Structure and mechanistic features of the prokaryotic minimal RNase P
- Institute of Pharmaceutical Chemistry, Philipps-University Marburg,, Germany
- Department of Structural Biology, Max Planck Institute of Biophysics, Germany
- Center for Synthetic Microbiology and Department of Chemistry, Philipps-University Marburg, Germany
- Max Planck Institute of Biophysics, Germany
- Philipps-Universitaet Marburg, Germany
Abstract
Endonucleolytic removal of 5'-leader sequences from tRNA precursor transcripts (pre-tRNAs) by RNase P is essential for protein synthesis. Beyond RNA-based RNase P enzymes, protein-only versions of the enzyme exert this function in various Eukarya (there termed PRORPs) and in some bacteria (Aquifex aeolicus and close relatives); both enzyme types belong to distinct subgroups of the PIN domain metallonuclease superfamily. Homologs of Aquifex RNase P (HARPs) are also expressed in some other bacteria and many archaea, where they coexist with RNA-based RNase P and do not represent the main RNase P activity. Here we solved the structure of the bacterial HARP from Halorhodospira halophila by cryo-EM revealing a novel screw-like dodecameric assembly. Biochemical experiments demonstrate that oligomerization is required for RNase P activity of HARPs. We propose that the tRNA substrate binds to an extended spike-helix (SH) domain that protrudes from the screw-like assembly to position the 5'-end in close proximity to the active site of the neighboring dimer. The structure suggests that eukaryotic PRORPs and prokaryotic HARPs recognize the same structural elements of pre-tRNAs (tRNA elbow region and cleavage site). Our analysis thus delivers the structural and mechanistic basis for pre-tRNA processing by the prokaryotic HARP system.
Data availability
Coordinates and structure factors have been deposited within the protein data bank (PDB) and the electron microscopy data bank (EMDB) under accession codes: 7OG5 and EMD-12878. The authors declare that all other data supporting the findings of this study are available within the article and its supplementary information files.
Article and author information
Author details
Pietro Ivan Giammarinaro
Funding
Deutsche Forschungsgemeinschaft (HA 1672/19-1)
- Roland Karl Hartmann
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Copyright
© 2021, Feyh et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
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Structure and mechanistic features of the prokaryotic minimal RNase P
eLife 10:e70160.
https://doi.org/10.7554/eLife.70160
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