1ZBI

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

Summary for 1ZBI

• Entry DOI: 10.2210/pdb1zbi/pdb
• Related: 1ZBF 1ZBL
• Descriptor: 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)
• Functional Keywords: rnase h, rna/dna hybrid, dde motif, hydrolase-rna-dna complex, hydrolase/rna/dna
• Biological source: Bacillus halodurans
• Cellular location: Cytoplasm (Potential): Q9KEI9
• Total number of polymer chains: 4
• Total formula weight: 40230.90

Authors

Nowotny, M.,Gaidamakov, S.A.,Crouch, R.J.,Yang, W. (deposition date: 2005-04-08, release date: 2005-07-12, Last modification date: 2023-08-23)

Primary citation

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

Experimental method

X-RAY DIFFRACTION (1.85 Å)