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Information on EC 6.5.1.4 - RNA 3'-terminal-phosphate cyclase (ATP) and Organism(s) Escherichia coli and UniProt Accession P46850
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6.5.1.4 RNA 3'-terminal-phosphate cyclase (ATP)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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Word Map
- 6.5.1.4
-
phosphodiester
-
cyclization
- ligases
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nucleotidylation
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adenylylation
- cyclases
- polynucleotide
- eucarya
- pre-rrna
- oligoribonucleotides
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ribozyme
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3',5'-phosphodiester
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alpha-32patp
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cyclase-like
-
2'-phosphate
The taxonomic range for the selected organisms is: Escherichia coli
The expected taxonomic range for this enzyme is: Bacteria, Eukaryota, Archaea
The expected taxonomic range for this enzyme is: Bacteria, Eukaryota, Archaea
Reaction Schemes
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[RNA]-3'-(3'-phospho-ribonucleoside)
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[RNA]-3'-(2',3'-cyclophospho)-ribonucleoside
Synonyms
rcl1p, rna 3'-terminal phosphate cyclase, rna 3'-phosphate cyclase, rna cyclase, st-rtc, 
more
topSYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
RNA 3'-phosphate cyclase
RNA 3'-terminal phosphate cyclase
RNA cyclase
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RNA-3'-phosphate cyclase
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-
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RtcA
RNA 3'-terminal phosphate cyclase
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-
-
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REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Ligation
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-
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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
85638-41-1
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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
ATP + RNA 3'-terminal-phosphate
AMP + diphosphate + RNA terminal-2',3'-cyclic-phosphodiester
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-
?
ATP + 5S rRNA
AMP + ?
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modified by ligation of [5'-P]pCp to the 3'-terminus
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?
ATP + AAAAUAAAAGpCp
AMP + diphosphate + AAAAUAAAAGpC-2',3'-cyclic phosphate
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-
-
ir
ATP + DNA 5'-terminal-phosphate
AMP + AppDNA
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RtcA also catalyzes adenylylation of 5'-phosphate ends of DNA strands to form AppDNA product
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-
?
ATP + human U14 snoRNA
AMP + ?
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modified by ligation of [5'-P]pCp to the 3'-terminus
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?
ATP + RNA 2'-terminal-phosphate
?
-
the rate of 2'-phosphate cyclization by RtcA is five orders of magnitude slower than 3'-phosphate cyclization, notwithstanding that RtcA binds with similar affinity to RNA3'p and RNA2'p substrates
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-
?
ATP + RNA 3'-terminal-phosphate
AMP + diphosphate + RNA terminal-2',3'-cyclic phosphate
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RtcA catalyzes the synthesis of RNA 2',3'-cyclic phosphate ends via an ATP-dependent pathway comprising three nucleotidyl transfer steps: reaction of RtcA with ATP to form a covalent RtcA-(histidinyl-N)-AMP intermediate and release diphosphate, transfer of AMP from RtcA 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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-
?
ATP + RNA 3'-terminal-phosphate
AMP + diphosphate + RNA terminal-2',3'-cyclic-phosphodiester
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-
?
ATP + RNA 5'-terminal-phosphate
AMP + AppRNA
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RtcA also catalyzes adenylylation of 5'-phosphate ends of RNA strands to form AppRNA product
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-
?
ATP + [RNA 3'-phosphate cyclase]-L-histidine
[RNA 3'-phosphate cyclase]-Ntau-(5'-adenylyl)-L-histidine + diphosphate
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-
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?
ATP + [RNA]-3'-(3'-phospho-ribonucleoside)
AMP + diphosphate + [RNA]-3'-(2',3'-cyclophospho)-ribonucleoside
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-
-
-
?
GTP + RNA 3'-terminal-phosphate
GMP + diphosphate + RNA terminal-2',3'-cyclic-phosphate
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-
-
-
?
[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)
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-
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-
?
[RNA]-3'-ribonucleoside-3'-(5'-diphosphoadenosine)
[RNA]-3'-(2',3'-cyclophospho)-ribonucleoside + AMP
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-
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?
ATP + RNA 3'-terminal-phosphate
AMP + diphosphate + RNA terminal-2',3'-cyclic-phosphate
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-
-
?
ATP + RNA 3'-terminal-phosphate
AMP + diphosphate + RNA terminal-2',3'-cyclic-phosphate
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-
?
ATP + RNA 3'-terminal-phosphate
AMP + diphosphate + RNA terminal-2',3'-cyclic-phosphate
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RtcA can quantitatively cyclize 8-mer, 6-mer, and 4-mer RNA3'p substrates
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?
additional information
?
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nonessential as demonstrated by knockout experiments
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?
additional information
?
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nonessential as demonstrated by knockout experiments
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?
additional information
?
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nucleoside 3'-monophosphates and nucleoside 5',3'-bisphosphates are no substrates
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?
additional information
?
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precise function is not known, may be responsible for generating or regenerating cyclic phosphate RNA ends required by RNA ligases
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?
additional information
?
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precise function is not known, may be responsible for generating or regenerating cyclic phosphate RNA ends required by RNA ligases
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?
additional information
?
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RtcA readily adenylylates the 5'-phosphate at a 5'-PO4/3'-OH nick in duplex DNA but is unable to covert the nicked DNA-adenylate to a sealed phosphodiester
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?
additional information
?
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the enzyme is incapable of phosphodiester synthesis (i.e., ligation) following adenylation of the 5'-terminal phosphate
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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
ATP + [RNA 3'-phosphate cyclase]-L-histidine
[RNA 3'-phosphate cyclase]-Ntau-(5'-adenylyl)-L-histidine + diphosphate
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-
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?
ATP + [RNA]-3'-(3'-phospho-ribonucleoside)
AMP + diphosphate + [RNA]-3'-(2',3'-cyclophospho)-ribonucleoside
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-
-
-
?
[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)
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?
[RNA]-3'-ribonucleoside-3'-(5'-diphosphoadenosine)
[RNA]-3'-(2',3'-cyclophospho)-ribonucleoside + AMP
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?
additional information
?
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nonessential as demonstrated by knockout experiments
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?
additional information
?
-
-
nonessential as demonstrated by knockout experiments
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?
additional information
?
-
precise function is not known, may be responsible for generating or regenerating cyclic phosphate RNA ends required by RNA ligases
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?
additional information
?
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precise function is not known, may be responsible for generating or regenerating cyclic phosphate RNA ends required by RNA ligases
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?
COFACTOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
ATP
ATP-dependent conversion of the 3'-phosphate to the 2',3'-cyclic phosphodiester
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Mg2+
additional information
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
additional information
?
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the rate of 2'-phosphate cyclization by RtcA is five orders of magnitude slower than 3'-phosphate cyclization, notwithstanding that RtcA binds with similar affinity to RNA3'p and RNA2'p substrates
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pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
pH RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
metabolism
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 PPi, 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
metabolism
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RtcA might serve an end healing function in an RNA repair pathway, by converting RNA 2'-phosphates, which cannot be spliced by RtcB, to 2',3'-cyclic phosphates that can be sealed
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
homodimer
the apoenzyme of Escherichia coli RtcA crystallizes as a disulfide-linked homodimer and reveales a fold composed of four tandem modules, each comprising a four-stranded beta sheet overlying two alpha helices, X-ray diffraction
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
hanging drop vapor diffusion technique, 2 orthorhombic crystal forms, space group P2(1)2(1)2(1), unit-cell dimensions a : 101.8 A, b : 126.6 A and c : 128.8 A, and P2(1)2(1)2 with unit cell dimensions a : 125.8 A, b : 133.5 A, c : 51.0 A
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
F251A
considerably reduced activity compared to wild-type enzyme, about 30%
H309A
P131G
considerably reduced activity compared to wild-type enzyme, about 35%
Y284A
considerably reduced activity compared to wild-type enzyme (12%)
H309A
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mutant is unreactive with either 3'-phosphate RNA end or 2'-phosphate RNA end
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
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
Genschik, P.; Drabikowski, K.; Filipowicz, W.
Characterization of the Escherichia coli RNA 3'-terminal phosphate cyclase and its sigma54-regulated operon
J. Biol. Chem.
273
25516-25526
1998
Escherichia coli (P46850), Escherichia coli, Escherichia coli YMC10 (P46850)
Billy, E.; Hess, D.; Hofsteenge, J.; Filipowicz, W.
Characterization of the adenylation site in the RNA 3'-terminal phosphate cyclase from Escherichia coli
J. Biol. Chem.
274
34955-34960
1999
Escherichia coli (P46849), Escherichia coli
Palm, G.J.; Billy, E.; Filipowicz, W.; Wlodawer, A.
Crystal structure of RNA 3'-terminal phosphate cyclase, a ubiquitous enzyme with unusual topology
Structure Fold. Des.
8
13-23
2000
Escherichia coli (P46849), Escherichia coli
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
Tanaka, N.; Smith, P.; Shuman, S.
Structure of the RNA 3-phosphate cyclase-adenylate intermediate illuminates nucleotide specificity and covalent nucleotidyl transfer
Structure
18
449-457
2010
Escherichia coli (P46849)
Chakravarty, A.K.; Shuman, S.
RNA 3'-phosphate cyclase (RtcA) catalyzes ligase-like adenylylation of DNA and RNA 5'-monophosphate ends
J. Biol. Chem.
286
4117-4122
2011
Escherichia coli
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
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