Allosteric activation of the SPRTN protease by ubiquitin maintains genome stability

Sophie Dürauer, Hyun-Seo Kang, Christian Wiebeler, Yuka Machida, Dina S. Schnapka, Denitsa Yaneva, Christian Renz, Maximilian J. Götz, Pedro Weickert, Abigail C. Major, Aldwin S. Rahmanto, Sophie M. Gutenthaler-Tietze, Lena J. Daumann, Petra Beli, Helle D. Ulrich, Michael Sattler, Yuichi J. Machida, Nadine Schwierz and Julian Stingele ()
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Sophie Dürauer: Ludwig-Maximilians-Universität München
Hyun-Seo Kang: Helmholtz Munich
Christian Wiebeler: University of Augsburg
Yuka Machida: National Cancer Institute
Dina S. Schnapka: Ludwig-Maximilians-Universität München
Denitsa Yaneva: Ludwig-Maximilians-Universität München
Christian Renz: Institute of Molecular Biology gGmbH
Maximilian J. Götz: Ludwig-Maximilians-Universität München
Pedro Weickert: Ludwig-Maximilians-Universität München
Abigail C. Major: University of Augsburg
Aldwin S. Rahmanto: Institute of Molecular Biology gGmbH
Sophie M. Gutenthaler-Tietze: Heinrich-Heine Universität Düsseldorf
Lena J. Daumann: Heinrich-Heine Universität Düsseldorf
Petra Beli: Institute of Molecular Biology gGmbH
Helle D. Ulrich: Institute of Molecular Biology gGmbH
Michael Sattler: Helmholtz Munich
Yuichi J. Machida: National Cancer Institute
Nadine Schwierz: University of Augsburg
Julian Stingele: Ludwig-Maximilians-Universität München

Nature Communications, 2025, vol. 16, issue 1, 1-17

Abstract: Abstract The DNA-dependent protease SPRTN maintains genome stability by degrading toxic DNA-protein crosslinks (DPCs). To understand how SPRTN’s promiscuous protease activity is confined to cleavage of crosslinked proteins, we reconstitute the repair of DPCs including their modification with SUMO and ubiquitin chains in vitro. We discover that DPC ubiquitylation strongly activates SPRTN independently of SPRTN’s known ubiquitin-binding domains. Using protein structure prediction, MD simulations and NMR spectroscopy we reveal that ubiquitin binds to SPRTN’s protease domain, promoting an open, active conformation. Replacing key interfacial residues prevents allosteric activation of SPRTN by ubiquitin, leading to genomic instability and cell cycle defects in cells expressing truncated SPRTN variants that cause premature aging and liver cancer in Ruijs-Aalfs syndrome patients. Collectively, our results reveal a ubiquitin-dependent regulatory mechanism that ensures SPRTN activity is deployed precisely when and where it is needed.

Date: 2025
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DOI: 10.1038/s41467-025-61224-z

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