FC0055
Peroxisome proliferator-activated receptor gamma (PPAR-γ)  -  DNA

Biological function
The peroxisome proliferator-activated receptors (PPARs) are nuclear receptors. These multi-domain transcription factors bind to DNA elements from which they regulate gene expression.

Domain organization/sequence features
PPAR-γ forms heterodimers with the retinoid X receptor (RXR). The PPAR-c ligand binding domain (LBD) cooperates with both DNA-binding domains (DBDs) to enhance response-element binding. The A/B segment of PPAR-γ is a potent transcriptional activator, contains a phosphorylation site and can interact with other proteins. The A/B segments are highly dynamic, lacking folded substructures despite their gene-activation properties.

Structural evidence
However, the A/B segments could not be visualized in any of the three complexes, presumably because of their high mobility. The dynamic properties were examined using amide hydrogen/ deuterium exchange mass spectrometry (H/D-Ex). In all samples, the most rapidly exchanging region was the A/B portion. Sequence alignments further demonstrate that these receptors lack significant stretches of hydrophobic residues and/or a meaningful level of amino-acid conservation in their A/B regions. The A/B domains are intrinsically flexible as they were not observable in the crystal structure. These receptor portions are also not conserved in sequence. The intrinsic flexibility in this receptor portion of PPAR-γ was independently verified by H/D- Ex. Three distinct PPAR-c ligands did not substantially impact the ordering of the A/B regions.

Biochemical evidence
PPAR-γ LBD interface with RXR-a DBD contributes to the DNA binding of the complex. Phe 347 is near the surface of the LBD, and distant from both the ligand-binding pocket and coactivator docking sites and DNA binding assays show that the Phe347Ala-mutant PPAR-γ negatively affects PPRE binding.

Structure/Mechanism
Phe347 positioned on the surface of a receptor LBD can strongly influence DNA binding, confirming the ability of the PPAR-γ LBD, through domain–domain interactions, to affect the receptors’ DNA-binding properties.

Mechanism category
competitive binding

Posttranslational modification
The phosphorylation site within the A/B segment and can interact with other receptor domains or regulatory proteins.

Significance
The LBD can also have an important function in modulating DNA binding depending on the manner in which the complex is organized. The fuzzy A/B segment dynamically modulates the interactions between the two DBDs, which could provide selective gene modulation properties by imparting a graded set of response element affinities.