9PD0

Panoptes OptS minimal CRISPR polymerase (mCpol) with non-hydrolyzable ligand ApCpp from Klebsiella pneumoniae strain KP67

Summary for 9PD0

• Entry DOI: 10.2210/pdb9pd0/pdb
• Related: 9MNR
• Descriptor: Panoptes OptS minimal CRISPR polymerase (mCpol), DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER, MAGNESIUM ION, ... (4 entities in total)
• Functional Keywords: antiphage defense systems, nucleotide cyclases, cyclic nucleotides, antiviral protein
• Biological source: Klebsiella pneumoniae
• Total number of polymer chains: 4
• Total formula weight: 60564.78

Authors

Dinh, D.M.,Morehouse, B.R. (deposition date: 2025-06-29, release date: 2025-09-24, Last modification date: 2025-12-10)

Primary citation

Sullivan, A.E.,Nabhani, A.,Izrailevsky, D.S.,Schinkel, K.,Hoffman, C.R.K.,Robbins, L.K.,Nagy, T.A.,Duncan, M.L.,Ledvina, H.E.,Erbse, A.H.,Kibby, E.M.,Tak, U.,Dinh, D.M.,Ednacot, E.M.Q.,Nguyen, C.M.,Burroughs, A.M.,Aravind, L.,Whiteley, A.T.,Morehouse, B.R.
The Panoptes system uses decoy cyclic nucleotides to defend against phage.
Nature, 647:988-996, 2025

PubMed Abstract: Bacteria combat phage infection using antiphage systems and many systems generate nucleotide-derived second messengers upon infection that activate effector proteins to mediate immunity. Phages respond with counter-defences that deplete these second messengers, leading to an escalating arms race with the host. Here we outline an antiphage system we call Panoptes that indirectly detects phage infection when phage proteins antagonize the nucleotide-derived second-messenger pool. Panoptes is a two-gene operon, optSE, wherein OptS is predicted to synthesize a nucleotide-derived second messenger and OptE is predicted to bind that signal and drive effector-mediated defence. Crystal structures show that OptS is a minimal CRISPR polymerase (mCpol) domain, a version of the polymerase domain found in type III CRISPR systems (Cas10). OptS orthologues from two distinct Panoptes systems generated cyclic dinucleotide products, including 2',3'-cyclic diadenosine monophosphate (2',3'-c-di-AMP), which we showed were able to bind the soluble domain of the OptE transmembrane effector. Panoptes potently restricted phage replication, but phages that had loss-of-function mutations in anti-cyclic oligonucleotide-based antiphage signalling system (CBASS) protein 2 (Acb2) escaped defence. These findings were unexpected because Acb2 is a nucleotide 'sponge' that antagonizes second-messenger signalling. Our data support the idea that cyclic nucleotide sequestration by Acb2 releases OptE toxicity, thereby initiating inner membrane disruption, leading to phage defence. These data demonstrate a sophisticated immune strategy that bacteria use to guard their second-messenger pool and turn immune evasion against the virus.

PubMed: 41034579
DOI: 10.1038/s41586-025-09557-z

Experimental method

X-RAY DIFFRACTION (2.42 Å)