Functions as an E3 ubiquitin-protein ligase. Binds phospholipid vesicles containing phosphatidylinositol 3-phosphate. S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + N(6)-ubiquitinyl-[acceptor protein]-L-lysine. Protein modification; protein ubiquitination. The FYVE domain mediates phosphatidylinositol 3-phosphate binding and is necessary and sufficient for targeting to endosome and vacuole membranes. Present with 195 molecules/cell in log phase SD medium.