{
  "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.",
  "abstract_shown": true,
  "affiliations": [
    "State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University , Hohhot 010020 ,",
    "State Key Laboratory of Genetics and Development of Complex Phenotypes, Department of Biochemistry and Biophysics, School of Life Sciences, Fudan University , Shanghai 200438 ,",
    "Center for mRNA Translational Research, Fudan University , Shanghai 200438 ,"
  ],
  "article_type": "research article",
  "arxiv": null,
  "author_total": 3,
  "authors": [
    {
      "affs": [
        0,
        1
      ],
      "name": "Jie Zhang",
      "orcid": "0009-0004-8506-531X"
    },
    {
      "affs": [
        1
      ],
      "name": "Yuqi Yao",
      "orcid": "0009-0000-7232-4926"
    },
    {
      "affs": [
        1,
        2
      ],
      "name": "Jinbiao Ma",
      "orcid": "0000-0002-0232-1786"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/br8c0dmx4haxv.bib",
  "cited_by": 0,
  "doi": "10.1093/nar/gkag1053",
  "fulltext_url": "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13717195/?tool=EBI",
  "id": "br8c0dmx4haxv",
  "issns": [
    "0305-1048",
    "1362-4962"
  ],
  "landing_url": "https://academic.oup.com/nar/article/doi/10.1093/nar/gkag1053/9004261",
  "language": "eng",
  "licence": "CC-BY-NC-4.0",
  "licence_label": "CC BY-NC 4.0",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by-nc/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "heading",
      "AcademicSubjects/SCI00010"
    ],
    [
      "heading",
      "Nucleic Acid Enzymes"
    ]
  ],
  "openalex": null,
  "pdf_url": "https://academic.oup.com/nar/article-pdf/54/20/gkag1053/72579603/gkag1053.pdf",
  "pmcid": "PMC13717195",
  "pmid": "42953968",
  "published": "2026-10-01",
  "publisher": "Oxford University Press (OUP)",
  "ris": "https://research.draconitic.com/paper/br8c0dmx4haxv.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:18:50Z",
      "native_id": "10.1093/nar/gkag1053",
      "source": "crossref",
      "url": "https://academic.oup.com/nar/article/doi/10.1093/nar/gkag1053/9004261"
    },
    {
      "first_seen": "2026-10-31T00:20:37Z",
      "native_id": "PMC:PMC13717195",
      "source": "europepmc",
      "url": "https://europepmc.org/article/PMC/PMC13717195"
    },
    {
      "first_seen": "2026-11-01T00:20:44Z",
      "native_id": "MED:42953968",
      "source": "europepmc",
      "url": "https://europepmc.org/article/MED/42953968"
    },
    {
      "first_seen": "2026-11-02T12:21:33Z",
      "native_id": "PMC13717195",
      "source": "pmc",
      "url": "https://doi.org/10.1093/nar/gkag1053"
    }
  ],
  "subjects": [
    {
      "field": "biochemistry",
      "origin": "issn:0305-1048",
      "subfield": "molecular-biology"
    }
  ],
  "title": "Metal-ion coordination drives active-site remodeling for backsplicing in circularly permuted group II introns",
  "title_text": "Metal-ion coordination drives active-site remodeling for backsplicing in circularly permuted group II introns",
  "type": "peer-reviewed",
  "updated_at": "2026-11-02T12:21:33Z",
  "url": "https://research.draconitic.com/paper/br8c0dmx4haxv",
  "venue": "Nucleic Acids Research",
  "versions": []
}