What is the nature of the homeodomain? What other DNA-binding domain does it most resemble?

Question

blues · Answer

Basically, a homeodomain consists of three alpha helices connected by short loops. The two N terminal helices are side by side and antiparallel - that is, the N terminal end of one associates with the C terminal domain of the other and vice versa. The third C terminal helix is roughly perpendicular to the other two so the whole structure looks like a + sign.

The C terminal helix is the one which does the DNA binding - if I remember correctly, it binds the major groove typically, though not always, in a sequence specific manner. The N terminus - not the N terminal helices but a few unstructured residues after the helices - bind to the minor groove as well and provide some extra energetic stability.

That should get you started.

anonymous · Answer

@blues great, thanks for your help

blues · Answer

You're quite welcome!

blues · Answer

By the way, please feel free to go on asking protein and bioinformatics questions!