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Figure 2 | BMC Structural Biology

Figure 2

From: A previously unobserved conformation for the human Pex5p receptor suggests roles for intrinsic flexibility and rigid domain motions in ligand binding

Figure 2

Comparison of the new structure and previously determined Pex5p(C) structures. A. Superposition of the new (blue) and old (cyan) apo-Pex5p(C) structures and the liganded structure (yellow). The arrows represent the rotation axes suggested by DynDom to describe the dynamic domain movements in the molecule. The green axis corresponds to the transition between the two apo forms. The red axis relates the new apo structure to the liganded structure and the orange one the old apo structure to the liganded structure. B. Disruption of the PTS1 binding site in the apo structures, caused by the movement away of the N-terminal half-molecule. The new apo structure is in blue, the old apo structure in cyan, and the liganded structure in yellow. The C-terminus of SCP2 is shown in gray, entering the binding site. In the apo structures, for example, the salt bridge between Arg557 from the C-terminal half (TPR7) and Glu residues 383 and 385 from the N-terminal half (TPR2) is broken. The positions of the 4 asparagine residues that intimately interact with the PTS1 motif are also shown. C. Comparison of the FEEEN motif and the 7C loop in the new apo-Pex5p(C) conformation (blue) with the previously described apo-structure (cyan) and SCP2-bound (yellow) structure [9]. The Sr2+ ion in the new structure is indicated as a green sphere, and the FEEEN motif in red. The position of the 7C loop is also given.

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