8WT6

Cryo-EM structure of the IS621 recombinase in complex with bridge RNA, donor DNA, and target DNA in the pre-strand exchange state

Summary for 8WT6

• Entry DOI: 10.2210/pdb8wt6/pdb
• EMDB information: 37827
• Descriptor: IS621 transposase, bridge RNA, target DNA, ... (8 entities in total)
• Functional Keywords: holliday junction, rna dependent recombinase, recombination-dna-rna complex, recombination/dna/rna
• Biological source: Escherichia coli; More
• Total number of polymer chains: 10
• Total formula weight: 312918.34

Authors

Hiraizumi, M.,Yamashita, K.,Nishimasu, H. (deposition date: 2023-10-18, release date: 2024-06-26, Last modification date: 2024-07-17)

Primary citation

Hiraizumi, M.,Perry, N.T.,Durrant, M.G.,Soma, T.,Nagahata, N.,Okazaki, S.,Athukoralage, J.S.,Isayama, Y.,Pai, J.J.,Pawluk, A.,Konermann, S.,Yamashita, K.,Hsu, P.D.,Nishimasu, H.
Structural mechanism of bridge RNA-guided recombination.
Nature, 630:994-1002, 2024

PubMed Abstract: Insertion sequence (IS) elements are the simplest autonomous transposable elements found in prokaryotic genomes. We recently discovered that IS110 family elements encode a recombinase and a non-coding bridge RNA (bRNA) that confers modular specificity for target DNA and donor DNA through two programmable loops. Here we report the cryo-electron microscopy structures of the IS110 recombinase in complex with its bRNA, target DNA and donor DNA in three different stages of the recombination reaction cycle. The IS110 synaptic complex comprises two recombinase dimers, one of which houses the target-binding loop of the bRNA and binds to target DNA, whereas the other coordinates the bRNA donor-binding loop and donor DNA. We uncovered the formation of a composite RuvC-Tnp active site that spans the two dimers, positioning the catalytic serine residues adjacent to the recombination sites in both target and donor DNA. A comparison of the three structures revealed that (1) the top strands of target and donor DNA are cleaved at the composite active sites to form covalent 5'-phosphoserine intermediates, (2) the cleaved DNA strands are exchanged and religated to create a Holliday junction intermediate, and (3) this intermediate is subsequently resolved by cleavage of the bottom strands. Overall, this study reveals the mechanism by which a bispecific RNA confers target and donor DNA specificity to IS110 recombinases for programmable DNA recombination.

PubMed: 38926616
DOI: 10.1038/s41586-024-07570-2

Experimental method

ELECTRON MICROSCOPY (2.5 Å)