[Go] Advice on adding an enzyme function

[Rama Balakrishnan]

I am not very enthusiastic either about substrate specific terms.
I am not sure if we have consistently added substrate-specific terms.  
Long time back (really long time back) I was told that if the  
mechanism of catalysis is the same between substrates, then we don't  
want to create substrate specific terms.

Rama

On May 21, 2008, at 9:26 AM, Jim Hu wrote:

> 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
>>>>>> _______________________________________________
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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
>> fax: +1-607-255-6683
>> _______________________________________________
>> Go mailing list
>> Go at geneontology.org
>> http://fafner.stanford.edu/mailman/listinfo/go
>
> =====================================
> 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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