Structure of the lambda complex at 2.5 A resolution: details of the repressor-operator interactions.
The crystal structure of a complex containing the DNA-binding domain of lambda repressor and a lambda operator site was determined at 2.5 A resolution and refined to a crystallographic R factor of 24.2 percent. The complex is stabilized by an extensive network of hydrogen bonds between the protein and the sugar-phosphate backbone. Several side chains form hydrogen bonds with sites in the major groove, and hydrophobic contacts also contribute to the specificity of binding. The overall arrangement of the complex is quite similar to that predicted from earlier modeling studies, which fit the protein dimer against linear B-form DNA. However, the cocrystal structure reveals important side chain-side chain interactions that were not predicted from the modeling or from previous genetic and biochemical studies.
Jordan
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Department of Biophysics, Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205.
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D001482:Base Composition; D001483:Base Sequence; D001665:Binding Sites; D055598:Chemical Phenomena; D002621:Chemistry; D003460:Crystallization; D004247:DNA / Q000378:metabolism*; D004268:DNA-Binding Proteins; D005973:Glutamine / Q000378:metabolism; D006860:Hydrogen Bonding; D008969:Molecular Sequence Data; D015394:Molecular Structure; D009690:Nucleic Acid Conformation; D009875:Operator Regions, Genetic; D011485:Protein Binding; D011487:Protein Conformation; D012097:Repressor Proteins / Q000235:genetics / Q000378:metabolism*; D013403:Sugar Phosphates / Q000378:metabolism; D014157:Transcription Factors / Q000378:metabolism*; D014764:Viral Proteins; D054334:Viral Regulatory and Accessory Proteins
D004268:DNA-Binding Proteins; D012097:Repressor Proteins; D013403:Sugar Phosphates; D014157:Transcription Factors; D014764:Viral Proteins; D054334:Viral Regulatory and Accessory Proteins; C016649:phage repressor proteins; D005973:Glutamine; D004247:DNA