3D Structure of the CAMP Receptor Protein
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
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
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
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
Martin Mulligan's Page on CRPPurves WK, David S, Orians GH, Heller HC.
Life: The Science of Biology 6th ed. 2001. Gordonsville, Virginia: Sinauer
Weaver, Robert P. Molecular Biology 2nd ed. 2002. New
York: McGraw-Hill Companies, Inc.