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Catabolite Activator Protein
Exploring the Structure
CAP recognizes a specific sequence of DNA, binding only to special sites next to genes involved in energy production. The recognition is provided by interactions between CAP amino acids and DNA bases in the major groove. This picture, from PDB entry 1cgp, shows how two arginines and a glutamate reach over and form specific hydrogen bonds with the DNA bases. Notice also the big bend in the DNA at the thymine-adenine base pair at center. CAP also interacts with many sites on the phosphate backbone of the DNA, strengthening the binding. PDB entry 1cgp has a break in the DNA chain at a key point in the backbone (shown with a star), but you can explore how CAP interacts with this site in PDB entry 1j59.A list of all CAP structures in the PDB as of December, 2003, is available here. For more information on CAP, click here. To explore CAP from a genomic perspective, take a look at the Protein of the Month feature at the European Bioinformatics Institute.
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Last changed by: A.Honegger,