sjm41
commented
2 years ago Revisiting this ticket and looking closer at the given references:
- the abstract of PMID:10964424 (referenced on both terms) says these enzymes are classified as lyases (not transferases or hydrolases!)
- PMID: 22748813 (referenced on GO:0008933) confirms this, saying "The fourth and final class of PG lytic enzymes is the lytic transglycosylase. By definition, these enzymes are not true “hydrolases” because they do not require water to catalyze PG cleavage. They are very similar to muramidases in that they cleave the β(1 → 4) linkages between N-acetylmuramyl and N-acetylglucosaminyl residues of the PG ([Fig. 1]), but they form a N-acetyl-1,6-anhydro-muramyl moiety residue during glycosidic cleavage and thus belong to a different mechanistic class than the lysozymes
Now, searching within the EC lyase class for 'transglycosylase', I see these 2 terms: 4.2.2.n1 peptidoglycan lytic exotransglycosylase 4.2.2.n2 peptidoglycan lytic endotransglycosylase
So I think the tasks here become:
- [x] Change EC xref on GO:0008932 (lytic endotransglycosylase activity) to 4.2.2.n2
- [x] Remove EC xref of EC:3.2.1.- on GO:0008933 (lytic transglycosylase activity)
- [x] Change parent on GO:0008933 (lytic transglycosylase activity) from 'GO:0016757 ! transferase activity, transferring glycosyl groups' to 'GO:0016837 carbon-oxygen lyase activity, acting on polysaccharides (EC:4.2.2.-)
- [x] Change EC reference on GO:0016837 (carbon-oxygen lyase activity, acting on polysaccharides) definition from [EC:4.2.-.-] to [EC:4.2.2.-]
hdrabkin
Something odd here:
[Term] id: GO:0008933 name: lytic transglycosylase activity namespace: molecular_function def: "Catalysis of the specific cleavage of the beta-(1->4) glycosidic linkage between N-acetylmuramyl and N-acetylglucosaminyl residues in peptidoglycan, with the concomitant formation of 1,6-anhydro-N-acetylmuramyl residues." [PMID:10964424, PMID:22748813] synonym: "murein transglycosylase B activity" NARROW [] synonym: "peptidoglycan lytic transglycosylase activity" EXACT [] xref: EC:3.2.1.- is_a: GO:0016757 ! transferase activity, transferring glycosyl groups is_a: GO:0061783 ! peptidoglycan muralytic activity
It has xref of EC:3.2.1.- (Hydrolases -> Glycosylases -> Glycosidases, ie. enzymes hydrolyzing O- and S-glycosyl compounds) but is has parent "is_a: GO:0016757 ! glycosyltransferase activity"
Also the only child of that term is: [Term] id: GO:0008932 name: lytic endotransglycosylase activity namespace: molecular_function def: "Catalysis of the specific cleavage of the beta-(1->4) glycosidic linkage between N-acetylmuramyl and N-acetylglucosaminyl residues in peptidoglycan, with the concomitant formation of 1,6-anhydro-N-acetylmuramyl residues. Acts on linkages within peptidoglycan chains (i.e. not at the ends) to produce shorter strands with 1,6-anhydromuramic acid ends." [PMID:10964424, PMID:9642199] synonym: "murein lytic endotransglycosylase E activity" NARROW [] xref: EC:2.4.99.- is_a: GO:0008933 ! lytic transglycosylase activity
This one does have a transferase EC xref of EC:2.4.99.- (Transferases -> Glycosyltransferases -> Transferring other glycosyl groups)
The EC xrefs above are for grouping terms, so both should probably be removed? I don't easily see an existing EC for these specific reactions. (haven't checked Rhea)
From the definitions, it looks like they are both hydrolases, so the parent on GO:0008933 should be changed to "hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553" (which correctly has EC xref 3.2.1.-)?