When synthesizing nucleotides (either purines or pyrimidines), I know some steps require you to activate a carbonyl O in order to get the amine group. In the image down below, you can see this. In this case, amine groups are coming from Asp and Glu. What I would like to know is, how do you know when to use which amino acid group? From what I've seen so far, I don't commonly see Asn or Gln being used.
I'm also confused by the intermediates produced by these two reactions (they are not shown in the image). I was told that IMP --> adenylosuccinate yields an acyl-phosphate intermediate; Xanthylate ---> GMP yields an acyl-AMP intermediate. My question is, how can you get either of these two intermediates?? The only way I can get and acyl- group at all is if the phosphates were to attach to the amino acids; not the substrates.
So yes, when activating something, I don't know if the phosphates will attach to the substrate or the amino acids, and I don't understand why Asp and Gln are always used as amine donors.
I tried looking for some mechanisms, but I couldn't find any, unfortunately. Any help would be greatly appreciated, though!