3D Structure of the CAMP Receptor Protein

CPK Color Scheme C O N P S

The cAMP Receptor Protein (CRP, also known as CAP) acts as a transcriptional activator that binds to DNA. More specifically, the CRP binds to the low-molecular weight compound adenosine 3',5'-cyclic monophosphate, which more commonly is know as cyclic AMP, or cAMP. Then the CRP-cAMP complex binds to DNA upstream of the promoter region (Purves et al. 2001). The binding equates to a more efficient binding rate of RNA polymerase to the promoter and an increased level of transcription of the structural genes (Weaver 2002). This current view is the entire complex of DNA bound to the CRP Protein. Further modifications of this complex will focus on strictly the CRP protein.

Click here to highlight just the DNA of the cAMP-CRP complex for clarification purposes.

From this point forward we will discuss the protein in this complex, which you can see in more detail by clicking here.

Click here to reset the chime image back to the initial view at any point.

The cAMP receptor protein is a dimer of two identical subunits. Each subunit consists of 209 amino acids in length. Click here to view the backbone of CRP (gray ribbons indicate the CRP, whereas the orange is the backbone of the DNA).

(You may find that it's easier to see the gray ribbons if you rotate the molecule by clicking here).

Now click here to eliminate the DNA entirely from the image and focus on the CRP.

To see the distinctions between the two subunits of the cRP click here (one subunit is green in this view and the other is blue).

Each monomer of the protein contains two structural and functional domains, namely the N and C terminal domains. The N-terminal domain (which is relatively amino acids 1-140), contains the cAMP nucleotide binding site. The C-terminal is a region of 50-60 amino acids that contain a helix-turn-helix DNA binding site. By clicking here you can see the distinctions between the secondary structure, wherein the beta-pleated sheets are yellow and the alpha-helices are magenta. This provides you with a sense of the location of the helix-turn-helix for the C-terminus, as well as the nucleotide binding site (N-terminus).

Click here to zoom in on the image.

This magnification of the cAMP-CRP complex illustrates that CRP bends DNA when it binds (upon the site). The binding of cAMP changes the conformation of the protein so that the DNA binding alpha helices are brought into the correct alignment in order to be able to recognize and therein bind at the appropriate site.Thus cAMP binding alters the internal bonding patterns within the dimer (CRP) (Mulilgan 1999). Here are some general characteristics of the CRP binding site, which reveals a lot about the protein itself: CRP-cAMP will bind to nonspecific DNA as well as to its specific DNA binding site, which has been found to be a 26 base-pair region of DNA. Research has also shown that amino acid sidechains form hydrogen bonds with the DNA bases as follows: Arg180 to G7; Glu181 to C5; and Arg185 to G5. Click here to see where H-bonds are located.

Nucleotide sequencing and analysis of CRP binding sites established an imperfect 5 base-pair palindrome: TGTGA---N6---TCACA. Yet, the functionally significant nucleotides line 11 base-pairs on both sides of the axis of symmetry. The reason why this information is included is due to the fact that it suggests the the two half sites are not purely identical, which is the case in all real CRP binding sites. Actually, the binding sites for most DNA-binding proteins have this same characteristic. The hypothesis for this: perfect binding sites would be too strong for the cell to be completely functional. Thus all known CRP binding sites have different half site sequences. By clicking on the following button, you can see the different amino acids (each is labeled by a different color) and with a good eye can tell that the two subunit binding domains are not exactly the same.

This tutorial was created as an undergraduate assignment at Davidson College.

References:

Kogoy, John. (2003). CPK Color Scheme. Permission Granted to Utilize in this page.

Mulligan, Martin E. (1999). cAMP Receptor Protein.

Molecular Martin Mulligan's Page on CRP

Purves WK, David S, Orians GH, Heller HC. Life: The Science of Biology 6th ed. 2001. Gordonsville, Virginia: Sinauer Associates, Inc.

Weaver, Robert P. Molecular Biology 2nd ed. 2002. New York: McGraw-Hill Companies, Inc.