Lipocalin-type prostaglandin (PG) D synthase (L-PGDS) is a multi functional protein that functions as a PGD2 synthesizing enzyme, a scavenger of various lipophilic ligands, and an amyloid β chaperone in the brain. L-PGDS is a member of the lipocalin superfamily and has the ability to bind various lipophilic molecules, such as prostanoid, retinoid, bile pigment, and amyloid β peptide. However, the molecular mechanism for this wide variety of ligand binding is not fully understood. In this study, we determined the NMR structures of recombinant mouse L-PGDS and a L-PGDS/PGH2 analog. L-PGDS has a typical lipocalin fold, consisting of an eight-stranded β-barrel and a single α-helix. The interior of the barrel forms a hydrophobic cavity and the upper end of the barrel is open. The size of the barrel was found to be larger than those of other lipocalins and the cavity contained two pockets. The results of NMR titration, kinetic and molecular docking experiments revealed that PGH2 and retinoic acid occupied the hydrophilic pockets 1 and 2, respectively. A structural comparison of the L-PGDS/PGH2 analog complex with apo-L-PGDS showed that the H2-helix, CD-loop, and EF-loop located at the upper end of the β-barrel undergo a conformational change and cover the entrance of the cavity upon U-46619 binding. These results indicate that the two binding sites in the large cavity are responsible for the broad ligand specificity of L-PGDS in its induced-fit mechanism.
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