|MadSci Network: Biochemistry|
Sorry I did not respond earlier to your question - I have been on vacation...
I am not sure which angle you want in answering your question - whether you are interested in specificity of enzymes in binding one over the other, or whether you want to know why organisms would evolve to have enzymes that only bind to one over the other. From your comments, it seems like you might like both answered.
ATP is found in high concentrations in cells, while GTP is in much lower concentrations. The ratio of ATP to AMP in the cell is very important, such that use of large amounts of ATP for energy can cause apoptosis (cell death). GTP is not required to maintain such a balance, so it is a good "alternative" energy source - its consumption will not lead to cell death. Since it is in small quanitites, there is also the possibility to have finer regulation of energy use when fine-tuned energy use is important. These are some general reasons that GTP exists at all.
As for the question about structural reasons for the specificity of an enzyme for ATP versus GTP, your general comment was basically correct. In looking for publications discussing this issue, I found a paper by a group who solved the crystal structure of the protein Transglutaminase 3. In just looking at the binding pocket they could see that "the specificity for binding by guanine nucleotides versus adenine nucleotides is conferred by the pattern of hydrogen bond donors and acceptor interactions with the major-groove face of the guanine" nucleotide.
Hope this helps! Sorry I am so late.
Ahvazi B, Boeshans KM, Steinert PM. Crystal structure of transglutaminase 3 in complex with GMP: structural basis for nucleotide specificity. J Biol Chem. 2004 Jun 18;279(25):26716-25. (www.jbc.org/cgi/content/full/279/25/26716)
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