Summary information and primary citation
- PDB-id
- 5swm; SNAP-derived features in text and JSON formats;
DNAproDB
- Class
- hydrolase-RNA-DNA
- Method
- X-ray (1.5 Å)
- Summary
- Bacillus halodurans rnase h mutant d132n in complex with 12-mer frna-DNA hybrid
- Reference
- Pallan PS, Prakash TP, de Leon AR, Egli M (2016): "Limits of RNA 2'-OH Mimicry by Fluorine: Crystal Structure of Bacillus halodurans RNase H Bound to a 2'-FRNA:DNA Hybrid." Biochemistry, 55, 5321-5325. doi: 10.1021/acs.biochem.6b00849.
- Abstract
- RNase H1 cleaves the RNA strand of RNA:DNA hybrids. Replacement of RNA 2'-hydroxyls by fluorine (FRNA) is commonly used to stabilize aptamers and siRNAs. However, FRNA:DNA hybrids fail to elicit RNase H activity. The underlying reasons are unclear, as 2'-OH groups are not directly involved in cleavage. We determined the crystal structure of Bacillus halodurans RNase H bound to a FRNA:DNA hybrid. The structure points to dynamic (slippage of the FRNA:DNA hybrid relative to the enzyme), geometric (different curvatures of FRNA:DNA and RNA:DNA hybrids), and electronic reasons (Mg(2+) absent from the active site of the FRNA:DNA complex) for the loss of RNaseH activity.
