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Journal of Biochemistry Advance Access originally published online on November 17, 2008
Journal of Biochemistry 2009 145(2):169-175; doi:10.1093/jb/mvn154
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© The Authors 2008. Published by Oxford University Press on behalf of the Japanese Biochemical Society. All rights reserved

Compact Packing of Lipocalin-type Prostaglandin D Synthase Induced by Binding of Lipophilic Ligands*

Katsuaki Inoue1, Naoto Yagi1, Yoshihiro Urade2 and Takashi Inui3,4,{dagger}

1Research & Utilization Division, Japan Synchrotron Radiation Research Institute, 1-1-1 Koto, Sayo, Hyogo 679-5198; 2Department of Molecular Behavioral Biology, Osaka Bioscience Institute, 6-2-4 Furuedai, Suita, Osaka 565-0874; 3Laboratory of Protein Sciences, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka 599-8531; and 4Department of Food and Nutrition, Tsu City College, 157 Ishinden-Nakano, Tsu, Mie 514-0112, Japan

{dagger}To whom correspondence should be addressed. Tel: +81-72-254-9473, Fax: +81-72-254-9474, E-mail: inuit{at}bioinfo.osakafu-u.ac.jp

Received September 8, 2008; Accepted November 3, 2008


  Abstract

Lipocalin-type prostaglandin (PG) D synthase (L-PGDS) is a multi-functioning protein belonging to the lipocalin family, acting as a PGD2-synthesizing enzyme and as an extracellular transporter for small lipophilic molecules. In the present study, to clarify the conformational changes of lipocalin proteins induced by binding of lipophilic ligands, such as all-trans-retinoic acid (RA), bilirubin (BR) and biliverdin (BV), we measured small-angle X-ray scattering (SAXS) of L-PGDS and that of two other lipocalins, β-lactoglobulin (βLG) and retinol-binding protein (RBP). L-PGDS bound all three ligands with high affinity, while βLG and RBP could bind only RA. The radius of gyration was estimated to be 19.4 Å for L-PGDS, and 18.8 Å for L-PGDS/RA, 17.3 Å for L-PGDS/BR and 17.8 Å for L-PGDS/BV complexes, indicating that L-PGDS became compact after binding of these ligands. Alternatively, the radius of gyration of βLG and RBP was 20.3 and 26.2 Å, respectively, and was almost the same before and after RA binding. Based on the SAXS data, we found that the compact packing upon binding ligands is a special feature of L-PGDS and it may be ascribed to the conformational flexibility of L-PGDS molecule itself, which underlies the high-affinity for its ligands.

Key Words: broad selectivity, compact packing, conformational change, radius of gyration, SAXS

Abbreviations: βLG, β-lactoglobulin; BR, bilirubin; BV, biliverdin; Kd, dissociation constant; L-PGDS, lipocalin-type prostaglandin D synthase; PG, prostaglandin; RA, all-trans-retinoic acid; RBP, retinol-binding protein; Rg, radius of gyration; SAXS, small-angle X-ray scattering

*Part of this work was presented at the 33rd FEBS Congress and 11th IUBMB Conference, Athens, Greece, June 28–July 3, 2008.


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