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The solution structures of the trp repressor-operator DNA complex

H Zhang1, D Zhao, M Revington

  • 1Stanford Magnetic Resonance Laboratory, CA 94305-5055.

Journal of Molecular Biology
|May 13, 1994
PubMed
Summary
This summary is machine-generated.

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The study reveals the precise 3D structure of Escherichia coli trp holorepressor bound to operator DNA. This complex formation involves significant DNA deformation and specific repressor-DNA interactions, crucial for gene regulation.

Area of Science:

  • Molecular Biology
  • Structural Biology
  • Biochemistry

Background:

  • The Escherichia coli trp holorepressor regulates tryptophan biosynthesis genes.
  • Understanding repressor-DNA complex structures is key to elucidating gene regulation mechanisms.

Purpose of the Study:

  • To determine the solution structures of the complex between Escherichia coli trp holorepressor and operator DNA.
  • To characterize the structural changes and interactions upon complex formation.

Main Methods:

  • Nuclear Magnetic Resonance (NMR) spectroscopy, including 2D NOESY and 3D NOESY-HMQC.
  • Restrained molecular dynamics and simulated annealing calculations.
  • Use of selectively deuterated and uniformly 15N-labeled samples.

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Main Results:

  • High-resolution structures of the repressor-DNA complex were obtained with low RMSD values.
  • DNA undergoes significant deformation from B-DNA to accommodate the repressor's helix-turn-helix (HTH) motif.
  • The repressor's core structure remains largely unchanged, but the L-tryptophan binding pocket and HTH segment show alterations.
  • N-terminal residues (2-17) are disordered and do not interact with DNA.
  • Direct hydrogen bonds between repressor residues and operator DNA bases were identified and are consistent with experimental data.

Conclusions:

  • The determined solution structures provide atomic-level insights into trp holorepressor-operator DNA recognition.
  • DNA bending and specific protein-DNA interactions mediated by the HTH domain are critical for repression.
  • Structural plasticity in both the repressor and DNA facilitates high-affinity binding.