The DIPP1 family binds IP8 in catalytically-productive twist-boat and chair conformations and associates in a ligand-dependent manner

Casa-Florez, David, Whitfield, Hayley, Pérez-Cañadillas, Jose M., Monterroso, Begoña, Riley, Andrew M., Márquez-Moñino, Maria A., Shipton, Megan L., Sanz-Aparicio, Julia, Brearley, Charles A., Potter, Barry V. L. and González, Beatriz (2026) The DIPP1 family binds IP8 in catalytically-productive twist-boat and chair conformations and associates in a ligand-dependent manner. International Journal of Biological Macromolecules. ISSN 0141-8130

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Abstract

Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1) is a Nudix hydrolase involved in inositol pyrophosphate (PP-InsP) metabolism, critical for cellular signaling, energy homeostasis, and stress responses. We report crystallographic and computational studies that reveal 1,5-bis-diphosphoinositol tetrakisphosphate (IP8) binds to DIPP1 in two catalytically-productive inositol ring conformations. IP8 hydrolysis at the 1-position requires a twist-boat conformation, whereas at the 5-position a canonical chair conformation is adopted. Additionally, structural and biophysical characterization shows that the DIPP1 family undergoes ligand-sensitive changes in the association state that might be further modulated by salt concentration and/or phosphate ions. Taken together, these results advance our understanding of DIPP1 in the dynamic regulation of inositol pyrophosphate signaling networks. They provide a detailed view of DIPP1 substrate recognition and suggest oligomerization as a novel regulatory mechanism, with broader implications for phosphate sensing and functional protein–protein interactions.

Item Type:	Article
Additional Information:	Data availability: All the atomic coordinates and the structure factors of the crystal structures are deposited in the Protein Data Bank (https://www.rcsb.org) under the submission codes 9T49 and 9T4A (DIPP1/PCP-IP8 in 1PP-SP mode); 9 T48 (DIPP1-R89S/PCP-IP8 in 1PP-TB and 1PP-SP modes); 9T4B (DIPP1-R89S/PCP-IP8 in 5PP mode); 9T4C (DIPP1-H91E/PCP-IP8 in 1PP-SP and out-mode); 9T4D (DIPP1-R41A/5-IP7); 9T4G (DIPP1/IP6); 9T4H (DIPP1-R41A/IP6); 9T4I (DIPP1-R89S/IP6); 9T4J (DIPP1-H91E/IP6); 9T4K (DIPP1-H91M/IP6); 9T4L (DIPP1-E108N/IP6); 9T4M (DIPP1-N112S/IP6); 9T4E (DIPP1); 9T4F (DIPP1-E108N). Acknowledgements: We are grateful to the European Synchrotron Radiation Facility for provision of synchrotron radiation facilities and we would like to thank the staff of the ESRF and EMBL Grenoble for assistance and support in using beamlines ID23-1, ID23-2, ID30-B and ID30-A3 (BAG proposal numbers MX2364 and MX2465). We also thank the Synchrotron Radiation Source at ALBA (Barcelona, Spain) for providing beamtime and assistance with the BL13-XALOC beamline. We gratefully acknowledge Prof. Martín Martínez-Ripoll for his valuable assistance with updating and maintenance of the scientific software used in this work. We also thank Dr. Lourdes Infantes for her assistance with in silico protein-ligand structural prediction. We thank Paula Sanz-Benito for valuable technical assistance. We thank Carlota Menéndez Linacero for her help in setting up the 5-IP7 biosynthesis. We thank the Biophysical Techniques Facility at IQF Blas Cabrera for access to the DSF equipment and for excellent assistance (A. González-Vega) with DLS experiments, and the Molecular Interactions Facility at CIB Margarita Salas (J.R. Luque-Ortega) for assistance in AUC experiments. The authors acknowledge the computational resources provided by the Galician Supercomputing Center (CESGA). The FinisTerrae III supercomputer and its permanent data storage system were funded by the NextGeneration EU 2021 Recovery, Transformation and Resilience Plan (ICT2021-006904), the Pluriregional Operational Programme of Spain 2014–2020 of the European Regional Development Fund (ERDF) (ICTS-2019-02-CESGA-3), and the State Programme for the Promotion of Scientific and Technical Research of Excellence, within the State Plan for Scientific and Technical Research and Innovation 2013–2016, State Subprogramme for Scientific and Technical Infrastructures and Equipment of ERDF (CESG15-DE-3114).
Uncontrolled Keywords:	inositol polyphosphate,inositol pyrophosphate,ip8,dipp1,nudix hydrolase,twist-boat
Faculty \ School:	Faculty of Science > School of Biological Sciences
UEA Research Groups:	Faculty of Science > Research Groups > Plant Sciences Faculty of Science > Research Groups > Molecular Microbiology
Depositing User:	LivePure Connector
Date Deposited:	11 Jun 2026 13:48
Last Modified:	14 Jun 2026 05:37
URI:	https://ueaeprints.uea.ac.uk/id/eprint/103378
DOI:	10.1016/j.ijbiomac.2026.152715

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