMZDMBWJUHKJPS-UHFFFAOYSA-M
K
Query on K

Download Ideal Coordinates CCD File 
W [auth E]POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
H [auth A],
O [auth C],
R [auth D],
T [auth E],
Z [auth F]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.221 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.886α = 67.93
b = 72.162β = 86.71
c = 72.692γ = 86.86
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swedish Research CouncilSweden10350

Revision History  (Full details and data files)

  • Version 1.0: 2021-02-03
    Type: Initial release
  • Version 2.0: 2021-04-07
    Changes: Atomic model, Data collection, Database references
  • Version 3.0: 2023-09-27
    Changes: Atomic model, Data collection, Database references, Derived calculations, Refinement description, Source and taxonomy, Structure summary
  • Version 3.1: 2024-01-24
    Changes: Refinement description