The solution structure of the Sac7d/DNA complex: A small-angle X-ray scattering study

Small-angle X-ray scattering has been used to study the structure of the mu ltimeric complexes that form between double-stranded DNA and the archaeal c hromatin protein Sac7d from Sulfolobus acidocaldarius. Scattering data from complexes of Sac7d with a defined 32-mer oligonucleotide, with poly[d(GC)] , and with E. coli DNA indicate that the protein binds along the surface of an extended DNA structure. Molecular models of fully saturated Sac7d/DNA c omplexes were constructed using constraints from crystal structure and solu tion binding data. Conformational space was searched systematically by vary ing the parameters of the models within the constrained set to find the bes t fits between the X-ray scattering data and simulated scattering curves. T he best fits were obtained for models composed of repeating segments of B-D NA with sharp kinks at contiguous protein binding sites. The results are co nsistent with extrapolation of the X-ray crystal structure of a 1:1 Sac7d/o ctanucleotide complex [Robinson, H., et al, (1998) Nature 392, 202-205] to polymeric DNA. The DNA conformation in our multimeric Sac7d/DNA model has t he base pairs tilted by about 35 degrees and displaced 3 Angstrom from the helix axis. There is a large roll between two base pairs at the protein-ind uced kink site, resulting in an overall bending angle of about 70 degrees f or Sac7d binding, Regularly repeating bends in the fully saturated complex result in a zigzag structure with negligible compaction of DNA. The Sac7d m olecules in the model form a unique structure with two left-handed helical ribbons winding around the outside of the right-handed duplex DNA.