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M28 family peptidase mappings #385

Closed gocentral closed 9 years ago

gocentral commented 17 years ago

It seems like M28 is not restricted to proteases....

actually the mapping is from InterPro:IPR003137 which is PA associated (this isn't the peptidase domain'...anyway there appear to be a number of pombe and cerevisiae proteins in this family which aren't peptidases and this corroborates what Neil says below.

Thanks

Val

Neil Rawlings wrote:

> Hello Val, > > The product of the yjr126c gene is classified in MEROPS as a > non-peptidase homologue in family M28 (it is such a divergent member of > the family that it can't be assigned to a subfamily). This is on the > basis that the third of the five zinc ligands has been replaced (Glu > replaced with Arg - residue 494; not even a single base change). All > peptidase members of this family have the motifs HXD and EE and it is > the second E that has changed. So it has both active site residues and > four out of five zinc ligands. If there is no biochemical evidence that > it is active, then it probably isn't; but six out of seven conserved essential residues could well be indicative > of a sequencing error. > > Neither Tre1 not Tre2 are peptidases. Again both are members of > peptidase family M28 and both have both catalytic residues and three of > the five metal ligands replaced. > > There are two Schizosaccharomyces pombe M28 homologues that do have a > complete active site: the products of the SPCC1919.12c (UniProt O94479) > and SPCC1259.02c (UniProt:O94702) genes. For Saccharomyces, > aminopeptidase Y and glutaminyl cyclase possess all active site > residues, and though both are enzymes, the latter is not known to be a > peptidase. Family M28 is one of several peptidase families to include > enzymes other than peptidases which have the same active site/metal > ligands.

Reported by: ValWood

Original Ticket: "geneontology/annotation-issues/385":https://sourceforge.net/p/geneontology/annotation-issues/385

gocentral commented 17 years ago

Original comment by: mah11

gocentral commented 17 years ago

Logged In: YES user_id=545117 Originator: NO

I've removed the annotation from IPR003137 as the domain appears in a lot of proteins lacking peptidase activity but as a general policy we don't remove enzyme annotation just because a family is known to contain a couple of catalytically members cos otherwise we'd have none left. Inactive family members will have to be manually annotated.

Sandra

Original comment by: orchard

gocentral commented 17 years ago

Original comment by: orchard