[DEPRECATED] Gene Ontology / Ontology requests / #11077 demethoxyubiquinone mono-oxygenase

Antonia Lock - 2014-08-14

ps. the length of the substrate appears to be species specific,
is demethoxyubiquinone = 2-octoprenyl-3-methyl-6-methoxy-1,4-benzoquinone ?

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Tanya Berardini - 2014-08-15

labels: --> enzymes

assigned_to: Tanya Berardini
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Tanya Berardini - 2014-08-15

Information gathering stage:

on length of Q: "The number of isoprene units in the tail of Q is designated by n; n = 6 in S. cerevisiae, 9 in C. elegans, and 10 in Homo sapiens."

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3066048/

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Tanya Berardini - 2014-08-25

Hi Antonia,

I was reviewing the Metacyc page for this pathway:

http://biocyc.org/META/NEW-IMAGE?type=PATHWAY&object=PWY-5872&detail-level=3

The step you're interested in is the penultimate one, right?

http://biocyc.org/META/NEW-IMAGE?type=REACTION&object=RXN-9236&detail-level=3

You may want to annotate to 'oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, GO:0016705' + 'ubiquinone biosynthetic process'. The function is cross-referenced to EC 1.14.-.- which is what the metacyc reaction references as well.

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Antonia Lock - 2014-08-29

Cheers,
I changed GO:0016709 to GO:0016705

Is there are term for the MF to convert between 5-demethoxyubiquinone-10 and ubiquinone-10?

E. coli ubiF is annotated to
GO:0008682 - 2-octoprenyl-3-methyl-6-methoxy-1,4-benzoquinone hydroxylase activity

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Tanya Berardini - 2014-09-02

I suggest that you use this term:

GO:0061542, 3-demethylubiquinone-n 3-O-methyltransferase activity

http://biocyc.org/META/NEW-IMAGE?type=EC-NUMBER&object=EC-2.1.1.64&detail-level=3

I'll add more synonyms.

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Tanya Berardini - 2014-09-02

status: open --> closed
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Tanya Berardini - 2014-09-02

Added synonyms:
+synonym: " 2-octaprenyl-3-methyl-5-hydroxy-6-methoxy-1,4-benzoquinone methyltransferase" NARROW []
+synonym: " OMHMB-methyltransferase" RELATED []
+synonym: " S-adenosyl-L-methionine:2-octaprenyl-3-methyl-5-hydroxy-6-methoxy-1,4-benzoquinone-O-methyltransferase" RELATED []
+synonym: "5-demethylubiquinone-9 methyltransferase" NARROW []
+synonym: "5-demethylubiquinone-10 methyltransferase" NARROW []
+synonym: "demethoxyubiquinone monooxygenase" RELATED []

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Antonia Lock - 2014-09-02

ah thanks! appreciate it, was pulling my hair a bit

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Antonia Lock - 2014-09-03

In the paper they call it a demethoxy-ubiquinone hydroxylase - is this also a synonym?

Also, in cerevisiae COQ3 is annotated to this term (GO:0061542, 3-demethylubiquinone-n 3-O-methyltransferase activity) however, CAT5 is apparently the functional ortholog....how does this work?

Last edit: Antonia Lock 2014-09-03

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Tanya Berardini - 2014-09-05

Will add this as a synonym: demethoxy-ubiquinone hydroxylase.

Don't know what to tell you about CAT5/COQ3. More of an annotation question than an ontology one. Maybe discuss with SGD curators?

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Antonia Lock - 2014-09-05

I'll ask Val to take a look at the paper if she think it's right.

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Valerie Wood - 2014-09-07

Hi,

Sorry I didn't see this thread. I didn't look at the paper but the the monoxygenase and the methytransferase appear to be different ...(coq3 and coq7)

This is what I sent to SGD earlier. I think there is a mix-uop

Val

According to KEGG
coq7 is
http://www.genome.jp/kegg-bin/get_htext?ko00001+K06134
EC:1.14.13.-

so maybe the wiki page and the wormbase description are incorrect?

The reaction is
2-Polyprenyl-3-methyl-6-methoxy-1,4-benzoquinone + Oxygen + NADPH + H+ <=> 2-Polyprenyl-3-methyl-5-hydroxy-6-methoxy-1,4-benzoquinone + NADP+ + H2O

do you think
demethoxyubiquinone monooxygenase
is the correct term for COQ7 and should this be removed as a synonym of
GO:0061542

Val

On 07/09/2014 16:56, Valerie Wood wrote:

Hi,

Antonia and I were wondering if S. cerevisiae COQ7 should be annotated to
GO:0061542
Name 3-demethylubiquinone-n 3-O-methyltransferase activity

http://en.wikipedia.org/wiki/COQ7

Its odd because SGD have COq3 annotated to this activity form IMP (all of the other annotations are IDA and IEA), but coq3 looks more like a methyltransferase

To me it seems possible that COQ7 should be demethoxyubiquinone monooxygenase, but

demethoxyubiquinone monooxygenase is a related synonym of
3-demethylubiquinone-n 3-O-methyltransferase activity which seems wrong?

Val

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Tanya Berardini - 2014-09-08

Pls. keep me in the loop so that I can update the synonyms if necessary. Thanks.

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Tanya Berardini - 2014-09-08

status: closed --> pending
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Valerie Wood - 2014-09-09

I think this is what we need to do.
Correct me if I am wrong.
Val

NTR: demethoxyubiquinone monooxygenase
synonym: demethoxy-ubiquinone hydroxylase
def:
2-Polyprenyl-3-methyl-6-methoxy-1,4-benzoquinone + Oxygen + NADPH + H+ <=> 2-Polyprenyl-3-methyl-5-hydroxy-6-methoxy-1,4-benzoquinone + NADP+ + H2O

actually.....probably they should be synonyms of this existing term?
GO:0008682 2-octoprenyl-3-methyl-6-methoxy-1,4-benzoquinone hydroxylase activity
the only annotation to this is E.coli UbiF http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0008682#term=annotation
which is coq7
http://www.genome.jp/kegg-bin/show_pathway?ko00130+K03184

remove synonym demethoxyubiquinone monooxygenase from
GO:0061542 3-demethylubiquinone-n 3-O-methyltransferase activity

val

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Valerie Wood - 2014-09-09

status: pending --> open
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KM Van Auken - 2014-09-09

Hi,

I just reviewed the enzymology and the worm description and I think the description we have is okay.

I agree with Val's suggestions above to remove the hydroxylase and monooxygenase synonyms from GO:0061542 and add them to GO:0008682.

The existing annotations for coq3 to the methyltransferase term and coq7/cat5 to the monooxygenase term are thus correct, although the latter could be updated to the more granular term, if I understand correctly.

This reference was also helpful: http://www.ncbi.nlm.nih.gov/pubmed/24911838

Thanks,
--Kimberly

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- Valerie Wood - 2014-09-10
  
  Hi Kimberly,
  
  Thanks, you're right, all the annotations are correct, it was just the
  synonyms which were confusing, so nobody was locating the specific term.
  
  VAl
  
  On 09/09/2014 18:51, KM Van Auken wrote:
  
  Hi,
  
  I just reviewed the enzymology and the worm description and I think
  the description we have is okay.
  
  I agree with Val's suggestions above to remove the hydroxylase and
  monooxygenase synonyms from GO:0061542 and add them to GO:0008682.
  
  The existing annotations for coq3 to the methyltransferase term and
  coq7/cat5 to the monooxygenase term are thus correct, although the
  latter could be updated to the more granular term, if I understand
  correctly.
  
  This reference was also helpful:
  http://www.ncbi.nlm.nih.gov/pubmed/24911838
  
  Thanks,
  --Kimberly
  
  [ontology-requests:#11077]
  http://sourceforge.net/p/geneontology/ontology-requests/11077
  demethoxyubiquinone mono-oxygenase
  
  Status: open
  Group: None
  Labels: enzymes
  Created: Thu Aug 14, 2014 01:10 PM UTC by Antonia Lock
  Last Updated: Tue Sep 09, 2014 08:40 AM UTC
  Owner: Tanya Berardini
  
  Hello!
  
  Just after a bit of annotation advice, I want to annotate coq7 to its
  MF by IMP evidence.
  
  In the pombe deletion mutant demethoxyubiquinone-10 accumulates, and
  no coenzyme Q10 is observed. PMID:18808426
  
  The enzyme is commonly referred to as "demethoxyubiquinone mono-oxygenase"
  eg
  http://www.wormbase.org/species/c_elegans/gene/WBGene00000536#03-9e-3
  http://en.wikipedia.org/wiki/COQ7
  
  are these the correct MF terms?:
  
  GO:0016709 oxidoreductase activity, acting on paired donors, with
  incorporation or reduction of molecular oxygen, NAD(P)H as one donor,
  and incorporation of one atom of oxygen
  
  GO:0008682 2-octoprenyl-3-methyl-6-methoxy-1,4-benzoquinone
  hydroxylase activity
  
  cheers!
  
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Tanya Berardini - 2014-09-09

-synonym: "demethoxy-ubiquinone hydroxylase" RELATED [GOC:al]
-synonym: "demethoxyubiquinone monooxygenase" RELATED []

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Tanya Berardini - 2014-09-09

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Tanya Berardini - 2014-09-09

status: open --> closed-fixed
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Tanya Berardini - 2014-09-09

Closing now that the 'bad' synonyms are gone.

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Tanya Berardini - 2014-09-09

+synonym: "demethoxyubiquinone monooxygenase" RELATED [GOC:vw]
+synonym: "demethoxy-ubiquinone hydroxylase" RELATED [GOC:vw]

Added to GO:0008682

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demethoxyubiquinone mono-oxygenase

The DEPRECATED legacy location of the GO, see http://geneontology.org

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#11077 demethoxyubiquinone mono-oxygenase

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