GO:0033898 is a subreaction of GO:0033897 about go-ontology

[raymond91125]

It seems enzymes that carry out just the half rxn may be different from the full rxn ones.
EC:4.6.1.22 was used to annotate CRISPR-associated proteins, e.g. https://www.uniprot.org/uniprotkb/U2UMQ6/entry that appear to be different from those annotated with EC:4.6.1.19 at UniProt.

[sjm41]

Hi @raymond91125

Thanks for looking into this.

I see there is only a single reviewed (SwissProt) entry at UniPort with EC:4.6.1.22 manually assigned to it:
https://www.uniprot.org/uniprotkb/A0Q7Q2/entry
This is "CRISPR-associated endonuclease Cas12a (cas12a)" from the bacterium Francisella tularensis subsp. novicida.

The annotation comes from PMID: 28431230. That paper does say that Cas12a reaction is a "RNA cleavage reactions dependent on the presence of the 2’-hydroxyl group in the ribonucleotide upstream of the scissile phosphate typically proceed via acid-base (rather than metal-dependent) catalysis and yield products containing 5’-hydroxyl and 2’,3’-cyclic phosphate groups."
So, the EC:4.6.1.22 annotation does seem to be correct here?

(I note that EC:4.6.1.22 does not appear to be annotated to any Bacillus subtilis proteins, despite its EC name of "Bacillus subtilis ribonuclease activity ribonuclease activity".)

However, looking again at GO:0033897, I see that its associated RHEA:68052 has the comment saying "Multi-step reaction: RHEA:67796 and RHEA:68056"

and RHEA:67796 is: "a ribonucleotidyl-ribonucleotide-RNA = a 3'-end 2',3'-cyclophospho-ribonucleotide-RNA + a 5'-end dephospho-ribonucleoside-RNA", that RHEA says corresponds to MetaCyc:RXN-19924.

So, both MetaCyc and RHEA state that that GO:0033898 (= RHEA:67796 / MetaCyc:RXN-19924) is a sub-reaction of GO:0033897 (= EC:4.6.1.19 / RHEA:68052 / MetaCyc:3.1.27.5-RXN), in which case it should be obsoleted in GO.

@kaxelsen
Could you confirm:
i) that the EC:4.6.1.22 annotation to A0Q7Q2 (cas12a) from PMID:28431230 is correct?
ii) whether RHEA:67796 = MetaCyc:RXN-19924 = EC:4.6.1.22 = GO:0033898? (there is currently no direct link between RHEA:67796 and EC:4.6.1.22 in RHEA, though this is implied via the shared MetaCyc:RXN-19924 xref)