3SZ1

Human PPAR gamma ligand binding domain in complex with luteolin and myristic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.207 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Mode of peroxisome proliferator-activated receptor gamma activation by luteolin.

Puhl, A.C.Bernardes, A.Silveira, R.L.Yuan, J.Campos, J.L.Saidemberg, D.M.Palma, M.S.Cvoro, A.Ayers, S.D.Webb, P.Reinach, P.S.Skaf, M.S.Polikarpov, I.

(2012) Mol.Pharmacol. 81: 788-799

  • DOI: 10.1124/mol.111.076216

  • PubMed Abstract: 
  • The peroxisome proliferator-activated receptor γ (PPARγ) is a target for treatment of type II diabetes and other conditions. PPARγ full agonists, such as thiazolidinediones (TZDs), are effective insulin sensitizers and anti-inflammatory agents, but t ...

    The peroxisome proliferator-activated receptor γ (PPARγ) is a target for treatment of type II diabetes and other conditions. PPARγ full agonists, such as thiazolidinediones (TZDs), are effective insulin sensitizers and anti-inflammatory agents, but their use is limited by adverse side effects. Luteolin is a flavonoid with anti-inflammatory actions that binds PPARγ but, unlike TZDs, does not promote adipocyte differentiation. However, previous reports suggested variously that luteolin is a PPARγ agonist or an antagonist. We show that luteolin exhibits weak partial agonist/antagonist activity in transfections, inhibits several PPARγ target genes in 3T3-L1 cells (LPL, ORL1, and CEBPα) and PPARγ-dependent adipogenesis, but activates GLUT4 to a similar degree as rosiglitazone, implying gene-specific partial agonism. The crystal structure of the PPARγ ligand-binding domain (LBD) reveals that luteolin occupies a buried ligand-binding pocket (LBP) but binds an inactive PPARγ LBD conformer and occupies a space near the β-sheet region far from the activation helix (H12), consistent with partial agonist/antagonist actions. A single myristic acid molecule simultaneously binds the LBP, suggesting that luteolin may cooperate with other ligands to bind PPARγ, and molecular dynamics simulations show that luteolin and myristic acid cooperate to stabilize the Ω-loop among H2', H3, and the β-sheet region. It is noteworthy that luteolin strongly suppresses hypertonicity-induced release of the pro-inflammatory interleukin-8 from human corneal epithelial cells and reverses reductions in transepithelial electrical resistance. This effect is PPARγ-dependent. We propose that activities of luteolin are related to its singular binding mode, that anti-inflammatory activity does not require H12 stabilization, and that our structure can be useful in developing safe selective PPARγ modulators.


    Organizational Affiliation

    Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, SP, Brazil.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Peroxisome proliferator-activated receptor gamma
A, B
278Homo 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 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MYR
Query on MYR

Download SDF File 
Download CCD File 
B
MYRISTIC ACID
C14 H28 O2
TUNFSRHWOTWDNC-UHFFFAOYSA-N
 Ligand Interaction
KNA
Query on KNA

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Download CCD File 
A
nonanoic acid
C9 H18 O2
FBUKVWPVBMHYJY-UHFFFAOYSA-N
 Ligand Interaction
LU2
Query on LU2

Download SDF File 
Download CCD File 
B
2-(3,4-dihydroxyphenyl)-5,7-dihydroxy-4H-chromen-4-one
Luteolin
C15 H10 O6
IQPNAANSBPBGFQ-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
LU2EC50: 2300 nM (98) BINDINGDB
LU2IC50: 21800 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.207 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 92.260α = 90.00
b = 62.150β = 101.67
c = 119.130γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
PDB_EXTRACTdata extraction
SCALAdata scaling
MAR345dtbdata collection
PHENIXrefinement
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-03-21
    Type: Initial release
  • Version 1.1: 2013-06-19
    Type: Database references