The Enzyme Database

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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 = [RNA ligase]-Nτ-(5′-guanosyl-phosphono)-L-histidine + diphosphate
(1b) [RNA ligase]-Nτ-(5′-guanosyl-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 = [RNA ligase]-Nτ-(5′-guanosyl-phosphono)-L-histidine + diphosphate
(2c) [RNA ligase]-Nτ-(5′-guanosyl-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 catalyses 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, PDB
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. [DOI] [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. [DOI] [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. [DOI] [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. [DOI] [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. [DOI] [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. [DOI] [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. [DOI] [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. [DOI] [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. [DOI] [PMID: 26858100]
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