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The DNA binding arm of lambda repressor: critical contacts from a flexible region
N D Clarke1, L J Beamer, H R Goldberg
1Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205.
Science (New York, N.Y.)
|October 11, 1991
Summary
Flexible protein segments, like the first six residues of phage lambda repressor, are crucial for specific DNA binding. This study reveals how these flexible regions precisely interact with DNA, refining our understanding of DNA-protein recognition.
Area of Science:
- Molecular Biology
- Structural Biology
- Genetics
Background:
- Proteins can bind specific DNA sequences even with flexible segments.
- The N-terminal residues of phage lambda repressor are vital for DNA binding.
- Previous models suggested a symmetrical interaction, but flexibility complicates this.
Purpose of the Study:
- To investigate the role of the flexible N-terminal residues of phage lambda repressor in site-specific DNA binding.
- To determine the structural basis for the interaction between these residues and the DNA operator site.
- To refine the understanding of DNA-protein recognition mechanisms.
Main Methods:
- Low-temperature X-ray crystallography was employed to obtain high-resolution structural data.
- Codon-directed saturation mutagenesis was used to probe the functional importance of specific residues.
- Analysis of functional sequences revealed conserved patterns in key positions.
Main Results:
- A high-resolution crystal structure (1.8 Å) elucidated the interactions of residues Lys3, Lys4, and Lys5.
- Lysine residues at positions 3 and 4 form multiple hydrogen bonds with guanine bases.
- Lysine at position 5 interacts with the DNA phosphate backbone, indicating a specific binding mode.
- The study identified conserved sequence patterns: [X]1-[X]2-[Lys or Arg]3-[Lys]4-[Lys or Arg]5-[X]6.
Conclusions:
- Flexible protein segments can mediate specific DNA recognition through precise interactions.
- The N-terminal residues of phage lambda repressor play a critical role in binding specificity.
- The observed interactions challenge traditional models of operator site alignment, suggesting a revised understanding of DNA-protein complex symmetry.