Ccaatg

_ Signal molecule

Regulator protein subunit

Regulator protein subunit

DNA binding regulator proteins

DNA binding regulator proteins

FIGURE 7.45 Helix-Turn-Helix (HTH) and Helix-Loop-Helix (HLH) Motifs

A simple bend versus a loop in the protein is the structural feature distinguishing between these DNA-binding proteins.

C-terminus

C-terminus }

heHcies 1 ' LooP

N a helicies N-terminus

\ i helicies N-terminus

Turn

N-terminus

A) Helix-turn-helix B) Helix-loop-helix of the DNA-binding domain is different, the HTH motif that actually binds to the DNA is almost identical to that found in the lambda CI repressor (Fig. 7.46).

The leucine zipper is found in many eukaryotic transcription factors, including the Fos, Jun and Myc proteins that are involved in control of cell division and carcino-genesis. A leucine zipper motif consists of an a-helix with leucine residues every seventh amino acid. In addition, the amino acids halfway between the leucines are usually hydrophobic. Because there are 3.6 amino acids per turn, these hydrophobic residues form a strip down the side of the a-helix (Fig. 7.48). Two such a-helices can bind together by their hydrophobic strips forming a zipper structure. The actual binding of DNA is due to basic residues in front of the zipper region.

leucine zipper One type of DNA-binding motif common in proteins

FIGURE 7.46 Binding of Helix-Turn-Helix (HTH) Motif to DNA

A typical HTH protein is a dimer with two sets of a-helices, labeled a2 and a3, that actually bind to the DNA. B) The pairs of a-helices fit into two adjacent major groves in the DNA. In panel B only the a2 and a3 helices are indicated to show how they interact with the DNA. The HTH shown is the phage lambda CI repressor.

FIGURE 7.46 Binding of Helix-Turn-Helix (HTH) Motif to DNA

A typical HTH protein is a dimer with two sets of a-helices, labeled a2 and a3, that actually bind to the DNA. B) The pairs of a-helices fit into two adjacent major groves in the DNA. In panel B only the a2 and a3 helices are indicated to show how they interact with the DNA. The HTH shown is the phage lambda CI repressor.

FIGURE 7.47 Helix-Turn-Helix Motif of Cro Protein from Lambda

Lambda Cro protein is shown bound to DNA (orange). A) The two HTH recognition helices (red) of Cro sit in the major groove of the DNA according to the model of Brian Matthews. B) Schematic diagram of the Cro dimer. C) Space-filling model of Cro dimer bound to bent B-DNA. The sugar-phosphate backbone of DNA is orange and the bases are yellow. From: Introduction to Protein Structure by Brandon & Tooze, 2nd ed., 1999. Garland Publishing, Inc., New York and London.

Zinc fingers are widely distributed in DNA binding proteins. Each zinc finger recognizes three bases in the DNA.

A zinc finger consists of a central zinc atom with a segment of 25-30 amino acid residues arranged around it (Fig. 7.49). In the classic version of the Zn finger, the Zn is bound to two cysteines, which lie in a very short piece of b-sheet—a b-hairpin—and two histidines, which lie in a short a-helix. The far end of the a-helix protrudes into the major groove of the DNA. Over a thousand zinc finger proteins are known, and zinc finger One type of DNA-binding motif common in proteins

FIGURE 7.48 Leucine Zipper Protein Binding DNA

A) The leucine zipper consists of two a-helixes that have hydrophobic zones and basic ends.

B) The helixes of the leucine zipper binds to each other by their hydrophobic regions and to DNA by their basic regions. The basic end region fits into the major groove of the DNA. Because the basic regions are roughly parallel and open up around the DNA, the two helical segments resemble a zipper.

C-terminus

Hydrophobic surface

Leucine zipper protein

I N-terminus a m

' Hydrophobic surfaces bind together oar » :

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