Comparative X-ray structures of the major binding protein for the immunosuppressant FK506 (tacrolimus) in unliganded form and in complex with FK506 and rapamycin

Abstract

FK506 (tacrolimus) is a natural product now approved in the US and Japan for organ transplantation. FK506, in complex with its 12 kDa cytosolic receptor (FKBP12), is a potent agonist of immunosuppression through the inhibition of the phosphatase activity of calcineurin. Rapamycin (sirolimus), which is itself an immunosuppressant by a different mechanism, completes with FK506 for binding to FKBP12 and thereby acts as an antagonist of calcineurin inhibition. We have solved the X-ray structure of unliganded FKBP12 and of FKBP12 in complex with FK506 and with rapamycin; these structures show localized differences in conformation and mobility in those regions of the protein that are known, by site-directed mutagenesis, to be involved in calcineurin inhibition. A comparison of 16 additional X-ray structures of FKBP12 in complex with FKBP12-binding ligands, where those structures were determined from different crystal forms with distinct packing arrangements, lends significance to the observed structural variability and suggests that it represents an intrinsic functional characteristic of the protein. Similar differences have been observed for FKBP12 before, but were considered artifacts of crystal-packing interactions. We suggest that immunosuppressive ligands express their differential effects in part by modulating the conformation of FKBP12, in agreement with mutagenesis experiments on the protein, and not simply through differences in the ligand structures themselves.

Structure of the large FK506-binding protein FKBP51, an Hsp90-binding protein and a component of steroid receptor complexes

“…2). The major difference in the structures occurs in the ''80s'' loop (FKBP51 residues 110-125), a region known to show the most variations among the characterized FKBP domains (40). The PPIase activity of FKBP51 is 0.48 ϫ 10 6 M Ϫ1 ⅐s Ϫ1 (41), comparable to that of FKBP12, 0.64 ϫ 10 6 M Ϫ1 ⅐s Ϫ1 (42).…”

Structural analysis uncovers a role for redox in regulating FKBP13, an immunophilin of the chloroplast thylakoid lumen

“…The ␤ 6 -strand, which is unique to AtFKBP13, is formed by strands ␤ 6a and ␤ 6b connected by a short loop. Alignment between AtFKBP13 and representatives of other FKBPs, namely human HsFKB12 (29) and the macrophage infectivity potentiator protein from Legionella pneumophila, LpMIP (30), through the Dali server (31), gives the rms deviation values of 1.3 Å (with a Z-value of 17.5) and 1.4 Å (with a Z-value of 17.2), respectively (Fig. 1B).…”

Elucidating the Substrate Specificity and Condensation Domain Activity of FkbP, the FK520 Pipecolate-Incorporating Enzyme

“…The immunosuppressant natural products rapamycin, FK506, and FK520 possess macrocyclic lactone scaffolds that provide conformational constraints required for recognition by their binding proteins (the FKBPs) (15)(16)(17)(18) and interaction of the drug-FKBP complexes with downstream target proteins such as calcineurin (37) and FRAP (38). While the FK506/520 and rapamycin scaffolds possess differing polyketide portions, the common core motif contains the sole amino acid moiety, the six-membered L-pipecolate (shaded portions of Figure 1).…”

“…Critical to the interaction between the macrolide and the FKBP is a pipecolate moiety, which extends into the PPIase active site (15)(16)(17)(18). This group is derived from L-pipecolic acid, a nonproteinogenic, six-membered proline analogue.…”