Print

Print

Hello Guillermo,

 

because you are talking about conformational changes during the catalytic cycle, they should be very conserved along homologous enzymes. Discussing known examples of similar catalytic movements in homologous enzymes would strengthen your argument.

During my PhD, I was working on Zn-metallocarboxypeptidases, such as carboxypeptidase A, carboxypeptidase B and carboxypeptidsase T. CPT is a bacterial enzyme while CPA and CPB belong to mammals. CPT has identity of ~20% with CPA and CPB. Nevertheless, the catalytic induced fit movement of the Tyr248 loop upon substrate binding is believed to be the same in all these 3 enzymes.

 

Thank you,

Andrey

 

 

From: CCP4 bulletin board <[log in to unmask]> on behalf of Guillermo Montoya <[log in to unmask]>
Sent: Wednesday, February 1, 2017 10:32 AM
To: [log in to unmask]
Subject: Re: [ccp4bb] comparison of different protein states
 
Dear all, 

 thanks for your 
input


cheers!!


G.



On 1 Feb 2017, at 17:17, Debanu <[log in to unmask]> wrote:

Dear Xavier,
Great point and reminder!
Thanks,
Debanu

On Feb 1, 2017, at 6:44 AM, Boaz Shaanan <[log in to unmask]> wrote:

Hi,
One possible (formal, I should say) way around this would be to use one of the homology modeling servers (my favourite recently is phyre2 but go for any server you prefer) and feed it with the sequence of the protein in your structure as if you're trying to get its structure in the''apo'' form (a wrong term, as was pointed out on the bb recently). I'm quite certain that with the degree of conservation you mentioned it'll superpose extremely well on the other ''apo'' structure. This should satisfy the referee I would think (it's not me though).
Cheers,
Boaz


-------- Original message --------
From: Guillermo Montoya <[log in to unmask]>
Date: 01/02/2017 07:40 (GMT+02:00)
To: [log in to unmask]
Subject: [ccp4bb] comparison of different protein states


Dear all, 

first of all sorry for this off-topic question. I am requesting your help to 
find some papers  to convince one referee about the comparison
of two different protein states.

In our manuscript we show the crystal structure of an 
enzyme. This structure represents the enzyme after catalysis in complex with the product.
 In the discussion we have superimposed the enzyme in the apo conformation 
and the enzyme after catalysis in complex with the product 
and we have  commented the conformational changes observed
between these 2 states to propose a model.

The point of the referee is that this comparison is not valid because the 
enzymes that we used in the comparison belong to different species.
They are not the same protein.

However, and this is stated by us  in the figs and the manuscript, these two proteins are 
40% identical and 60% conserved, the polypeptide length is the same, and
the key amino acids and the domain structure are fully conserved. They are 
obviously orthologs.

IŽd really appreciate if you can send me some literature/information
to support our approach 

Thanks a lot for your input


best 




Guillermo Montoya, Prof., Dr.
Research Director, Protein Structure and Function Programme 
Novo Nordisk Foundation Center for Protein Research
Faculty of Health and Medical Sciences, University of Copenhagen,
Blegdamsvej 3A, DK-2200 Copenhagen, Denmark