2G8I: B. Halodurans Rnase H Catalytic Domain D192n Mutant In Complex With Mn2+ And RnaDNA HYBRID (NON-P Nick At The Active Site)

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.
PDB ID: 2G8IDownload
MMDB ID: 102956
PDB Deposition Date: 2006/3/2
Updated in MMDB: 2012/09
Experimental Method:
x-ray diffraction
Resolution: 1.65  Å
Source Organism:
Bacillus halodurans
Similar Structures:
Biological Unit for 2G8I: trimeric; determined by author
Molecular Components in 2G8I
Label Count Molecule
Protein (1 molecule)
Ribonuclease H
Molecule annotation
Nucleotides(2 molecules)
Molecule annotation
Molecule annotation
Chemicals (6 molecules)
* Click molecule labels to explore molecular sequence information.

Citing MMDB