4V8X の概要
| エントリーDOI | 10.2210/pdb4v8x/pdb |
| 分子名称 | 16S ribosomal RNA, 30S RIBOSOMAL PROTEIN S10, 30S RIBOSOMAL PROTEIN S11, ... (61 entities in total) |
| 機能のキーワード | ribosome, toxin-antitoxin, ribosome-dependent nuclease, mrna degradation, translation regulation |
| 由来する生物種 | ESCHERICHIA COLI 詳細 |
| タンパク質・核酸の鎖数 | 118 |
| 化学式量合計 | 4522358.49 |
| 構造登録者 | |
| 主引用文献 | Feng, S.,Chen, Y.,Kamada, K.,Wang, H.,Tang, K.,Wang, M.,Gao, Y. Yoeb-Ribosome Structure: A Canonical Rnase that Requires the Ribosome for its Specific Activity. Nucleic Acids Res., 41:9549-, 2013 Cited by PubMed Abstract: As a typical endoribonuclease, YoeB mediates cellular adaptation in diverse bacteria by degrading mRNAs on its activation. Although the catalytic core of YoeB is thought to be identical to well-studied nucleases, this enzyme specifically targets mRNA substrates that are associated with ribosomes in vivo. However, the molecular mechanism of mRNA recognition and cleavage by YoeB, and the requirement of ribosome for its optimal activity, largely remain elusive. Here, we report the structure of YoeB bound to 70S ribosome in pre-cleavage state, revealing that both the 30S and 50S subunits participate in YoeB binding. The mRNA is recognized by the catalytic core of YoeB, of which the general base/acid (Glu46/His83) are within hydrogen-bonding distance to their reaction atoms, demonstrating an active conformation of YoeB on ribosome. Also, the mRNA orientation involves the universally conserved A1493 and G530 of 16S rRNA. In addition, mass spectrometry data indicated that YoeB cleaves mRNA following the second position at the A-site codon, resulting in a final product with a 3'-phosphate at the newly formed 3' end. Our results demonstrate a classical acid-base catalysis for YoeB-mediated RNA hydrolysis and provide insight into how the ribosome is essential for its specific activity. PubMed: 23945936DOI: 10.1093/NAR/GKT742 主引用文献が同じPDBエントリー |
| 実験手法 | X-RAY DIFFRACTION (3.35 Å) |
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