2ZK1

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

Summary for 2ZK1

• Entry DOI: 10.2210/pdb2zk1/pdb
• Related: 2ZK0 2ZK2 2ZK3 2ZK4 2ZK5 2ZK6
• Descriptor: Peroxisome proliferator-activated receptor gamma, (5E,14E)-11-oxoprosta-5,9,12,14-tetraen-1-oic acid (3 entities in total)
• Functional Keywords: anti parallel helix sandwich, activator, alternative splicing, diabetes mellitus, disease mutation, dna-binding, metal-binding, nucleus, obesity, phosphoprotein, polymorphism, receptor, transcription, transcription regulation, zinc, zinc-finger
• Biological source: Homo sapiens (Human)
• Cellular location: Nucleus: P37231
• Total number of polymer chains: 2
• Total formula weight: 65694.17

Authors

Waku, T.,Shiraki, T.,Oyama, T.,Fujimoto, Y.,Morikawa, K. (deposition date: 2008-03-12, release date: 2009-02-24, Last modification date: 2024-11-20)

Primary citation

Waku, T.,Shiraki, T.,Oyama, T.,Fujimoto, Y.,Maebara, K.,Kamiya, N.,Jingami, H.,Morikawa, K.
Structural insight into PPARgamma activation through covalent modification with endogenous fatty acids
J.Mol.Biol., 385:188-199, 2009

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 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.

PubMed: 18977231
DOI: 10.1016/j.jmb.2008.10.039

Experimental method

X-RAY DIFFRACTION (2.61 Å)