2g8f | pdb_00002g8f

B. halodurans RNase H catalytic domain E188A mutant in complex with Mg2+ and RNA/DNA hybrid (non-P nick at the active site)

spinqualitylabelsall models 2g8f, resolution 1.65Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 2g8f is a 3 chain structure with sequence from Alkalihalobacillus halodurans. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Method: X-ray diffraction, Resolution 1.65Å Ligands: CL, MG Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Function RNH1_HALH5 Endonuclease that specifically degrades the RNA of RNA-DNA hybrids. Evolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMed 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. Stepwise analyses of metal ions in RNase H catalysis from substrate destabilization to product release.,Nowotny M, Yang W EMBO J. 2006 May 3;25(9):1924-33. Epub 2006 Apr 6. PMID:16601679 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See Also Ribonuclease 3D structures

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