Dynamic Fluctuations Provide the Basis of a Conformational Switch Mechanism in Apo Cyclic AMP Receptor Protein
Figure 1
Holo CRP crystal structure and functional sites.
A. The CRP structure in complex with DNA and cAMP (PDB: 1CGP). The N-terminal cAMP binding domains (V1-N133), the C-terminal DNA binding domains (V139-R209) and the hinge regions (L134-D138) connecting the two domains in subunits A/B are represented in cyan/ice blue, dark pink/light pink and green/yellow, respectively. The α-helices C, D, E, F and bound cAMP molecules are indicated for both subunits. B. The residues for the primary cAMP binding -G71, E72, R82, S83, T127, S128 (subunit B)-, the secondary cAMP binding –E58, A135, R180-, the specific DNA binding –R180, E181, R185-, the nonspecific DNA interactions –R169, Q170, S179, and the RNAp interaction –A156-Q164 (AR1) are labeled. The residues are colored white, blue, red and green corresponding to the residue types non-polar, basic, acidic and polar, respectively. The approximate position of the secondary cAMP is placed, considering the dimer CRP with four cAMPs (PDB: 2CGP). Figures are generated using VMD 1.8.7 [68].