Summary information and primary citation
- PDB-id
-
2g8f;
DSSR-derived features in text and
JSON formats
- Class
- hydrolase-RNA-DNA
- Method
- X-ray (1.65 Å)
- Summary
- B. halodurans rnase h catalytic domain e188a mutant in
complex with mg2+ and RNA-DNA hybrid (non-p nick at the
active site)
- Reference
-
Nowotny M, Yang W (2006): "Stepwise
analyses of metal ions in RNase H catalysis from
substrate destabilization to product release."
Embo J., 25, 1924-1933. doi:
10.1038/sj.emboj.7601076.
- Abstract
- In two-metal catalysis, metal ion A has been proposed
to activate the nucleophile and metal ion B to stabilize
the transition state. We recently reported crystal
structures of RNase H-RNA/DNA substrate complexes obtained
at 1.5-2.2 Angstroms. We have now determined and report
here structures of reaction intermediate and product
complexes of RNase H at 1.65-1.85 Angstroms. The movement
of the two metal ions suggests how they may facilitate RNA
hydrolysis during the catalytic process. Firstly, metal ion
A may assist nucleophilic attack by moving towards metal
ion B and bringing the nucleophile close to the scissile
phosphate. Secondly, metal ion B transforms from an
irregular coordination in the substrate complex to a more
regular geometry in the product complex. The exquisite
sensitivity of Mg(2+) to the coordination environment
likely destabilizes the enzyme-substrate complex and
reduces the energy barrier to form product. Lastly, product
release probably requires dissociation of metal ion A,
which is inhibited by either high concentrations of
divalent cations or mutation of an assisting protein
residue.
