ntr: ubiquinone biosynthesis methyltransferases

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(This is related to Item 1151948)

I found a nice review about this, PMID: 11583838.

It says the chain lengths of the polyprenyl tail is as follows: -6 units in cerevisiae -7 units in bacillus spp -8 units in E coli -9 units in R. capsulatus -10 units in G. suboxidans (p. 137 and discussion in section 7.2)

So we should probably add (n)prenyl-6-methoxy-1,4-benzoquinone methyltransferase activity terms for all these substrates, and maybe put a comment saying that the length of the polyprenyl tail varies from organism to organism and that unless there is direct evidence for the substrate, the parent term 'poly prenyl-6-methoxy-1,4-benzoquinone methyltransferase activity' should be used.

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Also: There is another methylation reaction in the ubiquinone synthesis pathway, 2-octaprenyl-3-methyl-5-hydroxy-6-methoxy-1,4-benzoquinol (demethylmenaquinone) -> ubiquinol (menaquinone?) (section 4.3.2).

You may want to run this by Kirll to make sure this is right.

Thanks

Pascale

Reported by: pgaudet

Original Ticket: "geneontology/ontology-requests/2396":https://sourceforge.net/p/geneontology/ontology-requests/2396

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• assigned_to: nobody --> jl242

Original comment by: pgaudet

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Logged In: YES user_id=451873

Have contacted Kirill for advice again.

Original comment by: jl242

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yes this looks fine to me

Kirill

Original comment by: kiri11

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Right, so just to check, these are the new terms I'll be adding:

2-heptaprenyl-6-methoxy-1,4-benzoquinone methyltransferase activity 2-nonaprenyl-6-methoxy-1,4-benzoquinone methyltransferase activity 2-decaprenyl-6-methoxy-1,4-benzoquinone methyltransferase activity

with defs:

2-heptaprenyl-6-methoxy-1,4-benzoquinone methyltransferase activity Catalysis of the reaction: 2-heptaprenyl-6-methoxy-1,4-benzoquinone + S-adenosyl-L-methionine = 2-heptaprenyl-3-methyl-6-methoxy-1,4-benzoquinone + S-adenosyl-L-homocysteine.

2-nonaprenyl-6-methoxy-1,4-benzoquinone methyltransferase activity Catalysis of the reaction: 2-nonaprenyl-6-methoxy-1,4-benzoquinone + S-adenosyl-L-methionine = 2-nonaprenyl-3-methyl-6-methoxy-1,4-benzoquinone + S-adenosyl-L-homocysteine.

2-decaprenyl-6-methoxy-1,4-benzoquinone methyltransferase activity Catalysis of the reaction: 2-decaprenyl-6-methoxy-1,4-benzoquinone + S-adenosyl-L-methionine = 2-decaprenyl-3-methyl-6-methoxy-1,4-benzoquinone + S-adenosyl-L-homocysteine.

and comment:

Note that the polyprenyl sidechain substrate for these methyltransferases varies in length between species, for example, 6 units in S. cerevisae, 8 units in E. coli and 10 units in G. suboxidans. Where the length of the substrate polyprenyl chain is unknown, the term '2-polyprenyl-6-methoxy-1,4-benzoquinone methyltransferase activity ; GO:0008425' should be used.

Original comment by: jl242

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• milestone: --> TermGenie

Original comment by: jl242

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Thanks Jane.

Are you also going to add the other reaction? 2-octaprenyl-3-methyl-5-hydroxy-6-methoxy-1,4-benzoquinol (demethylmenaquinone) -> ubiquinol (menaquinone?)

I don't know what the activity would be called.

Pascale

Original comment by: pgaudet

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Ah yes - that's called '2-octaprenyl-3-methyl-5-hydroxy-6-methoxy-1,4-benzoquinone methyltransferase' (see PMID: 1479344) - will add that too.

Original comment by: jl242

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• labels: --> New term request
• status: open --> closed-accepted

Original comment by: jl242

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Logged In: YES user_id=451873

Added new terms:

2-heptaprenyl-6-methoxy-1,4-benzoquinone methyltransferase activity ; GO:0043428 2-nonaprenyl-6-methoxy-1,4-benzoquinone methyltransferase activity ; GO:0043429 2-decaprenyl-6-methoxy-1,4-benzoquinone methyltransferase activity ; GO:0043430

as children of '2-polyprenyl-6-methoxy-1,4-benzoquinone methyltransferase activity ; GO:0008425'

and

2-octaprenyl-3-methyl-5-hydroxy-6-methoxy-1,4-benzoquinone methyltransferase ; GO:0043431

as a child of 'O-methyltransferase activity ; GO:0008171'

Original comment by: jl242