DNA Polymerase: Structural Homology, Conformational Dynamics, and the Effects of Carcinogenic DNA Adducts
Figure 4
Structure of bacteriophage T7 polymerase bound to a DNA primer-template containing a dG-AAF adduct at the templating position (PDB# 1X9M) [32]. (a) The overall shape of T7 polymerase resembles a human right hand forming fingers (green circle), thumb (blue circle), and palm (not highlighted). T7 also contains thioredoxin, a processivity factory, in addition to the polymerase and exonuclease domains. The AAF adduct (green) inserts behind the O helix (yellow), locking the helix in a distorted open conformation, inhibiting the binding of dNTPs. (b) Close-up view of active site. The AAF moiety (grey with green space filling) is inserted into a hydrophobic pocket behind the O helix stacking with a flipped out Phe528 (brown, with brown space filling), which is buried in the native structure. The adducted guanine is in an anti conformation placing the hydrogen bond acceptors and donors away from the nucleotide binding position. This position is further stabilized by hydrogen bonds to Arg566 and Asp534. The AAF moiety pushes the O helix forward, causing Tyr530 (pink with pink space filling) to stack on top of the DNA, occupying the nucleotide binding site which occludes a dNTP from binding. Residues 537–557 have been removed for simplified visualization (ends are circled red).
