In proteins, the helix-turn-helix (HTH) is a major structural motif capable of binding DNA. It is composed of two α helices joined by a short strand of amino acids and is found in many proteins that regulate gene expression.
Its discovery was based on similarities between the genes for Cro, CAP, and λ repressor, which share a common 20-25 amino acid sequence that facilitates DNA recognition. In particular, recognition and binding to DNA is done by the two α helices, one occupying the N-terminal end of the motif, the other at the C-terminus. In most cases, such as in the Cro repressor, the second helix contributes most to DNA recognition, and hence it is often called the "recognition helix". It binds to the major groove of DNA through a series of hydrogen bonds and various Van der Waals interactions with exposed bases. The other α helix stablizes the interaction between protein and DNA, but does not play a particularly strong role in its recognition.
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References
- Brennan RG, Matthews BW. "The helix-turn-helix DNA binding motif." J. Biol. Chem. 264: 1903- 1906 (1989) PMID 2644244 (full text PDF)
- Matthews BW, Ohlendorf DH, Anderson WF, Takeda Y. "Structure of the DNA-binding region of lac repressor inferred from its homology with cro repressor." Proc Natl Acad Sci U S A. 1982 Mar;79(5):1428-32. PMID 6951187 (full text PDF)
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