[Go] Advice on adding an enzyme function

[Alexander Diehl]

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 
> 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
>>> _______________________________________________
>>> Go mailing list
>>> Go at geneontology.org
>>> http://fafner.stanford.edu/mailman/listinfo/go
>>
>>
>


-- 
Alexander Diehl, Ph.D.
Senior Scientific Curator
Mouse Genome Informatics
The Jackson Laboratory
600 Main Street
Bar Harbor, ME  04609

email:  adiehl at informatics.jax.org
work:  +1 (207) 288-6427
fax:  +1 (207) 288-6131