6SSR | pdb_00006ssr

Crystal structure of Human Microsomal Glutathione S-Transferase 2 at 3.8 Angstroms resolution

• PDB DOI: https://doi.org/10.2210/pdb6SSR/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Komagataella pastoris
• Mutation(s): No 
• Membrane Protein: Yes  OPMPDBTMMemProtMDmpstruc


• Deposited: 2019-09-09 Released: 2021-02-03 
• Deposition Author(s): Thulasingam, M., Nji, E., Rinaldo-Matthis, A., Haeggstrom, J.Z.
• Funding Organization(s): Swedish Research Council

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.80 Å
• R-Value Free: 
  0.337 (Depositor), 0.342 (DCC) 
• R-Value Work: 
  0.305 (Depositor), 0.312 (DCC) 
• R-Value Observed: 
  0.307 (Depositor) 

Starting Model: experimental

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

• PubMed: 33741927 
• DOI: https://doi.org/10.1038/s41467-021-21924-8
• Primary Citation 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.

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Organizational Affiliation: 
• Department of Medical Biochemistry and Biophysics, Division of Chemistry II, Karolinska Institutet, Solnavägen 9, 171 65 Stockholm, Sweden. [e-mail].
Department of Biochemistry and Biophysics, Stockholm University, Svante Arrhenius väg 16, 106 91 Stockholm, Sweden.
Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden.
BioStruct-Africa, Stockholm, Sweden.
Department of Medical Biochemistry and Biophysics, Division of Chemistry II, Karolinska Institutet, Solnavägen 9, 171 65 Stockholm, Sweden.
Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden.
Department of Medical Biochemistry and Biophysics, Division of Chemistry II, Karolinska Institutet, Solnavägen 9, 171 65 Stockholm, Sweden. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: native gel electrophoresis

Macromolecule Content 

• Total Structure Weight: 52.4 kDa 
• Atom Count: 3,148 
• Modeled Residue Count: 401 
• Deposited Residue Count: 459 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Microsomal glutathione S-transferase 2	A, B, C	153	Homo sapiens	Mutation(s): 0  Gene Names: MGST2, GST2 EC: 2.5.1.18 (PDB Primary Data), 1.11.1 (UniProt), 4.4.1.20 (UniProt) 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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.80 Å
• R-Value Free:  0.337 (Depositor), 0.342 (DCC) 
• R-Value Work:  0.305 (Depositor), 0.312 (DCC) 
• R-Value Observed: 0.307 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 109.942	α = 90
b = 151.149	β = 90
c = 70.251	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-02-03 
Deposition Author(s): Thulasingam, M., Nji, E., Rinaldo-Matthis, A., Haeggstrom, J.Z.

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Funding Organization	Location	Grant Number
Swedish Research Council	Sweden	10350

Revision History  

• Version 1.0: 2021-02-03
  Type: Initial release
  
• Version 1.1: 2021-04-07
  Changes: Data collection, Database references
• Version 1.2: 2024-01-24
  Changes: Data collection, Database references, Refinement description