[DEPRECATED] Gene Ontology / Annotation issues / #758 taxon violation: GO:0051289 "protein homotetramerization"

#758 taxon violation: GO:0051289 "protein homotetramerization"

Status: closed-accepted

Owner: Jennifer Deegan

Labels: None

Priority: 5

Updated: 2010-01-13

Created: 2010-01-12

Creator: Emily Boyce

Private: No

GO:0051289 "protein homotetramerization" only_in NCBITaxon:2759 "Eukaryota"

- Rule needs removing.

Thackray SJ, Bruckmann C, Anderson JL, Campbell LP, Xiao R, Zhao L, Mowat CG, Forouhar F, Tong L, Chapman SK.
Histidine 55 of tryptophan 2,3-dioxygenase is not an active site base but regulates catalysis by controlling substrate binding. Biochemistry. 2008 Oct 7;47(40):10677-84. Epub 2008 Sep 11.
'The enzyme discussed here is a prokaryotic TDO from Xanthomonas campestris (the causative agent of black rot in cabbages), which shares 34% sequence identity with human TDO. The enzyme is a homotetramer that displays high substrate specificity, catalyzing the oxidation of l-Trp, 5-F-Trp, and 6-F-Trp (1).'

Discussion

Midori Harris - 2010-01-13

assigned_to: nobody --> jenclark
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Jennifer Deegan - 2010-01-13

I have moved this back to cellular organisms.

Thanks,

Jen

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Jennifer Deegan - 2010-01-13

status: open --> closed-accepted
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Pascale Gaudet - 2010-01-13

Jen:

Isn't this a potentientally universal process?

Pascale

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Jennifer Deegan - 2010-01-13

VIruses too you reckon? Shall I just remove the restriction then?

Jen

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Pascale Gaudet - 2010-01-13

Jen,

I would remove it. You might want an opinion from a biochemist - but this is a basic property of proteins (to be able to dimerize, tetramerize, etc). For those process I think you're better off being 'generous' and allow all organisms - as far as I know, no specific process evolved to do this. One example Ifound is the HIV RT which is a heterodimer - I am sure there are many more of all sort of subunit arrangements.

Pascale

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Jennifer Deegan - 2010-01-13

Hi Pascale,

It turns out that this term inherits the restriction from cellular component biogenesis and cellular component organisation which are both only_in_taxon cellular organisms. Shall I just remove both of these links? I'm not sure that we lose much.

Jen

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Pascale Gaudet - 2010-01-13

I would remove the restrictions, yes.

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Jennifer Deegan - 2010-01-13

Okay, will do. This is quite an interesting area actually. The whole virus thing has been really interesting in the way it affects the taxon rules. I have written down what I have found out on the wiki:

http://gocwiki.geneontology.org/index.php/Taxon-GO_Checks_and_Commentary_-_Part_4

In the meantime I will get rid of these restrictions.

Thanks,

Jen

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