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. 2016 Aug 5;3:37. doi: 10.3389/fmolb.2016.00037

Figure 2.

Figure 2

Residues involved in Φ29 TP/DNA polymerase interaction. Ribbon representation of the Φ29 TP/DNA polymerase heterodimer. DNA polymerase is colored in blue except for TPR1 (pale yellow), TPR2 (dark blue) and thumb (light green) subdomains. TP N-terminal, intermediate and priming domains are colored in red, green and orange, respectively. (A) Close-up view of the TP intermediate domain residues R158 and R169, proposed to make salt bridges with DNA polymerase residues E291 and E322 of the TPR1 subdomain, respectively. (B) Close-up view of the TP priming domain residues E191 and D198, proposed to interact with the DNA polymerase thumb subdomain residues K575 and K557, respectively. (C) The proposed stacking interactions between TP priming domain residues R256, Q253, and Y250, and DNA polymerase residues R96 (exonuclease domain) and E419 (TPR2 subdomain) are indicated. (D) Close-up view of the proposed interaction between TP priming domain residues R256 and E252 with DNA polymerase residues R96 (exonuclease domain) and L416 and G417 (TPR2 subdomain). Coordinates of the Φ29 TP/DNA polymerase heterodimer are from PDB ID 2EX3 (Kamtekar et al., 2006). The figure was made using the Pymol software (http://www.pymol.org).