You are using a web browser that is not fully supported by this website. Some features may not work as intended. For the best experience, please use one of the recommended browsers.
Opening Image: AMP-PNP at the catalytic site of F1-ATPase. The Mg2+ is shown in lime green.
to spacefill AMP-PNP, an analog of ATP in which the oxygen atom between the β and γ phosphates is replaced by a nitrogen atom.
In the previous tutorial we saw that the conformations of βT and βR are vastly different. We might expect that the side chains at the catalytic site are arranged differently in the two states, and this is the case.
We begin with the R-state containing AMP-PNP in place of ATP. The Mg2+ is directly liganded to the hydroxyl group of Thr-163 and the β and γ phosphates of AMP-PNP. Carboxylate oxygen atoms of Glu-192 and Asp-256 also interact with Mg2+ through water molecules (not shown). [Note: uncheck the boxes to simplify the display of the target group.]
Three side chains interact electrostatically with the γ phosphate:
Recall that the nucleotide-binding (middle) domain is disrupted as the catalytic site opens. In particular, two α helices directly involved in nucleotide binding move apart during the R→T transition.
Toggle between the R (liganded) and T (unliganded) states. The critical helices are highlighted in green.
Rotate each image with the mouse to sight along a helix axis. Note that the two helices are parallel in the R state. Then each model.
The critical side chains are arranged differently in the R (closed) and T (open) states.
Toggle expanded views of the filled and empty catalytic site.
The loss of binding energy arising from departure of the ligands is compensated in part by new interactions between the side chains in the empty site.
spacefill of critical side chains. The reorientation of the helices in the T state allows Glu-199 to hydrogen bond to Thr-163, whereas Asp-256 is hydrogen bonded to Lys-162. In addition, Glu-192 forms an ion pair with Arg-189.