Structural analysis of lipocalin-type prostaglandin D synthase complexed with biliverdin by small-angle X-ray scattering and multi-dimensional NMR |
| |
Authors: | Yuya Miyamoto Shigenori Nishimura Katsuaki Inoue Shigeru Shimamoto Takuya Yoshida Ayano Fukuhara Mao Yamada Yoshihiro Urade Naoto Yagi Tadayasu Ohkubo Takashi Inui |
| |
Institution: | 1. Laboratory of Protein Sciences, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka 599-8531, Japan;2. Research and Utilization Division, Japan Synchrotron Radiation Research Institute, 1-1-1 Koto, Sayo, Hyogo 679-5198, Japan;3. Laboratory of Biophysical Chemistry, Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan;4. Department of Molecular Behavioral Biology, Osaka Bioscience Institute, 6-2-4 Furuedai, Suita, Osaka 565-0874, Japan |
| |
Abstract: | Lipocalin-type prostaglandin D synthase (L-PGDS) acts as both a PGD2 synthase and an extracellular transporter for small lipophilic molecules. From a series of biochemical studies, it has been found that L-PGDS has an ability to bind a variety of lipophilic ligands such as biliverdin, bilirubin and retinoids in vitro. Therefore, we considered that it is necessary to clarify the molecular structure of L-PGDS upon binding ligand in order to understand the physiological relevance of L-PGDS as a transporter protein. We investigated a molecular structure of L-PGDS/biliverdin complex by small-angle X-ray scattering (SAXS) and multi-dimensional NMR measurements, and characterized the binding mechanism in detail. SAXS measurements revealed that L-PGDS has a globular shape and becomes compact by 1.3 Å in radius of gyration on binding biliverdin. NMR experiments revealed that L-PGDS possessed an eight-stranded antiparallel β-barrel forming a central cavity. Upon the titration with biliverdin, some cross-peaks for residues surrounding the cavity and EF-loop and H2-helix above the β-barrel shifted, and the intensity of other cross-peaks decreased with signal broadenings in 1H–15N heteronuclear single quantum coherence spectra. These results demonstrate that L-PGDS holds biliverdin within the β-barrel, and the conformation of the loop regions above the β-barrel changes upon binding biliverdin. Through such a conformational change, the whole molecule of L-PGDS becomes compact. |
| |
Keywords: | |
本文献已被 ScienceDirect 等数据库收录! |
|