Active Site Of Enzymes

Question

[miquelduranfrigola]

Hi all,

I have a list of UniprotACs corresponding to enzymes (no structure available for most of them). I'd like to identify residues in the active site. For now, I am looking at InterPro and extracting regions with the tag "site". Is this good practice? Any better option?

Many thanks in advance,

Miquel

[Diwan]

If the list is small, you can do homology modeling and look at cavities + key residues. (or) atleast for few you can do a sanity check to see if the regions you had extracted resembles an active site in a model.

Answer 1

[Neilfws]

In a UniProt record, the key that you are looking for in the feature table is ACT_SITE. For example in P00720 (T4 lysozyme):

FT   ACT_SITE     11     11       Proton donor. 
FT   ACT_SITE     20     20       Nucleophile.

So you could grep for that, or parse the record with the parsing library of your choice.