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Information on EC 6.5.1.8 - 3'-phosphate/5'-hydroxy nucleic acid ligase
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6.5.1.8 3'-phosphate/5'-hydroxy nucleic acid ligaseIUBMB 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 . 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 . The metazoan enzyme requires activating cofactors in order to achieve multiple turnover catalysis .
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The expected taxonomic range for this enzyme is: Eukaryota, Archaea, Bacteria
Reaction Schemes
+
5'-hydroxy-(ribonucleotide)m
+
=
+
+
+
+
+
=
+
+
(ribonucleotide)n-2',3'-cyclophosphate
+
5'-hydroxy-(ribonucleotide)m
+
+
=
+
+
Synonyms
rtcb-1, rtcb1, rtcb rna ligase, trna-splicing ligase, rna-splicing ligase, 
more
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SYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
3'-P RNL
MXAN_0280
MXAN_4982
RNA-splicing ligase
rtcB
Rtcb-1
RtcB1
Trl1
tRNA splicing ligase
rtcB
-
-
-
-
rtcB
-
subunit of tRNA splicing ligase, also known as HSPC117, C22orf28, FAAP, or D10Wsu52e
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REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
(ribonucleotide)n-2',3'-cyclophosphate + 5'-hydroxy-(ribonucleotide)m + GTP + H2O = (ribonucleotide)n+m + GMP + diphosphate
(2) overall reaction
-
-
-
(ribonucleotide)n-2',3'-cyclophosphate + H2O = (ribonucleotide)n-3'-phosphate
(2a)
-
-
-
(ribonucleotide)n-3'-(5'-diphosphoguanosine) + 5'-hydroxy-(ribonucleotide)m = (ribonucleotide)n+m + GMP
(ribonucleotide)n-3'-phosphate + 5'-hydroxy-(ribonucleotide)m + GTP = (ribonucleotide)n+m + GMP + diphosphate
(1) overall reaction
-
-
-
5'-guanosyl [RNA ligase]-Ntau-phosphono-L-histidine + (ribonucleotide)n-3'-phosphate = (ribonucleotide)n-3'-(5'-diphosphoguanosine) + [RNA ligase]-L-histidine
GTP + [RNA ligase]-L-histidine = 5'-guanosyl [RNA ligase]-Ntau-phosphono-L-histidine + diphosphate
[RNA ligase]-Ntau-(5'-guanosyl-phosphono)-L-histidine + (ribonucleotide)n-3'-phosphate = (ribonucleotide)n-3'-(5'-diphosphoguanosine) + [RNA ligase]-L-histidine
(2c)
-
-
-
(ribonucleotide)n-3'-(5'-diphosphoguanosine) + 5'-hydroxy-(ribonucleotide)m = (ribonucleotide)n+m + GMP
(1c)
-
-
-
(ribonucleotide)n-3'-(5'-diphosphoguanosine) + 5'-hydroxy-(ribonucleotide)m = (ribonucleotide)n+m + GMP
(2d)
-
-
-
5'-guanosyl [RNA ligase]-Ntau-phosphono-L-histidine + (ribonucleotide)n-3'-phosphate = (ribonucleotide)n-3'-(5'-diphosphoguanosine) + [RNA ligase]-L-histidine
(1b)
-
-
-
5'-guanosyl [RNA ligase]-Ntau-phosphono-L-histidine + (ribonucleotide)n-3'-phosphate = (ribonucleotide)n-3'-(5'-diphosphoguanosine) + [RNA ligase]-L-histidine
catalytic reaction mechanism, detailed overview
-
-
-
GTP + [RNA ligase]-L-histidine = 5'-guanosyl [RNA ligase]-Ntau-phosphono-L-histidine + diphosphate
(1a)
-
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-
GTP + [RNA ligase]-L-histidine = 5'-guanosyl [RNA ligase]-Ntau-phosphono-L-histidine + diphosphate
(2b)
-
-
-
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PATHWAY SOURCE
PATHWAYS
-
-
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SYSTEMATIC NAME
IUBMB Comments
poly(ribonucleotide)-3'-phosphate:5'-hydroxy-poly(ribonucleotide) ligase (GMP-forming)
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].
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SUBSTRATE
PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
(ribonucleotide)10-3'-phosphate + 5'-hydroxy-(ribonucleotide)10 + dGTP
(ribonucleotide)20 + dGMP + diphosphate
(ribonucleotide)10-3'-phosphate + 5'-hydroxy-(ribonucleotide)10 + GTP
(ribonucleotide)20 + GMP + diphosphate
(ribonucleotide)10-3'-phosphate + 5'-hydroxy-(ribonucleotide)10 + ITP
(ribonucleotide)20 + IMP + diphosphate
(ribonucleotide)20-3'-phosphate + 5'-hydroxy-(ribonucleotide)20 + GTP
(ribonucleotide)40 + GMP + diphosphate
(ribonucleotide)n-2',3'-cyclophosphate + 5'-hydroxy-(ribonucleotide)m + ATP + H2O
(ribonucleotide)n+m + AMP + diphosphate
(ribonucleotide)n-2',3'-cyclophosphate + 5'-hydroxy-(ribonucleotide)m + CTP + H2O
(ribonucleotide)n+m + CMP + diphosphate
(ribonucleotide)n-2',3'-cyclophosphate + 5'-hydroxy-(ribonucleotide)m + GTP + H2O
(ribonucleotide)n+m + GMP + diphosphate
(ribonucleotide)n-2',3'-cyclophosphate + 5'-hydroxy-(ribonucleotide)m + UTP + H2O
(ribonucleotide)n+m + UMP + diphosphate
(ribonucleotide)n-3'-(5'-diphosphoguanosine) + 5'-hydroxy-(ribonucleotide)m
(ribonucleotide)n+m + GMP
(ribonucleotide)n-3'-phosphate + 5'-hydroxy-(ribonucleotide)m + 2-aminopurine-riboside-5'-triphosphate
(ribonucleotide)n+m + 2-aminopurine-riboside-5'-monophosphate + diphosphate
-
about 20% activity with 0.1 mM 2-aminopurine triphosphate compared to GTP
-
-
?
(ribonucleotide)n-3'-phosphate + 5'-hydroxy-(ribonucleotide)m + 2-mercaptopurine-riboside-5'-triphosphate
(ribonucleotide)n+m + 2-mercaptopurine-riboside-5'-monophosphate + diphosphate
-
about 25% activity with 0.1 mM 2-mercaptopurine triphosphate compared to GTP
-
-
?
(ribonucleotide)n-3'-phosphate + 5'-hydroxy-(ribonucleotide)m + 6-chloropurine-riboside-5'-triphosphate
(ribonucleotide)n+m + 6-chloropurine-riboside-5'-monophosphate + diphosphate
-
about 1% activity with 0.1 mM 6-chloropurine triphosphate compared to GTP
-
-
?
(ribonucleotide)n-3'-phosphate + 5'-hydroxy-(ribonucleotide)m + 6-O-methylguanosine triphosphate
(ribonucleotide)n+m + 6-O-methylguanosine phosphate + diphosphate
-
about 45% activity with 0.1 mM 6-O-methyl triphosphate compared to GTP
-
-
?
(ribonucleotide)n-3'-phosphate + 5'-hydroxy-(ribonucleotide)m + ATP
(ribonucleotide)n+m + AMP + diphosphate
-
about 22% activity with 0.1 mM ATP compared to GTP
-
-
?
(ribonucleotide)n-3'-phosphate + 5'-hydroxy-(ribonucleotide)m + CTP
(ribonucleotide)n+m + CMP + diphosphate
-
about 18% activity with 0.1 mM CTP compared to GTP
-
-
?
(ribonucleotide)n-3'-phosphate + 5'-hydroxy-(ribonucleotide)m + GTP
(ribonucleotide)n+m + GMP + diphosphate
(ribonucleotide)n-3'-phosphate + 5'-hydroxy-(ribonucleotide)m + ITP
(ribonucleotide)n+m + IMP + diphosphate
-
about 75% activity with 0.1 mM ITP compared to GTP
-
-
?
(ribonucleotide)n-3'-phosphate + 5'-hydroxy-(ribonucleotide)m + UTP
(ribonucleotide)n+m + UMP + diphosphate
-
about 85% activity with 0.1 mM UTP compared to GTP
-
-
?
(ribonucleotide)n-3'-phosphate + 5'-phospho-(ribonucleotide)m + GTP
(ribonucleotide)n+m + GMP + diphosphate
-
overall reaction
-
?
(truncated 16S rRNA)-3'-phosphate + 5'-hydroxy-RNA43 + GTP
16S rRNA + GMP + diphosphate
-
endoribonuclease MazF, the toxin component of the toxin-antitoxin module mazEF, specifically cleaves the 16S rRNA of 70S ribosomes at an ACA site located at positions 15001502. Thereby, the ribosome loses a 3'-terminal 16S rRNA fragment of 43 nucleotides. RNA ligase RtcB catalyzes the religation of the truncated 16S rRNA present in specialized ribosomes. Thereby their ability to translate canonical mRNAs is fully restored
-
-
?
5'-guanosyl [RNA ligase]-NT-phosphono-L-histidine + (ribonucleotide)n-3'-phosphate
(ribonucleotide)n-3'-(5'-diphosphoguanosine) + [RNA ligase]-L-histidine
-
RtcB transfers GMP to the RNA 3'-phosphate end
-
?
5'-guanosyl [RNA ligase]-Ntau-phosphono-L-histidine + (ribonucleotide)n-3'-phosphate
(ribonucleotide)n-3'-(5'-diphosphoguanosine) + [RNA ligase]-L-histidine
GTP + [RNA ligase]-L-histidine
5'-guanosyl [RNA ligase]-NT-phosphono-L-histidine + diphosphate
-
-
-
?
GTP + [RNA ligase]-L-histidine
5'-guanosyl [RNA ligase]-Ntau-phosphono-L-histidine + diphosphate
(ribonucleotide)10-3'-phosphate + 5'-hydroxy-(ribonucleotide)10 + dGTP
(ribonucleotide)20 + dGMP + diphosphate
in the absence of Archease, RtcB-catalyzed RNA ligation proceeds efficiently with GTP and substantially less efficiently with dGTP and ITP. Inclusion of Archease in ligation reaction mixtures enables efficient utilization of GTP, dGTP, ATP or ITP
-
-
?
(ribonucleotide)10-3'-phosphate + 5'-hydroxy-(ribonucleotide)10 + dGTP
(ribonucleotide)20 + dGMP + diphosphate
in the absence of Archease, RtcB-catalyzed RNA ligation proceeds efficiently with GTP and substantially less efficiently with dGTP and ITP. Inclusion of Archease in ligation reaction mixtures enables efficient utilization of GTP, dGTP, ATP or ITP
-
-
?
(ribonucleotide)10-3'-phosphate + 5'-hydroxy-(ribonucleotide)10 + GTP
(ribonucleotide)20 + GMP + diphosphate
in the absence of Archease, RtcB-catalyzed RNA ligation proceeds efficiently with GTP and substantially less efficiently with dGTP and ITP. Inclusion of Archease in ligation reaction mixtures enables efficient utilization of GTP, dGTP, ATP or ITP
-
-
?
(ribonucleotide)10-3'-phosphate + 5'-hydroxy-(ribonucleotide)10 + GTP
(ribonucleotide)20 + GMP + diphosphate
in the absence of Archease, RtcB-catalyzed RNA ligation proceeds efficiently with GTP and substantially less efficiently with dGTP and ITP. Inclusion of Archease in ligation reaction mixtures enables efficient utilization of GTP, dGTP, ATP or ITP
-
-
?
(ribonucleotide)10-3'-phosphate + 5'-hydroxy-(ribonucleotide)10 + ITP
(ribonucleotide)20 + IMP + diphosphate
in the absence of Archease, RtcB-catalyzed RNA ligation proceeds efficiently with GTP and substantially less efficiently with dGTP and ITP. Inclusion of Archease in ligation reaction mixtures enables efficient utilization of GTP, dGTP, ATP or ITP
-
-
?
(ribonucleotide)10-3'-phosphate + 5'-hydroxy-(ribonucleotide)10 + ITP
(ribonucleotide)20 + IMP + diphosphate
in the absence of Archease, RtcB-catalyzed RNA ligation proceeds efficiently with GTP and substantially less efficiently with dGTP and ITP. Inclusion of Archease in ligation reaction mixtures enables efficient utilization of GTP, dGTP, ATP or ITP
-
-
?
(ribonucleotide)20-3'-phosphate + 5'-hydroxy-(ribonucleotide)20 + GTP
(ribonucleotide)40 + GMP + diphosphate
-
-
overall reaction, phosphodiester bond synthesis is rate limiting
-
?
(ribonucleotide)20-3'-phosphate + 5'-hydroxy-(ribonucleotide)20 + GTP
(ribonucleotide)40 + GMP + diphosphate
-
-
overall reaction
-
?
(ribonucleotide)n-2',3'-cyclophosphate + 5'-hydroxy-(ribonucleotide)m
(ribonucleotide)n+m
generation of substrate by cleavage of the intron-containing pre-tRNA with the Methanocaldococcus jannaschii tRNA splicing endonuclease
RtcB-catalyzed ligation incorporates the phosphate of the cyclic phosphate into the phosphodiester bond. ATP or GTP is not required
-
?
(ribonucleotide)n-2',3'-cyclophosphate + 5'-hydroxy-(ribonucleotide)m
(ribonucleotide)n+m
generation of substrate by cleavage of the intron-containing pre-tRNA with the Methanocaldococcus jannaschii tRNA splicing endonuclease
RtcB-catalyzed ligation incorporates the phosphate of the cyclic phosphate into the phosphodiester bond. ATP or GTP is not required
-
?
(ribonucleotide)n-2',3'-cyclophosphate + 5'-hydroxy-(ribonucleotide)m
(ribonucleotide)n+m
generation of substrate by cleavage of the intron-containing pre-tRNA with the Methanocaldococcus jannaschii tRNA splicing endonuclease
-
-
?
(ribonucleotide)n-2',3'-cyclophosphate + 5'-hydroxy-(ribonucleotide)m
(ribonucleotide)n+m
generation of substrate by cleavage of the intron-containing pre-tRNA with the Methanocaldococcus jannaschii tRNA splicing endonuclease
-
-
?
(ribonucleotide)n-2',3'-cyclophosphate + 5'-hydroxy-(ribonucleotide)m + ATP + H2O
(ribonucleotide)n+m + AMP + diphosphate
about 78% activity with 0.1 mM ATP compared to GTP
-
-
?
(ribonucleotide)n-2',3'-cyclophosphate + 5'-hydroxy-(ribonucleotide)m + ATP + H2O
(ribonucleotide)n+m + AMP + diphosphate
about 60% activity with 0.1 mM ATP compared to GTP
-
-
?
(ribonucleotide)n-2',3'-cyclophosphate + 5'-hydroxy-(ribonucleotide)m + ATP + H2O
(ribonucleotide)n+m + AMP + diphosphate
about 60% activity with 0.1 mM ATP compared to GTP
-
-
?
(ribonucleotide)n-2',3'-cyclophosphate + 5'-hydroxy-(ribonucleotide)m + CTP + H2O
(ribonucleotide)n+m + CMP + diphosphate
about 70% activity with 0.1 mM CTP compared to GTP
-
-
?
(ribonucleotide)n-2',3'-cyclophosphate + 5'-hydroxy-(ribonucleotide)m + CTP + H2O
(ribonucleotide)n+m + CMP + diphosphate
about 60% activity with 0.1 mM CTP compared to GTP
-
-
?
(ribonucleotide)n-2',3'-cyclophosphate + 5'-hydroxy-(ribonucleotide)m + CTP + H2O
(ribonucleotide)n+m + CMP + diphosphate
about 60% activity with 0.1 mM CTP compared to GTP
-
-
?
(ribonucleotide)n-2',3'-cyclophosphate + 5'-hydroxy-(ribonucleotide)m + GTP + H2O
(ribonucleotide)n+m + GMP + diphosphate
-
-
-
?
(ribonucleotide)n-2',3'-cyclophosphate + 5'-hydroxy-(ribonucleotide)m + GTP + H2O
(ribonucleotide)n+m + GMP + diphosphate
about 80% activity with 0.01 mM GTP
-
-
?
(ribonucleotide)n-2',3'-cyclophosphate + 5'-hydroxy-(ribonucleotide)m + GTP + H2O
(ribonucleotide)n+m + GMP + diphosphate
-
-
-
-
?
(ribonucleotide)n-2',3'-cyclophosphate + 5'-hydroxy-(ribonucleotide)m + GTP + H2O
(ribonucleotide)n+m + GMP + diphosphate
-
-
-
-
?
(ribonucleotide)n-2',3'-cyclophosphate + 5'-hydroxy-(ribonucleotide)m + GTP + H2O
(ribonucleotide)n+m + GMP + diphosphate
-
-
-
?
(ribonucleotide)n-2',3'-cyclophosphate + 5'-hydroxy-(ribonucleotide)m + GTP + H2O
(ribonucleotide)n+m + GMP + diphosphate
about 75% activity with 0.01 mM GTP
-
-
?
(ribonucleotide)n-2',3'-cyclophosphate + 5'-hydroxy-(ribonucleotide)m + GTP + H2O
(ribonucleotide)n+m + GMP + diphosphate
-
-
-
?
(ribonucleotide)n-2',3'-cyclophosphate + 5'-hydroxy-(ribonucleotide)m + GTP + H2O
(ribonucleotide)n+m + GMP + diphosphate
about 75% activity with 0.01 mM GTP
-
-
?
(ribonucleotide)n-2',3'-cyclophosphate + 5'-hydroxy-(ribonucleotide)m + GTP + H2O
(ribonucleotide)n+m + GMP + diphosphate
-
-
-
-
?
(ribonucleotide)n-2',3'-cyclophosphate + 5'-hydroxy-(ribonucleotide)m + GTP + H2O
(ribonucleotide)n+m + GMP + diphosphate
substrate for ligation is a 20mer RNA strand with 5'-OH and 2',3'-cyclic phosphate ends
overall reaction
-
?
(ribonucleotide)n-2',3'-cyclophosphate + 5'-hydroxy-(ribonucleotide)m + GTP + H2O
(ribonucleotide)n+m + GMP + diphosphate
substrate mimicks the broken tRNAGlu(UUC) anticodon stem-loop generated by Kluyveromyces lactis gamma-toxin, leaving 2',3'-cyclic phosphate and 5'-OH ends
overall reaction
-
?
(ribonucleotide)n-2',3'-cyclophosphate + 5'-hydroxy-(ribonucleotide)m + GTP + H2O
(ribonucleotide)n+m + GMP + diphosphate
-
-
-
-
?
(ribonucleotide)n-2',3'-cyclophosphate + 5'-hydroxy-(ribonucleotide)m + GTP + H2O
(ribonucleotide)n+m + GMP + diphosphate
-
-
-
?
(ribonucleotide)n-2',3'-cyclophosphate + 5'-hydroxy-(ribonucleotide)m + GTP + H2O
(ribonucleotide)n+m + GMP + diphosphate
-
overall reaction
-
?
(ribonucleotide)n-2',3'-cyclophosphate + 5'-hydroxy-(ribonucleotide)m + UTP + H2O
(ribonucleotide)n+m + UMP + diphosphate
about 75% activity with 0.1 mM UTP compared to GTP
-
-
?
(ribonucleotide)n-2',3'-cyclophosphate + 5'-hydroxy-(ribonucleotide)m + UTP + H2O
(ribonucleotide)n+m + UMP + diphosphate
about 60% activity with 0.1 mM UTP compared to GTP
-
-
?
(ribonucleotide)n-2',3'-cyclophosphate + 5'-hydroxy-(ribonucleotide)m + UTP + H2O
(ribonucleotide)n+m + UMP + diphosphate
about 60% activity with 0.1 mM UTP compared to GTP
-
-
?
(ribonucleotide)n-2',3'-cyclophosphate + H2O
(ribonucleotide)n-3'-phosphate
-
-
-
?
(ribonucleotide)n-2',3'-cyclophosphate + H2O
(ribonucleotide)n-3'-phosphate
-
-
-
?
(ribonucleotide)n-3'-(5'-diphosphoguanosine) + 5'-hydroxy-(ribonucleotide)m
(ribonucleotide)n+m + GMP
-
-
-
?
(ribonucleotide)n-3'-(5'-diphosphoguanosine) + 5'-hydroxy-(ribonucleotide)m
(ribonucleotide)n+m + GMP
-
-
-
?
(ribonucleotide)n-3'-phosphate + 5'-hydroxy-(ribonucleotide)m + GTP
(ribonucleotide)n+m + GMP + diphosphate
-
-
-
-
?
(ribonucleotide)n-3'-phosphate + 5'-hydroxy-(ribonucleotide)m + GTP
(ribonucleotide)n+m + GMP + diphosphate
-
overall reaction, RtcB is required for ligation of endogenous intron-containing pre-tRNAs
-
?
(ribonucleotide)n-3'-phosphate + 5'-hydroxy-(ribonucleotide)m + GTP
(ribonucleotide)n+m + GMP + diphosphate
-
-
-
-
?
(ribonucleotide)n-3'-phosphate + 5'-hydroxy-(ribonucleotide)m + GTP
(ribonucleotide)n+m + GMP + diphosphate
-
100% activity with 0.01 mM GTP
-
-
?
(ribonucleotide)n-3'-phosphate + 5'-hydroxy-(ribonucleotide)m + GTP
(ribonucleotide)n+m + GMP + diphosphate
-
-
-
-
?
(ribonucleotide)n-3'-phosphate + 5'-hydroxy-(ribonucleotide)m + GTP
(ribonucleotide)n+m + GMP + diphosphate
-
overall reaction, substrate 5'-hydroxy-(ribonucleotide)m can be composed of all ribonucleotides or all deoxynucleotides
-
?
(ribonucleotide)n-3'-phosphate + 5'-hydroxy-(ribonucleotide)m + GTP
(ribonucleotide)n+m + GMP + diphosphate
-
-
-
-
?
(ribonucleotide)n-3'-phosphate + GTP
? + GMP
substrate is a 20-mer HORNAp
RtcB1 efficiently converts the linear substrate to a circular RNA species as a consequence of intramolecular ligation plus multimers
-
?
(ribonucleotide)n-3'-phosphate + GTP
? + GMP
substrate is a 20-mer HORNAp
RtcB2 efficiently converts the linear substrate to a circular RNA species as a consequence of intramolecular ligation plus multimers. Isoform Rtcb2 is 5fold less effectively than isoform RtcB1
-
?
(ribonucleotide)n-3'-phosphate + GTP
? + GMP
substrate is a 20-mer HORNAp
RtcB1 efficiently converts the linear substrate to a circular RNA species as a consequence of intramolecular ligation plus multimers
-
?
(ribonucleotide)n-3'-phosphate + GTP
? + GMP
substrate is a 20-mer HORNAp
RtcB2 efficiently converts the linear substrate to a circular RNA species as a consequence of intramolecular ligation plus multimers. Isoform Rtcb2 is 5fold less effectively than isoform RtcB1
-
?
5'-guanosyl [RNA ligase]-Ntau-phosphono-L-histidine + (ribonucleotide)n-3'-phosphate
(ribonucleotide)n-3'-(5'-diphosphoguanosine) + [RNA ligase]-L-histidine
-
-
-
?
5'-guanosyl [RNA ligase]-Ntau-phosphono-L-histidine + (ribonucleotide)n-3'-phosphate
(ribonucleotide)n-3'-(5'-diphosphoguanosine) + [RNA ligase]-L-histidine
substrate for ligation is a 20-mer RNA strand with 5'-OH and 3'-monophosphate ends
-
-
?
5'-guanosyl [RNA ligase]-Ntau-phosphono-L-histidine + (ribonucleotide)n-3'-phosphate
(ribonucleotide)n-3'-(5'-diphosphoguanosine) + [RNA ligase]-L-histidine
-
-
-
?
GTP + [RNA ligase]-L-histidine
5'-guanosyl [RNA ligase]-Ntau-phosphono-L-histidine + diphosphate
-
-
-
?
GTP + [RNA ligase]-L-histidine
5'-guanosyl [RNA ligase]-Ntau-phosphono-L-histidine + diphosphate
-
-
-
?
additional information
?
-
-
ATP and CTP are at least 3 orders of magnitude less effective as phosphate donors compared to GTP
-
-
?
additional information
?
-
RtcB executes a three-step ligation pathway, consisting of reaction of His337 of the enzyme with GTP to form a covalent RtcB-(histidinyl-N)-GMP intermediate, transfer of guanylate to a polynucleotide 3'-phosphate to form a polynucleotide-(3')pp(5')G intermediate, and (iii) attack of a 5'-OH on the N(3')pp(5')G end to form the splice junction. Presence of GTP is required
-
-
?
additional information
?
-
RtcB seals broken tRNA-like stem-loop structures with 2',3'-cyclic phosphate and 5'-OH ends to form a splice junction with a 2'-OH, 3',5'-phosphodiester
-
-
?
additional information
?
-
sealing of a 2',3'-cyclic phosphate end by RtcB requires GTP, is contingent on formation of the RtcBGMP adduct, and involves a kinetically valid RNA(3')pp(5')G intermediate. RtcB catalyzes the hydrolysis of a 2',3'-cyclic phosphate to a 3'-phosphate at a rate that is at least as fast as the rate of ligation. NTP requirement for ligation is satisfied by GTP and 6-O-methyl guanosine triphosphate and inosine triphosphate. 6-chloropurine ribonucleoside triphosphate, 2-aminopurine ribonucleoside triphosphate and ATP are inactive
-
-
?
additional information
?
-
-
the enzyme joins RNA 2',3'-cyclic phosphate or RNA 3'-phosphate ends to 5'-OH RNA ends in a multistep pathway whereby the enzyme hydrolyzes RNA 2',3'-cyclic phosphate to RNA 3'-phosphate, transfers GMP from GTP to RNA 3'-phosphate to form to RNAppG, and directs the attack of 5'-OH on RNAppG to form a 3'-5' phosphodiester splice junction
-
-
?
additional information
?
-
isoform Rtcb1 displays DNA ligase and DNA 3'-capping activities on a 12-mer pDNAp strand
-
-
?
additional information
?
-
isoform Rtcb1 displays DNA ligase and DNA 3'-capping activities on a 12-mer pDNAp strand
-
-
?
additional information
?
-
-
isoform Rtcb1 displays DNA ligase and DNA 3'-capping activities on a 12-mer pDNAp strand
-
-
?
additional information
?
-
isoform Rtcb2 displays DNA ligase and DNA 3'-capping activities on a 12-mer pDNAp strand
-
-
?
additional information
?
-
isoform Rtcb2 displays DNA ligase and DNA 3'-capping activities on a 12-mer pDNAp strand
-
-
?
additional information
?
-
-
isoform Rtcb2 displays DNA ligase and DNA 3'-capping activities on a 12-mer pDNAp strand
-
-
?
additional information
?
-
isoform Rtcb1 displays DNA ligase and DNA 3'-capping activities on a 12-mer pDNAp strand
-
-
?
additional information
?
-
isoform Rtcb1 displays DNA ligase and DNA 3'-capping activities on a 12-mer pDNAp strand
-
-
?
additional information
?
-
isoform Rtcb2 displays DNA ligase and DNA 3'-capping activities on a 12-mer pDNAp strand
-
-
?
additional information
?
-
isoform Rtcb2 displays DNA ligase and DNA 3'-capping activities on a 12-mer pDNAp strand
-
-
?
additional information
?
-
three-step mechanism for catalysis of the ligation of 3'-P and 5'-OH RNA termini by RtcB. In the activation step, cleavage of the phosphoanhydride bond between the alpha and beta phosphoryl groups of GTP occurs during transfer of GMP to the 3'-P terminus of an RNA strand to form a guanylylate-activated intermediate. In the cyclization step, the 2'-OH on the terminal ribose attacks the GMP-activated 3'-P to generate a 2',3'-cyclic phosphate and release GMP. In the ligation step, the 5'-OH terminus of a second RNA strand attacks the cyclic phosphate to form a 3',5'-phosphodiester bond
-
-
?
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NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
(ribonucleotide)n-2',3'-cyclophosphate + 5'-hydroxy-(ribonucleotide)m + GTP + H2O
(ribonucleotide)n+m + GMP + diphosphate
(ribonucleotide)n-3'-phosphate + 5'-hydroxy-(ribonucleotide)m + GTP
(ribonucleotide)n+m + GMP + diphosphate
(ribonucleotide)n-2',3'-cyclophosphate + 5'-hydroxy-(ribonucleotide)m + GTP + H2O
(ribonucleotide)n+m + GMP + diphosphate
-
-
-
?
(ribonucleotide)n-2',3'-cyclophosphate + 5'-hydroxy-(ribonucleotide)m + GTP + H2O
(ribonucleotide)n+m + GMP + diphosphate
-
-
-
-
?
(ribonucleotide)n-2',3'-cyclophosphate + 5'-hydroxy-(ribonucleotide)m + GTP + H2O
(ribonucleotide)n+m + GMP + diphosphate
-
-
-
-
?
(ribonucleotide)n-2',3'-cyclophosphate + 5'-hydroxy-(ribonucleotide)m + GTP + H2O
(ribonucleotide)n+m + GMP + diphosphate
-
-
-
?
(ribonucleotide)n-2',3'-cyclophosphate + 5'-hydroxy-(ribonucleotide)m + GTP + H2O
(ribonucleotide)n+m + GMP + diphosphate
-
-
-
?
(ribonucleotide)n-2',3'-cyclophosphate + 5'-hydroxy-(ribonucleotide)m + GTP + H2O
(ribonucleotide)n+m + GMP + diphosphate
-
-
-
-
?
(ribonucleotide)n-2',3'-cyclophosphate + 5'-hydroxy-(ribonucleotide)m + GTP + H2O
(ribonucleotide)n+m + GMP + diphosphate
-
-
-
-
?
(ribonucleotide)n-2',3'-cyclophosphate + 5'-hydroxy-(ribonucleotide)m + GTP + H2O
(ribonucleotide)n+m + GMP + diphosphate
-
-
-
?
(ribonucleotide)n-3'-phosphate + 5'-hydroxy-(ribonucleotide)m + GTP
(ribonucleotide)n+m + GMP + diphosphate
-
-
-
-
?
(ribonucleotide)n-3'-phosphate + 5'-hydroxy-(ribonucleotide)m + GTP
(ribonucleotide)n+m + GMP + diphosphate
-
-
-
-
?
(ribonucleotide)n-3'-phosphate + 5'-hydroxy-(ribonucleotide)m + GTP
(ribonucleotide)n+m + GMP + diphosphate
-
-
-
-
?
(ribonucleotide)n-3'-phosphate + 5'-hydroxy-(ribonucleotide)m + GTP
(ribonucleotide)n+m + GMP + diphosphate
-
-
-
-
?
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COFACTOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
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METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Mg2+
Mn2+
Zn2+
additional information
Mn2+
prior to binding GTP, a single manganese ion is bound to RtcB
Mn2+
the RtcB/Mn2+ structure shows two Mn2+ ions at the active site. The enzyme's substrate-induced GTP binding site and the putative reactive RNA ends are in the vicinity of the binuclear Mn2+ active center
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ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
archease
-
archease stimulates the activity of the human tRNA ligase complex with high efficiency only in the presence of GTP
-
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DISEASE
TITLE OF PUBLICATION
LINK TO PUBMED
Trauma, Nervous System
Crystal structure of human archease, a key cofactor of tRNA splicing ligase complex.
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TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.00018
(ribonucleotide)10-3'-phosphate
pH 7.0, 70°C, ligation reaction
-
0.00055
(ribonucleotide)10-3'-phosphate
pH 7.0, 70°C, presence of archease, ligation reaction
-
0.0122
(ribonucleotide)20-3'-phosphate
-
pH 7.4, 70°C, presence of archease
-
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ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
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SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SOURCE
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LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY
GeneOntology No.
LITERATURE
SOURCE
a subset of RtcB is associated with the endoplasmic reticulum
brenda
a subset of RtcB is associated with the nuclear envelope
brenda
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GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
malfunction
-
RNAi knockdown of rtcb-1 lowers endoplasmic reticulum stress response in vivo
physiological function
physiological function
archease and RtcB from Pyrococcus horikoshii function in tandem, with Archease altering the catalytic properties of the RNA ligase. Catalytic concentrations of archease are sufficient to activate RtcB, and Archease accelerates both the RNA 3'-P guanylylation and ligation steps. Archease can alter the NTP specificity of RtcB such that ATP, dGTP or ITP is used efficiently. RtcB variants that have inactivating substitutions in the guanine-binding pocket can be rescued by the addition of archease. Substitution of the archease metal-binding re