9OVC

Structure of Geobacillus stearothermophilus RNase P ribozyme in 10 mM Mg2+

Summary for 9OVC

• Entry DOI: 10.2210/pdb9ovc/pdb
• EMDB information: 70897
• Descriptor: RNase P ribozyme, MAGNESIUM ION (2 entities in total)
• Functional Keywords: ribozyme, rna, rnase p
• Biological source: Geobacillus stearothermophilus
• Total number of polymer chains: 1
• Total formula weight: 136397.90

Authors

Lee, Y.-T.,Skeparnias, I.,Stagno, J.R.,Wang, Y.-X. (deposition date: 2025-05-29, release date: 2026-05-20)

Primary citation

Lee, Y.T.,Degenhardt, M.F.S.,Skeparnias, I.,Chen, S.Y.,Bhoge, B.A.,Tarasov, S.G.,Dyba, M.A.,Zhang, J.,Stagno, J.R.,Wang, Y.X.
Structural basis for protein-free catalysis by ribonuclease P ribozyme.
Nat Commun, 2026

PubMed Abstract: Ribonuclease P (RNase P) is an essential metallonuclease found in all three domains of life. However, the structural basis for the ancient RNase P RNA component acting alone as a ribozyme and catalytic metal-ion chemistry remains unknown. We report a series of cryo-EM structures, at resolutions of 2.8-3.5 Å, of the Geobacillus stearothermophilus RNase P aporibozyme (apoE) in various states of the catalytic cycle. The formation of both the tetraloop/tetraloop-receptor interaction and the interdigitated double T-loop motif in the substrate-specificity domain facilitates substrate binding. The apoE uses two metal ions for catalysis, suggesting a catalytic mechanism and evolutionary importance of the RNase P ribozyme to function without its protein component. Together, our data portray the regulatory RNA-RNA interfaces, dynamic structures, and cation traffic that confer function to a trans-acting ribozyme.

PubMed: 41986363
DOI: 10.1038/s41467-026-71597-4

Experimental method

ELECTRON MICROSCOPY (2.97 Å)