2ZK2

Human peroxisome proliferator-activated receptor gamma ligand binding domain complexed with glutathion conjugated 15-deoxy-delta12,14-prostaglandin J2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.26 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.247 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural insight into PPARgamma activation through covalent modification with endogenous fatty acids

Waku, T.Shiraki, T.Oyama, T.Fujimoto, Y.Maebara, K.Kamiya, N.Jingami, H.Morikawa, K.

(2009) J.Mol.Biol. 385: 188-199

  • DOI: 10.1016/j.jmb.2008.10.039
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Peroxisome proliferator-activated receptor (PPAR) gamma is a nuclear receptor that regulates lipid homeostasis, and several fatty acid metabolites have been identified as PPARgamma ligands. Here, we present four crystal structures of the PPARgamma li ...

    Peroxisome proliferator-activated receptor (PPAR) gamma is a nuclear receptor that regulates lipid homeostasis, and several fatty acid metabolites have been identified as PPARgamma ligands. Here, we present four crystal structures of the PPARgamma ligand binding domain (LBD) covalently bound to endogenous fatty acids via a unique cysteine, which is reportedly critical for receptor activation. The structure analyses of the LBD complexed with 15-deoxy-Delta(12,14)-prostaglandin J(2) (15d-PGJ(2)) revealed that the covalent binding of 15d-PGJ(2) induced conformational changes in the loop region following helix H2', and rearrangements of the side-chain network around the created covalent bond in the LBD. Point mutations of these repositioned residues on the loop and helix H3 almost completely abolished PPARgamma activation by 15d-PGJ(2), indicating that the observed structural alteration may be crucial for PPARgamma activation by the endogenous fatty acid. To address the issue of partial agonism of endogenous PPARgamma ligands, we took advantage of a series of oxidized eicosatetraenoic acids (oxoETEs) as covalently bound ligands to PPARgamma. Despite similar structural and chemical properties, these fatty acids exhibited distinct degrees of transcriptional activity. Crystallographic studies, using two of the oxoETE/PPARgamma LBD complexes, revealed that transcriptional strength of each oxoETE is associated with the difference in the loop conformation, rather than the interaction between each ligand and helix H12. These results suggest that the loop conformation may be responsible for the modulation of PPARgamma activity. Based on these results, we identified novel agonists covalently bound to PPARgamma by in silico screening and a cell-based assay. Our crystallographic study of LBD complexed with nitro-233 demonstrated that the expected covalent bond is indeed formed between this newly identified agonist and the cysteine. This study presents the structural basis for the activation and modulation mechanism of PPARgamma through covalent modification with endogenous fatty acids.


    Organizational Affiliation

    Takara Bio Endowed Division, Department of Biomolecular Recognition, Institute for Protein Research, Osaka University, Open Laboratories of Advanced Bioscience and Biotechnology, Suita, Osaka, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Peroxisome proliferator-activated receptor gamma
A, B
286Homo sapiensMutation(s): 0 
Gene Names: PPARG (NR1C3)
Find proteins for P37231 (Homo sapiens)
Go to Gene View: PPARG
Go to UniProtKB:  P37231
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PTG
Query on PTG

Download SDF File 
Download CCD File 
A
(5E,14E)-11-oxoprosta-5,9,12,14-tetraen-1-oic acid
15-deoxy-delta(12,14)-prostaglandin J2
C20 H28 O3
VHRUMKCAEVRUBK-XOVNXQNQSA-N
 Ligand Interaction
GSH
Query on GSH

Download SDF File 
Download CCD File 
A
GLUTATHIONE
C10 H17 N3 O6 S
RWSXRVCMGQZWBV-WDSKDSINSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.26 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.247 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 93.381α = 90.00
b = 61.347β = 103.02
c = 118.687γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
CNSphasing
HKL-2000data reduction
HKL-2000data collection
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-02-24
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance