Structural basis for protein-free catalysis by ribonuclease P ribozyme

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.

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Publication Details

Journal
Nature Communications
Published
2026-04-15
DOI
https://doi.org/10.1038/s41467-026-71597-4
Primary Topic
RNA and protein synthesis mechanisms
Type
article
Field-Weighted Citation Impact
0.00

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article

Structural basis for protein-free catalysis by ribonuclease P ribozyme

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RNA and protein synthesis mechanisms
article

Structural basis for protein-free catalysis by ribonuclease P ribozyme

Szu-Yun Chen, Bapurao A. Bhoge, Yun‐Xing Wang, Sergey G. Tarasov, Yun-Tzai Lee, Maximilia Frazão de Souza Degenhardt, Ilias Skeparnias, Jinwei Zhang, Jason R. Stagno, Marzena Dyba
article en

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.

Nature Communications
National Institute of Diabetes and Digestive and Kidney Diseases (US), Protein Express (United States) (US), Frederick National Laboratory for Cancer Research (US), National Cancer Institute (US)
National Cancer Institute, National Institute of Diabetes and Digestive and Kidney Diseases
Openalex Percentile: Top 16%
RNA and protein synthesis mechanisms
DOIOpen Access PDFOpenAlex
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