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
On 1 Feb 2017, at 17:17, Debanu <[log in to unmask]> wrote:
Dear Xavier,Great point and reminder!Thanks,DebanuHi,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 tofind some papers to convince one referee about the comparisonof two different protein states.
In our manuscript we show the crystal structure of anenzyme. This structure represents the enzyme after catalysis in complex with the product.In the discussion we have superimposed the enzyme in the apo conformationand the enzyme after catalysis in complex with the productand we have commented the conformational changes observedbetween these 2 states to propose a model.
The point of the referee is that this comparison is not valid because theenzymes 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 are40% identical and 60% conserved, the polypeptide length is the same, andthe key amino acids and the domain structure are fully conserved. They areobviously orthologs.
IŽd really appreciate if you can send me some literature/informationto support our approach
Thanks a lot for your input
best
Guillermo Montoya, Prof., Dr.Research Director, Protein Structure and Function ProgrammeNovo Nordisk Foundation Center for Protein Research
Faculty of Health and Medical Sciences, University of Copenhagen,
Blegdamsvej 3A, DK-2200 Copenhagen, Denmarkweb: www.cpr.ku.dk