Transcriptional control

In this part of this practical we will look in structural detail at a number of examples of the specific recognition between DNA and proteins and how it is controlled.

A prokaryotic repressor

An example of a prokaryotic repressor is the trp repressor, which regulates the synthesis of the amino acid tryptophan by negative feed-back. A schematic view of this control is shown in this figure.
Organization and control
        of trp operon

The protein is a dimer binding to an inverted repeat in the DNA. The protein has a helix-turn-helix motif which is found in many bacterial repressors.
A PDB entry of a protein-DNA complex is found, as well as entries for various other forms of the protein.

Download the complex. The DNA in the complex is a variant of the normal DNA operon to which the protein normally binds. Locate the helix-turn-helix motif in the repressor!

Q. 1.  What are the nature of the direct contacts between the protein and the DNA? Are there any hydrogen bonds?

Download also the repressor without the tryptophan (the aporepressor). Superimpose the proteins and compare the conformation of the repressor with and without the amino acid.

Q. 2. What changes occur in the protein?

Q. 3. How can that explain the effect of the tryptophan?

Eukaryotic transcription factors

Eukaryotic transcription factors have widely different types of folds. There are some families of transcription factors with helix-turn-helix motifs. Other types of transcription factors still bind to DNA using a alpha helix in the major groove. We will look at a couple of families to see some of the variability in their folds.

Zinc finger domains

A number of transcription factors are called zinc fingers, but they are divided in a number of families that are not really related. One type is what is also called the classic Zn finger domain. An example is the Zif268 protein, a mammalian protein now called Egr1 (Early growth response 1). The protein has 543 amino acids. There are three Zn-finger domains in the protein and in the database SMART it is drawn like this (the purple rectangles "low-complexity regions", possibly flexible regions in the protein.

The crystal structure is known only for the DNA-binding part of the protein. Download this protein in complex with DNA!

Q. 4.  How are the Zn ions coordinated? What is the role of the Zn ion in the domain?

Q. 5.  Describe how the Zn-finger binds to the DNA! What hydrogen bonds between the protein and the DNA do you find (use only one of the Zn fingers)?

Another type of Zn finger is found in the DNA-binding domain of the glucocorticoid receptor.

Q. 6.  How are the Zn ions coordinated in this protein?

Q. 7.  How is the DNA recognized in this complex?

Leucine zipper

Many transcription factors have a simple design using a leucine zipper to form a dimer. The leucine zipper is a short coiled-coil of alpha helices.

Find a leucine zipper-DNA complex in the data bank.

Q. 8.  How is the DNA bound in this complex?

The zipper region is characterized by a regular pattern of leucine with a distance of 7 amino acid residues along the sequence.

Q. 9.  Explain this pattern by looking at the interactions in the zipper region!

Practical "Transcription", Lars Liljas