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EC Tree
IUBMB Comments The enzyme converts the 3'-terminal phosphate of various RNA substrates into the 2',3'-cyclic phosphodiester in an ATP-dependent reaction. Catalysis occurs by a three-step mechanism, starting with the activation of the enzyme by ATP, forming a phosphoramide bond between adenylate and a histidine residue [5,6]. The adenylate group is then transferred to the 3'-phosphate terminus of the substrate, forming the capped structure [RNA]-3'-(5'-diphosphoadenosine). Finally, the enzyme catalyses an attack of the vicinal O-2' on the 3'-phosphorus, which results in formation of cyclic phosphate and release of the adenylate. The enzyme also has a polynucleotide 5' adenylylation activity . cf. EC 6.5.1.5, RNA 3'-terminal-phosphate cyclase (GTP).
The taxonomic range for the selected organisms is: Homo sapiens The expected taxonomic range for this enzyme is: Bacteria, Eukaryota, Archaea
Reaction Schemes
+
[RNA]-3'-(3'-phospho-ribonucleoside)
=
+
+
[RNA]-3'-(2',3'-cyclophospho)-ribonucleoside
Synonyms
rcl1p, rna 3'-terminal phosphate cyclase, rna 3'-phosphate cyclase, rna cyclase, st-rtc,
more
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RNA 3'-phosphate cyclase
-
-
RNA 3'-terminal phosphate cyclase
RNA-3'-phosphate cyclase
-
-
-
-
RNA 3'-terminal phosphate cyclase
-
-
-
-
RNA 3'-terminal phosphate cyclase
-
-
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ATP + [RNA]-3'-(3'-phospho-ribonucleoside) = AMP + diphosphate + [RNA]-3'-(2',3'-cyclophospho)-ribonucleoside
formation of a covalent cyclase-AMP intermediate
-
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RNA-3'-phosphate:RNA ligase (cyclizing, AMP-forming)
The enzyme converts the 3'-terminal phosphate of various RNA substrates into the 2',3'-cyclic phosphodiester in an ATP-dependent reaction. Catalysis occurs by a three-step mechanism, starting with the activation of the enzyme by ATP, forming a phosphoramide bond between adenylate and a histidine residue [5,6]. The adenylate group is then transferred to the 3'-phosphate terminus of the substrate, forming the capped structure [RNA]-3'-(5'-diphosphoadenosine). Finally, the enzyme catalyses an attack of the vicinal O-2' on the 3'-phosphorus, which results in formation of cyclic phosphate and release of the adenylate. The enzyme also has a polynucleotide 5' adenylylation activity [7]. cf. EC 6.5.1.5, RNA 3'-terminal-phosphate cyclase (GTP).
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ATP + oligodeoxyribonucleotide 3'-terminal phosphate
AMP + diphosphate + oligodeoxyribonucleotide-2',3'-cyclic-phosphate
500fold poorer substrate than oligoribonucleotide 3'-terminal phosphate
-
-
?
ATP + RNA 3'-terminal-phosphate
?
the enzyme could be involved in the maintenance of cyclic ends in tRNA splicing intermediates or in the cyclization of the 3' end of U6 sbRNA
-
-
?
ATP + RNA 3'-terminal-phosphate
AMP + diphosphate + RNA terminal-2',3'-cyclic-phosphate
oligoribonucleotides
-
?
ATP + (Ap)npAp
AMP + ?
-
pure oligoribonucleotide
-
?
ATP + (Up)10pGp
AMP + ?
-
pure oligoribonucleotide
-
?
ATP + 5S rRNA-pCp
AMP + ?
-
-
-
?
ATP + AAAAUAAAAGCp
AMP + ?
-
pure oligoribonucleotide
-
?
ATP + AAAAUAAAAGp
AMP + ?
-
pure oligoribonucleotide
-
?
ATP + AAAAUAAAAGpCp
AMP + diphosphate + AAAAUAAAAGpC-2',3'-cyclic phosphate
-
-
-
-
ir
ATP + AUGp
AMP + ?
-
pure oligoribonucleotide
-
?
ATP + CCCCACCCCGp
AMP + ?
-
pure oligoribonucleotide
-
?
ATP + CCCCCACCCCGCp
AMP + ?
-
pure oligoribonucleotide
-
?
ATP + RNA 2'-terminal-phosphate
?
-
-
-
-
?
ATP + RNA 3'-terminal-phosphate
?
-
role in RNA processing
-
-
?
ATP + RNA 3'-terminal-phosphate
AMP + diphosphate + RNA terminal-2',3'-cyclic-phosphate
ATP + RNA 3'-terminal-phosphate
AMP + diphosphate + RNA terminal-2',3'-cyclic-phosphodiester
-
-
-
?
ATP + tobacco mosaic virus RNA
AMP + ?
-
fragments modified by ligation of pGp, pAp, or pCp
-
?
ATP + tRNA-pNp
AMP + ?
-
-
-
?
ATP + [RNA 3'-phosphate cyclase]-L-histidine
[RNA 3'-phosphate cyclase]-Ntau-(5'-adenylyl)-L-histidine + diphosphate
-
-
-
-
?
ATP + [RNA]-3'-(3'-phospho-ribonucleoside)
AMP + diphosphate + [RNA]-3'-(2',3'-cyclophospho)-ribonucleoside
-
-
-
-
?
ATPgammaS + RNA 3'-terminal-phosphate
AMP + thiodiphosphate + RNA terminal-2',3'-cyclic-phosphate
CTP + RNA 3'-terminal-phosphate
CMP + diphosphate + RNA terminal-2',3'-cyclic-phosphate
GTP + RNA 3'-terminal-phosphate
GMP + diphosphate + RNA terminal-2',3'-cyclic-phosphate
UTP + RNA 3'-terminal-phosphate
UMP + diphosphate + RNA terminal-2',3'-cyclic-phosphate
[RNA 3'-phosphate cyclase]-Ntau-(5'-adenylyl)-L-histidine + [RNA]-3'-(3'-phospho-ribonucleoside)
[RNA 3'-phosphate cyclase]-L-histidine + [RNA]-3'-ribonucleoside-3'-(5'-diphosphoadenosine)
-
-
-
-
?
[RNA]-3'-ribonucleoside-3'-(5'-diphosphoadenosine)
[RNA]-3'-(2',3'-cyclophospho)-ribonucleoside + AMP
-
-
-
-
?
additional information
?
-
ATP + RNA 3'-terminal-phosphate
AMP + diphosphate + RNA terminal-2',3'-cyclic-phosphate
-
-
-
?
ATP + RNA 3'-terminal-phosphate
AMP + diphosphate + RNA terminal-2',3'-cyclic-phosphate
-
-
-
?
ATP + RNA 3'-terminal-phosphate
AMP + diphosphate + RNA terminal-2',3'-cyclic-phosphate
-
-
-
?
ATP + RNA 3'-terminal-phosphate
AMP + diphosphate + RNA terminal-2',3'-cyclic-phosphate
-
-
-
-
?
ATP + RNA 3'-terminal-phosphate
AMP + diphosphate + RNA terminal-2',3'-cyclic-phosphate
-
no activity with dATP
-
?
ATP + RNA 3'-terminal-phosphate
AMP + diphosphate + RNA terminal-2',3'-cyclic-phosphate
-
ir
-
?
ATP + RNA 3'-terminal-phosphate
AMP + diphosphate + RNA terminal-2',3'-cyclic-phosphate
-
(Up)10Gp is cyclized at a faster rate than tRNAApGp or AUGp
-
?
ATP + RNA 3'-terminal-phosphate
AMP + diphosphate + RNA terminal-2',3'-cyclic-phosphate
-
human U6 small nuclear RNA
-
?
ATPgammaS + RNA 3'-terminal-phosphate
AMP + thiodiphosphate + RNA terminal-2',3'-cyclic-phosphate
-
-
-
-
?
ATPgammaS + RNA 3'-terminal-phosphate
AMP + thiodiphosphate + RNA terminal-2',3'-cyclic-phosphate
-
ir
-
?
CTP + RNA 3'-terminal-phosphate
CMP + diphosphate + RNA terminal-2',3'-cyclic-phosphate
-
-
-
-
?
CTP + RNA 3'-terminal-phosphate
CMP + diphosphate + RNA terminal-2',3'-cyclic-phosphate
-
reaction proceeds 15-20 times slower than in presence of ATP
-
-
?
GTP + RNA 3'-terminal-phosphate
GMP + diphosphate + RNA terminal-2',3'-cyclic-phosphate
-
-
-
-
?
GTP + RNA 3'-terminal-phosphate
GMP + diphosphate + RNA terminal-2',3'-cyclic-phosphate
-
reaction proceeds 15-20 times slower than in presence of ATP
-
-
?
UTP + RNA 3'-terminal-phosphate
UMP + diphosphate + RNA terminal-2',3'-cyclic-phosphate
-
-
-
-
?
UTP + RNA 3'-terminal-phosphate
UMP + diphosphate + RNA terminal-2',3'-cyclic-phosphate
-
reaction proceeds 15-20 times slower than in presence of ATP
-
-
?
additional information
?
-
-
ATP/diphosphate exchange reaction not detected
-
-
?
additional information
?
-
-
trinucleotides are the shortest oligonucleotides able to act as substrates, ribonucleoside 3'-phosphates and ribonucleoside 5',3'-phosphates are no substrates
-
?
additional information
?
-
-
the enzyme is incapable of phosphodiester synthesis (i.e., ligation) following adenylation of the 5'-terminal phosphate
-
-
?
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ATP + RNA 3'-terminal-phosphate
?
the enzyme could be involved in the maintenance of cyclic ends in tRNA splicing intermediates or in the cyclization of the 3' end of U6 sbRNA
-
-
?
ATP + RNA 3'-terminal-phosphate
?
-
role in RNA processing
-
-
?
ATP + [RNA 3'-phosphate cyclase]-L-histidine
[RNA 3'-phosphate cyclase]-Ntau-(5'-adenylyl)-L-histidine + diphosphate
-
-
-
-
?
ATP + [RNA]-3'-(3'-phospho-ribonucleoside)
AMP + diphosphate + [RNA]-3'-(2',3'-cyclophospho)-ribonucleoside
-
-
-
-
?
[RNA 3'-phosphate cyclase]-Ntau-(5'-adenylyl)-L-histidine + [RNA]-3'-(3'-phospho-ribonucleoside)
[RNA 3'-phosphate cyclase]-L-histidine + [RNA]-3'-ribonucleoside-3'-(5'-diphosphoadenosine)
-
-
-
-
?
[RNA]-3'-ribonucleoside-3'-(5'-diphosphoadenosine)
[RNA]-3'-(2',3'-cyclophospho)-ribonucleoside + AMP
-
-
-
-
?
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ATP
-
requires ATP as cofactor, other ribonucleoside triphosphates are used very inefficiently
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Ca2+
-
only 5% of the activation by Mg2+
K+
-
optimal concentration: 150-200 mM
Na+
-
optimal concentration: 150-200 mM
Mg2+
-
required
Mg2+
-
maximal activity at 4-5 mM
Mn2+
-
only 5% of the activation by Mg2+
Mn2+
-
cannot replace Mg2+ in activation
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Vanadyl-ribonucleoside complex
-
-
-
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Colorectal Neoplasms
Next-generation sequencing analysis of multiplex families with atypical psychosis.
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0.0017
ATP
-
-
0.006
ATPgammaS
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-
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additional information
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-
additional information
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-
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8 - 10.5
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8.0-9.0: maximal activity, 10.5: 70% of maximal activity
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30
-
similar rates of reaction at 25°C, 30°C, and 37°C
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0 - 37
-
0°C: 25% of maximal activity, 12°C: 60% of maximal activity, 25-37°C: maximal activity
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-
Uniprot
brenda
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-
brenda
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brenda
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-
brenda
-
-
brenda
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metabolism
-
synthesis of RNA 2',3'-cyclic phosphate ends via an ATP-dependent pathway comprising three nucleotidyl transfer steps: reaction of Rtc with ATP to form a covalent Rtc-(histidinyl-N)-AMP intermediate and release diphosphate, transfer of AMP from Rtc1 to an RNA 3'-phosphate to form an RNA(3')pp(5')A intermediate; and attack by the terminal nucleoside O2' on the 3'-phosphate to form an RNA 2',3'-cyclic phosphate product and release AMP
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RTCA_HUMAN
366
0
39337
Swiss-Prot
other Location (Reliability: 2 )
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38000 - 40000
-
glycerol density gradient sedimentation, gel filtration
39400
-
calculated from cDNA
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monomer
-
1 * 38000-40000, SDS-PAGE
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E14A
-
activity very low, only 4% of RNA is cyclized compared to 95% with wild-type enzyme
H326A
-
almost same activiy like wild-type enzyme
H52A
-
half activity compared to wild-type enzyme
Q51A
-
almost same activiy like wild-type enzyme
H320A
-
enzyme inactive
H320A
-
mutant is unreactive with either 3'-phosphate RNA end or 2'-phosphate RNA end
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20
-
3-4 h, 50% loss of activity
4
-
3 d, 50% loss of activity
42
-
5 min, 55% loss of activity
50
-
5 min, 95% loss of activity
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not affected by several cycles of freezing and thawing
-
resistant to protease digestion
-
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-70°C, stable for at least 3 months
-
-70°C, stable for at least 6 months
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4°C, 50% loss of activity after 3 days
-
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using Ni-NTA chromatography
-
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overexpression in Escherichia coli
cloned and overexpressed in Escherichia coli as fusion protein with glutathione S-transferase
-
expressed in Escherichia coli
-
expressed in Escherichia coli as a His-tagged fusion protein
-
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Reinberg, D.; Arenas, J.; Hurwitz, J.
The enzymatic conversion of 3'-phosphate terminated RNA chains to 2',3'-cyclic phosphate derivatives
J. Biol. Chem.
260
6088-6097
1985
Homo sapiens
brenda
Filipowicz, W.; Konarska, M.; Gross, H.J.; Shatkin, A.J.
RNA 3'-terminal phosphate cyclase activity and RNA ligation in HeLa cell extract
Nucleic Acids Res.
11
1405-1418
1983
Homo sapiens, Xenopus laevis
brenda
Vicente, O.; Filipowicz, W.
Purification of RNA 3'-terminal phosphate cyclase from HeLa cells
Eur. J. Biochem.
17
431-439
1988
Homo sapiens
brenda
Filipowicz, W.; Vicente, O.
RNA 3'-terminal phosphate cyclase from HeLa cells
Methods Enzymol.
181
499-510
1990
Homo sapiens, Xenopus laevis
brenda
Genschik, P.; Billy, E.; Swianiewicz, M.; Filipowicz, W.
The human RNA 3'-terminal phosphate cyclase is a member of a new family of proteins conserved in eucarya, bacteria and archaea
EMBO J.
16
2955-2967
1997
Homo sapiens (O00442), Homo sapiens
brenda
Gu, J.; Shumyatsky, G.; Makan, N.; Reddy, R.
Formation of 2',3'-cyclic phosphates at the 3' end of human U6 small nuclear RNA in vitro. Identification of 2',3'-cyclic phosphates at the 3' ends of human signal recognition particle and mitochondrial RNA processing RNAs
J. Biol. Chem.
272
21989-21993
1997
Homo sapiens
brenda
Filipowicz, W.; Billy, E.; Drabikowski, K.; Genschik, P.
Cyclases of the 3'-terminal phosphate in RNA: a new family of RNA processing enzymes conserved in Eucarya, Bacteria and Archaea
Acta Biochim. Pol.
45
895-906
1998
Aquifex aeolicus, Arabidopsis thaliana, Danio rerio, Saccharomyces cerevisiae, Caenorhabditis elegans, Dictyostelium discoideum, Drosophila melanogaster, Escherichia coli, Homo sapiens, Methanocaldococcus jannaschii, Mus musculus, no activity in Bacillus subtilis, no activity in Haemophilus influenzae, no activity in Mycoplasma genitalium, no activity in Synechocystis sp., Pseudomonas aeruginosa, Schizosaccharomyces pombe, Toxoplasma gondii, Xenopus sp., no activity in Helicobacter pylori
brenda
Billy, E.; Wegierski, T.; Nasr, F.; Filipowicz, W.
Rcl1p, the yeast protein similar to the RNA 3'-phosphate cyclase, associates with U3 snoRNP and is required for 18S rRNA biogenesis
EMBO J.
19
2115-2126
2000
Saccharomyces cerevisiae, Homo sapiens, Mus musculus
brenda
Tanaka, N.; Shuman, S.
Structure-activity relationships in human RNA 3-phosphate cyclase
RNA
15
1865-1874
2009
Homo sapiens, Escherichia coli (P46849), Escherichia coli
brenda
Das, U.; Shuman, S.
2-Phosphate cyclase activity of RtcA: a potential rationale for the operon organization of RtcA with an RNA repair ligase RtcB in Escherichia coli and other bacterial taxa
RNA
19
1355-1362
2013
Escherichia coli, Homo sapiens
brenda
Filipowicz, W.
RNA 3-terminal phosphate cyclases and cyclase-like proteins
Postepy Biochem.
62
327-334
2016
Escherichia coli, Homo sapiens
brenda