Helix-turn-helix

This  motif  have  of  two    -helices  divided  by  a  short  (four-amino   acid) peptide  sequence  which  forms  a   -turn that shown in above figure.  When the transcription factor binds to the DNA one of the helices, called as the recognition helix, lies in the main groove of the DNA double helix that also shown in the figure. The helix-turn-helix motif was originally   exposed   in particular   transcription   factors   which   play   major   roles   in Drosophila   early development.   These  proteins  each  contain  a  60-amino  acid DNA-binding   region  called as  a  homeodomain   (encoded  by  a  DNA  sequence by as  a homeobox).  The homeodomain has four    -helices in those helices II and III are the classic helix-turn-helix motif.  Because the real discovery, the helix-turn-helix motif has been found in a wide range of transcription factors, involving various which have no role in development.

Zinc finger

Several kinds of zinc finger have been reported, two of that are the C2H2 finger, the C4   finger.  The C2H2   zinc finger is a loop of 12 amino acids with two cysteines and two histidines at the base of the loop that tetrahedrally coordinate a zinc ion in the figure. This forms a compact structure of two β-strands and one α- helix. The α-helix holds a number of conserved basic amino acids and interacts straightly with the DNA, binding in the main groove of the double helix. The Transcription factors that have zinc fingers often contain various such motifs, arranged such that α-helix of each contacts the DNA. Certainly RNA polymerase III transcription   factor A have nine zinc fingers! The SP1 transcription factor that binds to the SP1 box has 3 zinc fingers.

Figure:  (a) Helix-turn-helix  motif of a DNA-binding protein; (b) binding of the helix-turn-helix to target DNA showing the recognition helix lying in the main groove of the DNA.