[Go] Advice on adding an enzyme function

[Pankaj Jaiswal]

I support substrate-specific child terms for catalytic activities. It 
makes a lot of sense not only in species specific annotation but also in 
spatio-temporal functions as well, because the same molecules can use 
different substrates in different time and space in the same organism.

Pankaj

Alexander Diehl wrote:
> Jane,
> 
> There is precedent in the GO for such substrate-specific child terms, 
> for instance, 'xanthoxin dehydrogenase activity ; GO:0010301' is a child 
> of 'alcohol dehydrogenase activity ; GO:0004022' and 'sirohydrochlorin 
> ferrochelatase activity ; GO:0051266' and 'ferrochelatase activity ; 
> GO:0004325'.  There are many other examples.
> 
> However, perhaps Harold or others with strong backgrounds in 
> biochemistry will have a different bias (it's only 7 am EDT right now)
> 
> Thanks,
> 
> Alex
> 
> 
> Jane Lomax wrote:
>> Hi Alex - both the euk and prok enzymes act on spermine and 
>> spermidine, but the euk enzyme also acts on a range of other 
>> alkane-alpha,omega-diamine substrates including putrescine and http://dev.gramene.org/db/markers/marker_view
http://dev.gramene.org/db/markers/marker_view
>> 1,3-diaminopropane. In an assay, the prok enzyme does not act on 
>> putrescine and 1,3-diaminopropane.
>>
>> So I think you're suggesting I add child terms to GO:0004145, such as 
>> 'spermine N-acetyltransferase activity' etc?
>>
>> Jane
>>
>>
>> Alexander Diehl wrote:
>>> Jane,
>>>
>>> I would vote no, if the following conditions are true:
>>>
>>> 1)  When presented with any of the eukaryotic substrates, the 
>>> prokaryotic enzyme catalyzes the same reaction as the eukaryotic one.
>>>
>>> 2)  When presented with any of the prokaryotic substrates, the 
>>> eukaryotic enzyme catalyzes the same reaction as the prokaryotic one.
>>>
>>> When you say that the prokaryotic enzyme acts on a different range of 
>>> alkane-alpha,omega-diamine substrates, do you mean that it has a 
>>> different range of substrates available in the organisms where it is 
>>> found, or that it cannot act upon the substances found in eukaryotic 
>>> organisms.?
>>>
>>> If the latter is true, I would vote yes, and create substrate 
>>> specific terms for GO:0004145.
>>>
>>> -- Alex
>>>
>>>
>>> Jane Lomax wrote:
>>>> Hi - do we have any guidelines anywhere for when to add an enzyme 
>>>> function term or not? I had a look on the wiki and in the 
>>>> documentation and couldn't see anything. If not, perhaps we should 
>>>> add something - it seems that there have been quite a few 
>>>> discussions in this area and might be good to capture it all somewhere.
>>>>
>>>> Anyhow, my dilemma is this - we have a term 'diamine 
>>>> N-acetyltransferase activity ;  GO:0004145' which has EC 2.3.1.57. 
>>>> The EC is based on the eukaryotic enzyme, and the reaction catalysed 
>>>> is: acetyl-CoA + an alkane-alpha,omega-diamine = CoA + an 
>>>> N-acetyldiamine. Several different substrates (i.e. 
>>>> alkane-alpha,omega-diamines) are acted upon.
>>>>
>>>> The equivalent prokaryotic enzyme has essentially the same reaction, 
>>>> *but* acts on a different range of alkane-alpha,omega-diamine 
>>>> substrates.
>>>>
>>>> So should I add a new term for the prokaryotic function or not?
>>>>
>>>> thanks,
>>>>
>>>> Jane
>>>> _______________________________________________
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>>>> Go at geneontology.org
>>>> http://fafner.stanford.edu/mailman/listinfo/go
>>>
>>>
>>
> 
> 

-- 
Pankaj Jaiswal
G-15, Bradfield Hall
Dept. of Plant Breeding and Genetics
Cornell University
Ithaca, NY-14853, USA

Ph. +1-607-255-3103 / 4199
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