[Go] Advice on adding an enzyme function

[Jim Hu]

Hi guys,

I'm not enthusiastic about substrate-specific child terms.  There are  
too many possible substrates and it seems like this would be better as  
a with CheBI.  Substrate class specific child terms, sure - leaving  
aside what makes a group of substrates members of a class.  I'd also  
hate to get bogged down in arguments about whether a particular  
substrate is physiologically significant.

Jim

On May 21, 2008, at 10:48 AM, Pankaj Jaiswal wrote:

> 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
>>>>> _______________________________________________
>>>>> Go mailing list
>>>>> 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
> fax: +1-607-255-6683
> _______________________________________________
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=====================================
Jim Hu
Associate Professor
Dept. of Biochemistry and Biophysics
2128 TAMU
Texas A&M Univ.
College Station, TX 77843-2128
979-862-4054


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