Rebuilt 3D structure of the chloroplast f1 ATPase-tentoxin complex

The F1 part of the chloroplast H+ adenosine triphosphate (ATP)‐synthase (CF1) strongly interacts with tentoxin, a natural fungous cyclic tetrapeptide known to inhibit the chloroplast enzyme and not the mammalian mitochondrial enzyme. Whereas the synthesis or the hydrolysis of ATP requires the stepwise rotation of the protein rotor γ within the (αβ)3 crown, only one molecule of tentoxin is needed to fully inhibit the complex. With the help of an original homology modeling technique, based on robust distance geometry protocols, we built a tridimensional model of the α3β3γ CF1 subcomplex (3200 residues), in which we introduced three different nucleotide occupancies to check their possible influence on the tentoxin binding site. Simultaneous comparison of three available high‐resolution X‐ray structures of F1, performed with a local structural alignment search tool, led to characterizing common structural blocks and the distorsions experienced by the complex during the catalytic turnover. The common structural blocks were used as a starting point of the spinach CF1 structure rebuilding. Finally, tentoxin was docked into its putative binding site of the reconstructed structure. The docking method was initially validated in the mitochondrial enzyme by its ability to relocate nucleotides into their original position in the crystal. Tentoxin binding was found possible to the two α/β interfaces associated with the empty and adenosine diphosphate (ADP)‐loaded catalytic sites, but not to the one associated with the ATP‐loaded site. These results suggest a mechanism of CF1 inhibition by one molecule of tentoxin, by the impossibility of the α/β interface bearing tentoxin to pass through the ATP‐loaded state. Proteins 2002;49:302–320. © 2002 Wiley‐Liss, Inc.