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

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

ATP + (ribonucleotide)n-3'-hydroxyl + 5'-phospho-(ribonucleotide)m = (ribonucleotide)n+m + AMP + diphosphate (overall reaction) [RN:R07640];
(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

R07640;
(other) R00436
Reaction

ATP [CPD:C00002];
(ribonucleotide)n-3'-hydroxyl;
5'-phospho-(ribonucleotide)m;
[RNA ligase]-L-lysine;
[RNA ligase]-N6-(5'-adenylyl)-L-lysine;
5'-(5'-diphosphoadenosine)-(ribonucleotide)m

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.

EC 6.5.1.3 created 1976, modified 2016

1  [PMID:4342972]

Silber R, Malathi VG, Hurwitz J.

Purification and properties of bacteriophage T4-induced RNA ligase.

Proc Natl Acad Sci U S A 69:3009-13 (1972)
DOI:10.1073/pnas.69.10.3009

2  [PMID:4373468]

Cranston JW, Silber R, Malathi VG, 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 249:7447-56 (1974)

3  [PMID:320212]

Sugino A, Snoper TJ, Cozzarelli NR

Bacteriophage T4 RNA ligase. Reaction intermediates and interaction of substrates.

J Biol Chem 252:1732-8 (1977)

4  [PMID:6194411]

Romaniuk PJ, Uhlenbeck OC

Joining of RNA molecules with RNA ligase.

Methods Enzymol 100:52-9 (1983)
DOI:10.1016/0076-6879(83)00045-2

5  [PMID:14962393]

Ho CK, Wang LK, Lima CD, Shuman S

Structure and mechanism of RNA ligase.

Structure 12:327-39 (2004)
DOI:10.1016/j.str.2004.01.011

6  [PMID:17018278]

Nandakumar J, Shuman S, Lima CD

RNA ligase structures reveal the basis for RNA specificity and conformational changes that drive ligation forward.

Cell 127:71-84 (2006)
DOI:10.1016/j.cell.2006.08.038