inositol kinases - errata and suggestions

[gocentral]

Hi,

I was annotating an Arabidopsis gene with inositol kinase acitivty. GOing through the ontology I realised there might be a need to reorganise this section (see GO:0004428 and children).

I think it might make sense to have the parentage as follows:

inositol or phosphatidylinositol kinase activity (GO:004428)

• myo-inositol kinase activity
• myo-inositol 3-kinase activity inositol polyphosphate kinase activity
• inositol trikisphosphate kinase activity (a child of this could be GO:0008440 and GO:0035299)
• inositol tetrakisphosphate kinase activity (a child of this could be GO:0047325 and GO:0047326)
• inositol pentakisphosphate kinase activity (a child of this could be GO:0035299), etc...
• phosphatidylinositol phosphate kinase activity (and children... already exists)

errata:

- GO:0035300 and GO:0008440 say "... trisphosphate...", it should be "...trikisphosphate...". (for example see PMID 10926925). Definitions need to be updated accordingly.

- GO:0019140 better defined by 'myo-inositol 3-kinase activity'

Thanks Christophe

Reported by: c_tissier

Original Ticket: "geneontology/ontology-requests/2825":https://sourceforge.net/p/geneontology/ontology-requests/2825

[gocentral]

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Hi Christophe,

We get our enzyme names and reaction definitions from the IUBMB nomenclature recommendations, so perhaps you might need to speak to them on this issue? I've dealt with them in the past and pointed out possible errors, and they were very quick to respond. If you let us know their response, we can update GO accordingly.

Thanks! Amelia Ireland.

Original comment by: girlwithglasses

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From the other item on this topic: GO:0047325 name: inositol tetrakisphosphate 1-kinase activity def: Catalysis of the reaction: 1D-myo-inositol 3,4,5,6-tetrakisphosphate + ATP = 1D-myo-inositol 1,3,4,5,6-pentakisphosphate + ADP.

this is wrong. Too granular. Definition should be: def: Catalysis of the reaction: 1D-myo-inositol tetrakisphosphate + ATP = 1D-myo-inositol pentakisphosphate + ADP.

the current definition should be given to a child of "inositol tetrakisphosphate 1-kinase activity" and this child should be "inositol 3,4,5,6-tetrakisphosphate 1-kinase activity".

Original comment by: girlwithglasses

[gocentral]

• summary: errata and suggestion --> inositol kinases - errata and suggestions

Original comment by: girlwithglasses

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Re: the first erratum in the initial post -

According to IUPAC, 'trisphosphate' is correct; there is no such thing as 'trikisphosphate' (it is an error in PMID 10926925, and is not found elsewhere in PubMed).

http://www.chem.qmul.ac.uk/iupac/misc/phospho.html

m

Original comment by: mah11

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Hi,

I have contacted IUBMB. I will let you know of their reply.

Christophe

Original comment by: c_tissier

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I've added two grouping terms:

inositol tetrakisphosphate kinase activity ; GO:0051765 inositol trisphosphate kinase activity ; GO:0051766

With the suggestion regarding "inositol tetrakisphosphate 1-kinase activity" (below) and the like, we'll wait and see what IUBMB say, but for the time being, I've added the precise names (e.g. inositol 3,4,5,6- tetrakisphosphate 1-kinase activity) as exact synonyms for the terms.

Original comment by: girlwithglasses

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• assigned_to: nobody --> girlwithglasses

Original comment by: girlwithglasses

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Chris,

Did you ever hear back from IUBMB?

Tanya

Original comment by: tberardini

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no, I did not.

Chris

Original comment by: c_tissier

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Hi everyone,

Can we come up with a solution and close this item? I would like to clear this temporary term from my list. Thanks!

Donghui

Original comment by: donghui

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Hi,

This item has been open for a long time. Please comment to let us know whether you would like it to remain assigned to you, or would prefer it to be reassigned. (You don't necessarily have to work on it immediately if you keep it; we just need to know whether it's still on your list.)

Thanks, Midori & David Ontology development group managers

Original comment by: mah11

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• assigned_to: girlwithglasses --> nobody

Original comment by: mah11

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superseded by SF 1849773 https://sourceforge.net/tracker/?func=detail&atid=440764&aid=1849773&group\_id=36855

Original comment by: mah11

[gocentral]

• status: open --> closed-out-of-date

Original comment by: mah11