Structures and activation mechanism of the Gabija anti-phage system

Jing Li, Rui Cheng, Zhiming Wang, Wuliu Yuan, Jun Xiao, Xinyuan Zhao, Xinran Du, Shiyu Xia, Lianrong Wang, Bin Zhu () and Longfei Wang ()
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Jing Li: Wuhan University
Rui Cheng: Huazhong University of Science and Technology
Zhiming Wang: Wuhan University
Wuliu Yuan: Wuhan University
Jun Xiao: Wuhan University
Xinyuan Zhao: Huazhong University of Science and Technology
Xinran Du: Wuhan University
Shiyu Xia: California Institute of Technology
Lianrong Wang: Wuhan University
Bin Zhu: Huazhong University of Science and Technology
Longfei Wang: Wuhan University

Nature, 2024, vol. 629, issue 8011, 467-473

Abstract: Abstract Prokaryotes have evolved intricate innate immune systems against phage infection1–7. Gabija is a highly widespread prokaryotic defence system that consists of two components, GajA and GajB8. GajA functions as a DNA endonuclease that is inactive in the presence of ATP9. Here, to explore how the Gabija system is activated for anti-phage defence, we report its cryo-electron microscopy structures in five states, including apo GajA, GajA in complex with DNA, GajA bound by ATP, apo GajA–GajB, and GajA–GajB in complex with ATP and Mg2+. GajA is a rhombus-shaped tetramer with its ATPase domain clustered at the centre and the topoisomerase–primase (Toprim) domain located peripherally. ATP binding at the ATPase domain stabilizes the insertion region within the ATPase domain, keeping the Toprim domain in a closed state. Upon ATP depletion by phages, the Toprim domain opens to bind and cleave the DNA substrate. GajB, which docks on GajA, is activated by the cleaved DNA, ultimately leading to prokaryotic cell death. Our study presents a mechanistic landscape of Gabija activation.

Date: 2024
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DOI: 10.1038/s41586-024-07270-x

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