title: Recognition of a DNA operator by the repressor of phage 434: a view at high resolution.
abstract: The repressors of temperate bacteriophages such as 434 and lambda control transcription by binding to a set of DNA operator sites. The different affinity of repressor for each of these sites ensures efficient regulation. High-resolution x-ray crystallography was used to study the DNA-binding domain of phage 434 repressor in complex with a synthetic DNA operator. The structure shows recognition of the operator by direct interactions with base pairs in the major groove, combined with the sequence-dependent ability of DNA to adopt the required conformation on binding repressor. In particular, a network of three-centered bifurcated hydrogen bonds among base pairs in the operator helps explain why 434 repressor prefers certain sites over others. These bonds, which stabilize the conformation of the bound DNA, can form only with certain sequences.
authors.affiliation: Department of Biochemistry and Molecular Biology, Harvard University, Cambridge, MA 02138.
authors.forename: A K
authors.initials: AK
authors.lastname: Aggarwal
authors.forename: D W
authors.initials: DW
authors.lastname: Rodgers
authors.forename: M
authors.initials: M
authors.lastname: Drottar
authors.forename: M
authors.initials: M
authors.lastname: Ptashne
authors.forename: S C
authors.initials: SC
authors.lastname: Harrison
mesh_terms: D001482:Base Composition; D001483:Base Sequence; D001665:Binding Sites; D004247:DNA / Q000378:metabolism*; D004268:DNA-Binding Proteins; D006860:Hydrogen Bonding; D015394:Molecular Structure; D009690:Nucleic Acid Conformation; D009875:Operator Regions, Genetic; D011485:Protein Binding; D011487:Protein Conformation; D012097:Repressor Proteins / Q000378:metabolism*; D012984:Software; D014157:Transcription Factors / Q000378:metabolism*; D014764:Viral Proteins / Q000378:metabolism*; D054334:Viral Regulatory and Accessory Proteins; D014961:X-Ray Diffraction
chemical_list: D004268:DNA-Binding Proteins; D012097:Repressor Proteins; D014157:Transcription Factors; D014764:Viral Proteins; D054334:Viral Regulatory and Accessory Proteins; C016649:phage repressor proteins; D004247:DNA