Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 47.98 kDa 
• Atom Count: 4117 
• Modelled Residue Count: 417 
• Deposited Residue Count: 418 
• Unique protein chains: 1

5J41

Glutathione S-transferase bound with hydrolyzed Piperlongumine

• PDB DOI: 10.2210/pdb5J41/pdb

• Classification: transferase/transferase inhibitor
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-03-31 Released: 2016-11-30 
• Deposition Author(s): Harshbarger, W., Gondi, S., Ficarro, S., Hunter, J., Udayakumar, D., Gurbani, D., Marto, J., Westover, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.19 Å
• R-Value Free: 0.186 
• R-Value Work: 0.163 
• R-Value Observed: 0.164 

Literature

Structural and Biochemical Analyses Reveal the Mechanism of Glutathione S-Transferase Pi 1 Inhibition by the Anti-cancer Compound Piperlongumine.

Harshbarger, W., Gondi, S., Ficarro, S.B., Hunter, J., Udayakumar, D., Gurbani, D., Singer, W.D., Liu, Y., Li, L., Marto, J.A., Westover, K.D.

(2017) J Biol Chem 292: 112-120

• PubMed: 27872191 
• DOI: 10.1074/jbc.M116.750299
• Primary Citation of Related Structures:  
  5J41


• PubMed Abstract: 
  

Glutathione S-transferase pi 1 (GSTP1) is frequently overexpressed in cancerous tumors and is a putative target of the plant compound piperlongumine (PL), which contains two reactive olefins and inhibits proliferation in cancer cells but not normal cells. PL exposure of cancer cells results in increased reactive oxygen species and decreased GSH. These data in tandem with other information led to the conclusion that PL inhibits GSTP1, which forms covalent bonds between GSH and various electrophilic compounds, through covalent adduct formation at the C7-C8 olefin of PL, whereas the C2-C3 olefin of PL was postulated to react with GSH. However, direct evidence for this mechanism has been lacking. To investigate, we solved the X-ray crystal structure of GSTP1 bound to PL and GSH at 1.1 Å resolution to rationalize previously reported structure activity relationship studies. Surprisingly, the structure showed that a hydrolysis product of PL (hPL) was conjugated to glutathione at the C7-C8 olefin, and this complex was bound to the active site of GSTP1; no covalent bond formation between hPL and GSTP1 was observed. Mass spectrometry (MS) analysis of the reactions between PL and GSTP1 confirmed that PL does not label GSTP1. Moreover, MS data also indicated that nucleophilic attack on PL at the C2-C3 olefin led to PL hydrolysis. Although hPL inhibits GSTP1 enzymatic activity in vitro, treatment of cells susceptible to PL with hPL did not have significant anti-proliferative effects, suggesting that hPL is not membrane-permeable. Altogether, our data suggest a model wherein PL is a prodrug whose intracellular hydrolysis initiates the formation of the hPL-GSH conjugate, which blocks the active site of and inhibits GSTP1 and thereby cancer cell proliferation.

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Organizational Affiliation: 

From the Departments of Biochemistry and Radiation Oncology, The University of Texas Southwestern Medical Center, Dallas, Texas 75390 and [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutathione S-transferase P	A, B	209	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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GSH	D [auth A], G [auth B]	GLUTATHIONE C10 H17 N3 O6 S RWSXRVCMGQZWBV-WDSKDSINSA-N
3LF	C [auth A], F [auth B]	3-(3,4,5-trimethoxyphenyl)propanoic acid C12 H16 O5 ZCYXGVJUZBKJAI-UHFFFAOYSA-N
MES	E [auth A], H [auth B]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.19 Å
• R-Value Free: 0.186 
• R-Value Work: 0.163 
• R-Value Observed: 0.164 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.495	α = 90
b = 89.458	β = 98.235
c = 69.001	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2016-03-31 
• Released Date: 2016-11-30 
Deposition Author(s): Harshbarger, W., Gondi, S., Ficarro, S., Hunter, J., Udayakumar, D., Gurbani, D., Marto, J., Westover, K.

Revision History  

• Version 1.0: 2016-11-30
  Type: Initial release
  
• Version 1.1: 2016-12-21
  Changes: Database references
• Version 1.2: 2017-01-18
  Changes: Database references