title: Crystal packing interaction that blocks crystallization of a site-specific DNA binding protein-DNA complex.
abstract: We present here three high-resolution crystal structures of complexes between the DNA-binding domain of the heat-shock transcription factor (HSF) and DNA oligomers. Although the DNA oligomers contain HSF's specific binding sequence, called a heat-shock element, the crystal structures do not contain the specific protein-DNA complex. In one crystal structure, the 10 base pair DNA oligomer is statically disordered. In the other two related structures, the 12 base pair DNA oligomers are in unique positions, but the protein-DNA contacts in these two crystals are not sequence specific. In all three structures, the DNA appears to act as a rigid, polyanion scaffold to support columns of proteins in a crystalline lattice. A robust crystal packing interface between protein monomers obscures the true DNA-binding surface, known from previous genetic and biochemical studies. By redesigning the protein to interfere with the crystal lattice contacts, we were able to obtain physiologically relevant crystals in a specific protein-DNA complex. Thus, a crystal-packing interface was able to prevent the weak, but physiological relevant interactions between a protein and DNA.
authors.affiliation: Department of Molecular and Cell Biology, University of California, Berkeley, California, USA.
authors.forename: O
authors.initials: O
authors.lastname: Littlefield
authors.forename: H C
authors.initials: HC
authors.lastname: Nelson
mesh_terms: D001665:Binding Sites; D003460:Crystallization; D018360:Crystallography, X-Ray / Q000379:methods*; D004247:DNA / Q000737:chemistry*; D004268:DNA-Binding Proteins / Q000737:chemistry*; D005656:Fungal Proteins / Q000737:chemistry; D006360:Heat-Shock Proteins / Q000737:chemistry; D007716:Kluyveromyces / Q000737:chemistry; D009690:Nucleic Acid Conformation; D025941:Protein Interaction Mapping / Q000379:methods; D029701:Saccharomyces cerevisiae Proteins; D014157:Transcription Factors / Q000737:chemistry
chemical_list: D004268:DNA-Binding Proteins; D005656:Fungal Proteins; C067168:HSF1 protein, S cerevisiae; D006360:Heat-Shock Proteins; D029701:Saccharomyces cerevisiae Proteins; D014157:Transcription Factors; D004247:DNA