[Go] Advice on adding an enzyme function

[Alexander Diehl]

I agree if there is no difference in the mechanism of catalysis that we 
should not create substrate specific terms.  However, selectivity among 
classes of substrates suggests mechanistic differences to me.  In no way 
would I advocate create of enzyme terms for every possible substrate, 
only among classes of substrate that are handled in varied mechanistic ways.

-- Alex


Rama Balakrishnan wrote:
> 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


-- 
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