Fig. 2: Interplay between Pup-binding and the Dop-loop conformation.
a Crystal structure of Dop with the Dop-loop inserted into the empty active site. Dop is colored green except for the Dop-loop that is colored purple. The unresolved 7-residue stretch of the Dop-loop is depicted as a purple dashed line. b Close-up of the molecular interactions mediated by the first helix (DLη1) of the Dop-loop. Polar interactions are represented as black dashed lines. c Comparison of the interactions mediated by the Dop-loop in different conformations. Sequence of the Dop-loop in the resolved region is colored purple while for the disordered part it is colored gray. The regions forming helices or β-strands were outlined as solid or dashed black boxes, respectively. Interactions between Dop (green) and the Dop-loop (purple) are indicated as black dashed lines, including hydrogen bonds, hydrophobic and electrostatic interactions assigned with a distance cut-off of 4 Å. d Zoomed-in view of the interactions between the resolved Dop-loop region (purple) and Dop (green) as observed in all Pup-bound structures in this study (here shown on the example of the Dop-PupE-ADP-MgF3(H2O)− structure). Polar interactions are represented as black dashed lines. e Structural comparison of active site residues as observed in the Dop-loop-inserted structure (gray) and a Pup-bound Dop structure (shown on the example of the Dop-PupE-ADP-MgF3(H2O)− complex) (green, red, light-orange and purple). Red arrows indicate the movements induced by Pup-binding, while black arrows suggest strong steric clashes. The unresolved or omitted parts of the Dop-loop were depicted as dashed lines (gray or purple) with the ends of the loop represented as filled dots.
