GO:0017042 name: glycosylceramidase activity (EC:3.2.1.62)

[sjm41]

MetaCyc:RXN-13785 corresponds to EC:3.2.1.62 (https://biocyc.org/META/NEW-IMAGE?object=RXN-13785)

It's current an xref on this GO term:

id: GO:0008422 name: beta-glucosidase activity def: "Catalysis of the hydrolysis of terminal, non-reducing beta-D-glucose residues with release of beta-D-glucose." [EC:3.2.1.21, PMID:12594539] xref: EC:3.2.1.21 xref: MetaCyc:3.2.1.21-RXN xref: MetaCyc:RXN-13785 xref: RHEA:69647 {source="skos:narrowMatch"} xref: RHEA:69655 {source="skos:narrowMatch"} is_a: GO:0015926 ! glucosidase activity

But it should be moved to this term:

id: GO:0017042 name: glycosylceramidase activity def: "Catalysis of the reaction: glycosyl-N-acylsphingosine + H2O = a sugar + N-acylsphingosine." [PMID:10692580, PMID:9762914] synonym: "cerebrosidase activity" RELATED [EC:3.2.1.62] synonym: "glycosyl ceramide glycosylhydrolase activity" RELATED [EC:3.2.1.62] synonym: "glycosyl-N-acylsphingosine glycohydrolase activity" RELATED [EC:3.2.1.62] xref: EC:3.2.1.62 xref: MetaCyc:GLYCOSYLCERAMIDASE-RXN is_a: GO:0004553 ! hydrolase activity, hydrolyzing O-glycosyl compounds

Also, looks like the definition and synonyms of GO:0017042 should be updated to match the EC description: https://enzyme.expasy.org/EC/3.2.1.62

glycosyl-N-acylsphingosine + H2O <=> N-acylsphingosine + a sugar a beta-D-galactosyl-N-acylsphingosine + H2O <=> a ceramide + beta-D-galactose a flavonoid-O-beta-D-glucoside + H2O <=> a flavonoid + beta-D-glucose

[sjm41]

Actually, MetaCyc:RXN-13785 is for a specific instance of EC:3.2.1.62.

Correct MetaCyc xrefs for glycosylceramidase activity/EC:3.2.1.62 are: RXN-22900 GLUCOSYLCERAMIDASE-RXN (already present) GALACTOSYLCERAMIDASE-RXN

[sjm41]

@pgaudet I've fixed the MetaCyc xrefs here, but haven't updated the definition and synonyms of GO:0017042 to match the EC description, so reassigning to you.

[sjm41]

@pgaudet :

The EC:3.2.1.62 entry lists 3 reactions for this activity: glycosyl-N-acylsphingosine + H2O <=> N-acylsphingosine + a sugar a beta-D-galactosyl-N-acylsphingosine + H2O <=> a ceramide + beta-D-galactose a flavonoid-O-beta-D-glucoside + H2O <=> a flavonoid + beta-D-glucose

Should we list all of those in the GO:0017042 def?

[sjm41]

@pgaudet I just bumped into this issue again.

id: GO:0017042 name: glycosylceramidase activity namespace: molecular_function def: "Catalysis of the reaction: glycosyl-N-acylsphingosine + H2O = a sugar + N-acylsphingosine." [PMID:10692580, PMID:9762914] synonym: "cerebrosidase activity" RELATED [EC:3.2.1.62] synonym: "glycosyl ceramide glycosylhydrolase activity" RELATED [EC:3.2.1.62] synonym: "glycosyl-N-acylsphingosine glycohydrolase activity" RELATED [EC:3.2.1.62] xref: EC:3.2.1.62 xref: MetaCyc:GALACTOSYLCERAMIDASE-RXN xref: MetaCyc:GLYCOSYLCERAMIDASE-RXN xref: MetaCyc:RXN-22900 is_a: GO:0004553 ! hydrolase activity, hydrolyzing O-glycosyl compounds

EC:3.2.1.62 covers three separate reactions, as indicated by the 3 different MetaCyc mappings (one of which, MetaCyc:GALACTOSYLCERAMIDASE-RXN, is shared with GO:0004336 galactosylceramidase activity [EC:3.2.1.46])

There is no RHEA mapping to EC:3.2.1.62.

There is 1 EXP annotation to GO:0017042.

Maybe we should:

• keep the current definition and name
• only map to the corresponding MetaCyc:GLYCOSYLCERAMIDASE-RXN
• make the EC mapping a broadMatch

?

[sjm41]

id: GO:0102669 name: isoflavone-7-O-glucoside beta-glucosidase activity namespace: molecular_function def: "Catalysis of the reaction: daidzein 7-O-beta-D-glucoside + H2O = daidzein + beta-D-glucose." [EC:3.2.1.-, GOC:pz] xref: MetaCyc:RXN-3591 is_a: GO:0004553 ! hydrolase activity, hydrolyzing O-glycosyl compounds

MetaCyc:RXN-3591 maps to RHEA:69683 in RHEA.

MetaCyc:RXN-3591 says that this reaction equation differs from the official Enzyme Commission reaction equations for this EC entry = EC:3.2.1.62 = GO:0017042 glycosylceramidase activity

So, GO:0102669 could either be merged into GO:0017042, or should become a child of it (with the new RHEA:69683 xref), depending on what we decide to do with GO:0017042.

[sjm41]

After discussions with @pgaudet and looking at CHEBI:

1. Keep GO:0017042 glycosylceramidase activity with its current definition, but make EC:3.2.1.62 broadMatch and only have the single MetaCyc:GLYCOSYLCERAMIDASE-RXN (exactMatch) mapping.

2. For GO:0004336 galactosylceramidase activity, make EC:3.2.1.46, MetaCyc:GALACTOSYLCERAMIDASE-RXN, RHEA:14297 all exactMatch xrefs.

3. For GO:0004348 glucosylceramidase activity, make EC:3.2.1.45, MetaCyc:GLUCOSYLCERAMIDASE-RXN, RHEA:13269 all exactMatch xrefs.

4. Ignore the MetaCyc:RXN-22900 reaction, since MetaCyc say "No enzyme has been identified for this reaction in this database."

5. Obsolete GO:0102669 isoflavone-7-O-glucoside beta-glucosidase activity - no annotations, only reference is to MetaCyc:RXN-3591 which says "this reaction equation differs from the official Enzyme Commission reaction"

Then make relationships look like this:

glycosylceramidase activity (GO:0017042)
    |_galactosylceramidase activity (GO:0004336)
    |_glucosylceramidase activity (GO:0004348)

[sjm41]

@pgaudet Just this bit left to do here: Obsolete GO:0102669 isoflavone-7-O-glucoside beta-glucosidase activity - no annotations, only reference is to MetaCyc:RXN-3591 which says "this reaction equation differs from the official Enzyme Commission reaction"