PDBsum entry 1fcz

Gene regulation

PDB id

1fcz

Contents

			Protein chain

					235 a.a. *

			Ligands

					156


					LMU

			Waters ×305

* Residue conservation analysis

References listed in PDB file

Key reference

Title

Structural basis for isotype selectivity of the human retinoic acid nuclear receptor.

Authors

B.P.Klaholz, A.Mitschler, D.Moras.

Ref.

J Mol Biol, 2000, 302, 155-170. [DOI no: 10.1006/jmbi.2000.4032]

PubMed id

10964567

Abstract

The human retinoic acid receptor (hRAR) belongs to the family of nuclear receptors that regulate transcription in a ligand-dependent way. The isotypes RARalpha,beta and gamma are distinct pharmacological targets for retinoids that are involved in the treatment of various skin diseases and cancers, in particular breast cancer and acute promyelocytic leukemia. Therefore, synthetic retinoids have been developed aiming at isotype selectivity and reduced side-effects. We report the crystal structures of three complexes of the hRARgamma ligand-binding domain (LBD) bound to agonist retinoids that possess selectivity either for RARgamma (BMS184394) or for RARbeta/gamma (CD564), or that are potent for all RAR-isotypes (panagonist BMS181156). The high resolution data (1.3-1. 5 A) provide a description at the atomic level of the ligand pocket revealing the molecular determinants for the different degrees of ligand selectivity. The comparison of the complexes of the chemically closely related retinoids BMS184394 and CD564 shows that the side-chain of Met272 adopts different conformations depending on the presence of a hydrogen bond between its sulfur atom and the ligand. This accounts for their different isotype selectivity. On the other hand, the difference between the pan- and the RARbeta, gamma-selective agonist is probably due to a steric discrimination at the level of the 2-naphthoic acid moiety of CD564. Based on this study, we propose a model for a complex with the RARgamma-specific agonist CD666 that shows the possible applications for structure-based drug design of RAR isotype-selective retinoids.



	Figure 2. Figure 2. Detail of the W-loop showing the non-planar peptide linkage between Ser215 and Ala216, and the double conformation of Ser215 that allows the formation of different hydrogen bonds for the stabilization of the W-loop (stereo view). The s[A]-weighted 2 mF[o] -DF[c] electron density map (colored in blue) at 1.30 Å resolution is contoured at 1.5s.		Figure 3. Figure 3. The chemical similarity of the RARg-selective BMS184394 and the RARb,g-selective CD564 allows to attribute their different selectivity to their respective hydroxyl and keto groups (stereo views). (a) Final model of the BMS184394 complex depicted with the initial refinement-unbiased s[A]-weighted mF[o] -F[c] omit map (colored in violet) at 1.47 Å resolution contoured at 3.2s. The protein part is colored in green and the ligand in red. Although a racemic mixture has been used in co-crystallization only the R-enantiomer of BMS184394 is present exhibiting a hydrogen bond to the Met272 sulfur atom. (b) The CD564 complex with the ligand fitted to its electron density (s[A]-weighted mF[o] -F[c] omit map at 1.30 Å resolution contoured at 3.2s, colored in orange). The protein part is colored in blue and the ligand in orange. (c) The pocket superposition obtained by a least-squares fit of the BMS184394 and CD564 complexes illustrates that the conformation of the Met272 side-chain depends on the interaction pattern with the ligand. The movement of Met272 is mediated to Ile389 and Leu386. Note that Ile389 and Ser390 exhibit two independent conformations for each structure that are depicted in green and yellow for the BMS184394 complex and in blue and violet for the CD564 complex.

Secondary reference #1

Title

Enantiomer discrimination illustrated by high-Resolution crystal structures of the human nuclear receptor hrargamma.

Authors

B.P.Klaholz, A.Mitschler, M.Belema, C.Zusi, D.Moras.

Ref.

Proc Natl Acad Sci U S A, 2000, 97, 6322-6327. [DOI no: 10.1073/pnas.97.12.6322]

PubMed id

10841540

Full text

Abstract



	Figure 1. Fig. 1. Stereo representation of the ligand-binding pocket of the crystal structure of the hRAR LBD with the bound active enantiomer BMS270394 (shown in orange). The final model is depicted with the ligand fitted to the electron density map (colored in red) that has been calculated at the very beginning of the refinement in absence of the ligand. The [A]-weighted F[obs] F[calc] map (18) at 1.59-Å resolution is contoured at 3.2 . Distances in yellow indicate hydrogen bonds and salt bridges between ligand and residues, whereas van der Waals contacts are shown in blue. RAR selectivity of the ligand is achieved by its hydroxyl group, which forms a hydrogen bond with the sulfur of Met-272, corresponding to isoleucines in RAR and . H3, H5, H10, and H11 indicate helices, and L6/7 the loop between helix 6 and 7.		Figure 2. Fig. 2. Structure of hRAR LBD bound to the inactive BMS270395 and its comparison with the BMS270394 complex (stereo representations) (A). The BMS270395 complex with the initial refinement-unbiased [A]-weighted F[obs] F[calc] map at 1.67 Å resolution contoured at 3.2 and colored in violet. The map clearly indicates two possible positions for the fluorine atom, corresponding to two different ligand conformations. The up and down orientations of the fluorine atom have occupancies of 40/60%, respectively (colored in green and red, pointing to Ile-275 and Ala-234, respectively) (B). Superposition of the hRAR LBD complexes of both enantiomers as obtained by a least-squares fit. The position of the hydroxyl group oxygen is strictly conserved to maintain the hydrogen bond to Met-272; BMS270395 therefore adopts a conformation different from that observed for BMS270394 (C). Detailed view of the part of the ligand pocket where the ligand exhibits unfavorable contacts. The color code for distances is that of Fig. 1. The fluorine atom exhibits close contacts for both the up and down orientation, whereas the salt bridge between the carboxylate group and Arg-278 is weaker compared with the BMS270394 complex.