Extended Data Fig. 6: Structures of dimeric HNH endonuclease complexes with DNA and their comparison with the dimeric HNH active site of PsCap5.
From: Activation of CBASS Cap5 endonuclease immune effector by cyclic nucleotides

HNH endonuclease I-PpoI18 (PDB ID: 1A74, with the catalytic ions modeled based on the complex with cleaved DNA PDB ID: 1A73) and Hpy99I19 (PDB ID: 3GOX). In the displayed Hpy99I structure, the N-terminal β-barrel (residues 1–53), a linker (residues 54–64) and the residues of the HNH domain which approach the major groove of the DNA for sequence-specific interactions (residues 79-98) have been omitted for clarity. The phage T4 Endo VII20 (PDB ID: 2QNC) cleaves two symmetrical strands of a four-way junction DNA. For all proteins, a front and a side views of a DNA-binding surface colored by electrostatic potential are shown; the conserved ββα structural elements of the dimer approaching duplex DNA for cleavage from the minor groove side is colored in green, the catalytic ions are shown as green spheres and the catalytic His residues shown as red sticks. A front view of a DNA binding surface of dimeric HNH endonuclease of PsCap5 tetramer, formed by the active conformation protomers A and C. The view also includes the inactive protomers B and D. The side view of HNH endonuclease domains A/C only and of the four endonuclease domains of the tetramer. The two structural Mg2+ ions are positioned in-between of the catalytic ions. A model of HNH endonuclease domains A/C interactions with DNA is based on the structure of Colicin E9 HNH endonuclease monomer with DNA22 (PDB ID: 1V15).