8SP3

Asymmetric dimer of MapSPARTA bound with gRNA/tDNA hybrid

Summary for 8SP3

• Entry DOI: 10.2210/pdb8sp3/pdb
• EMDB information: 40673
• Descriptor: TIR-APAZ, short pAgo, guide RNA, ... (5 entities in total)
• Functional Keywords: short prokaryotic argonaute, oligomerization, tir, nadase activity, bacterial immune system, mapsparta, immune system
• Biological source: Maribacter polysiphoniae; More
• Total number of polymer chains: 8
• Total formula weight: 251164.12

Authors

Shen, Z.F.,Yang, X.Y.,Fu, T.M. (deposition date: 2023-05-01, release date: 2023-08-23, Last modification date: 2023-09-20)

Primary citation

Shen, Z.,Yang, X.Y.,Xia, S.,Huang, W.,Taylor, D.J.,Nakanishi, K.,Fu, T.M.
Oligomerization-mediated activation of a short prokaryotic Argonaute.
Nature, 621:154-161, 2023

PubMed Abstract: Although eukaryotic and long prokaryotic Argonaute proteins (pAgos) cleave nucleic acids, some short pAgos lack nuclease activity and hydrolyse NAD(P) to induce bacterial cell death. Here we present a hierarchical activation pathway for SPARTA, a short pAgo consisting of an Argonaute (Ago) protein and TIR-APAZ, an associated protein. SPARTA progresses through distinct oligomeric forms, including a monomeric apo state, a monomeric RNA-DNA-bound state, two dimeric RNA-DNA-bound states and a tetrameric RNA-DNA-bound active state. These snapshots together identify oligomerization as a mechanistic principle of SPARTA activation. The RNA-DNA-binding channel of apo inactive SPARTA is occupied by an auto-inhibitory motif in TIR-APAZ. After the binding of RNA-DNA, SPARTA transitions from a monomer to a symmetric dimer and then an asymmetric dimer, in which two TIR domains interact through charge and shape complementarity. Next, two dimers assemble into a tetramer with a central TIR cluster responsible for hydrolysing NAD(P). In addition, we observe unique features of interactions between SPARTA and RNA-DNA, including competition between the DNA 3' end and the auto-inhibitory motif, interactions between the RNA G2 nucleotide and Ago, and splaying of the RNA-DNA duplex by two loops exclusive to short pAgos. Together, our findings provide a mechanistic basis for the activation of short pAgos, a large section of the Ago superfamily.

PubMed: 37494956
DOI: 10.1038/s41586-023-06456-z

Experimental method

ELECTRON MICROSCOPY (3.52 Å)