title: The DNA binding arm of lambda repressor: critical contacts from a flexible region.
abstract: Segments of protein that do not adopt a well-ordered conformation in the absence of DNA can still contribute to site-specific recognition of DNA. The first six residues (NH2-Ser1-Thr2-Lys3-Lys4-Lys5-Pro6-) of phage lambda repressor are flexible but are important for site-specific binding. Low-temperature x-ray crystallography and codondirected saturation mutagenesis were used to study the role of this segment. All of the functional sequences have the form [X]1-[X]2-[Lys or Arg]3-[Lys]4-[Lys or Arg]5-[X]6. A high-resolution (1.8 angstrom) crystal structure shows that Lys3 and Lys4 each make multiple hydrogen bonds with guanines and that Lys5 interacts with the phosphate backbone. The symmetry of the complex breaks down near the center of the site, and these results suggest a revision in the traditional alignment of the six lambda operator sites.
authors.affiliation: Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205.
authors.forename: N D
authors.initials: ND
authors.lastname: Clarke
authors.forename: L J
authors.initials: LJ
authors.lastname: Beamer
authors.forename: H R
authors.initials: HR
authors.lastname: Goldberg
authors.forename: C
authors.initials: C
authors.lastname: Berkower
authors.forename: C O
authors.initials: CO
authors.lastname: Pabo
mesh_terms: D000595:Amino Acid Sequence; D010582:Bacteriophage lambda / Q000235:genetics; D004279:DNA, Viral / Q000737:chemistry*; D004268:DNA-Binding Proteins; D014644:Genetic Variation; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D012097:Repressor Proteins / Q000737:chemistry*; D014764:Viral Proteins; D054334:Viral Regulatory and Accessory Proteins / Q000737:chemistry*; D014961:X-Ray Diffraction
chemical_list: D004279:DNA, Viral; D004268:DNA-Binding Proteins; D012097:Repressor Proteins; D014764:Viral Proteins; D054334:Viral Regulatory and Accessory Proteins; C016649:phage repressor proteins