4L96

Structure of the complex between the F360L PPARgamma mutant and the ligand LT175 (space group I222)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.38 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.183 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural basis of the transactivation deficiency of the human PPAR gamma F360L mutant associated with familial partial lipodystrophy.

Lori, C.Pasquo, A.Montanari, R.Capelli, D.Consalvi, V.Chiaraluce, R.Cervoni, L.Loiodice, F.Laghezza, A.Aschi, M.Giorgi, A.Pochetti, G.

(2014) Acta Crystallogr.,Sect.D 70: 1965-1976

  • DOI: 10.1107/S1399004714009638
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The peroxisome proliferator-activated receptors (PPARs) are transcription factors that regulate glucose and lipid metabolism. The role of PPARs in several chronic diseases such as type 2 diabetes, obesity and atherosclerosis is well known and, for th ...

    The peroxisome proliferator-activated receptors (PPARs) are transcription factors that regulate glucose and lipid metabolism. The role of PPARs in several chronic diseases such as type 2 diabetes, obesity and atherosclerosis is well known and, for this reason, they are the targets of antidiabetic and hypolipidaemic drugs. In the last decade, some rare mutations in human PPARγ that might be associated with partial lipodystrophy, dyslipidaemia, insulin resistance and colon cancer have emerged. In particular, the F360L mutant of PPARγ (PPARγ2 residue 388), which is associated with familial partial lipodystrophy, significantly decreases basal transcriptional activity and impairs stimulation by synthetic ligands. To date, the structural reason for this defective behaviour is unclear. Therefore, the crystal structure of PPARγ F360L together with the partial agonist LT175 has been solved and the mutant has been characterized by circular-dichroism spectroscopy (CD) in order to compare its thermal stability with that of the wild-type receptor. The X-ray analysis showed that the mutation induces dramatic conformational changes in the C-terminal part of the receptor ligand-binding domain (LBD) owing to the loss of van der Waals interactions made by the Phe360 residue in the wild type and an important salt bridge made by Arg357, with consequent rearrangement of loop 11/12 and the activation function helix 12 (H12). The increased mobility of H12 makes the binding of co-activators in the hydrophobic cleft less efficient, thereby markedly lowering the transactivation activity. The spectroscopic analysis in solution and molecular-dynamics (MD) simulations provided results which were in agreement and consistent with the mutant conformational changes observed by X-ray analysis. Moreover, to evaluate the importance of the salt bridge made by Arg357, the crystal structure of the PPARγ R357A mutant in complex with the agonist rosiglitazone has been solved.


    Related Citations: 
    • Crystal structure of the peroxisome proliferator-activated receptor gamma (PPARgamma) ligand binding domain complexed with a novel partial agonist: a new region of the hydrophobic pocket could be exploited for drug design.
      Montanari, R.,Saccoccia, F.,Scotti, E.,Crestani, M.,Godio, C.,Gilardi, F.,Loiodice, F.,Fracchiolla, G.,Laghezza, A.,Tortorella, P.,Lavecchia, A.,Novellino, E.,Mazza, F.,Aschi, M.,Pochetti, G.
      (2008) J.Med.Chem. 51: 7768


    Organizational Affiliation

    Istituto di Cristallografia, CNR, Via Salaria, Km 29,300, Monterotondo Stazione, 00015 Roma, Italy.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Peroxisome proliferator-activated receptor gamma
A
275Homo sapiensMutation(s): 1 
Gene Names: PPARG (NR1C3)
Find proteins for P37231 (Homo sapiens)
Go to Gene View: PPARG
Go to UniProtKB:  P37231
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
LRG
Query on LRG

Download SDF File 
Download CCD File 
A
(2S)-2-(biphenyl-4-yloxy)-3-phenylpropanoic acid
C21 H18 O3
TZTPJJNNACUQQR-FQEVSTJZSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
LRGEC50: 480 - 560 nM (99) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.38 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.183 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 67.170α = 90.00
b = 112.000β = 90.00
c = 116.800γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
REFMACrefinement
HKL-2000data collection
AMoREphasing
CNSrefinement
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-06-25
    Type: Initial release
  • Version 1.1: 2016-11-23
    Type: Database references