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Structural basis for lysophosphatidylserine recognition by GPR34

Tamaki Izume, Ryo Kawahara, Akiharu Uwamizu, Luying Chen, Shun Yaginuma, Jumpei Omi, Hiroki Kawana, Fumiya K. Sano, Tatsuki Tanaka, Kazuhiro Kobayashi, Hiroyuki H. Okamoto, Yoshiaki Kise, Tomohiko Ohwada, Junken Aoki, Wataru Shihoya, Osamu Nureki
doi: https://doi.org/10.1101/2023.02.15.528751
Tamaki Izume
1Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo 113-0033, Japan
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Ryo Kawahara
1Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo 113-0033, Japan
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Akiharu Uwamizu
2Department of Health Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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Luying Chen
3Department of Organic and Medicinal Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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Shun Yaginuma
2Department of Health Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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Jumpei Omi
2Department of Health Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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Hiroki Kawana
2Department of Health Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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Fumiya K. Sano
1Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo 113-0033, Japan
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Tatsuki Tanaka
1Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo 113-0033, Japan
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Kazuhiro Kobayashi
1Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo 113-0033, Japan
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Hiroyuki H. Okamoto
1Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo 113-0033, Japan
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Yoshiaki Kise
1Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo 113-0033, Japan
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Tomohiko Ohwada
3Department of Organic and Medicinal Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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  • For correspondence: ohwada@mol.f.u-tokyo.ac.jp jaok@mol.f.u-tokyo.ac.jp wtrshh9@gmail.com nureki@bs.s.u-tokyo.ac.jp
Junken Aoki
2Department of Health Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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  • For correspondence: ohwada@mol.f.u-tokyo.ac.jp jaok@mol.f.u-tokyo.ac.jp wtrshh9@gmail.com nureki@bs.s.u-tokyo.ac.jp
Wataru Shihoya
1Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo 113-0033, Japan
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  • For correspondence: ohwada@mol.f.u-tokyo.ac.jp jaok@mol.f.u-tokyo.ac.jp wtrshh9@gmail.com nureki@bs.s.u-tokyo.ac.jp
Osamu Nureki
1Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo 113-0033, Japan
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  • For correspondence: ohwada@mol.f.u-tokyo.ac.jp jaok@mol.f.u-tokyo.ac.jp wtrshh9@gmail.com nureki@bs.s.u-tokyo.ac.jp
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Abstract

GPR34 is a recently identified G-protein coupled receptor, which has an immunomodulatory role and recognizes lysophosphatidylserine (LysoPS) as a putative ligand. Here, we report cryo-electron microscopy structures of human GPR34-Gi complex bound with either the LysoPS analogue S3E-LysoPS, which contains an ethoxy group at the sn-1 position, or M1, a derivative of S3E-LysoPS in which oleic acid is substituted with a metabolically stable aromatic fatty acid surrogate. In both structures, the ligand-binding pocket is laterally open toward the membrane, allowing lateral entry of lipidic agonists into the cavity. The amine and carboxylate groups of the serine moiety are recognized by the charged residue cluster, and the aromatic fatty acid surrogate of M1 forms stable hydrophobic interactions with the cavity, thus acting as a superagonist. Molecular dynamics simulations further account for the LysoPS-regioselectivity of GPR34. Thus, using a series of structural and physiological experiments, we provide evidence that chemically unstable 2-acyl LysoPS is the physiological ligand for GPR34, suggesting its short signal duration. Overall, we anticipate the present structures will pave the way for development of novel anticancer drugs that specifically target GPR34.

Competing Interest Statement

O.N. is a co-founder and scientific advisor for Curreio. All other authors declare no competing interests.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission.
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Posted February 16, 2023.
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Structural basis for lysophosphatidylserine recognition by GPR34
Tamaki Izume, Ryo Kawahara, Akiharu Uwamizu, Luying Chen, Shun Yaginuma, Jumpei Omi, Hiroki Kawana, Fumiya K. Sano, Tatsuki Tanaka, Kazuhiro Kobayashi, Hiroyuki H. Okamoto, Yoshiaki Kise, Tomohiko Ohwada, Junken Aoki, Wataru Shihoya, Osamu Nureki
bioRxiv 2023.02.15.528751; doi: https://doi.org/10.1101/2023.02.15.528751
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Structural basis for lysophosphatidylserine recognition by GPR34
Tamaki Izume, Ryo Kawahara, Akiharu Uwamizu, Luying Chen, Shun Yaginuma, Jumpei Omi, Hiroki Kawana, Fumiya K. Sano, Tatsuki Tanaka, Kazuhiro Kobayashi, Hiroyuki H. Okamoto, Yoshiaki Kise, Tomohiko Ohwada, Junken Aoki, Wataru Shihoya, Osamu Nureki
bioRxiv 2023.02.15.528751; doi: https://doi.org/10.1101/2023.02.15.528751

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