9IWN

X-ray structure of human PPARalpha ligand binding domain-intrinsic fatty acid (E. coli origin)-PGC1alpha coactivator peptide co-crystals obtained by cross-seeding

Summary for 9IWN

• Entry DOI: 10.2210/pdb9iwn/pdb
• Descriptor: Peroxisome proliferator-activated receptor alpha, Peroxisome proliferator-activated receptor gamma coactivator 1-alpha, PALMITIC ACID, ... (5 entities in total)
• Functional Keywords: nuclear receptor, protein-ligand complex, ppar, coactivator, pgc1a, transcription
• Biological source: Homo sapiens (human); More
• Total number of polymer chains: 2
• Total formula weight: 32857.54

Authors

Kamata, S.,Honda, A.,Yashiro, S.,Komori, Y.,Shimamura, A.,Hosoda, A.,Oyama, T.,Ishii, I. (deposition date: 2024-07-25, release date: 2025-05-07)

Primary citation

Kamata, S.,Honda, A.,Yashiro, S.,Kaneko, C.,Komori, Y.,Shimamura, A.,Masuda, R.,Oyama, T.,Ishii, I.
Competitive Ligand-Induced Recruitment of Coactivators to Specific PPAR alpha / delta / gamma Ligand-Binding Domains Revealed by Dual-Emission FRET and X-Ray Diffraction of Cocrystals.
Antioxidants, 14:-, 2025

PubMed Abstract: Peroxisome proliferator-activated receptors (PPARs), composed of the α/δ/γ subtypes, are ligand-activated nuclear receptors/transcription factors that sense endogenous fatty acids or therapeutic drugs to regulate lipid/glucose metabolism and oxidative stress. PPAR forms a multiprotein complex with a retinoid X receptor and corepressor complex in an unliganded/inactive state, and ligand binding induces the replacement of the corepressor complex with the coactivator complex to initiate the transcription of various genes, including the metabolic and antioxidant ones. We investigated the processes by which the corepressor is replaced with the coactivator or in which two coactivators compete for the PPARα/δ/γ-ligand-binding domains (LBDs) using single- and dual-emission fluorescence resonance energy transfer (FRET) assays. Single-FRET revealed that the respective PPARα/δ/γ-selective agonists (pemafibrate, seladelpar, and pioglitazone) induced the dissociation of the two corepressor peptides, NCoR1 and NCoR2, from the PPARα/δ/γ-LBDs and the recruitment of the two coactivator peptides, CBP and TRAP220. Meanwhile, dual-FRET demonstrated that these processes are simultaneous and that the four coactivator peptides, CBP, TRAP220, PGC1α, and SRC1, were competitively recruited to the PPARα/δ/γ-LBDs with different preferences upon ligand activation. Furthermore, the five newly obtained cocrystal structures using X-ray diffraction, PPARα-LBDs-NCoR2/CBP/TRAP220/PGC1α and PPARγ-LBD-NCoR2, were co-analyzed with those from our previous studies. This illustrates that these coactivators bound to the same PPARα-LBD loci via their consensus LXXLL motifs in the liganded state; that NCoR1/NCoR2 corepressors bound to the same loci via the IXXXL sequences within their consensus LXXXIXXXL motifs in the unliganded state; and that ligand activation induced AF-2 helix 12 formation that interfered with corepressor binding and created a binding space for the coactivator. These PPARα/γ-related biochemical and physicochemical findings highlight the coregulator dynamics on limited PPARα/δ/γ-LBDs loci.

PubMed: 40298866
DOI: 10.3390/antiox14040494

Experimental method

X-RAY DIFFRACTION (1.59 Å)