Hatchet ribozyme structure and implications for cleavage mechanism

Proc Natl Acad Sci U S A. 2019 May 28;116(22):10783-10791. doi: 10.1073/pnas.1902413116. Epub 2019 May 14.


Small self-cleaving ribozymes catalyze site-specific cleavage of their own phosphodiester backbone with implications for viral genome replication, pre-mRNA processing, and alternative splicing. We report on the 2.1-Å crystal structure of the hatchet ribozyme product, which adopts a compact pseudosymmetric dimeric scaffold, with each monomer stabilized by long-range interactions involving highly conserved nucleotides brought into close proximity of the scissile phosphate. Strikingly, the catalytic pocket contains a cavity capable of accommodating both the modeled scissile phosphate and its flanking 5' nucleoside. The resulting modeled precatalytic conformation incorporates a splayed-apart alignment at the scissile phosphate, thereby providing structure-based insights into the in-line cleavage mechanism. We identify a guanine lining the catalytic pocket positioned to contribute to cleavage chemistry. The functional relevance of structure-based insights into hatchet ribozyme catalysis is strongly supported by cleavage assays monitoring the impact of selected nucleobase and atom-specific mutations on ribozyme activity.

Keywords: catalysis; cleavage; hatchet; noncoding RNA; ribozyme.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Catalysis
  • Hepatitis Delta Virus / enzymology
  • Nucleic Acid Conformation
  • RNA, Catalytic* / chemistry
  • RNA, Catalytic* / metabolism
  • RNA, Viral / chemistry
  • RNA, Viral / metabolism


  • RNA, Catalytic
  • RNA, Viral

Associated data

  • PDB/6JQ5
  • PDB/6JQ6