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

1  [PMID:6828385]

Filipowicz W, Konarska M, Gross HJ, Shatkin AJ.

RNA 3'-terminal phosphate cyclase activity and RNA ligation in HeLa cell extract.

Nucleic Acids Res 11:1405-18 (1983)
DOI:10.1093/nar/11.5.1405

2  [PMID:2581947]

Reinberg D, Arenas J, Hurwitz J.

The enzymatic conversion of 3'-phosphate terminated RNA chains to 2',3'-cyclic phosphate derivatives.

J Biol Chem 260:6088-97 (1985)

3  [PMID:9184239]

Genschik P, Billy E, Swianiewicz M, Filipowicz W

The human RNA 3'-terminal phosphate cyclase is a member of a new family of proteins conserved in Eucarya, Bacteria and Archaea.

EMBO J 16:2955-67 (1997)
DOI:10.1093/emboj/16.10.2955

4  [PMID:9738023]

Genschik P, Drabikowski K, Filipowicz W

Characterization of the Escherichia coli RNA 3'-terminal phosphate cyclase and its sigma54-regulated operon.

J Biol Chem 273:25516-26 (1998)
DOI:10.1074/jbc.273.39.25516

5  [PMID:10574971]

Billy E, Hess D, Hofsteenge J, Filipowicz W

Characterization of the adenylation site in the RNA 3'-terminal phosphate cyclase from Escherichia coli.

J Biol Chem 274:34955-60 (1999)
DOI:10.1074/jbc.274.49.34955

6  [PMID:19690099]

Tanaka N, Shuman S

Structure-activity relationships in human RNA 3'-phosphate cyclase.

RNA 15:1865-74 (2009)
DOI:10.1261/rna.1771509

7  [PMID:21098490]

Chakravarty AK, Shuman S

RNA 3'-phosphate cyclase (RtcA) catalyzes ligase-like adenylylation of DNA and RNA 5'-monophosphate ends.

J Biol Chem 286:4117-22 (2011)
DOI:10.1074/jbc.M110.196766

8  [PMID:23945037]

Das U, Shuman S

2'-Phosphate cyclase activity of RtcA: a potential rationale for the operon organization of RtcA with an RNA repair ligase RtcB in Escherichia coli and other bacterial taxa.

RNA 19:1355-62 (2013)
DOI:10.1261/rna.039917.113