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The Structural Basis of ATP as an Allosteric Modulator

Figure 6

The energy landscape of ATP binding to the substrate ATP-binding site of the UMP kinase as a function of the progress of ATP binding.

(A) The six snapshots of the substrate ATP-binding pathway represent the following configurations: A, the unbound state; B, the “encounter complex”; C, an intermediate state in which ATP does not interact with Lys10, Ser12 and Lys161; D, the relatively high-energy state; E; an intermediate state in which ATP interacts with Lys10, Ser12, Arg57, and Lys161; F, the fully bound state. The 165-DGVFTSDP-172 motif of UMP kinase in the recognition of the adenine moiety of ATP is shown in magenta. The ATP and its interacting residues are shown as sticks, whereas subunit A of the UMP kinase is shown in pale cyan. The green dashes represent hydrogen bonds. The hydrogen atoms are not displayed for clarity. The error bars represent standard deviations of binding energies for the 20 snapshots from 20 trajectories.

Figure 6

doi: https://doi.org/10.1371/journal.pcbi.1003831.g006