5JCW

Crystal Structure of hGSTP1-1 with Glutathione Adduct of Phenethyl Isothiocyanate

• PDB DOI: https://doi.org/10.2210/pdb5JCW/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-04-15 Released: 2016-10-12 
• Deposition Author(s): Kumari, V., Ji, X.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.193 
• R-Value Work: 0.154 
• R-Value Observed: 0.155 

Starting Model: experimental

Literature

Irreversible Inhibition of Glutathione S-Transferase by Phenethyl Isothiocyanate (PEITC), a Dietary Cancer Chemopreventive Phytochemical.

Kumari, V., Dyba, M.A., Holland, R.J., Liang, Y.H., Singh, S.V., Ji, X.

(2016) PLoS One 11: e0163821-e0163821

• PubMed: 27684484 
• DOI: https://doi.org/10.1371/journal.pone.0163821
• Primary Citation of Related Structures:  
  5JCU, 5JCW


• PubMed Abstract: 
  

  Dietary isothiocyanates abundant as glucosinolate precursors in many edible cruciferous vegetables are effective for prevention of cancer in chemically-induced and transgenic rodent models. Some of these agents, including phenethyl isothiocyanate (PEITC), have already advanced to clinical investigations. The primary route of isothiocyanate metabolism is its conjugation with glutathione (GSH), a reaction catalyzed by glutathione S-transferase (GST). The pi class GST of subunit type 1 (hGSTP1) is much more effective than the alpha class GST of subunit type 1 (hGSTA1) in catalyzing the conjugation. Here, we report the crystal structures of hGSTP1 and hGSTA1 each in complex with the GSH adduct of PEITC. We find that PEITC also covalently modifies the cysteine side chains of GST, which irreversibly inhibits enzymatic activity.

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Organizational Affiliation: 

Center for Cancer Research, National Cancer Institute, Frederick, Maryland, United States of America.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 48.68 kDa 
• Atom Count: 3,894 
• Modelled Residue Count: 418 
• Deposited Residue Count: 420 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutathione S-transferase P	A, B	210	Homo sapiens	Mutation(s): 0  Gene Names: GSTP1, FAEES3, GST3 EC: 2.5.1.18
UniProt & NIH Common Fund Data Resources
Find proteins for P09211 (Homo sapiens) Explore P09211  Go to UniProtKB:  P09211
PHAROS:  P09211 GTEx:  ENSG00000084207

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GVX	C [auth A], K [auth B]	L-gamma-glutamyl-S-[(2-phenylethyl)carbamothioyl]-L-cysteinylglycine C19 H26 N4 O6 S2 WSGBVCNCZSZCGE-KBPBESRZSA-N
GSH	J [auth A]	GLUTATHIONE C10 H17 N3 O6 S RWSXRVCMGQZWBV-WDSKDSINSA-N
MPD	D [auth A], L [auth B]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N
ACT	E [auth A], M [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
CA	F [auth A], G [auth A], H [auth A], I [auth A], N [auth B], O [auth B], P [auth B], Q [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.193 
• R-Value Work: 0.154 
• R-Value Observed: 0.155 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.365	α = 90
b = 88.943	β = 97.85
c = 69.483	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
DENZO	data reduction
SCALEPACK	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-10-12 
Deposition Author(s): Kumari, V., Ji, X.

Revision History  

• Version 1.0: 2016-10-12
  Type: Initial release
  
• Version 1.1: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Structure summary
• Version 1.2: 2023-09-27
  Changes: Refinement description