Question: GO:0008682 | 3-demethoxyubiquinol 3-hydroxylase activity (obsoletion or taxon restriction)

[ValWood]

I used

GO:0008682 | 3-demethoxyubiquinol 3-hydroxylase activity
for S. pombe coq7

@sylvainpoux pointed out that this should be more correctly

GO:0160224 | 3-demethoxyubiquinone 3-hydroxylase (NADH) activity

but I notice that Rhea maps many coq7 (including human) to
GO:0008682 | 3-demethoxyubiquinol 3-hydroxylase activity
https://www.uniprot.org/uniprotkb/?query=rhea:50908

My question is, should GO:0008682 | 3-demethoxyubiquinol 3-hydroxylase activity exist, and if so, should it be taxon restricted ?
There are only 2 EXP annotations

UniProtKB:O74826 | coq7 | enables | GO:0008682    3-demethoxyubiquinol 3-hydroxylase activity | ECO:0000315   IMP | PMID:18808426 |   | 284812 Schizosaccharomyces pombe (strain 972 / ATCC 24843) | PomBase |  
UniProtKB:P75728 | ubiF | enables | GO:0008682    3-demethoxyubiquinol 3-hydroxylase activity | ECO:0000315   IMP | PMID:10802164 |   | 83333 Escherichia coli (strain K12) | EcoliWiki

I will. remove the PomBase annotation today.

[ValWood]

[ValWood]

Hi @pgaudet could you ask Rhe for feedback, and then assign back to me to action

[sylvainpoux]

Hi @ValWood,

Here is the content of coq7 in S.pombe:

CC FUNCTION: Catalyzes the hydroxylation of 2-polyprenyl-3-methyl-6-methoxy-1,4-benzoquinol (DMQH2) during ubiquinone biosynthesis. {EXP|Ref.3}· Also catalyzes the hydroxylation of the 5-methoxy-2-methyl-3-(all-trans-polyprenyl)benzoquinone at the C6 position and participates in the biosynthesis of ubiquinone. {MODM|HAMAP-Rule:MF_03194}
CC CATALYTIC ACTIVITY
Reaction=a 5-methoxy-2-methyl-3-(all-trans-polyprenyl)benzene-1,4-diol + AH2 + O2 = a 3-demethylubiquinol + A + H2O [Rhea:50908]
EC=1.14.99.60
Evidence={MODM|HAMAP-Rule:MF_03194, EXP|Ref.3}
CC CATALYTIC ACTIVITY
Reaction=a 5-methoxy-2-methyl-3-(all-trans-polyprenyl)benzoquinone + NADH + O2 = a 3-demethylubiquinone + NAD(+) + H2O [Rhea:81211]
EC=1.14.13.253
Evidence={MODM|HAMAP-Rule:MF_03194}
PhysiologicalDirection=Left-to-right [Rhea:81212] {MODM|HAMAP-Rule:MF_03194}

An old paper (PMID:18808426) showed this GO:0008682 | 3-demethoxyubiquinol 3-hydroxylase activity. But according to a recent paper (PMID:38425362), COQ7 mediates GO:0160224 | 3-demethoxyubiquinone 3-hydroxylase (NADH) activity.

Thanks

Sylvain

[ValWood]

I agree, as does the author of PMID:18808426, so the question is, should we have GO:0008682 in GO. If yes, I think it should probably be "only in prokaryotes"?

[pgaudet]

GO:0160224 was recently created, see #29305

GO:0008682 only mentions 'acceptor', without mentioning which. I think GO:0160224 should be a child of GO:0008682.

I am not sure why you propose the TC bacteria on GO:0008682; I dont find any papers describing the acceptor.

Does anyone know if there are acceptors other than NAD for this reaction?

@kaxelsen
Thanks, Pascale

[ValWood]

I was suggesting a taxon restriction "Never in eukaryotes" on GO:0008682 3-demethoxyubiquinol 3-hydroxylase activity
if it is a valid term (because it appears to have EXP annotations for bacteria). These might be incorrect. I have no clue.