Has E3 ubiquitin-protein ligase activity and may target misfolded substrates towards proteasomal degradation. Regulates the activity of some serine/threonine-protein phosphatases by E3 ubiquitin-protein ligase activity. Required for responses to biotic and abiotic stresses such as auxin, abscisic acid (ABA), low and high temperature and darkness, probably through the activation of serine/threonine-protein phosphatase and the subsequent modification of the plasma membrane composition. Regulates the chloroplastic Clp proteolytic activity in response to stresses. Ubiquitylates FtsH1, a component of the chloroplast FtsH protease, and affects protein degradation in chloroplasts. Mediates plastid precursor degradation to prevent cytosolic precursor accumulation, together with the molecular chaperone HSC70-4. Mediates ubiquitination of transit peptides and thereby led to their degradation through the ubiquitin-proteasome system. 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. Interacts with HSC70-4, PP2AA1, PP2AA3 and PP2A5, as well as with UBC8, UBC9 and UBC10. Interacts also with the chloroplastic proteolytic subunits ClpP4, FtsH1 and FtsH2. By abiotic stresses such as chilling, heat-shock and salts (selenate and NaCl). The U-box domain is required for the ubiquitin protein ligase activity.