1ZBI

Bacillus halodurans RNase H catalytic domain mutant D132N in complex with 12-mer RNA/DNA hybrid

1ZBI の概要

• エントリーDOI: 10.2210/pdb1zbi/pdb
• 関連するPDBエントリー: 1ZBF 1ZBL
• 分子名称: 5'-R(*GP*AP*CP*AP*CP*CP*UP*GP*AP*UP*UP*C)-3', 5'-D(*GP*AP*AP*TP*CP*AP*GP*GP*TP*GP*TP*C)-3', ribonuclease H-related protein, ... (5 entities in total)
• 機能のキーワード: rnase h, rna/dna hybrid, dde motif, hydrolase-rna-dna complex, hydrolase/rna/dna
• 由来する生物種: Bacillus halodurans
• 細胞内の位置: Cytoplasm (Potential): Q9KEI9
• タンパク質・核酸の鎖数: 4
• 化学式量合計: 40230.90

構造登録者

Nowotny, M.,Gaidamakov, S.A.,Crouch, R.J.,Yang, W. (登録日: 2005-04-08, 公開日: 2005-07-12, 最終更新日: 2023-08-23)

主引用文献

Nowotny, M.,Gaidamakov, S.A.,Crouch, R.J.,Yang, W.
Crystal Structures of RNase H Bound to an RNA/DNA Hybrid: Substrate Specificity and Metal-Dependent Catalysis.
Cell(Cambridge,Mass.), 121:1005-1016, 2005

PubMed Abstract: RNase H belongs to a nucleotidyl-transferase superfamily, which includes transposase, retroviral integrase, Holliday junction resolvase, and RISC nuclease Argonaute. We report the crystal structures of RNase H complexed with an RNA/DNA hybrid and a mechanism for substrate recognition and two-metal-ion-dependent catalysis. RNase H specifically recognizes the A form RNA strand and the B form DNA strand. Structure comparisons lead us to predict the catalytic residues of Argonaute and conclude that two-metal-ion catalysis is a general feature of the superfamily. In nucleases, the two metal ions are asymmetrically coordinated and have distinct roles in activating the nucleophile and stabilizing the transition state. In transposases, they are symmetrically coordinated and exchange roles to alternately activate a water and a 3'-OH for successive strand cleavage and transfer by a ping-pong mechanism.

PubMed: 15989951
DOI: 10.1016/j.cell.2005.04.024

実験手法

X-RAY DIFFRACTION (1.85 Å)