Structural Insights into E. coli Porphobilinogen Deaminase during Synthesis and Exit of 1-Hydroxymethylbilane
Figure 5
Loop dynamics during pyrrole chain elongation.
A. Plot of distance between centers of mass of the loop residues (42–60) and the active site residues (11, 19, 84, 131, 132, 155, 176, 242) to track the loop movement in the different stages of the simulation. B. Interaction of K55 with E88 (open loop conformation denoted in blue color) and with V306, E305 and Q243 (closed loop conformation denoted in green color) regulate the loop movement in DPM stage. C. Distance graphs depicting the interaction of D50 with R149 during DPM stage to regulate loop movement (along with K55 interactions); interaction of D50 with R149 (black), D50 with G150 (red) and K55 with E88 (green), involved in loop movement during the P3M stage; Interaction of K55 with E239 (black) and G60 with E88 (red) involved in loop movement during the P4M stage.