Ligases;
Forming phosphoric-ester bonds;
Ligases that form phosphoric-ester bonds (only sub-subclass identified to date)
BRITE hierarchy

RNA-3'-phosphate:RNA ligase (cyclizing, AMP-forming)

ATP + [RNA]-3'-(3'-phospho-ribonucleoside) = AMP + diphosphate + [RNA]-3'-(2',3'-cyclophospho)-ribonucleoside (overall reaction) [RN:R04274];
(1a) ATP + [RNA 3'-phosphate cyclase]-L-histidine = [RNA 3'-phosphate cyclase]-Ntau-(5'-adenylyl)-L-histidine + diphosphate;
(1b) [RNA 3'-phosphate cyclase]-Ntau-(5'-adenylyl)-L-histidine + [RNA]-3'-(3'-phospho-ribonucleoside) = [RNA 3'-phosphate cyclase]-L-histidine + [RNA]-3'-ribonucleoside-3'-(5'-diphosphoadenosine);
(1c) [RNA]-3'-ribonucleoside-3'-(5'-diphosphoadenosine) = [RNA]-3'-(2',3'-cyclophospho)-ribonucleoside + AMP

R04274
Reaction

ATP [CPD:C00002];
[RNA]-3'-(3'-phospho-ribonucleoside);
[RNA 3'-phosphate cyclase]-L-histidine;
[RNA 3'-phosphate cyclase]-Ntau-(5'-adenylyl)-L-histidine;
[RNA]-3'-ribonucleoside-3'-(5'-diphosphoadenosine)

The enzyme converts the 3'-terminal phosphate of various RNA substrates into the 2',3'-cyclic phosphodiester in an ATP-dependent reaction. Catalysis occurs by a three-step mechanism, starting with the activation of the enzyme by ATP, forming a phosphoramide bond between adenylate and a histidine residue [5,6]. The adenylate group is then transferred to the 3'-phosphate terminus of the substrate, forming the capped structure [RNA]-3'-(5'-diphosphoadenosine). Finally, the enzyme catalyses an attack of the vicinal O-2' on the 3'-phosphorus, which results in formation of cyclic phosphate and release of the adenylate. The enzyme also has a polynucleotide 5' adenylylation activity [7]. cf. EC 6.5.1.5, RNA 3'-terminal-phosphate cyclase (GTP).

EC 6.5.1.4 created 1986, modified 1989, modified 2013, modified 2016