EC - RNA ligase (ATP)

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IntEnz Enzyme Nomenclature


Accepted name:
RNA ligase (ATP)
Other names:
RNA ligase
polyribonucleotide ligase
polyribonucleotide synthase (ATP)
ribonucleic ligase
poly(ribonucleotide):poly(ribonucleotide) ligase (AMP-forming)
Systematic name:
poly(ribonucleotide)-3'-hydroxyl:5'-phospho-poly(ribonucleotide) ligase (ATP)



The enzyme catalyses the ligation of RNA strands with 3'-hydroxyl and 5'-phosphate termini, forming a phosphodiester and sealing certain types of single-strand breaks in RNA. Catalysis occurs by a three-step mechanism, starting with the activation of the enzyme by ATP, forming a phosphoramide bond between adenylate and a lysine residue. The adenylate group is then transferred to the 5'-phosphate terminus of the substrate, forming the capped structure 5'-(5'-diphosphoadenosine)-[RNA]. Finally, the enzyme catalyses a nucleophilic attack of the 3'-OH terminus on the capped terminus, which results in formation of the phosphodiester bond and release of the adenylate.

Links to other databases

Enzymes and pathways: NC-IUBMB , BRENDA , ExplorEnz , ENZYME@ExPASy , KEGG , MetaCyc , UniPathway
Structural data: CSA , EC2PDB
Gene Ontology: GO:0003972
CAS Registry Number: 37353-39-2
UniProtKB/Swiss-Prot: (48) [show] [UniProt]


  1. Silber, R., Malathi, V.G. and Hurwitz, J.
    Purification and properties of bacteriophage T4-induced RNA ligase.
    Proc. Natl. Acad. Sci. USA 69: 3009-3013 (1972). [PMID: 4342972]
  2. Cranston, J. W., Silber, R., Malathi, V. G., Hurwitz, J.
    Studies on ribonucleic acid ligase. Characterization of an adenosine triphosphate-inorganic pyrophosphate exchange reaction and demonstration of an enzyme-adenylate complex with T4 bacteriophage-induced enzyme.
    J. Biol. Chem. 249: 7447-7456 (1974). [PMID: 4373468]
  3. Sugino, A., Snoper, T. J., Cozzarelli, N. R.
    Bacteriophage T4 RNA ligase. Reaction intermediates and interaction of substrates.
    J. Biol. Chem. 252: 1732-1738 (1977). [PMID: 320212]
  4. Romaniuk, P. J., Uhlenbeck, O. C.
    Joining of RNA molecules with RNA ligase.
    Meth. Enzymol. 100: 52-59 (1983). [PMID: 6194411]
  5. Ho, C. K., Wang, L. K., Lima, C. D., Shuman, S.
    Structure and mechanism of RNA ligase.
    Structure 12: 327-339 (2004). [PMID: 14962393]
  6. Nandakumar, J., Shuman, S., Lima, C. D.
    RNA ligase structures reveal the basis for RNA specificity and conformational changes that drive ligation forward.
    Cell 127: 71-84 (2006). [PMID: 17018278]

[EC created 1976, modified 2016]