1SJF

Crystal Structure of the Hepatitis Delta Virus Gemonic Ribozyme Precursor, with C75U mutaion, in Cobalt Hexammine solution

1SJF の概要

• エントリーDOI: 10.2210/pdb1sjf/pdb
• 関連するPDBエントリー: 1CX0 1DRZ 1SJF 1VBX 1VBY 1VBZ 1VC0 1VC5 1VC6 1VC7
• 分子名称: Hepatitis Delta virus ribozyme, U1 small nuclear ribonucleoprotein A, COBALT HEXAMMINE(III), ... (4 entities in total)
• 機能のキーワード: hdv, ribozyme, rna, u1a, precursor, translation-rna complex, translation/rna
• 由来する生物種: Homo sapiens (human); 詳細
• 細胞内の位置: Nucleus: P09012
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 36288.23

構造登録者

Ke, A.,Zhou, K.,Ding, F.,Cate, J.H.D.,Doudna, J.A. (登録日: 2004-03-03, 公開日: 2004-05-18, 最終更新日: 2024-05-29)

主引用文献

Ke, A.,Zhou, K.,Ding, F.,Cate, J.H.,Doudna, J.A.
A conformational switch controls hepatitis delta virus ribozyme catalysis.
Nature, 429:201-205, 2004

PubMed Abstract: Ribozymes enhance chemical reaction rates using many of the same catalytic strategies as protein enzymes. In the hepatitis delta virus (HDV) ribozyme, site-specific self-cleavage of the viral RNA phosphodiester backbone requires both divalent cations and a cytidine nucleotide. General acid-base catalysis, substrate destabilization and global and local conformational changes have all been proposed to contribute to the ribozyme catalytic mechanism. Here we report ten crystal structures of the HDV ribozyme in its pre-cleaved state, showing that cytidine is positioned to activate the 2'-OH nucleophile in the precursor structure. This observation supports its proposed role as a general base in the reaction mechanism. Comparison of crystal structures of the ribozyme in the pre- and post-cleavage states reveals a significant conformational change in the RNA after cleavage and that a catalytically critical divalent metal ion from the active site is ejected. The HDV ribozyme has remarkable chemical similarity to protein ribonucleases and to zymogens for which conformational dynamics are integral to biological activity. This finding implies that RNA structural rearrangements control the reactivity of ribozymes and ribonucleoprotein enzymes.

PubMed: 15141216
DOI: 10.1038/nature02522

実験手法

X-RAY DIFFRACTION (2.75 Å)