8X51

Structure of DNA-bound GajA dimer (focused refinement)

Summary for 8X51

• Entry DOI: 10.2210/pdb8x51/pdb
• EMDB information: 38058
• Descriptor: Endonuclease GajA, DNA (5'-D(*TP*TP*TP*AP*AP*TP*AP*AP*CP*CP*CP*GP*GP*TP*TP*AP*TP*TP*TP*TP*T)-3'), DNA (5'-D(*AP*AP*AP*AP*AP*TP*AP*AP*CP*CP*GP*GP*GP*TP*TP*AP*TP*TP*AP*AP*A)-3'), ... (4 entities in total)
• Functional Keywords: endonuclease, complex, dna binding, dna binding protein, dna binding protein-dna complex, dna binding protein/dna
• Biological source: Bacillus cereus VD045; More
• Total number of polymer chains: 4
• Total formula weight: 147119.51

Authors

Li, J.,Wang, Z.,Wang, L. (deposition date: 2023-11-16, release date: 2024-02-28, Last modification date: 2024-10-16)

Primary citation

Li, J.,Cheng, R.,Wang, Z.,Yuan, W.,Xiao, J.,Zhao, X.,Du, X.,Xia, S.,Wang, L.,Zhu, B.,Wang, L.
Structures and activation mechanism of the Gabija anti-phage system.
Nature, 629:467-473, 2024

PubMed Abstract: Prokaryotes have evolved intricate innate immune systems against phage infection. Gabija is a highly widespread prokaryotic defence system that consists of two components, GajA and GajB. GajA functions as a DNA endonuclease that is inactive in the presence of ATP. 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 Mg. 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.

PubMed: 38471529
DOI: 10.1038/s41586-024-07270-x

Experimental method

ELECTRON MICROSCOPY (2.92 Å)