Homeodomain motif

Dimer of the MAT alpha-2 protein from yeast, with two identical homeodomains, bound to a 21 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 helix-turn-helix motif contacting with the major groove in DNA (two alpha helix stretches separated by a short stretch without a defined secondary structure);
  2. a third helix stretch, that stays apart from DNA;
  3. a stretch without a defined secondary structure that interacts with DNA in the minor groove.

In addition, each particular protein has other regions that form the remainder of the molecule, not shown here.

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
—helix
Third helix
Contact in the minor groove

When you finish, click on

 


Note how the two recognition helices fit in successive positions of the major groove.

Spacefilling model, or spheres.

in a lighter shade of colour the peptide contacting with the minor groove.

Another protein with two homeodomain motifs
In this case, a heteodimer formed by a subunit of the former protein MAT alpha-2 and another from a similar protein, MAT A-1.