The GTPase Ypt7p from S. cerevisiae is involved in late endosome-to-vacuole transport and homotypic vacuole fusion. We present crystal structures of the GDP- and GppNHp-bound conformation of Ypt7p solved at 1.35 and 1.6 Å resolution, respectively. Despite the similarity of the overall structure to other Ypt/Rab proteins, Ypt7p displays small but significant differences. The Ypt7p-specific residues Tyr33 and Tyr37 cause a difference in the main chain trace of the RabSF2 region and form a characteristic surface epitope. Ypt7p•GppNHp does not display the helix α2, characteristic of the Ras-superfamily, but instead possess an extended loop L4/L5. Due to insertions in loops L3 and L7, the neighboring RabSF1 and RabSF4 regions are different in their conformations to those of other Ypt/Rab proteins.
Constantinescu, A. T., Rak, A., Alexandrov, K., Esters, H., Goody, R. S., & Scheidig, A. J. (2002). Rab-subfamily-specific regions of Ypt7p are structurally different from other RabGTPases. Structure, 10(4), 569–579. https://doi.org/10.1016/S0969-2126(02)00737-2