Structure of Arc represser in solution: evidence for a family of β-sheet DNA-binding proteins

Abstract

THE Arc represser^1–3, which is involved in the switch between lysis and lysogeny of Salmonella bacteriophage P22, does not belong to any of the known classes of DNA-binding proteins^4,5. Mutagenesis studies⁶ show that the DNA-binding region is located in the 15 N-terminal amino-acid residues. We have now determined the three-dimensional structure of the Arc dimer from an extensive set of inter proton-distance data obtained from ¹H NMR spectroscopy. A priori, intra- and inter-monomer nuclear Overhauser effects (NOEs) cannot be distinguished for a symmetric dimer. But by using the homology with the Escherichia coil Met represser⁷ we could interpret the NOEs unambiguously in an iterative structure refinement procedure. The final structure satisfies a large set of NOE constraints (1,352 for the dimer). It shows a strongly intertwined dimer, in which residues 8–14 of different monomers form an antiparallel β-sheet. A model for the Arc represser–operator complex can account for all available biochemical and genetic data. In this model two Arc dimers bind with their β-sheet regions in successive major grooves on one side of the DNA helix, similar to the Met repressor interaction. Thus, Arc and Met repressors are members of the same family of proteins, which contain an antiparallel β-sheet as the DNA-binding motif.