8SSG

Minimal protein-only/RNA-free Ribonuclease P from Hydrogenobacter thermophilus

Summary for 8SSG

• Entry DOI: 10.2210/pdb8ssg/pdb
• Descriptor: RNA-free ribonuclease P (2 entities in total)
• Functional Keywords: rna-free ribonuclease p, hydrolase, nuclease
• Biological source: Hydrogenobacter thermophilus TK-6
• Total number of polymer chains: 7
• Total formula weight: 157379.25

Authors

Mendoza, J.,Wilhelm, C.A.,Mallik, L.,Koutmos, M. (deposition date: 2023-05-08, release date: 2023-10-18, Last modification date: 2023-11-22)

Primary citation

Wilhelm, C.A.,Mallik, L.,Kelly, A.L.,Brotzman, S.,Mendoza, J.,Anders, A.G.,Leskaj, S.,Castillo, C.,Ruotolo, B.T.,Cianfrocco, M.A.,Koutmos, M.
Bacterial RNA-free RNase P: Structural and functional characterization of multiple oligomeric forms of a minimal protein-only ribonuclease P.
J.Biol.Chem., 299:105327-105327, 2023

PubMed Abstract: tRNAs are typically transcribed with extended 5' and 3' ends that must be removed before they attain their active form. One of the first steps of tRNA processing in nearly every organism is the removal of the 5' leader sequence by ribonuclease P (RNase P). Here, we investigate a recently discovered class of RNase P enzymes, Homologs of Aquifex RNase P (HARPs). In contrast to other RNase Ps, HARPs consist only of a metallonuclease domain and lack the canonical substrate recognition domain essential in other classes of proteinaceous RNase P. We determined the cryo-EM structure of Aquifex aeolicus HARP (Aq880) and two crystal structures of Hydrogenobacter thermophilus HARP (Hth1307) to reveal that both enzymes form large ring-like assemblies: a dodecamer in Aq880 and a tetradecamer in Hth1307. In both oligomers, the enzyme active site is 42 Å away from a positively charged helical region, as seen in other protein-only RNase P enzymes, which likely serves to recognize and bind the elbow region of the pre-tRNA substrate. In addition, we use native mass spectrometry to confirm and characterize the previously unreported tetradecamer state. Notably, we find that multiple oligomeric states of Hth1307 are able to cleave pre-tRNAs. Furthermore, our single-turnover kinetic studies indicate that Hth1307 cleaves pre-tRNAs from multiple species with a preference for native substrates. These data provide a closer look at the nuanced similarities and differences in tRNA processing across disparate classes of RNase P.

PubMed: 37806495
DOI: 10.1016/j.jbc.2023.105327

Experimental method

X-RAY DIFFRACTION (3.2 Å)