8JKZ

Cryo-EM structure of the prokaryotic SPARSA system complex

Summary for 8JKZ

• Entry DOI: 10.2210/pdb8jkz/pdb
• EMDB information: 36384
• Descriptor: Sir2 superfamily protein, Piwi domain protein, NICOTINAMIDE-ADENINE-DINUCLEOTIDE (3 entities in total)
• Functional Keywords: sparsa antiviral system, nadase, argonaute proteins, antiviral protein
• Biological source: Geobacter sulfurreducens; More
• Total number of polymer chains: 2
• Total formula weight: 120257.49

Authors

Xu, X.,Zhen, X.,Long, F. (deposition date: 2023-06-02, release date: 2024-01-24)

Primary citation

Zhen, X.,Xu, X.,Ye, L.,Xie, S.,Huang, Z.,Yang, S.,Wang, Y.,Li, J.,Long, F.,Ouyang, S.
Structural basis of antiphage immunity generated by a prokaryotic Argonaute-associated SPARSA system.
Nat Commun, 15:450-450, 2024

PubMed Abstract: Argonaute (Ago) proteins are ubiquitous across all kingdoms of life. Eukaryotic Agos (eAgos) use small RNAs to recognize transcripts for RNA silencing in eukaryotes. In contrast, the functions of prokaryotic counterparts (pAgo) are less well known. Recently, short pAgos in conjunction with the associated TIR or Sir2 (SPARTA or SPARSA) were found to serve as antiviral systems to combat phage infections. Herein, we present the cryo-EM structures of nicotinamide adenine dinucleotide (NAD)-bound SPARSA with and without nucleic acids at resolutions of 3.1 Å and 3.6 Å, respectively. Our results reveal that the APAZ (Analogue of PAZ) domain and the short pAgo form a featured architecture similar to the long pAgo to accommodate nucleic acids. We further identified the key residues for NAD binding and elucidated the structural basis for guide RNA and target DNA recognition. Using structural comparisons, molecular dynamics simulations, and biochemical experiments, we proposed a putative mechanism for NAD hydrolysis in which an H186 loop mediates nucleophilic attack by catalytic water molecules. Overall, our study provides mechanistic insight into the antiphage role of the SPARSA system.

PubMed: 38200015
DOI: 10.1038/s41467-023-44660-7

Experimental method

ELECTRON MICROSCOPY (3.6 Å)