
Bardia G. answered 07/05/19
B.S in Biochemistry and Molecular Biology from UC Davis
Why questions are difficult to answer in Biology, generally.
Guanosine Triphosphate (GTP) and Adenosine Triphosphate (ATP) are both high energy nucleotides with a purine as their glucosylamine (base) group with a very similar structure.
GTP is energetically equivalent in almost every regard to ATP and can be freely converted between the two forms by nucleoside diphosphate kinase (NDK).
One potential reason is that enzymes that bind GTP instead of ATP would be more specific and only active under certain conditions, such as those present during the Krebs cycle and gluconeogenesis.
Another reason is pure chance and that the enzymes of these pathways happened to do their job better when they bound GTP instead of ATP and the mutation stuck.