The Three-dimensional Structure of the Liver X Receptor β Reveals a Flexible Ligand-binding Pocket That Can Accommodate Fundamentally Different Ligands

Abstract

The structures of the liver X receptor LXR␤ (NR1H2) have been determined in complexes with two synthetic ligands, T0901317 and GW3965, to 2.1 and 2.4 Å, respectively. Together with its isoform LXR␣ (NR1H3) it regulates target genes involved in metabolism and transport of cholesterol and fatty acids. The two LXR␤ structures reveal a flexible ligand-binding pocket that can adjust to accommodate fundamentally different ligands. The ligand-binding pocket is hydrophobic but with polar or charged residues at the two ends of the cavity. T0901317 takes advantage of this by binding to His-435 close to H12 while GW3965 orients itself with its charged group in the opposite direction. Both ligands induce a fixed "agonist conformation" of helix H12 (also called the AF-2 domain), resulting in a transcriptionally active receptor.Liver X receptors (LXR) 1 are members of the superfamily of nuclear receptors. These transcription factors regulate target genes through a dynamic series of interactions with specific DNA response elements as well as transcriptional coregulators. The binding of ligand has profound effects on these interactions and has the potential to trigger both gene activation and, in some cases, gene silencing. There are 48 sequence-related nuclear receptors in humans and the family comprises receptors that recognize hormones, both steroidal and non-steroidal, but also receptors responding to metabolic intermediates and to xenobiotics. There are also a number of so-called orphan receptors where the natural ligand is unknown. Some of the receptors show a very specific and high affinity ligand binding, like the thyroid hormone receptors, whereas others have a substantially lower affinity for their ligands and are less discriminating in their ligand selectivity. Like many of the other nonsteroid hormone receptors, LXR functions as a heterodimer with the retinoid X receptor (RXR) to regulate gene expression (1, 2). Together with peroxisome proliferator-activated receptor (PPAR) and farnesoid X receptor (FXR), LXRs represent a subclass of so-called permissive RXR heterodimers. In this subclass, the RXR heterodimers can be activated independently by either the RXR ligand, the partner's ligand, or synergistically by both (3).LXRs consist of two closely related receptor isoforms encoded by separate genes, LXR␣ (NR1H3) and LXR␤ (NR1H2). LXR␣ shows tissue-restricted expression with the highest mRNA levels in the liver and somewhat lower levels in the kidney, small intestine, spleen, and adrenal gland (4, 5). In contrast, LXR␤ is ubiquitously expressed (6, 7). Both LXR isoforms can be activated by specific oxysterols that are formed in vivo (2,8,9). In view of the high degree of homology between the LXR isoforms (75% identity in the ligand-binding domain (LBD), 54% identity overall), it is perhaps not surprising that few subtypespecific biological responses have been described and that information on subtype selective ligands is limited. LXRs have been shown to regulate several genes involved in cholesterol and lipid homeos...

Ligand specificity and evolution of liver X receptors

“…Disorder probabilities were generally very similar across all LXRα and LXRβ sequences analyzed, whether analyzed by domain (DBD or LBD) or full-length protein sequence (Supplementary Table 3). One major difference was that ciLXR had no prediction of disorder in the first part of the LBD that includes the long helix-1 and the interloop region between helix-1 and helix-3, a region that is difficult to resolve crystallographically due to unclear electron density [19,33]. The low prediction of disorder in the ciLXR LBD contrasts markedly with all other LXRs analyzed, including that from the purple sea urchin (Supplementary Table 3).…”

“…High-resolution crystal structures of LXRs bound to various agonists have been published for human LXRα [33], mouse LXRα [34], and human LXRβ [18,19,35]. From these structures, a total of 31 amino acid residue positions have been shown to interact with ligands in LXRα and/or LXRβ.…”

“…Note that the planar 6-FC also manages to interact with the HBA. Alignment of 6-FC with T-0901317 in the orientation from a different crystal structure of hLXRβ [19] suggests a different pharmacophore (Fig. 5B) in which His-435 serves as a hydrogen bond donor (HBD; this residue is known from structural studies as having the capability of serving as either a HBD or HBA) [18].…”

“…This molecule conformation was used as a template. Similarly T-0901317 was extracted from the X-ray crystal structure 1PQC [19] and used as an alternate template. All other ligands were imported as sdf files and up to 255 conformations were generated with the Best conformer generation method, allowing a maximum energy difference of 20 kcal/mol with Discovery Studio Catalyst 1.7 (Accelrys, San Diego, CA).…”

Identification of a potent synthetic FXR agonist with an unexpected mode of binding and activation

“…For instance, recent studies with the androgen receptor show that side-chain rearrangements in the ligand-binding pocket can accommodate bulky extensions (34). Similarly, LXR␤ undergoes binding-pocket rearrangements that allow two ligands that differ greatly in size and shape to bind with high affinity (35). Finally, both the vitamin D receptor and ecdysone receptors exhibit the apparent ability to bind different ligands in distinct yet partially overlapping binding pockets (36,37).…”