8CDV

Rnase R bound to a 30S degradation intermediate (state II)

8CDV の概要

• エントリーDOI: 10.2210/pdb8cdv/pdb
• 関連するPDBエントリー: 8CDU
• EMDBエントリー: 16595 16596
• 分子名称: 16S rRNA, 30S ribosomal protein S12, 30S ribosomal protein S13, ... (19 entities in total)
• 機能のキーワード: ssu, 30s, rnase r, ribosomal degradation, turnover, ribosome
• 由来する生物種: Bacillus subtilis subsp. subtilis str. 168; 詳細
• タンパク質・核酸の鎖数: 19
• 化学式量合計: 809548.65

構造登録者

Paternoga, H.,Dimitrova-Paternoga, L.,Wilson, D.N. (登録日: 2023-02-01, 公開日: 2023-12-20, 最終更新日: 2024-03-13)

主引用文献

Dimitrova-Paternoga, L.,Kasvandik, S.,Beckert, B.,Granneman, S.,Tenson, T.,Wilson, D.N.,Paternoga, H.
Structural basis of ribosomal 30S subunit degradation by RNase R.
Nature, 626:1133-1140, 2024

PubMed Abstract: Protein synthesis is a major energy-consuming process of the cell that requires the controlled production and turnover of ribosomes. Although the past few years have seen major advances in our understanding of ribosome biogenesis, structural insight into the degradation of ribosomes has been lacking. Here we present native structures of two distinct small ribosomal 30S subunit degradation intermediates associated with the 3' to 5' exonuclease ribonuclease R (RNase R). The structures reveal that RNase R binds at first to the 30S platform to facilitate the degradation of the functionally important anti-Shine-Dalgarno sequence and the decoding-site helix 44. RNase R then encounters a roadblock when it reaches the neck region of the 30S subunit, and this is overcome by a major structural rearrangement of the 30S head, involving the loss of ribosomal proteins. RNase R parallels this movement and relocates to the decoding site by using its N-terminal helix-turn-helix domain as an anchor. In vitro degradation assays suggest that head rearrangement poses a major kinetic barrier for RNase R, but also indicate that the enzyme alone is sufficient for complete degradation of 30S subunits. Collectively, our results provide a mechanistic basis for the degradation of 30S mediated by RNase R, and reveal that RNase R targets orphaned 30S subunits using a dynamic mechanism involving an anchored switching of binding sites.

PubMed: 38326618
DOI: 10.1038/s41586-024-07027-6

実験手法

ELECTRON MICROSCOPY (4.73 Å)