gocentral
commented
15 years ago Here's some text from a discussion of an article that discusses the two different activities (SUMO endopeptidase vs. SUMO deconjugase) a little more explicitly. http://www.plantcell.org/cgi/rapidpdf/tpc.108.058669v1
In Arabidopsis, eight genes have been identified that encode proteins with high similarity to yeast Ulp1 (Kurepa et al., 2003; Murtas et al., 2003; Chosed et al., 2006; Colby et al., 2006). So far, At ULP1a, At ULP1c (OTS2), At ULP1d (OTS1), and ESD4 have been shown to have At SUMO1/2 endopeptidase activity in vitro (Chosed et al., 2006; Colby et al., 2006) (Figure 1). Despite OTS1 having SUMO1 endopeptidase activity in vitro, its role in vivo is largely directed toward the deconjugation of SUMOylated proteins. ThisSUMO deconjugating role also applies to OTS2, as shown by the increased levels of SUMOylated protein in the corresponding mutant backgrounds (Figure 4), and to ESD4 (Murtas et al., 2003). Since the major roles of OTS1, OTS2, and ESD4 seem to be mainly deconjugative, the question arises of which of these is the major SUMO maturation protease in Arabidopsis. One possibility is that the SUMO endopeptidase activity could be highly redundant and that most (if not all) Arabidopsis SUMO proteases contribute to some extent to proSUMO maturation. An alternative model could be that one or more Arabidopsis SUMO proteases is involved in proSUMO to SUMO maturation. This model applies in yeast, where only two SUMO proteases, Ulp1 and Ulp2, exist. Although Ulp2 has endopeptidase activity in vitro, Ulp1 is largely responsible for proSUMO maturation in vivo (Li and Hochstrasser, 2000).
Original comment by: kadreher
Several small proteins such as UB, SUMO, and Rub/NEDD need to proteolytically processed before they can be attached to a target.
This requires the cleavage of a peptide bond within UB, SUMO, etc. (process 1) This processing is done by a series of enzymes that generally seem to be cysteine proteases.
Once these small proteins are attached to a target protein via an isopeptide bond, they can be removed from the target by an isopeptidase activity. (process 2) This process is often carried out by the same enzymes that do the peptide cleavage described in process 1.
Please see the following paper for one example: http://www.plantphysiol.org/cgi/content/full/142/1/318
There are a series of terms that are children of small conjugating protein-specific protease activity (GO:0019783) such as:
SUMO-specific protease activity (GO:0016929)that sound like they could apply to either of these processes. However, the definition states:
Catalysis of the hydrolysis of SUMO, a small ubiquitin-related modifier, from previously sumoylated substrates.
This only relates to process 2. If I want to annotate a protein that has only been shown to act in process 1, then I do not know what molecular activity to assign to it, other than the general term "cysteine-type peptidase activity."
I am not sure if it would be possible to either a) amend the definition to include both process 1 and 2, or b) to create a new term. In some senses I lean toward the former because I think that many enzymes may be involved in process 1 or 2. But, I would be grateful for feedback from the GO curators.
Please note that the definition for "small conjugating protein-specific protease activity" also only applies to process 2: Catalysis of the hydrolysis of various forms of polymeric ubiquitin or ubiquitin-like sequences (e.g. APG8, ISG15, NEDD8, SUMO). Will remove ubiquitin-like sequences from larger leaving groups.
Sincerely, kate
Reported by: kadreher
Original Ticket: "geneontology/ontology-requests/5572":https://sourceforge.net/p/geneontology/ontology-requests/5572