Structure of the Escherichia coli Primase Zinc Site

The structure of the single zinc site in primase from Escherichia coli was studied using X-ray absorption spectroscopy (XAS). XAS provides information about the local structure (radius about 5 A) of atoms surrounding the metal and has been widely used to characterize metalloproteins. The edge region of the spectrum provides information about the chemical identity of the ligating atoms and their coordination geometry while the extended fine structure provides information about the number of ligating atoms and their average distance from the metal. The zinc site in native primase was found to be tetrahedrally ligated by three sulfurs at an average distance of 2.37 +/- 0.02 A and one histidine nitrogen located at a distance of 2.11 +/- 0.02 A. In the zinc site in the high-magnesium conformation of primase, one sulfur ligand is lost and one or two oxygen ligands are gained. Finally, when ATP was added to primase, the zinc site structure was altered to octahedral coordination with three sulfur and three oxygen (or nitrogen) ligands, one of which could be a histidine nitrogen. These results and others indicate that the primase zinc site functions similar to the essential zinc site from Escherichia coli RNA polymerase which can also be coordinated by its initiating nucleotide ATP [Wu, F. Y.-H., Huang, W.-J., Sinclair. R. B., & Powers, L. (1992) J. Biol. Chem. 267, 25560-25567]. In light of this. the high-magnesium conformation result suggests that high magnesium primase becomes inactive because the zinc is prevented from coordinating ATP.