Helix-turn-helix motif


A dimer of the Cro protein from lambda bacteriophage; only part of the protein is displayed, corresponding to its two helix-turn-helix motifs, bound to a 20 bp fragment of DNA.

Each chain is displayed using a different colour: the 2 DNA strands and 2 motifs in the dimeric protein.

The structure common with other proteins, and hence called the motif, consists of:

  1. a stretch of alpha helix, that fits in the major groove of DNA and directly interacts with bases in it, so called "recognition helix";
  2. a short stretch of peptide sharply bent forming a rigid hairpin (a turn);
  3. another alpha helix that stays apart from DNA and forms a fixed angle with the first one, thanks to the stiffness of the turn and to contacts between sidechains in both helices.

Quiz:

Identify each part of the molecule and pick the colour used for it in the model:
(click on a coloured square to assign that colour to the item at its right)
Recognition helix
Turn
Second alpha helix in the motif

When you finish, click on

 

These three components give the motif its name. In addition, each particular protein has other regions in alpha helix, turns and loops that participate in the motif structure, and the remainder of the protein molecule, not shown.

Spacefilling model, or spheres.

Another protein with two helix-turn-helix motifs
"Lambda repressor", a protein from the lambda bacteriophage, bound to DNA in the operator region.