A comprehensive structural and functional analysis of the ligand binding domain of the nuclear receptor superfamily reveals highly conserved signaling motifs and two distinct canonical forms through evolution

Abstract

Nuclear receptors (NRs) are transcriptional factors that play an essential role in all aspects of human development, metabolism and physiology. A prime example of a NR is the glucocorticoid receptor (GR). Structure‑wise, the GR is typical of the NR superfamily, while its signaling is a part of multiple physiological mechanisms. In this study, using the GR and the steroid hormone receptors as a basis, an analysis of the structure, function and evolution of the NR ligand binding domain was conducted, while a list of NR mutations was composed in order to examine the effects of the mutations on NR structure and function. The results proposed 7 conserved signaling motifs and identified the amino acid repeating pattern ‘LxxLL’ or ‘LLxxL’ in the ligand binding domains (LBDs) of the NRs. Phylogenetic analysis revealed 4 distinct monophyletic branches, and it proposed new evolutionary relations between the LBD of NRs. Furthermore, structural and functional comparisons through NR LBD structures and their corresponding ligands displayed two major canonical forms, one for the steroid hormone‑like cluster and another one for the thyroid hormone‑like cluster. Last but not least, a new sub‑cluster of estrogen receptor α with a specific canonical form has been identified. Although this sub‑cluster has 98% similarity in sequence level with all known ERα, shows more significant structural similarity with the ERβ members (RMSD <2Å) rather than the ERα. In particular, the Y537S mutation, which is very common in breast cancer, creates this new trans‑form of ERα'. ERα' is functionally and structurally more similar to ERβ, while still retaining some of its ERα characteristics. This new information may be of high importance in order to understand the signaling mechanisms underlying NRs and cancer.