Metal-ion coordination drives active-site remodeling for backsplicing in circularly permuted group II introns
- 1State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University , Hohhot 010020 ,
- 2State Key Laboratory of Genetics and Development of Complex Phenotypes, Department of Biochemistry and Biophysics, School of Life Sciences, Fudan University , Shanghai 200438 ,
- 3Center for mRNA Translational Research, Fudan University , Shanghai 200438 ,
Abstract
Circularly permuted (CP) group II introns are self-splicing ribozymes that undergo a sequential branching and backsplicing reaction to yield branched introns and circular exons (circRNAs). While the initial branching step is structurally characterized, the mechanistic principles that govern the subsequent large-scale active-site remodeling and stringent metal-ion specificity required for backsplicing remain poorly understood. Here, we present a series of high-resolution cryo-EM structures of the CP group II intron from Gluconacetobacter diazotrophicus PAL5 (Gdi-1), capturing the ribozyme at discrete stages along the branching -to- backsplicing pathway under distinct ionic conditions. Comparative analyses under K+/Mg2+, K+/Ca2+, and Cs+/Mg2+ conditions demonstrate that productive backsplicing relies on ion-specific coordination networks that govern 3′ splice site (3′SS) docking and catalytic center formation, revealing the precise metal-ion-coordinated conformational rearrangements and dynamic splice-site exchange mechanisms. Crucially, we identify a previously unrecognized, highly selective monovalent cation-binding site, K3, that structurally couples the γ–γ′ interaction to reassembly of the heteronuclear four-metal core, thereby promoting productive second-step active-site formation. Together, these findings establish a structural basis for metal-ion-dependent active-site remodeling during group II intron catalysis and provide mechanistic insights into metal-ion selectivity in circRNA biogenesis.
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BibTeX
@article{zhang2026metalion,
title = {{Metal-ion coordination drives active-site remodeling for backsplicing in circularly permuted group II introns}},
author = {Jie Zhang and Yuqi Yao and Jinbiao Ma},
journal = {Nucleic Acids Research},
year = {2026},
month = oct,
doi = {10.1093/nar/gkag1053},
url = {https://academic.oup.com/nar/article/doi/10.1093/nar/gkag1053/9004261},
note = {CC BY-NC 4.0},
}
RIS
TY - JOUR
TI - Metal-ion coordination drives active-site remodeling for backsplicing in circularly permuted group II introns
AU - Jie Zhang
AU - Yuqi Yao
AU - Jinbiao Ma
PY - 2026
DA - 2026/10/01
JO - Nucleic Acids Research
DO - 10.1093/nar/gkag1053
UR - https://academic.oup.com/nar/article/doi/10.1093/nar/gkag1053/9004261
AB - Circularly permuted (CP) group II introns are self-splicing ribozymes that undergo a sequential branching and backsplicing reaction to yield branched introns and circular exons (circRNAs). While the initial branching step is structurally characterized, the mechanistic principles that govern the subsequent large-scale active-site remodeling and stringent metal-ion specificity required for backsplicing remain poorly understood. Here, we present a series of high-resolution cryo-EM structures of the CP group II intron from Gluconacetobacter diazotrophicus PAL5 (Gdi-1), capturing the ribozyme at discrete stages along the branching -to- backsplicing pathway under distinct ionic conditions. Comparative analyses under K+/Mg2+, K+/Ca2+, and Cs+/Mg2+ conditions demonstrate that productive backsplicing relies on ion-specific coordination networks that govern 3′ splice site (3′SS) docking and catalytic center formation, revealing the precise metal-ion-coordinated conformational rearrangements and dynamic splice-site exchange mechanisms. Crucially, we identify a previously unrecognized, highly selective monovalent cation-binding site, K3, that structurally couples the γ–γ′ interaction to reassembly of the heteronuclear four-metal core, thereby promoting productive second-step active-site formation. Together, these findings establish a structural basis for metal-ion-dependent active-site remodeling during group II intron catalysis and provide mechanistic insights into metal-ion selectivity in circRNA biogenesis.
SN - 0305-1048
SN - 1362-4962
ER -