IntroductionIn eukaryotic cells, there are two major routes to the lysosome/vacuole after exiting the trans-Golgi network (TGN) (Hunziker and Geuze, 1996;Kornfeld and Mellman, 1989). One is the biosynthetic pathway by which the cell delivers newly synthesized lysosomal enzymes and membrane proteins for the biogenesis and maintenance of lysosomes/vacuoles. The transport vesicles carrying the cargo molecules are budded from the TGN and mostly target endosomes prior to arriving at lysosomes/vacuoles. The other route is the so-called endocytic pathway by which the cell delivers various internalized ligands and the receptors from the plasma membrane (PM) to lysosomes/vacuoles for degradation. The ligand-receptor complexes, for instance the EGF/EGF-receptor, are segregated into the internal vesicles of endosomes (Futter et al., 1996). Subsets of receptors that recycle back to the PM, such as transferrin receptor and low-density lipoprotein receptor, are sequestered into clathrin-coated vesicles at recycling endosomes and are removed from the degradative pathways. In both pathways, endosomes play central roles in the sorting of cargo molecules and indeed, endosomes are meeting places for membrane traffic from both routes.By an extensive genetic analysis in the yeast Saccharomyces cerevisiae, more than 50 of the Vps (vacuolar protein sorting) genes involved in membrane transport to vacuoles were isolated (Raymond et al., 1992). The class E Vps family, one of the sub-groups of Vps mutants, exhibits a modest degree of secretion of newly synthesized carboxypeptidase Y (CPY), a soluble vacuolar enzyme, compared with other sub-classes of Vps mutants. In class E Vps mutants, both the 60 kDa V-2997 SKD1 belongs to the AAA-ATPase family and is one of the mammalian class E Vps (vacuolar protein sorting) proteins. Previously we have reported that the overexpression of an ATPase activity-deficient form of SKD1 (suppressor of potassium transport growth defect), SKD1(E235Q), leads the perturbation of membrane transport through endosomes and lysosomes, however, the molecular mechanism behind the action of SKD1 is poorly understood. We have identified two SKD1-binding proteins, SBP1 and mVps2, by yeast two-hybrid screening and we assign them as mammalian class E Vps proteins. The primary sequence of SBP1 indicates 22.5% identity with that of Vta1p from Saccharomyces cerevisiae, which was recently identified as a novel class E Vps protein binding to Vps4p. In fact, SBP1 binds directly to SKD1 through its C-terminal region (198-309). Endogenous SBP1 is exclusively localized to cytosol, however it is redirected to an aberrant endosomal structure, the E235Q compartment, in the cells expressing SKD1(E235Q). The ATPase activity of SKD1 regulates both the membrane association of, and assembly of, a large hetero-oligomer protein complex, containing SBP1, which is potentially involved in membrane transport through endosomes and lysosomes. The N-terminal half (1-157) of human SBP1 is identical to lyst-interacting protein 5 and intriguingly, SKD...