MINE would be a great database to start: http://minedatabase.mcs.anl.gov/#/home

and their paper:

MINEs: open access databases of computationally predicted enzyme promiscuity products for untargeted metabolomics Article MINEs: Open access databases of computationally predicted en...

Thanks for your reply. My question is how do I find probable substrate/metabolite for my new enzyme. I went through your website but couldn't find option to input enzyme structure or PDB file. I would really appreciate if there is any way out.

You look at the possibility of it to be an adenosyl or guanydyl cyclase. Did you run a blast for your enzyme to see what you can pull?

You are saying that your enzyme has a structure (PDB structure), maybe the structural team has some opinions on the possible substrates?

Alternately you could make a mutant and perform proteomics-metabolomics to see if you have a change in your profiles.

Another possibility is that your enzyme is cycling peptides and I am not sure then how you would be able to identify the "metabolite"

Geremy I have digged this protein sequence by doing bioinformatic analysis based on the known cyclases (chemical reactions in which there is ring formation). I have only solved the structure of the protein and now I am looking for some natural possible substrates.

Making mutant is a different story if I see reaction with some substrates. My question is how do I find the probable biosynthetic pathway in which My protein will act as catalyst. I for sure know that it will fall in biosynthesis of some cyclisation product.

And thanks in advance.

I guess that cyclases in general are able to have very diverse biochemical activity depending on the nature of the substrate you could look at you structure and try to find the type of reaction that your enzyme might catalyze (e.g. hydrolase, carboxylase, etc... ). You could also look at the size of the "active site" that might give you a first hint at what could be your substrate in terms of size. I don't think that there is an universal way to get information on the substrate. my point on the mutant + omics strategy was that you could have another layer of information by knowing what types of pathways are perturbated when your cyclase is not expressed.