Structural basis of pre-tRNA intron removal by human tRNA splicing endonuclease

Mol Cell. 2023 Apr 20;83(8):1328-1339.e4. doi: 10.1016/j.molcel.2023.03.015. Epub 2023 Apr 6.

Abstract

Removal of the intron from precursor-tRNA (pre-tRNA) is essential in all three kingdoms of life. In humans, this process is mediated by the tRNA splicing endonuclease (TSEN) comprising four subunits: TSEN2, TSEN15, TSEN34, and TSEN54. Here, we report the cryo-EM structures of human TSEN bound to full-length pre-tRNA in the pre-catalytic and post-catalytic states at average resolutions of 2.94 and 2.88 Å, respectively. Human TSEN features an extended surface groove that holds the L-shaped pre-tRNA. The mature domain of pre-tRNA is recognized by conserved structural elements of TSEN34, TSEN54, and TSEN2. Such recognition orients the anticodon stem of pre-tRNA and places the 3'-splice site and 5'-splice site into the catalytic centers of TSEN34 and TSEN2, respectively. The bulk of the intron sequences makes no direct interaction with TSEN, explaining why pre-tRNAs of varying introns can be accommodated and cleaved. Our structures reveal the molecular ruler mechanism of pre-tRNA cleavage by TSEN.

Keywords: RNA metabolism; splicing mechanism; tRNA splicing; tRNA splicing endonuclease.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Endonucleases / genetics
  • Endoribonucleases* / genetics
  • Humans
  • Introns / genetics
  • Nucleic Acid Conformation
  • RNA Precursors* / genetics
  • RNA Precursors* / metabolism
  • RNA Splice Sites
  • RNA Splicing
  • RNA, Transfer / genetics
  • RNA, Transfer / metabolism

Substances

  • splicing endonuclease
  • RNA Precursors
  • Endoribonucleases
  • RNA, Transfer
  • RNA Splice Sites
  • TSEN15 protein, human
  • Endonucleases