Database of articles cited by EMDB/PDB/SASBDB data

Keywords
Structure methods	All X-ray diffraction NMR electron microscopy small angle scattering neutron diffraction fiber diffraction powder diffraction infrared spectroscopy EPR fluorescence transfer theoretical model Hybrid
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Journal
IF	>30 >20 >10 >5 all

Title	Structural mechanism of bridge RNA-guided recombination.
Journal, issue, pages	Nature, Vol. 630, Issue 8018, Page 994-991002, Year 2024
Publish date	Jun 26, 2024
Authors	Masahiro Hiraizumi / Nicholas T Perry / Matthew G Durrant / Teppei Soma / Naoto Nagahata / Sae Okazaki / Januka S Athukoralage / Yukari Isayama / James J Pai / April Pawluk / Silvana Konermann / Keitaro Yamashita / Patrick D Hsu / Hiroshi Nishimasu /
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- ...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.
External links	Nature / PubMed:38926616 / PubMed Central
Methods	EM (single particle)
Resolution	2.5 - 2.9 Å
Structure data	37827 8wt6 EMDB-37827, PDB-8wt6: Cryo-EM structure of the IS621 recombinase in complex with bridge RNA, donor DNA, and target DNA in the pre-strand exchange state Method: EM (single particle) / Resolution: 2.5 Å 37828 8wt7 EMDB-37828, PDB-8wt7: Cryo-EM structure of the IS621 recombinase in complex with bridge RNA, donor DNA, and target DNA in the pre-strand exchange locked state Method: EM (single particle) / Resolution: 2.7 Å 37829 8wt8 EMDB-37829, PDB-8wt8: Cryo-EM structure of the IS621 recombinase in complex with bridge RNA, donor DNA, and target DNA in the post-strand exchange state (Holliday junction intermediate) Method: EM (single particle) / Resolution: 2.9 Å 37830 8wt9 EMDB-37830, PDB-8wt9: Cryo-EM structure of the IS621 recombinase in complex with bridge RNA, donor DNA, and target DNA in the post-strand exchange state (Holliday junction resolution) Method: EM (single particle) / Resolution: 2.7 Å
Chemicals	ChemComp-MG: Unknown entry ChemComp-HOH: WATER
Source	escherichia coli (E. coli)
Keywords	RECOMBINATION/DNA/RNA / Holliday junction / RNA dependent recombinase / RECOMBINATION-DNA-RNA complex / RECOMBINATION/RNA/DNA / RECOMBINATION / RECOMBINATION-RNA-DNA complex