8KDA

Cryo-EM structure of Hydrogenobacter thermophilus minimal protein-only RNase P (HARP) in complex with pre-tRNAs

Summary for 8KDA

• Entry DOI: 10.2210/pdb8kda/pdb
• EMDB information: 37129
• Descriptor: RNA-free ribonuclease P, Aquifex aeolicus pre-tRNAVal, MAGNESIUM ION (3 entities in total)
• Functional Keywords: pre-trna processing, trna, pre-trna complex, hydrolase-rna complex, rna-free ribonuclease p, ribonuclease p, hydrolase/rna
• Biological source: Hydrogenobacter thermophilus DSM 653 (Hydrogenobacter thermophilus TK-6); More
• Total number of polymer chains: 17
• Total formula weight: 381641.35

Authors

Teramoto, T.,Adachi, N.,Yokogawa, T.,Koyasu, T.,Mayanagi, K.,Nakamura, T.,Senda, T.,Kakuta, Y. (deposition date: 2023-08-09, release date: 2024-08-14, Last modification date: 2025-07-16)

Primary citation

Teramoto, T.,Koyasu, T.,Yokogawa, T.,Adachi, N.,Mayanagi, K.,Nakamura, T.,Senda, T.,Kakuta, Y.
Structural basis of transfer RNA processing by bacterial minimal RNase P.
Nat Commun, 16:5456-5456, 2025

PubMed Abstract: Precursor tRNAs (pre-tRNAs) require nucleolytic removal of 5'-leader and 3'-trailer sequences for maturation, which is essential for proper tRNA function. The endoribonuclease RNase P exists in diverse forms, including RNA- and protein-based RNase P, and removes 5'-leader sequences from pre-tRNAs. Some bacteria and archaea possess a unique minimal protein-based RNase P enzyme, HARP, which forms dodecamers with twelve active sites. Here, we present cryogenic electron microscopy structures of HARP dodecamers complexed with five pre-tRNAs, and we show that HARP oligomerization enables specific recognition of the invariant distance between the acceptor stem 5'-end and the TψC-loop, functioning as a molecular ruler-a feature representing convergent evolution among RNase P enzymes. The HARP dodecamer uses only five active sites for 5'-leader cleavage, while we identify a 3'-trailer cleavage activity in the remaining seven sites. This elucidation reveals how small proteins evolve through oligomerization to adapt a pivotal biological function (5'-leader processing) and acquire a novel function (3'-trailer processing).

PubMed: 40593470
DOI: 10.1038/s41467-025-60002-1

Experimental method

ELECTRON MICROSCOPY (3.19 Å)