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Source ontology files for the Gene Ontology
http://geneontology.org/page/download-ontology
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2-polyprenyl-6-methoxy-1,4-benzoquinone methyltransferase activity terms #25682

Closed sjm41 closed 10 months ago

sjm41 commented 1 year ago

Similar to #25680....

Currently we have:

2-polyprenyl-6-methoxy-1,4-benzoquinone methyltransferase activity (GO:0008425) (EC:2.1.1.-, no RHEA)
    |__2-hexaprenyl-6-methoxy-1,4-benzoquinone methyltransferase activity (GO:0043334) (no EC/RHEA)
    |__2-heptaprenyl-6-methoxy-1,4-benzoquinone methyltransferase activity (GO:0043428) (no EC, RHEA:44756)
    |__2-octaprenyl-6-methoxy-1,4-benzoquinone methylase activity (GO:0043333) (EC:2.1.1.201, no RHEA)
    |__2-nonaprenyl-6-methoxy-1,4-benzoquinone methyltransferase activity (GO:0043429) (no EC/RHEA)
    |__2-decaprenyl-6-methoxy-1,4-benzoquinone methyltransferase activity (GO:0043430) (RHEA:44764)

Screenshot 2023-07-05 at 14 09 43

EC:2.1.1.201 says: Name: 2-methoxy-6-polyprenyl-1,4-benzoquinol methylase Reaction: a 2-methoxy-6-all-trans-polyprenyl-1,4-benzoquinol + S-adenosyl-L-methionine <=> a 6-methoxy-3-methyl-2-all-trans-polyprenyl-1,4-benzoquinol + H(+) + S-adenosyl-L-homocysteine

Comments: Ubiquinones from different organisms have a different number of prenyl units (for example, ubiquinone-6 in Saccharomyces, ubiquinone- 9 in rat and ubiquinone-10 in human), and thus the natural substrate for the enzymes from different organisms has a different number of prenyl units. However, the enzyme usually shows a low degree of specificity regarding the number of prenyl units.

So, I suggest:

sjm41 commented 10 months ago

@pgaudet I've done the xref corrections. What do you think about the obsoletion suggestion?

pgaudet commented 10 months ago

Dear all,

The proposal has been made to obsolete

GO:0043429 2-nonaprenyl-6-methoxy-1,4-benzoquinone methyltransferase activity GO:0043428 2-heptaprenyl-6-methoxy-1,4-benzoquinone methyltransferase activity GO:0043430 2-decaprenyl-6-methoxy-1,4-benzoquinone methyltransferase activity GO:0043334 2-hexaprenyl-6-methoxy-1,4-benzoquinone methyltransferase activity GO:0043333 2-octaprenyl-6-methoxy-1,4-benzoquinone methylase activity

since these represent species-specific substrates, as stated in the EC comment: "Ubiquinones from different organisms have a different number of prenyl units" and "However, the enzyme usually shows a low degree of specificity regarding the number of prenyl units.". These will be replaced by the parent term " GO:0008425 2-polyprenyl-6-methoxy-1,4-benzoquinone methyltransferase activity"

The parent of GO:0008425, 'GO:0030580 quinone cofactor methyltransferase activity' will also be obsoleted and replaced by GO:0008425, since these describe the same reaction.

Annotations are here: https://github.com/geneontology/go-annotation/issues/4866

You can comment on the ticket: https://github.com/geneontology/go-ontology/issues/25682

Thanks, Pascale