1rvb
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MG2+ BINDING TO THE ACTIVE SITE OF ECO RV ENDONUCLEASE: A CRYSTALLOGRAPHIC STUDY OF COMPLEXES WITH SUBSTRATE AND PRODUCT DNA AT 2 ANGSTROMS RESOLUTION
OverviewOverview
The type II restriction endonuclease EcoRV was crystallized as a complex, with the substrate DNA undecamer AAAGATATCTT (recognition sequence, underlined). These crystals diffract to much better resolution (2 A) than, was the case for the previously reported complex with the decamer, GGGATATCCC [Winkler, F. K., Banner, D. W., Oefner, C., Tsernoglou, D., Brown, R. S., Heathman, S. P., Bryan, R. K., Martin, P. D., Petratos, K., & Wilson, K. S. (1993) EMBO J. 12, 1781-1795]. The crystal structure, contains one dimer complex in the asymmetric unit and was solved by, molecular replacement. The same kinked DNA conformation characteristic for, enzyme-bound cognate DNA is observed. Crystals, soaked with Mg2+, show the, essential cofactor bound at only one active site of the dimer, and the DNA, is not cleaved. The Mg2+ has one oxygen from the scissile phosphodiester, group and two carboxylate oxygens, one form Asp74 and one from Asp90, in, its octahedral ligand sphere. The scissile phosphodiester group is pulled, by 1 A toward the Mg2+. After substrate cleavage in solution, isomorphous, crystals containing the enzyme--product--Mg2+ complex were obtained. In, this structure, each of the 5'-phosphate groups is bound to two Mg2+. The, kinked DNA conformation is essentially maintained, but the two central, adenines, 3' to the cleavage sites, form an unusual cross-strand base, stacking. The structures have been refined to R factors of 0.16 at 2.1-2.0, A resolution maintaining very good stereochemistry. On the basis of these, structures and inspired by recent kinetic data [Vipond, I. B., & Halford, S. E. (1994) Biochemistry (second paper of three in this issue)], we have, constructed a transition state model with two metals bound to the scissile, phosphorane group.
About this StructureAbout this Structure
1RVB is a Single protein structure of sequence from Escherichia coli with MG as ligand. Full crystallographic information is available from OCA.
ReferenceReference
Mg2+ binding to the active site of EcoRV endonuclease: a crystallographic study of complexes with substrate and product DNA at 2 A resolution., Kostrewa D, Winkler FK, Biochemistry. 1995 Jan 17;34(2):683-96. PMID:7819264
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