Protease that catalyzes two essential functions in the SUMO pathway: processing of full-length SUMOs to their mature forms and deconjugation of SUMO from targeted proteins. Cleaves precursors of SUM1 and SUM2, but not of SUM3 or SUM5. Able to release SUM1 and SUM2 from conjugates, but unable to cleave SUM3. Acts predominantly as an isopeptidase, cleaving SUMO-conjugated proteins better than SUMO peptides. Plays an important role in the control of flowering time. Hydrolysis of the alpha-linked peptide bond in the sequence Gly-Gly-|-Ala-Thr-Tyr at the C-terminal end of the small ubiquitin-like modifier (SUMO) propeptide, Smt3, leading to the mature form of the protein. A second reaction involves the cleavage of an epsilon-linked peptide bond between the C-terminal glycine of the mature SUMO and the lysine epsilon-amino group of the target protein. Inhibited by thiol reagent and N-ethylmaleimide, but not by ubiquitin aldehyde, pepstatin A or benzamidine HCl. Interacts with NUA (via N-terminus). Interacts with KIN10 (PubMed:20855607). The nuclear envelope localization is independent of the presence of the nuclear pore anchor NUA. Expressed in seedlings, leaves, shoots, flowers and roots. No circadian regulation. The N-terminal regulatory domain is required for peptidase activity in vitro. Early flowering under both long and short days and pleiotropic alterations in shoot development. Belongs to the peptidase C48 family.