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Information on EC 6.5.1.4 - RNA 3'-terminal-phosphate cyclase (ATP) and Organism(s) Homo sapiens and UniProt Accession O00442

for references in articles please use BRENDA:EC6.5.1.4
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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).
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Homo sapiens
UNIPROT: O00442
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The taxonomic range for the selected organisms is: Homo sapiens
The expected taxonomic range for this enzyme is: Bacteria, Eukaryota, Archaea
Reaction Schemes
hide(Overall reactions are displayed. Show all >>)
+
[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
SYNONYM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
RNA 3'-phosphate cyclase
-
-
RNA 3'-terminal phosphate cyclase
RNA cyclase
-
-
-
-
RNA-3'-phosphate cyclase
-
-
-
-
RtcA
-
-
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
ATP + [RNA]-3'-(3'-phospho-ribonucleoside) = AMP + diphosphate + [RNA]-3'-(2',3'-cyclophospho)-ribonucleoside
show the reaction diagram
formation of a covalent cyclase-AMP intermediate
-
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Ligation
-
-
-
-
SYSTEMATIC NAME
IUBMB Comments
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).
CAS REGISTRY NUMBER
COMMENTARY hide
85638-41-1
-
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
ATP + oligodeoxyribonucleotide 3'-terminal phosphate
AMP + diphosphate + oligodeoxyribonucleotide-2',3'-cyclic-phosphate
show the reaction diagram
500fold poorer substrate than oligoribonucleotide 3'-terminal phosphate
-
-
?
ATP + RNA 3'-terminal-phosphate
?
show the reaction diagram
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
show the reaction diagram
oligoribonucleotides
-
?
ATP + (Ap)npAp
AMP + ?
show the reaction diagram
-
pure oligoribonucleotide
-
?
ATP + (Up)10pGp
AMP + ?
show the reaction diagram
-
pure oligoribonucleotide
-
?
ATP + 5S rRNA-pCp
AMP + ?
show the reaction diagram
-
-
-
?
ATP + AAAAUAAAAGCp
AMP + ?
show the reaction diagram
-
pure oligoribonucleotide
-
?
ATP + AAAAUAAAAGp
AMP + ?
show the reaction diagram
-
pure oligoribonucleotide
-
?
ATP + AAAAUAAAAGpCp
AMP + diphosphate + AAAAUAAAAGpC-2',3'-cyclic phosphate
show the reaction diagram
-
-
-
-
ir
ATP + AUGp
AMP + ?
show the reaction diagram
-
pure oligoribonucleotide
-
?
ATP + CCCCACCCCGp
AMP + ?
show the reaction diagram
-
pure oligoribonucleotide
-
?
ATP + CCCCCACCCCGCp
AMP + ?
show the reaction diagram
-
pure oligoribonucleotide
-
?
ATP + RNA 2'-terminal-phosphate
?
show the reaction diagram
-
-
-
-
?
ATP + RNA 3'-terminal-phosphate
?
show the reaction diagram
-
role in RNA processing
-
-
?
ATP + RNA 3'-terminal-phosphate
AMP + diphosphate + RNA terminal-2',3'-cyclic-phosphate
show the reaction diagram
ATP + RNA 3'-terminal-phosphate
AMP + diphosphate + RNA terminal-2',3'-cyclic-phosphodiester
show the reaction diagram
-
-
-
?
ATP + tobacco mosaic virus RNA
AMP + ?
show the reaction diagram
-
fragments modified by ligation of pGp, pAp, or pCp
-
?
ATP + tRNA-pNp
AMP + ?
show the reaction diagram
-
-
-
?
ATP + [RNA 3'-phosphate cyclase]-L-histidine
[RNA 3'-phosphate cyclase]-Ntau-(5'-adenylyl)-L-histidine + diphosphate
show the reaction diagram
-
-
-
-
?
ATP + [RNA]-3'-(3'-phospho-ribonucleoside)
AMP + diphosphate + [RNA]-3'-(2',3'-cyclophospho)-ribonucleoside
show the reaction diagram
-
-
-
-
?
ATPgammaS + RNA 3'-terminal-phosphate
AMP + thiodiphosphate + RNA terminal-2',3'-cyclic-phosphate
show the reaction diagram
CTP + RNA 3'-terminal-phosphate
CMP + diphosphate + RNA terminal-2',3'-cyclic-phosphate
show the reaction diagram
GTP + RNA 3'-terminal-phosphate
GMP + diphosphate + RNA terminal-2',3'-cyclic-phosphate
show the reaction diagram
UTP + RNA 3'-terminal-phosphate
UMP + diphosphate + RNA terminal-2',3'-cyclic-phosphate
show the reaction diagram
[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)
show the reaction diagram
-
-
-
-
?
[RNA]-3'-ribonucleoside-3'-(5'-diphosphoadenosine)
[RNA]-3'-(2',3'-cyclophospho)-ribonucleoside + AMP
show the reaction diagram
-
-
-
-
?
additional information
?
-
NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
ATP + RNA 3'-terminal-phosphate
?
show the reaction diagram
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
?
show the reaction diagram
-
role in RNA processing
-
-
?
ATP + [RNA 3'-phosphate cyclase]-L-histidine
[RNA 3'-phosphate cyclase]-Ntau-(5'-adenylyl)-L-histidine + diphosphate
show the reaction diagram
-
-
-
-
?
ATP + [RNA]-3'-(3'-phospho-ribonucleoside)
AMP + diphosphate + [RNA]-3'-(2',3'-cyclophospho)-ribonucleoside
show the reaction diagram
-
-
-
-
?
[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)
show the reaction diagram
-
-
-
-
?
[RNA]-3'-ribonucleoside-3'-(5'-diphosphoadenosine)
[RNA]-3'-(2',3'-cyclophospho)-ribonucleoside + AMP
show the reaction diagram
-
-
-
-
?
COFACTOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
ATP
-
requires ATP as cofactor, other ribonucleoside triphosphates are used very inefficiently
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Ca2+
-
only 5% of the activation by Mg2+
K+
-
optimal concentration: 150-200 mM
Na+
-
optimal concentration: 150-200 mM
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
iodoacetamide
-
-
SDS
-
-
Sodium phosphate
-
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Vanadyl-ribonucleoside complex
-
-
-
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.0017 - 0.006
ATP
0.006
ATPgammaS
0.2
GTP
-
-
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
0.021
-
-
additional information
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
7.4
-
assay at
pH RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
8 - 10.5
-
8.0-9.0: maximal activity, 10.5: 70% of maximal activity
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
30
-
similar rates of reaction at 25°C, 30°C, and 37°C
37
-
assay at
TEMPERATURE RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
0 - 37
-
0°C: 25% of maximal activity, 12°C: 60% of maximal activity, 25-37°C: maximal activity
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
-
Uniprot
Manually annotated by BRENDA team
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
SOURCE
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY hide
GeneOntology No.
LITERATURE
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
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
UNIPROT
ENTRY NAME
ORGANISM
NO. OF AA
NO. OF TRANSM. HELICES
MOLECULAR WEIGHT[Da]
SOURCE
SEQUENCE
LOCALIZATION PREDICTION?
RTCA_HUMAN
366
0
39337
Swiss-Prot
other Location (Reliability: 2)
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
38000 - 40000
-
glycerol density gradient sedimentation, gel filtration
39000
-
SDS-PAGE
39400
-
calculated from cDNA
40000
-
SDS-PAGE
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
monomer
-
1 * 38000-40000, SDS-PAGE
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
D297A
-
enzyme inactive
E14A
-
activity very low, only 4% of RNA is cyclized compared to 95% with wild-type enzyme
H320A
H326A
-
almost same activiy like wild-type enzyme
H52A
-
half activity compared to wild-type enzyme
Q51A
-
almost same activiy like wild-type enzyme
R21A
-
enzyme inactive
R40A
-
enzyme inactive
R43A
-
enzyme inactive
Y294A
-
enzyme inactive
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
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
GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
not affected by several cycles of freezing and thawing
-
resistant to protease digestion
-
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
-70°C, stable for at least 3 months
-
-70°C, stable for at least 6 months
-
4°C, 50% loss of activity after 3 days
-
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
recombinant enzyme
-
using Ni-NTA chromatography
-
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
overexpression in Escherichia coli
cDNA characterized
-
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
-
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
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
Manually annotated by BRENDA team
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
Manually annotated by BRENDA team
Vicente, O.; Filipowicz, W.
Purification of RNA 3'-terminal phosphate cyclase from HeLa cells
Eur. J. Biochem.
17
431-439
1988
Homo sapiens
Manually annotated by BRENDA team
Filipowicz, W.; Vicente, O.
RNA 3'-terminal phosphate cyclase from HeLa cells
Methods Enzymol.
181
499-510
1990
Homo sapiens, Xenopus laevis
Manually annotated by BRENDA team
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
Manually annotated by BRENDA team
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
Manually annotated by BRENDA team
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
Manually annotated by BRENDA team
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
Manually annotated by BRENDA team
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
Manually annotated by BRENDA team
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
Manually annotated by BRENDA team
Filipowicz, W.
RNA 3-terminal phosphate cyclases and cyclase-like proteins
Postepy Biochem.
62
327-334
2016
Escherichia coli, Homo sapiens
Manually annotated by BRENDA team