FadR Binding with DNA

FadR binds to DNA with a winged helix turn helix motif. This particular motif is popular in many repressor proteins in prokaryotic cells. Helix turn helix motifs consist of a pair of helices connected by a tight turn of a few residues long. When bonded to DNA the first helix will connect by binding to the phosphate backbone. The turn aspect also binds to the backbone of DNA. The second helix, known as the recognition helix rests along the major groove of the DNA molecule. Here side chains of the helix will bind with the edges of the DNA base pairs. The wing part of the FadR motif is a loop a few residues down the protein that will deeply penetrate the minor groove.

The winged helix turn helix motif is found in each monomer of the protein. Each motif will bind to DNA in five specific areas. Each is shown in detail in the chime below by clicking the button next to the description.

FadR's w-hth motif binding to DNA

1) Residues 7-9 located right before the start of alpha helix 1 make several non specific bonds to the phosphate backbone.

2) At the start of alpha helix 2 there is contact between Glu 34 and the phosphate backbone. Also, Arg 35 donates two hydrogen bonds on the major groove side of the DNA strand. This represents the first alpha helix in the w-hth motif.

3) This area represents the turn in the w-hth motif. The side chain of Thr 44 hydrogen bonds to the phosphate backbone. Arg 45 is also involved in hydrogen bonding and bonds to the guanine at the -3 position.

4) The third alpha helix of the FadR Protein is the recognition helix in the w-hth motif. It binds to DNA with residues from its first turn only. Thr 46 contacts with a central base pair in the DNA helix. The next residue, Thr 47 hydrogen bonds to the phosphate backbone. Arg 49 also donates two hydrogen bonds to the phosphate backbone.

5) The last contact area in the DNA-FadR complex is from residues 63 through 69. This strand represents the wing part of the w-hth motif. These residues form a loop between two beta strands in the protein. This loop deeply penetrates the minor DNA groove.

Picture of the entire motif hilighting the specific parts of the winged helix turn helix

1 - pink

2- green

3 - blue

4-yellow

5-red