ATP-dependent RNA ligase

An ATP-dependent RNA ligase catalyzes RNA ligation using ATP to activate the joining chemistry. For the activity EC6.5.1.3, a $3^{\prime }$ hydroxyl group is joined to a $5^{\prime }$ phosphate, yielding a phosphodiester bond, adenosine monophosphate and inorganic pyrophosphate. The accepted activity name specifies both compatible terminal groups and an energy-coupled reaction.^[ref]

The reaction proceeds through distinct activation states. An adenylate group first attaches to a lysine residue of the RNA ligase, then transfers to the RNA $5^{\prime }$ phosphate. Attack by the $3^{\prime }$ hydroxyl group completes the junction and releases the adenylate as adenosine monophosphate.^[ref] The enzyme can enter another catalytic cycle, whereas the ATP-derived chemical inventory has changed.

For an idealized inventory, start with four nanomoles of one RNA end, three nanomoles of its compatible partner and two nanomoles of ATP. Assume initially unactivated enzyme, no preactivated RNA and no nucleotide regeneration. At most two nanomoles of joined product can form through the stated route, leaving at least two and one nanomoles of the respective fragments. A smaller enzyme amount can still process multiple substrate molecules over repeated cycles; the amount and activity of enzyme affect how quickly that limit is approached.

The original T4-induced ligase purification linked ATP dependence and end modification to measurable products, including evidence for intramolecular circularization under the tested conditions.^[ref] The end requirements distinguish this route from RtcB's GTP-dependent chemistry.