ATP-dependent synthetases and ligases

Synthetases and ligases are not classified as nucleotidyltransferases and phosphotransferases, but those that utilize ATP to activate a substrate for ligation catalyze nucleotidyl transfers or phospho transfers in activation steps. The mechanistic questions regarding these steps are analogous but not identical to those for the simple transferases. The chemical aspects of the adenylyl and phospho transfer steps should be the same for ATP-dependent synthetases and ligases as for the simpler transferases. However, enzymic catalysis frequently involves factors other than purely chemical rate enhancement of a single step. In the case of ATP-dependent synthetases and ligases, these factors include the requirement to bind several substrates in close proximity or the involvement of two or more sites in a polymer. In a few cases the complications imposed by the interactions 

DNA ligase and RNA ligase catalyze phosphodiester bond formation between 5 -phosphate and the 3 -hydroxyl ends of DNA or RNA. DNA ligases are required for DNA replication and RNA ligases are required for certain RNA splicing reactions. The function and overall reaction mechanism for DNA ligases are reviewed in Volume X of this series (80). The chemical mechanistic pathway for DNA ligase is outlined in reactions (23a)-(23c). 

These enzymes are not classified as nucleotidyltransferases, although they catalyze nucleotidyl group transfers in the course of activating the S -phosphoryl groups for the ligation process. The activation mechanism involves a covalent adenylyl-enzyme as an intermediate and a double displacement on of ATP (or NAD+). The chemical mechanism of the RNA ligase reaction is similar. The stereochemistry of these reactions is known for RNA ligase and is consistent with the mechanism as formulated above (81, 82). 

From a chemical standpoint the activation phases of the DNA and RNA ligase reactions [reactions (23a) and (23b)] are analogous to the pyrophosphorylase reactions discussed above, and the ligase phases [reaction (23c)] are analogous to the reactions catalyzed by the DNA and RNA polymerases. Both the pyro- 

The mechanism of action of glutamine synthetase has been extensively studied, and both the bacterial and mammalian enzymes were reviewed in Volume X of this series (83, 84). Many experimental approaches have been applied to the question of the chemical activation of the y-carboxyl group of glutamate and its reaction with ammonia. All of these experiments supported the stepwise chemical mechanism outlined in reactions (24a) and (24b) (8J), 

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