Fig. 1: Pup bound to Dop exhibits a more extensive network of interactions than Pup bound to ligase PafA. | Nature Communications

Fig. 1: Pup bound to Dop exhibits a more extensive network of interactions than Pup bound to ligase PafA.

From: Structures of prokaryotic ubiquitin-like protein Pup in complex with depupylase Dop reveal the mechanism of catalytic phosphate formation

Fig. 1

a Overview of the Dop-PupQ-AMP-PCP complex structure. In the complex, Dop is colored green, PupQΔN43 red, the partially resolved Dop-loop purple, and AMP-PCP is colored orange. The disordered part of the Dop-loop is represented as a purple dashed line and magnesium ions are represented as green spheres. b Comparison of Pup structures when bound to Dop (red) or to PafA (gray, PDB 4BJR). Dop and PafA are omitted for clarity. The relative rotation angles were measured between the central axes of the helices. c Schematic comparison of the interactions formed by Pup in the Dop-Pup and in the PafA-Pup complex. Sequences of Pup are colored red (Acel PupQΔN43) or gray (CgluPupEΔN37), and the residues forming the two orthogonal helices (helix 1 and helix 2) are outlined by black boxes. Dop-Pup and PafA-Pup interactions are indicated as black dashed lines, including hydrogen bonds, hydrophobic and electrostatic interactions assigned with a distance cut-off of 4 Å. Dop residues are colored green and PafA residues blue. d Molecular interactions formed by the C-terminal residue of Pup with Dop (green) or with PafA (blue). Only interacting residues are displayed and are shown in stick representation. Polar interactions are represented as black or gray dashed lines.

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