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The cavity in the hydrophobic core of Myb DNA-binding domain is reserved for DNA recognition and trans-activation

K Ogata1, C Kanei-Ishii, M Sasaki

  • 1Tsukuba Life Science Center, Institute of Physical and Chemical Research (RIKEN), Ibaraki, Japan.

Nature Structural Biology
|February 1, 1996
PubMed

Insights

The Myb protein

Area of Science:

  • Molecular Biology
  • Structural Biology
  • Biochemistry

Background:

  • The Myb DNA-binding domain comprises three imperfect repeats (R1, R2, R3), each with a helix-turn-helix motif.
  • Repeat R2 exhibits unique properties, including high thermal instability and an internal cavity within its hydrophobic core, unlike R1 and R3.
  • Understanding the structural dynamics of Myb repeats is crucial for elucidating its DNA-binding mechanism.

Purpose of the Study:

  • To investigate the role of conformational flexibility in the R2 repeat of the Myb DNA-binding domain.
  • To determine the impact of stabilizing the R2 structure on Myb's DNA-binding activity and trans-activation function.

Main Methods:

  • Nuclear Magnetic Resonance (NMR) structure analysis to identify structural features like cavities.
  • Site-directed mutagenesis to create cavity-filling mutations in the R2 repeat.
  • Assays to measure DNA-binding activity and trans-activation function of wild-type and mutant Myb proteins.

Main Results:

  • The R2 repeat displays slow conformational fluctuations, attributed to an internal cavity.
  • Mutations filling the cavity in R2 stabilize its structure.
  • Stabilization of R2 significantly impairs Myb's specific DNA-binding and trans-activation capabilities.

Conclusions:

  • The inherent conformational flexibility of the R2 repeat, linked to its cavity, is essential for Myb's DNA recognition.
  • Myb's DNA-binding activity is modulated by the dynamic properties of its R2 repeat.
  • Structural plasticity of Myb repeats plays a critical role in gene regulation.

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