 RNA ligase

An RNA ligase is an enzyme that catalyzes covalent joining of RNA ends. Its usefulness depends on the terminal groups it recognizes and the chemistry that activates the joining reaction. The activity classified as EC6.5.1.3, an ATP-dependent RNA ligase, joins $3^{\prime }$ hydroxyl group and $5^{\prime }$ phosphate termini while converting ATP to adenosine monophosphate and diphosphate.^[ref]

RtcB illustrates another route. It joins a $3^{\prime }$ phosphate to a $5^{\prime }$ hydroxyl group using GTP, and can process an RNA cyclic phosphate end before sealing. The substrate ends appropriate for one RNA ligase therefore need not be appropriate for another.^[ref]

For a specified assay, imagine two RNA fragments held in the correct alignment. One pair has the terminal groups accepted by the chosen RNA ligase; an otherwise sequence-identical pair carries a blocked end. A failure to join the second pair could reflect end chemistry even though the letters and alignment match. A meaningful comparison separates recognition, activation and final phosphodiester bond formation. Historically, purification of a T4-induced enzyme and tests of its labelled products connected the joining activity to a biochemical preparation.^[ref] That functional evidence goes beyond assigning an enzyme name from sequence resemblance alone.