Update EC xref on GO:0004325 ferrochelatase activity

[sjm41]

id: GO:0004325 name: ferrochelatase activity namespace: molecular_function def: "Catalysis of the reaction: heme B (protoheme) + H+ = Fe(2+) + protoporphyrin IX." [RHEA:22584] xref: EC:4.99.1.1 xref: KEGG_REACTION:R00310 xref: MetaCyc:PROTOHEMEFERROCHELAT-RXN xref: Reactome:R-HSA-189465 "FECH binds Fe2+ to PRIN9 to form heme" xref: RHEA:22584 is_a: GO:0016829 ! lyase activity

EC has been transferred to 4.98.1.1 https://www.enzyme-database.org/query.php?ec=4.99.1.1

@kaxelsen that website says the transfer happened in 2021, but I don't see the update here: https://enzyme.expasy.org/EC/4.99.1.1 Is there a synchrony problem??

Also, I think reference to EC:4.99.1.1 should be deleted from the comment on this entry: id: GO:0016851 name: magnesium chelatase activity namespace: molecular_function def: "Catalysis of the reaction: ATP + H(2)O + Mg(2+) + protoporphyrin IX = ADP + 2 H(+) + magnesium protoporphyrin IX + phosphate." [EC:6.6.1.1, RHEA:13961] comment: Note that this was EC:4.99.1.1. xref: EC:6.6.1.1 xref: KEGG_REACTION:R03877 xref: MetaCyc:RXN1F-20 xref: RHEA:13961 is_a: GO:0051003 ! ligase activity, forming nitrogen-metal bonds, forming coordination complexes

[kaxelsen]

Concerning EC 4.99.1.1 transferred to EC 4.98.1.1 You are quite right the SIB ENZYME data is not up to date. We have had problems with the curation tool that was old and needed to be replaced. This has now been done, and I have started working down the back-log. I hope to be up-to-date by release 2022_04 scheduled for September 28.

[pgaudet]

Since we make links to https://enzyme.expasy.org, we need to wait for the September update to update the xref.

[sjm41]

OK!

What do you think about removing "Note that this was EC:4.99.1.1." from the GO:0016851 entry. Seems a different reaction, and https://enzyme.expasy.org/EC/6.6.1.1 doesn't mention it.

[pgaudet]

Sounds good. I also updated the definition of GO:0016851 to match RHEA:

EC ATP + protoporphyrin IX + Mg(2+) + H(2)O <=> ADP + phosphate + Mg-protoporphyrin IX + 2 H(+)

RHEA ATP + H2O + Mg2+ + protoporphyrin IX = ADP + 3 H+ + Mg-protoporphyrin IX + phosphate

Not sure why there is a discrepancy.

[kaxelsen]

The reason is that IUBMB texts are not perfectly balanced for charge and mass, that is one of the improvements in Rhea. Protons are only added to IUBMB reactions when they are deemed to be an important part of the reaction.

[sjm41]

Regarding the backlog @kaxelsen mentions - sounds like there will be quite a lot of new/changed ECs to add or move in the Sept update. I can't remember if there's an existing process for this update to be coordinated with GO, so all xrefs will be updated as required?

[kaxelsen]

I don't think there is. Until now we (Rhea) have made lists of the EC numbers and GO terms concerned and informed @pgaudet .

[pgaudet]

I think this is done.

[sjm41]

Hi @pgaudet I think we still need to change 4.99.1.1 -> 4.98.1.1 on GO:0004325, don't we?

You said above that we should wait until September to do this since we make links to https://enzyme.expasy.org/, but I think we should make the change now given 4.99.1.1 is already invalid at all other places (https://www.enzyme-database.org, KEGG, MetaCyc...) and it's just EXPASY that is out of date. It's true that the hyperlink to EXPASY won't resolve until Sept, but I think that's OK - better that than report an obsolete EC number?

[pgaudet]

That was starting from a good intention but it's too confusing to keep track of true obsolete xrefs and not yet visible ones.