The GTP responsiveness of PI5P4Kβ evolved from a compromised trade-off between activity and specificity

Koh Takeuchi; Yoshiki Ikeda; Miki Senda; Ayaka Harada; Koji Okuwaki; Kaori Fukuzawa; So Nakagawa; Hong Yang Yu; Lisa Nagase; Misaki Imai; Mika Sasaki; Yu-Hua Lo; Doshun Ito; Natsuki Osaka; Yuki Fujii; Atsuo T Sasaki; Toshiya Senda

doi:10.1016/j.str.2022.04.004

The GTP responsiveness of PI5P4Kβ evolved from a compromised trade-off between activity and specificity

Structure. 2022 Jun 2;30(6):886-899.e4. doi: 10.1016/j.str.2022.04.004. Epub 2022 May 2.

Authors

Koh Takeuchi¹, Yoshiki Ikeda², Miki Senda³, Ayaka Harada³, Koji Okuwaki⁴, Kaori Fukuzawa⁵, So Nakagawa⁶, Hong Yang Yu⁷, Lisa Nagase³, Misaki Imai⁸, Mika Sasaki², Yu-Hua Lo³, Doshun Ito³, Natsuki Osaka⁹, Yuki Fujii¹⁰, Atsuo T Sasaki¹¹, Toshiya Senda¹²

Affiliations

¹ Molecular Profiling Research Center for Drug Discovery and Cellular Molecular Biotechnology Research Institute, National Institute of Advanced Science and Technology, Aomi, Koto, Tokyo 135-0063, Japan; Graduate School of Pharmacological Sciences, The University of Tokyo, Hongo, Bunkyo, Tokyo 113-0033, Japan. Electronic address: koh-takeuchi@mol.f.u-tokyo.ac.jp.
² Division of Hematology and Oncology, Department of Internal Medicine, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA.
³ Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Ibaraki 305-0801, Japan.
⁴ Department of Chemistry and Research Center for Smart Molecules, Rikkyo University, Toshima, Tokyo 171-8501, Japan.
⁵ School of Pharmacy and Pharmaceutical Sciences, Hoshi University, Shinagawa, Tokyo 142-8501, Japan.
⁶ Department of Molecular Life Sciences, Tokai University School of Medicine, Isehara, Kanagawa 259-1193, Japan.
⁷ Division of Hematology and Oncology, Department of Internal Medicine, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA; Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Ibaraki 305-0801, Japan.
⁸ Molecular Profiling Research Center for Drug Discovery and Cellular Molecular Biotechnology Research Institute, National Institute of Advanced Science and Technology, Aomi, Koto, Tokyo 135-0063, Japan; Graduate School of Pharmacological Sciences, The University of Tokyo, Hongo, Bunkyo, Tokyo 113-0033, Japan.
⁹ Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0052, Japan.
¹⁰ Graduate School of Science, Osaka City University, 3-3-138 Sugimoto, Sumiyoshi, Osaka 558-8585, Japan.
¹¹ Division of Hematology and Oncology, Department of Internal Medicine, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA; Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA; Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0052, Japan; Department of Neurosurgery, Brain Tumor Center at UC Gardner Neuroscience Institute, Cincinnati, OH 45267, USA. Electronic address: atsuo.sasaki@uc.edu.
¹² Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Ibaraki 305-0801, Japan; Department of Accelerator Science, School of High Energy Accelerator Science, SOKENDAI (The Graduate University for Advanced Studies), Oho, Tsukuba, Ibaraki 305-0801, Japan; Faculty of Pure and Applied Sciences, University of Tsukuba, Tennodai, Ibaraki 305-8571, Japan. Electronic address: toshiya.senda@kek.jp.

Abstract

Unlike most kinases, phosphatidylinositol 5-phosphate 4-kinase β (PI5P4Kβ) utilizes GTP as a physiological phosphate donor and regulates cell growth under stress (i.e., GTP-dependent stress resilience). However, the genesis and evolution of its GTP responsiveness remain unknown. Here, we reveal that PI5P4Kβ has acquired GTP preference by generating a short dual-nucleotide-recognizing motif called the guanine efficient association (GEA) motif. Comparison of nucleobase recognition with 660 kinases and 128 G proteins has uncovered that most kinases and PI5P4Kβ use their main-chain atoms for adenine recognition, while the side-chain atoms are required for guanine recognition. Mutational analysis of the GEA motif revealed that the acquisition of GTP reactivity is accompanied by an extended activity toward inosine triphosphate (ITP) and xanthosine triphosphate (XTP). Along with the evolutionary analysis data that point to strong negative selection of the GEA motif, these results suggest that the GTP responsiveness of PI5P4Kβ has evolved from a compromised trade-off between activity and specificity, underpinning the development of the GTP-dependent stress resilience.

Keywords: GTP; GTP sensor; PI5P4K; activity; evolution; kinase; specificity; stress resilience.

Publication types

Research Support, Non-U.S. Gov't
Research Support, N.I.H., Extramural

MeSH terms

GTP-Binding Proteins* / metabolism
Guanine
Guanosine Triphosphate / metabolism
Inosine Triphosphate* / metabolism

Substances

Inosine Triphosphate
Guanine
Guanosine Triphosphate
GTP-Binding Proteins

Abstract

Publication types

MeSH terms

Substances

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