IUBMB Enzyme Nomenclature

EC 6.5.1.8

Accepted name: 3'-phosphate/5'-hydroxy nucleic acid ligase

Reaction: (1) (ribonucleotide)n-3'-phosphate + 5'-hydroxy-(ribonucleotide)m + GTP = (ribonucleotide)n+m + GMP + diphosphate (overall reaction)
(1a) GTP + [RNA ligase]-L-histidine = 5'-guanosyl [RNA ligase]-Nτ-phosphono-L-histidine + diphosphate
(1b) 5'-guanosyl [RNA ligase]-Nτ-phosphono-L-histidine + (ribonucleotide)n-3'-phosphate = (ribonucleotide)n-3'-(5'-diphosphoguanosine) + [RNA ligase]-L-histidine
(1c) (ribonucleotide)n-3'-(5'-diphosphoguanosine) + 5'-hydroxy-(ribonucleotide)m = (ribonucleotide)n+m + GMP
(2) (ribonucleotide)n-2',3'-cyclophosphate + 5'-hydroxy-(ribonucleotide)m + GTP + H2O = (ribonucleotide)n+m + GMP + diphosphate (overall reaction)
(2a) (ribonucleotide)n-2',3'-cyclophosphate + H2O = (ribonucleotide)n-3'-phosphate
(2b) GTP + [RNA ligase]-L-histidine = 5'-guanosyl [RNA ligase]-Nτ-phosphono-L-histidine + diphosphate
(2c) 5'-guanosyl [RNA ligase]-Nτ-phosphono-L-histidine + (ribonucleotide)n-3'-phosphate = (ribonucleotide)n-3'-(5'-diphosphoguanosine) + [RNA ligase]-L-histidine
(2d) (ribonucleotide)n-3'-(5'-diphosphoguanosine) + 5'-hydroxy-(ribonucleotide)m = (ribonucleotide)n+m + GMP

Other name(s): rtcB (gene name)

Systematic name: poly(ribonucleotide)-3'-phosphate:5'-hydroxy-poly(ribonucleotide) ligase (GMP-forming)

Comments: The enzyme is a GTP- and Mn2+-dependent 3'-5' nucleic acid ligase with the ability to join RNA with 3'-phosphate or 2',3'-cyclic-phosphate ends to RNA with 5'-hydroxy ends. It can also join DNA with 3'-phosphate ends to DNA with 5'-hydroxy ends, provided the DNA termini are unpaired [6]. The enzyme is found in members of all three kingdoms of life, and is essential in metazoa for the splicing of intron-containing tRNAs. The reaction follows a three-step mechanism with initial activation of the enzyme by GTP hydrolysis, forming a phosphoramide bond between the guanylate and a histidine residue. The guanylate group is transferred to the 3'-phosphate terminus of the substrate, forming the capped structure [DNA/RNA]-3'-(5'-diphosphoguanosine). When a suitable 5'-OH end is available, the enzyme catalyses an attack of the 5'-OH on the capped end to form a 3'-5' phosphodiester splice junction, releasing the guanylate. When acting on an RNA 2',3'-cyclic-phosphate, the enzyme cayalyses an additional reaction, hydrolysing the cyclic phosphate to a 3'-phosphate [9]. The metazoan enzyme requires activating cofactors in order to achieve multiple turnover catalysis [8].

Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number:

References:

1. Tanaka, N., Meineke, B. and Shuman, S. RtcB, a novel RNA ligase, can catalyze tRNA splicing and HAC1 mRNA splicing in vivo. J. Biol. Chem. 286 (2011) 30253-30257. [PMID: 21757685]

2. Tanaka, N. and Shuman, S. RtcB is the RNA ligase component of an Escherichia coli RNA repair operon. J. Biol. Chem. 286 (2011) 7727-7731. [PMID: 21224389]

3. Tanaka, N., Chakravarty, A.K., Maughan, B. and Shuman, S. Novel mechanism of RNA repair by RtcB via sequential 2',3'-cyclic phosphodiesterase and 3'-phosphate/5'-hydroxyl ligation reactions. J. Biol. Chem. 286 (2011) 43134-43143. [PMID: 22045815]

4. Desai, K.K. and Raines, R.T. tRNA ligase catalyzes the GTP-dependent ligation of RNA with 3'-phosphate and 5'-hydroxyl termini. Biochemistry 51 (2012) 1333-1335. [PMID: 22320833]

5. Chakravarty, A.K., Subbotin, R., Chait, B.T. and Shuman, S. RNA ligase RtcB splices 3'-phosphate and 5'-OH ends via covalent RtcB-(histidinyl)-GMP and polynucleotide-(3')pp(5')G intermediates. Proc. Natl. Acad. Sci. USA 109 (2012) 6072-6077. [PMID: 22474365]

6. Chakravarty, A.K. and Shuman, S. The sequential 2',3'-cyclic phosphodiesterase and 3'-phosphate/5'-OH ligation steps of the RtcB RNA splicing pathway are GTP-dependent. Nucleic Acids Res. 40 (2012) 8558-8567. [PMID: 22730297]

7. Das, U., Chakravarty, A.K., Remus, B.S. and Shuman, S. Rewriting the rules for end joining via enzymatic splicing of DNA 3'-PO4 and 5'-OH ends. Proc. Natl. Acad. Sci. USA 110 (2013) 20437-20442. [PMID: 24218597]

8. Desai, K.K., Beltrame, A.L. and Raines, R.T. Coevolution of RtcB and Archease created a multiple-turnover RNA ligase. RNA 21 (2015) 1866-1872. [PMID: 26385509]

9. Maughan, W.P. and Shuman, S. Distinct contributions of enzymic functional groups to the 2',3'-cyclic phosphodiesterase, 3'-phosphate guanylylation, and 3'-ppG/5'-OH ligation steps of the Escherichia coli RtcB nucleic acid splicing pathway. J. Bacteriol. 198 (2016) 1294-1304. [PMID: 26858100]

[EC 6.5.1.8 created 2017]


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