Helix-Turn-Helix Motif
 
The helix-turn-helix motif was first identified as a conserved sequence element in the repressors encoded by the lambdoid phages of E. coli and Salmonella typhimurium. Subsequently this element has been found in a large variety of DNA-binding proteins, both in prokaryotes and in eukaryotes, and shows a very high degree of structural conservation. This DNA-binding domain consists of two short a-helices that usually are separated by a glycine residue. This amino acid in concert with its neighbors acts as a flexible hinge allowing the polypeptide chain to bend between the two helices so that they can make hydrophobic contacts with each other. These contacts preserve the relative orientation of the two helices and result in the formation of a compact tertiary structural domain. The
distal helix lies in the DNA major groove and the proximal helix contacts the sugar-phosphate backbone. Although the structure of this domain is highly conserved, the orientation of the recognition helix within the major groove is quite variable. This feature suggests that the motif is a structure that possesses a rigidity which is necessary for precise sequence recognition.
Related to the prokaryotic helix-turn-helix fold are protein folds of essentially the same fundamental structure, but which contain longer turns or loops. These eukaryotic variants include the homeodomain fold, which contains both a helix-turn-helix element and a short extended minor groove-tracking sequence, the POU-specific domain, and the helix-wing-helix fold. The latter fold contains an extended b sheet immediately following the recognition helix and is typified by hepatocyte nuclear factor 3 (HNF3) and the globular domain of the linker histones, H5 and H1. Whereas the prokaryotic proteins usually bind as homodimers and bind to palindromic DNA targets, the eukaryotic counterparts normally bind as monomers.
References
“Helix-Turn-Helix Motif” in , Vol. 2, pp. 1105–1106, by Andrew Travers, MRC Laboratory of Molecular Biology, Cambridge; “Helix-Turn-Helix Motif” in  (online), posting date: January 15, 2002, by Andrew Travers, MRC Laboratory of Molecular Biology, Cambridge.