Figure 4.

Model of Tag pol showing a view of the flexible loop containing the Y-GG/A motif. The loop follows the helical interdomain (yellow/blue) at the C-terminal end of the exonuclease domain (green) and runs out into a β-sheet of the active site (palm domain, blue). It is located close to the main groove on the surface of the protein, running from the upper left corner to the connection of palm and thumb domain in this presentation. The groove is known to harbour the template for DNA synthesis, the primer-end facing in the direction of the palm domain and the thumb (6). In this model derived from the crystal structure of T.gorgonarius DNA polymerase without ligands, Tyr387 is facing away from the groove and turned towards the fingers domain (pink) containing the dNTP binding motif B. It is reasonable to assume that the loop becomes reordered upon binding of the double-stranded DNA template (K.-P.Hopfner, personal communication).