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Mechanism of metal activation of human hematopoietic prostaglandin D synthase

A Corrigendum to this article was published on 01 May 2003

Abstract

Here we report the crystal structures of human hematopoietic prostaglandin (PG) D synthase bound to glutathione (GSH) and Ca2+ or Mg2+. Using GSH as a cofactor, prostaglandin D synthase catalyzes the isomerization of PGH2 to PGD2, a mediator for allergy response. The enzyme is a homodimer, and Ca2+ or Mg2+ increases its activity to 150% of the basal level, with half maximum effective concentrations of 400 μM for Ca2+ and 50 μM for Mg2+. In the Mg2+-bound form, the ion is octahedrally coordinated by six water molecules at the dimer interface. The water molecules are surrounded by pairs of Asp93, Asp96 and Asp97 from each subunit. Ca2+ is coordinated by five water molecules and an Asp96 from one subunit. The Asp96 residue in the Ca2+-bound form makes hydrogen bonds with two guanidium nitrogen atoms of Arg14 in the GSH-binding pocket. Mg2+ alters the coordinating water structure and reduces one hydrogen bond between Asp96 and Arg14, thereby changing the interaction between Arg14 and GSH. This effect explains a four-fold reduction in the Km of the enzyme for GSH. The structure provides insights into how Ca2+ or Mg2+ binding activates human hematopoietic PGD synthase.

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Figure 1: The structure of human H-PGDS.
Figure 2: The metal coordination structures of human H-PGDS.
Figure 3: Effect of metal ion on the PGDS activity.

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Protein Data Bank

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Acknowledgements

The authors are grateful to M. Tang, K. Miura and E. Yamashita at SPring-8 beamline 12B2, 40B2 and 44XU, respectively, for the fundamental data collection, and M. Kawamoto for his kind support in the data collection at SPring-8 beamline 41XU. The authors express their appreciation to O. Hayaishi, Osaka Bioscience Institute, for his generous support of this study. This study was funded by the PRESTO (T.I.) and CREST (Y.U.) projects, Japan Science and Technology Corporation, and is a part of 'Applied Research Pilot Project for the Industrial Use of Space' promoted by NASDA and the Japan Space Utilization Promotion Center, National Project on Protein Structural and Functional Analyses, and Osaka City.

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Correspondence to Yasushi Kai or Yoshihiro Urade.

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Inoue, T., Irikura, D., Okazaki, N. et al. Mechanism of metal activation of human hematopoietic prostaglandin D synthase. Nat Struct Mol Biol 10, 291–296 (2003). https://doi.org/10.1038/nsb907

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