8K0S

The Anoxybacillus pushchinoensis ORF-less Group IIC Intron HYER1 with 10-nt TRS at symmetric apo state

Summary for 8K0S

• Entry DOI: 10.2210/pdb8k0s/pdb
• EMDB information: 36779
• Descriptor: RNA (543-MER), MAGNESIUM ION (2 entities in total)
• Functional Keywords: orf-less group iic intron, ribozymes, rna
• Biological source: Anoxybacillus pushchinoensis
• Total number of polymer chains: 2
• Total formula weight: 412841.92

Authors

Zhu, H.Z.,Liu, J.J.G. (deposition date: 2023-07-10, release date: 2024-05-01, Last modification date: 2024-05-15)

Primary citation

Liu, Z.X.,Zhang, S.,Zhu, H.Z.,Chen, Z.H.,Yang, Y.,Li, L.Q.,Lei, Y.,Liu, Y.,Li, D.Y.,Sun, A.,Li, C.P.,Tan, S.Q.,Wang, G.L.,Shen, J.Y.,Jin, S.,Gao, C.,Liu, J.G.
Hydrolytic endonucleolytic ribozyme (HYER) is programmable for sequence-specific DNA cleavage.
Science, 383:eadh4859-eadh4859, 2024

PubMed Abstract: Ribozymes are catalytic RNAs with diverse functions including self-splicing and polymerization. This work aims to discover natural ribozymes that behave as hydrolytic and sequence-specific DNA endonucleases, which could be repurposed as DNA manipulation tools. Focused on bacterial group II-C introns, we found that many systems without intron-encoded protein propagate multiple copies in their resident genomes. These introns, named HYdrolytic Endonucleolytic Ribozymes (HYERs), cleaved RNA, single-stranded DNA, bubbled double-stranded DNA (dsDNA), and plasmids in vitro. HYER1 generated dsDNA breaks in the mammalian genome. Cryo-electron microscopy analysis revealed a homodimer structure for HYER1, where each monomer contains a Mg-dependent hydrolysis pocket and captures DNA complementary to the target recognition site (TRS). Rational designs including TRS extension, recruiting sequence insertion, and heterodimerization yielded engineered HYERs showing improved specificity and flexibility for DNA manipulation.

PubMed: 38301022
DOI: 10.1126/science.adh4859

Experimental method

ELECTRON MICROSCOPY (3.41 Å)