Structural determinants of the agonist-independent association of human peroxisome proliferator-activated receptors with coactivators

Lipid homeostasis is controlled by various nuclear receptors (NRs), including the peroxisome proliferator-activated receptors (PPAR alpha, delta, and gamma), which sense lipid levels and regulate their metabolism. Here we demonstrate that human PPARs have a high basal activity and show ligand-independent coactivator (CoA) association comparable with the NR constitutive androstane receptor. Using PPAR gamma as an example, we found that four different amino acid groups contribute to the ligand-independent stabilization of helix 12 of the PPAR ligand-binding domain. These are: (i) Lys(329) and Glu(499), mediating a charge clamp-type stabilization of helix 12 via a CoA bridge; (ii) Glu(352), Arg(425), and Tyr(505), directly stabilizing the helix via salt bridges and hydrogen bonds; (iii) Lys(347) and Asp(503), interacting with each other as well as contacting the CoA; and (iv) His(351), Tyr(355), His(477), and Tyr(501), forming a hydrogen bond network. These amino acids are highly conserved within the PPAR subfamily, suggesting that the same mechanism may apply for all three PPARs. Phylogenetic trees of helix 12 amino acid and nucleotide sequences of all crystallized NRs and all human NRs, respectively, indicated a close relationship of PPARs with constitutive androstane receptor and other constitutive active members of the NR superfamily. Taking together, the ligand-independent tight control of the position of the PPAR helix 12 provides an effective alternative for establishing an interaction with CoA proteins. This leads to high basal activity of PPARs and provides an additional view on PPAR signaling.