ExplorEnz: EC 6.5.1.3

6.5.1.3

Accepted name:

RNA ligase (ATP)

Reaction:

ATP + (ribonucleotide)_n-3′-hydroxyl + 5′-phospho-(ribonucleotide)_m = (ribonucleotide)_n+m + AMP + diphosphate (overall reaction)
(1a) ATP + [RNA ligase]-L-lysine = [RNA ligase]-N⁶-(5′-adenylyl)-L-lysine + diphosphate
(1b) [RNA ligase]-N⁶-(5′-adenylyl)-L-lysine + 5′-phospho-(ribonucleotide)_m = 5′-(5′-diphosphoadenosine)-(ribonucleotide)_m + [RNA ligase]-L-lysine
(1c) (ribonucleotide)_n-3′-hydroxyl + 5′-(5′-diphosphoadenosine)-(ribonucleotide)_m = (ribonucleotide)_n+m + AMP

Other name(s):

polyribonucleotide synthase (ATP); RNA ligase; polyribonucleotide ligase; ribonucleic ligase; poly(ribonucleotide):poly(ribonucleotide) ligase (AMP-forming)

Systematic name:

poly(ribonucleotide)-3′-hydroxyl:5′-phospho-poly(ribonucleotide) ligase (ATP)

Comments:

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.

References:

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

[EC 6.5.1.3 created 1976, modified 2016]