Structural and Dynamic Analysis of Lipocalin Type Prostaglandin D Synthase in its APO form and Substrate Analog Complex Form

Abstract

Lipocalin-type prostaglandin (PG) D synthase (L-PGDS) is endowed with dual functions as a PGD2-synthesizing enzyme and a transporter for lipophilic ligands in the central nervous system. The structure of apo-L-PGDS has already been reported, and substrate docking models and mutational studies has revealed the mechanism of activation of Cys65 and the important residues for substrate recognition at the barrel retion. However, the information of residues involved in the substrate recognition has been almost limited to the region around the catalytic center Cys65. Here, we present the first structure of mouse L-PGDS/substrate analog (U-46619) complex determined by using NMR. Structural and dynamic comparison with apo and complex form revealed that apo-L-PGDS has large open state with overall slow motions and becomes rigid closed state upon substrate analog binding. This conformational change induced the interaction of residues, which are located at the entrance region (H2-helix, CD-loop and EF-loop) with substrate analog. Especially, Phe55 and Pro110 cover the ω chain of the substrate via hydrophobic contacts and fix it in the cavity. Further mutational and kinetic studies demonstrated that the mutation of these residues causes the decrease of affinity for substrate, indicating that the entrance region of L-PGDS is important for the substrate recognition as well as the catalytic region in the barrel.