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Information on EC 3.1.13.B1 - 5'-3' exoribonuclease
for references in articles please use BRENDA:EC3.1.13.B1
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preliminary BRENDA-supplied EC number
EC Tree 3 Hydrolases
3.1 Acting on ester bonds
3.1.13 Exoribonucleases producing 5′-phosphomonoesters
3.1.13.B1 5'-3' exoribonuclease
The expected taxonomic range for this enzyme is: Bacteria, Eukaryota, Archaea
- 3.1.13.B1
-
decapping
-
sfrnas
-
deadenylation
- flaviviruses
-
exonucleolytic
-
pyrophosphohydrolase
-
exoribonucleolytic
-
p-bodies
- pre-rrnas
-
pacman
-
flaviviral
Reaction Schemes
showexonucleolytic cleavage in the 5'- to 3'-direction to yield nucleoside 5'-phosphates
Synonyms
5'-3' exoribonuclease, 5'-to-3' exoribonuclease, pab-rnase j, 5'-3' exoribonuclease 2, saci-acpsf2, sso-rnase j, tk-rnase j, more
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SYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
5'-to-3' exoribonuclease
aRNase J
Pab-RNase J
PAB1751
ribonuclease J
RNJ
Saci-aCPSF2
Saci2362
Sso-RNase J
SSO0386
TERMP 00146
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REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
exonucleolytic cleavage in the 5'- to 3'-direction to yield nucleoside 5'-phosphates
-
-
-
-
exonucleolytic cleavage in the 5'- to 3'-direction to yield nucleoside 5'-phosphates
cleavage scheme, Rail/Rat1 mechanism and mechanism of RNAPII termination, overview
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SUBSTRATE
PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
LITERATURE
COMMENTARY
Reversibility
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
miR-382 + H2O
nucleoside 5'-phosphate + ?
Substrates: substrate is a piwi-interacting RNA
Products: -
Products: -
?
piR-48164 + H2O
nucleoside 5'-phosphate + ?
Substrates: substrate is a piwi-interacting RNA
Products: -
Products: -
?
piR-58320 + H2O
nucleoside 5'-phosphate + ?
Substrates: substrate is a piwi-interacting RNA
Products: -
Products: -
?
piwi-interacting RNA + H2O
nucleoside 5'-phosphate + ?
Substrates: -
Products: -
Products: -
?
(A)40 + 38 H2O
adenosine + 39 AMP
Substrates: (A)40 is a 40-nt-long synthetic RNA harboring a single radioactively labeled A nucleotide at the 5'-end. When compared with the triphosphorylated RNA, SSSO-RNase J displayes a twofold higher velocity in degrading mono-phosphorylated RNA and RNA bearing a 5'-hydroxyl group
Products: -
Products: -
?
(A)40 + 38 H2O
adenosine + 39 AMP
Substrates: (A)40 is a 40-nt-long synthetic RNA harboring a single radioactively labeled A nucleotide at the 5'-end. When compared with the triphosphorylated RNA, SSSO-RNase J displayes a twofold higher velocity in degrading mono-phosphorylated RNA and RNA bearing a 5'-hydroxyl group
Products: -
Products: -
?
5'-pA(A)39 + H2O
40 AMP
Substrates: 5'-pA(A)39 is a 40-nt-long synthetic RNA harboring a 5'-monophosphate and a single radioactively labeled A nucleotide at the 5'-end. When compared with the triphosphorylated RNA, the enzyme displayes a twofold higher velocity in degrading mono-phosphorylated RNA and RNA bearing a 5'-hydroxyl group
Products: -
Products: -
?
5'-pA(A)39 + H2O
40 AMP
Substrates: 5'-pA(A)39 is a 40-nt-long synthetic RNA harboring a 5'-monophosphate and a single radioactively labeled A nucleotide at the 5'-end. When compared with the triphosphorylated RNA, the enzyme displayes a twofold higher velocity in degrading mono-phosphorylated RNA and RNA bearing a 5'-hydroxyl group
Products: -
Products: -
?
5'-pC-sR47 + H2O
5'-phosphomononucleotides
Substrates: sR47 RNA labeled either at its 5' end as a 5'-[32P]monophosphate. The enzyme is a highly processive 5'-to-3'-exoribonuclease.The principal product of the 5' end-labeled RNA is [32P]GMP as guanosine is the 5'-nucleotide of sR47. Single-stranded DNA is degraded by the enzyme, suggesting that the it does not discriminate between ribose and 2'-deoxyribose nucleosides. Double-stranded DNA is resistant to degradation. The enzyme requires a free 5' end to initiate degradation
Products: -
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?
5'-pC-sR47 + H2O
5'-phosphomononucleotides
Pyrococcus abyssi GE5 / CNCM I-1302 / DSM 25543
Substrates: sR47 RNA labeled either at its 5' end as a 5'-[32P]monophosphate. The enzyme is a highly processive 5'-to-3'-exoribonuclease.The principal product of the 5' end-labeled RNA is [32P]GMP as guanosine is the 5'-nucleotide of sR47. Single-stranded DNA is degraded by the enzyme, suggesting that the it does not discriminate between ribose and 2'-deoxyribose nucleosides. Double-stranded DNA is resistant to degradation. The enzyme requires a free 5' end to initiate degradation
Products: -
Products: -
?
5'-pppA(A)39 + H2O
ATP + 39 AMP
Substrates: 5'-pppA(A)39 is a 40-nt-long synthetic RNA harboring a 5'-triphosphate and a single radioactively labeled A nucleotide at the 5'-end. When compared with the triphosphorylated RNA, the enzyme displayes a twofold higher velocity in degrading mono-phosphorylated RNA and RNA bearing a 5'-hydroxyl group
Products: -
Products: -
?
5'-pppA(A)39 + H2O
ATP + 39 AMP
Substrates: 5'-pppA(A)39 is a 40-nt-long synthetic RNA harboring a 5'-triphosphate and a single radioactively labeled A nucleotide at the 5'-end. When compared with the triphosphorylated RNA, the enzyme displayes a twofold higher velocity in degrading mono-phosphorylated RNA and RNA bearing a 5'-hydroxyl group
Products: -
Products: -
?
5'-pppA(A)41 + H2O
ATP + 41 AMP
Substrates: 5'-pppA(A)41 is a 42-nt-long synthetic RNA harboring a 5'-tri-phosphate and a single radioactively labeled A nucleotide at the 5'-end. Decay of 5'-PPP-40A1 RNA results in either a single nucleotide or short oligoribonucleotides, indicating an exoribonucleolytic activity. Degradation with 5' to 3' directionality in vitro
Products: -
Products: -
?
5'-pppA(A)41 + H2O
ATP + 41 AMP
Substrates: 5'-pppA(A)41 is a 42-nt-long synthetic RNA harboring a 5'-tri-phosphate and a single radioactively labeled A nucleotide at the 5'-end. Decay of 5'-PPP-40A1 RNA results in either a single nucleotide or short oligoribonucleotides, indicating an exoribonucleolytic activity. Degradation with 5' to 3' directionality in vitro
Products: -
Products: -
?
FAD-capped RNA+ H2O
nucleoside 5'-phosphate + ?
Substrates: -
Products: -
Products: -
?
FAD-capped RNA+ H2O
nucleoside 5'-phosphate + ?
Substrates: -
Products: -
Products: -
?
FAD-capped RNA+ H2O
nucleoside 5'-phosphate + ?
-
Substrates: -
Products: -
Products: -
?
RNA + H2O
3'-phosphomononucleotides
Substrates: the translation initiation factor a/eIF2(g) binds to the 5'-tri-phosphate terminus of mRNA to protect from 5'-to-3' directional decay and counteract the activity of Sso-RNase J
Products: -
Products: -
?
RNA + H2O
3'-phosphomononucleotides
Substrates: the translation initiation factor a/eIF2(g) binds to the 5'-tri-phosphate terminus of mRNA to protect from 5'-to-3' directional decay and counteract the activity of Sso-RNase J
Products: -
Products: -
?
RNA + H2O
3'-phosphomononucleotides
Substrates: the enzyme plays a major role in mRNA turnover
Products: -
Products: -
?
RNA + H2O
3'-phosphomononucleotides
Substrates: the enzyme plays a major role in mRNA turnover
Products: -
Products: -
?
RNA + H2O
3'-phosphomononucleotides
Substrates: highly processive 5'-to-3'-exoribonuclease
Products: -
Products: -
?
additional information
?
-
Substrates: pre-tRNA(Trp) is a poor substrate
Products: -
Products: -
?
additional information
?
-
-
Substrates: pre-tRNA(Trp) is a poor substrate
Products: -
Products: -
?
additional information
?
-
Pyrococcus abyssi GE5 / CNCM I-1302 / DSM 25543
Substrates: pre-tRNA(Trp) is a poor substrate
Products: -
Products: -
?
additional information
?
-
Substrates: using synthetic RNAs as well as 5'-end-labeled natural mRNAs from Sulfolobus solfataricus, no hints for an endonucleolytic activity are obtained
Products: -
Products: -
?
additional information
?
-
-
Substrates: using synthetic RNAs as well as 5'-end-labeled natural mRNAs from Sulfolobus solfataricus, no hints for an endonucleolytic activity are obtained
Products: -
Products: -
?
additional information
?
-
Substrates: using synthetic RNAs as well as 5'-end-labeled natural mRNAs from Sulfolobus solfataricus, no hints for an endonucleolytic activity are obtained
Products: -
Products: -
?
additional information
?
-
Substrates: nuclear yeast Rat1 catalyzes exonucleolytic cleavage of RNA in the 5'- to 3'-direction to yield nucleoside 5'-phosphates, it forms a complex with Rai1 that stabilizes Rat1 and helps target 5x02 monophosphate RNA by its diphosphohydrolase activity. The efficiency of termination increases as the RNA transcript undergoing degradation by Rat1 gets longer, which suggests that Rat1 may generate a driving force for dissociating RNAPII from the template while degrading the nascent transcripts to catch up to the polymerase. Rat1/Rai1 itself is not sufficient to terminate RNAPII in vitro. Yeast Rat1/Rai1 does not terminate Escherichia coli RNAP, implying that a specific interaction between Rat1/Rai1 and RNAPII may be required for termination. Rat1/Rai1 do not show ATPase activity, ATP hydrolysis may be crucial to promote RNAPII termination but is not driven by Rat1/Rai1. The 5'-3' exoribonuclease activity of Rat1 is essential for RNAPII termination, quantification of the remaining RNAs after Rat1/Rai1 treatment without or with ATP
Products: -
Products: -
?
additional information
?
-
-
Substrates: nuclear yeast Rat1 catalyzes exonucleolytic cleavage of RNA in the 5'- to 3'-direction to yield nucleoside 5'-phosphates, it forms a complex with Rai1 that stabilizes Rat1 and helps target 5x02 monophosphate RNA by its diphosphohydrolase activity. The efficiency of termination increases as the RNA transcript undergoing degradation by Rat1 gets longer, which suggests that Rat1 may generate a driving force for dissociating RNAPII from the template while degrading the nascent transcripts to catch up to the polymerase. Rat1/Rai1 itself is not sufficient to terminate RNAPII in vitro. Yeast Rat1/Rai1 does not terminate Escherichia coli RNAP, implying that a specific interaction between Rat1/Rai1 and RNAPII may be required for termination. Rat1/Rai1 do not show ATPase activity, ATP hydrolysis may be crucial to promote RNAPII termination but is not driven by Rat1/Rai1. The 5'-3' exoribonuclease activity of Rat1 is essential for RNAPII termination, quantification of the remaining RNAs after Rat1/Rai1 treatment without or with ATP
Products: -
Products: -
?
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NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
LITERATURE
COMMENTARY
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
RNA + H2O
3'-phosphomononucleotides
Substrates: the translation initiation factor a/eIF2(g) binds to the 5'-tri-phosphate terminus of mRNA to protect from 5'-to-3' directional decay and counteract the activity of Sso-RNase J
Products: -
Products: -
?
RNA + H2O
3'-phosphomononucleotides
Substrates: the translation initiation factor a/eIF2(g) binds to the 5'-tri-phosphate terminus of mRNA to protect from 5'-to-3' directional decay and counteract the activity of Sso-RNase J
Products: -
Products: -
?
RNA + H2O
3'-phosphomononucleotides
Substrates: the enzyme plays a major role in mRNA turnover
Products: -
Products: -
?
RNA + H2O
3'-phosphomononucleotides
Substrates: the enzyme plays a major role in mRNA turnover
Products: -
Products: -
?
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METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Mg2+
additional information
additional information
the addition of divalent ions to the reaction buffer does not stimulate the reaction
additional information
-
the addition of divalent ions to the reaction buffer does not stimulate the reaction
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INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
initiation factor a/eIF2(gamma)
binding of translation initiation factor a/eIF2(gamma) to the 5'-end of mRNA counteracts the 5'-to-3' exoribonucleolytic activity in vitro. The factor binds by virtue of the gamma-subunit to the 5'-end of tri-phosphorylated mRNAs and thereby increases the stability of the 5'-part of mRNAs
-
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ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
ATP
ATP significantly enhances Rat1/Rai1-mediated RNAPII termination. The ATP-dependent effect seems to be unique to Rat1/Rai1. ATP addition does not stimulate the processivity of Rat1. Rather, it slightly reduces the exonuclease activity because 1 mM of ATP is sufficient to chelate the Mg2+ ion necessary for the nuclease activity of Rat1, suggesting that ATP affects Rat1-mediated termination in a somewhat different manner
additional information
NTP misincorporation induces RNAPII pausing and enhances termination by Rat1/Rai1. When ATP misincorporates into RNA transcripts, the elongation of RNAPII is significantly blocked, presumably due to the disruption and/or rearrangement of the RNAPII active center, RNAPII with a disrupted active center might be more effectively terminated by Rat1/Rai1
-
additional information
-
NTP misincorporation induces RNAPII pausing and enhances termination by Rat1/Rai1. When ATP misincorporates into RNA transcripts, the elongation of RNAPII is significantly blocked, presumably due to the disruption and/or rearrangement of the RNAPII active center, RNAPII with a disrupted active center might be more effectively terminated by Rat1/Rai1
-
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DISEASE
TITLE OF PUBLICATION
LINK TO PUBMED
Amyotrophic Lateral Sclerosis
SETX (senataxin), the helicase mutated in AOA2 and ALS4, functions in autophagy regulation.
Apraxias
SETX (senataxin), the helicase mutated in AOA2 and ALS4, functions in autophagy regulation.
Ataxia
SETX (senataxin), the helicase mutated in AOA2 and ALS4, functions in autophagy regulation.
Choriocarcinoma
Zika virus noncoding sfRNAs sequester multiple host-derived RNA-binding proteins and modulate mRNA decay and splicing during infection.
Dengue
Zika virus noncoding sfRNAs sequester multiple host-derived RNA-binding proteins and modulate mRNA decay and splicing during infection.
Frontotemporal Dementia
SETX (senataxin), the helicase mutated in AOA2 and ALS4, functions in autophagy regulation.
Hepatitis C
XRN1 Stalling in the 5' UTR of Hepatitis C Virus and Bovine Viral Diarrhea Virus Is Associated with Dysregulated Host mRNA Stability.
Infections
Expression of the Arabidopsis Xrn4p 5'-3' exoribonuclease facilitates degradation of tombusvirus RNA and promotes rapid emergence of viral variants in plants.
Muscular Atrophy, Spinal
SETX (senataxin), the helicase mutated in AOA2 and ALS4, functions in autophagy regulation.
Neoplasms
Upregulation of XRN2 acts as an oncogene in oral squamous cell carcinoma and correlates with poor prognosis.
Spinocerebellar Ataxias
SETX (senataxin), the helicase mutated in AOA2 and ALS4, functions in autophagy regulation.
Virus Diseases
Zika virus noncoding sfRNAs sequester multiple host-derived RNA-binding proteins and modulate mRNA decay and splicing during infection.
Zika Virus Infection
Zika virus noncoding sfRNAs sequester multiple host-derived RNA-binding proteins and modulate mRNA decay and splicing during infection.
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pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
7.5
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TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
65
95
activity increases with temperature up to 95Ā°C, the maximum temperature tested
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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
Highest Expressing Human Cell Lines
Cell Line LinksPlease wait a moment until the data is sorted. This message will disappear when the data is sorted.
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
evolution
yeast Rat1 is evolutionarily well conserved from yeast to human (Xrn2 in human)
physiological function
physiological function
the enzyme plays a major role in mRNA turnover
physiological function
yeast Rat1 is an essential nuclear protein. Within a complex with Rai1, the 5'-3' exoribonuclease Rat1 promotes termination of RNA polymerase II (RNAPII) on protein-coding genes. The 5'-3' exoribonuclease activity of Rat1 is essential for RNAPII termination. Rat1 forms a complex with Rai1 that stabilizes Rat1 and helps target 5' monophosphate RNA by its diphosphohydrolase activity. Within a complex with Rai1, the 5'-3' exoribonuclease Rat1 promotes termination of RNAPII on protein-coding genes, overview. RNAPII is prone to more effective termination by Rat1/Rai1 when its catalytic site is disrupted due to NTP misincorporation, implying that paused RNAPII, which is often found in vivo near termination sites, can adopt a similar configuration to Rat1/Rai1 and trigger termination. Rat1/Rai1 itself is not sufficient to terminate RNAPII in vitro. Multiple-mechanistic features contribute to Rat1-mediated termination of RNAPII. NTP misincorporation induces RNAPII pausing and enhances termination by Rat1/Rai1, Rat1/Rai1 more effectively terminates RNAPII when a non-cognate NTP (ATP, CTP or UTP), rather than cognate GTP. Exoribonuclease activity is required for Rat1 not only to approach RNAPII but also to accumulate a sufficient driving force to dislodge the polymerase from the DNA template
physiological function
5'-3' exoribonuclease XRN2 regulates the stability of telomeric repeat-containing RNA TERRA. Stabilization of TERRA alone is insufficient to drive alternative lengthening of telomeres, while depletion of XRN2 in alternative lengthening of telomeres-positive cells leads to a significant increase in TERRA R-loops and exacerbates alternative lengthening of telomeres activity
physiological function
aRNase J engages specifically with a Ski2-like helicase and the RNA exosome to exert control over RNA surveillance, at the vicinity of the ribosome. aRNase J interacts with proteins involved in RNA metabolism from transcription (RNA polymerase subunits), RNA modification (C/D guide RNP components) and RNA decay (RNA exosome) to translation (ribosomal proteins and translation initiation factors)
physiological function
aRNase J interacts with helicase ASH-Ski2 in vivo. An association of aRNase J with the ribosome is emphasized in absence of ASH-Ski2
physiological function
Xrn1 functions mainly as a transcriptional activator. Its disruption leads to a reduction of RNA polymerase II occupancy downstream of transcription start sites. Xrn1 modulates transcription initiation and elongation of its target genes. Pol II occupancy markedly increases near cleavage and polyadenylation sites in cells lacking Xrn1, whereas its activity decreases. Xrn1 is involved in transcription termination downstream of polyadenylation sites
physiological function
degradation of human piwi-interacting RNAs (piRNAs) is mostly dependent on the 5'-3' exoribonuclease pathway. XRN1 and XRN2 are involved in 68% of piRNA degradation, while exosomes contribute 32% in vitro. The presence of 3'-end 2'-O-methylation in piRNAs significantly reduces their degradation. Formation of stable secondary structures in piRNAs slows the rate of XRN1-mediated degradation
physiological function
-
5'-3' exoribonucleases, Xrn1 and Rat1, physically interact with the RNA 5' FAD cap and both possess FAD cap decapping (deFADding) activity and subsequently degrade the resulting RNA
physiological function
5'-3' exoribonucleases, Xrn1 and Rat1, physically interact with the RNA 5' FAD cap and both possess FAD cap decapping (deFADding) activity and subsequently degrade the resulting RNA. Levels of FAD caps are about 2fold higher in HEK-293T cells bearing a disrupted Xrn1 gene
physiological function
5'-3' exoribonucleases, Xrn1 and Rat1, physically interact with the RNA 5' FAD cap and both possess FAD cap decapping (deFADding) activity and subsequently degrade the resulting RNA
physiological function
-
the enzyme plays a major role in mRNA turnover
-
physiological function
Pyrococcus abyssi DSM 11836
-
aRNase J interacts with helicase ASH-Ski2 in vivo. An association of aRNase J with the ribosome is emphasized in absence of ASH-Ski2
-
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UNIPROT
ENTRY NAME
ORGANISM
NO. OF AA
NO. OF TRANSM. HELICES
MOLECULAR WEIGHT[Da]
SOURCE
SEQUENCE
LOCALIZATION PREDICTION
The reliability class of the localization prediction ranges from 1 (very reliable) to 5 (not reliable).
The reliability class of the localization prediction ranges from 1 (very reliable) to 5 (not reliable). F0LHN9_THEBM
Thermococcus barophilus (strain DSM 11836 / MP)
441
0
49367
TrEMBL
-
XRN1_YEAST
Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
1528
0
175460
Swiss-Prot
other Location (Reliability: 4)
XRN2_YEAST
Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
1006
0
115934
Swiss-Prot
-
Q4J6E1_SULAC
Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770)
422
0
47280
TrEMBL
-
Q5JH57_THEKO
Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)
444
0
49681
TrEMBL
-
RNJL_SACS2
Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)
492
0
54944
Swiss-Prot
Secretory Pathway (Reliability: 4)
RNJ_PYRAB
Pyrococcus abyssi (strain GE5 / Orsay)
451
0
50517
Swiss-Prot
-
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CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
crystal structure with three manganese ions coordinated by a sulfate molecule and the active site amino acid
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PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
E209A
significantly reduced activity compared with the wild type protein
H388A
significantly reduced activity compared with the wild type protein
H86A
significantly reduced activity compared with the wild type protein
E209A
Pyrococcus abyssi GE5 / CNCM I-1302 / DSM 25543
-
significantly reduced activity compared with the wild type protein
-
H388A
Pyrococcus abyssi GE5 / CNCM I-1302 / DSM 25543
-
significantly reduced activity compared with the wild type protein
-
H86A
Pyrococcus abyssi GE5 / CNCM I-1302 / DSM 25543
-
significantly reduced activity compared with the wild type protein
-
E203A/D233A/D235A
site-directed mutagenesis, mutation of three active site residues, mutant rat1EDD does not show 5'-3' exoribonuclease activity, and rat1EDD/Rai1 complex does not degrade RNAs or decrease RNAPII elongation, demonstrating that RNA degradation by exonuclease activity is critical to RNAPII termination
additional information
additional information
to address the biological significance of Saci-aCPSF2, a deletion mutant is constructed, and the influence of SaciaCPSF2 on the transcriptome profile is assessed employing high throughput RNA sequencing
additional information
-
to address the biological significance of Saci-aCPSF2, a deletion mutant is constructed, and the influence of SaciaCPSF2 on the transcriptome profile is assessed employing high throughput RNA sequencing
additional information
-
to address the biological significance of Saci-aCPSF2, a deletion mutant is constructed, and the influence of SaciaCPSF2 on the transcriptome profile is assessed employing high throughput RNA sequencing
-
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PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
recombinant His6-tagged Rat1 from Escherichia coli strain BL21 Codon-Plus (DE3) RIL by nickel affinity chromatography and anion exchange chromatography, followed by gel filtration
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CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
expression in Escherichia coli
recombinant overexpression of His6-tagged Rat1 in Escherichia coli strain BL21 Codon-Plus(DE3)RIL. The recombinant Rat1/Rai1 cannot terminate Escherichia coli RNAP in vitro and addition of each NTP has no effect either
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APPLICATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
medicine
women who subsequently develope preeclampsia show decreased expression of long non-coding RNA telomerase RNA component TERC in peripheral blood mononuclear cells early in pregnancy. XRN1 involved in the maturation of TERC is also reduced in pregnancy and 5-year follow-up. XRN1 and TERC are positively correlated at weeks 22-24 with a stronger association in the preeclampsia group
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REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Clouet-d'Orval, B.; Rinaldi, D.; Quentin, Y.; Carpousis, A.J.
Euryarchaeal beta-CASP proteins with homology to bacterial RNase J Have 5'- to 3'-exoribonuclease activity
J. Biol. Chem.
285
17574-17583
2010
Pyrococcus abyssi (Q9V076), Pyrococcus abyssi, Pyrococcus abyssi GE5 / CNCM I-1302 / DSM 25543 (Q9V076), Thermococcus kodakarensis (Q5JH57)
brenda
Märtens, B.; Amman, F.; Manoharadas, S.; Zeichen, L.; Orell, A.; Albers, S.V.; Hofacker, I.; Bläsi, U.
Alterations of the transcriptome of Sulfolobus acidocaldarius by exoribonuclease aCPSF2
PLoS One
8
e76569
2013
Sulfolobus acidocaldarius (Q4J6E1), Sulfolobus acidocaldarius, Sulfolobus acidocaldarius DSM 639 (Q4J6E1)
brenda
Hasenöhrl, D.; Konrat, R.; Bläsi, U.
Identification of an RNase J ortholog in Sulfolobus solfataricus: implications for 5'-to-3' directional decay and 5'-end protection of mRNA in crenarchaeota
RNA
17
99-107
2011
Saccharolobus solfataricus (Q980D0), Saccharolobus solfataricus, Saccharolobus solfataricus P2 (Q980D0)
brenda
Park, J.; Kang, M.; Kim, M.
Unraveling the mechanistic features of RNA polymerase II termination by the 5'-3' exoribonuclease Rat1
Nucleic Acids Res.
43
2625-2637
2015
Saccharomyces cerevisiae (Q02792), Saccharomyces cerevisiae
brenda
Balaratnam, S.; Hoque, M.E.; West, N.; Basu, S.
Decay of Piwi-interacting RNAs in human cells is primarily mediated by 5' to 3' exoribonucleases
ACS Chem. Biol.
17
1723-1732
2022
Homo sapiens (Q9H0D6), Homo sapiens (Q8IZH2)
brenda
Reiss, M.; Keegan, J.; Aldrich, A.; Lyons, S.M.; Flynn, R.L.
The exoribonuclease XRN2 mediates degradation of the long non-coding telomeric RNA TERRA
FEBS Lett.
597
1818-1836
2023
Homo sapiens (Q9H0D6)
brenda
Fischer, J.; Song, Y.S.; Yosef, N.; di Iulio, J.; Churchman, L.S.; Choder, M.
The yeast exoribonuclease Xrn1 and associated factors modulate RNA polymerase II processivity in 5 and 3 gene regions
J. Biol. Chem.
295
11435-11454
2020
Saccharomyces cerevisiae (P22147)
brenda
Phung, D.K.; Etienne, C.; Batista, M.; Langendijk-Genevaux, P.; Moalic, Y.; Laurent, S.; Liuu, S.; Morales, V.; Jebbar, M.; Fichant, G.; Bouvier, M.; Flament, D.; Clouet-dOrval, B.
RNA processing machineries in Archaea the 5'-3' exoribonuclease aRNase J of the beta-CASP family is engaged specifically with the helicase ASH-Ski2 and the 3'-5' exoribonucleolytic RNA exosome machinery
Nucleic Acids Res.
48
3832-3847
2020
Pyrococcus abyssi (Q9V076), Pyrococcus abyssi (F0LHN9), Pyrococcus abyssi DSM 11836 (F0LHN9)
brenda
Sharma, S.; Yang, J.; Doamekpor, S.K.; Grudizen-Nogalska, E.; Tong, L.; Kiledjian, M.
Identification of a novel deFADding activity in human, yeast and bacterial 5' to 3' exoribonucleases
Nucleic Acids Res.
50
8807-8817
2022
Homo sapiens (Q8IZH2), Escherichia coli (P77766), Saccharomyces cerevisiae
brenda
Lekva, T.; Roland, M.C.P.; Estensen, M.E.; Norwitz, E.R.; Tilburgs, T.; Henriksen, T.; Bollerslev, J.; Normann, K.R.; Magnus, P.; Olstad, O.K.; Aukrust, P.; Ueland, T.
Dysregulated non-coding telomerase RNA component and associated exonuclease XRN1 in leucocytes from women developing preeclampsia-possible link to enhanced senescence
Sci. Rep.
11
19735
2021
Homo sapiens (Q8IZH2)
brenda
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