Fig. 5: A model for DNA translocation and subunit coordination by phage T4 DNA packaging motor.
From: A viral genome packaging ring-ATPase is a flexibly coordinated pentamer
a The pentameric gp17 DNA packaging motor (five brown circles) alternates between a quiescent state and a DNA engaging active state when exposed to short 45-bp oligonucleotide DNA substrate (gray circles), with the ISD motor spending longer time in quiescent state than the WT motor (shown by blue deleterious symbol). b The pentameric motor adapts to DNA helix by interacting at ~2-bp intervals, leading to different subunits binding at different strengths, as shown by increasing color intensity with increasing strength of the grip. The surface view of the putative DNA-binding C-terminal domain of gp17 is used to illustrate DNA–motor interactions. Shown are the side views with the camera facing subunit #1. See Supplementary Video 1 for additional details. The subunit with the strongest grip (#1; cyan) fires ATP, causing 2-bp DNA translocation (n + 2). The adjacent subunit (#2) now attains the strongest grip, while the apo subunit (no ATP) re-loads ATP. The #2 subunit now fires, causing another 2-bp translocation (n + 2 + 2) and this cycle continues. c Cartoon schematic of b depicting the motor’s top view. DNA is shown in gray in the motor’s channel, with each small circle representing 2-bp of DNA. White arches represent DNA-binding grips, while the purple arches represent the strongest grips. Hexagons at the center of each subunit represent bound ATP. b, c correspond to WT motor, while d, e correspond to ISD motor. When an inactive motor subunit (black; subunit #2) is encountered (d, e), the motor pauses and readjusts DNA grip, which might involve backward DNA movement (“m” bp). The subunit with the strongest grip (#3) then fires causing DNA translocation and the cycle continues. The shapes depicted in the figure are shown in the bottom left corner of the figure.
