3.1.13.1: exoribonuclease II
This is an abbreviated version!
For detailed information about exoribonuclease II, go to the full flat file.
Word Map on EC 3.1.13.1
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3.1.13.1
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dnase
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nucleic
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pancreatic
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strand
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single-stranded
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endoribonuclease
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viruses
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polynucleotide
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endonuclease
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polyadenylation
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duplex
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polya
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ribonucleoproteins
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transcriptase
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rna-binding
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circrnas
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exosome
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phosphorylase
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chemokine
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dsrnas
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tata
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virion
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rpa
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nucleases
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stem-loops
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actinomycin
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helicase
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endonucleolytic
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dicer
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phosphodiester
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rna-dependent
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pronase
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intermedius
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oligoadenylate
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riboprobes
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rna-protein
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nucleolar
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ribozyme
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3'-terminal
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angiogenin
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argonaute
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encapsidation
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rna-induced
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pre-rrnas
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rna-dna
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antitoxin
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mip-1alpha
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snrnp
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medicine
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drosha
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degradation
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analysis
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norovirus
- 3.1.13.1
- dnase
- nucleic
- pancreatic
- strand
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single-stranded
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endoribonuclease
- viruses
- polynucleotide
- endonuclease
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polyadenylation
- duplex
- polya
- ribonucleoproteins
- transcriptase
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rna-binding
-
circrnas
-
exosome
- phosphorylase
- chemokine
- dsrnas
- tata
- virion
- rpa
- nucleases
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stem-loops
- actinomycin
- helicase
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endonucleolytic
- dicer
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phosphodiester
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rna-dependent
- pronase
- intermedius
- oligoadenylate
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riboprobes
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rna-protein
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nucleolar
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ribozyme
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3'-terminal
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angiogenin
-
argonaute
-
encapsidation
-
rna-induced
- pre-rrnas
- rna-dna
- antitoxin
-
mip-1alpha
-
snrnp
- medicine
- drosha
- degradation
- analysis
- norovirus
Reaction
Exonucleolytic cleavage in the 3'- to 5'- direction to yield nucleoside 5'-phosphates =
Synonyms
3'-5'exoribonuclease, 3’-5’exoribonuclease, 5'->3' exoribonuclease 2, AB205_0003320, Dis, Dis3, EC 3.1.4.20, exonuclease ISG20, More, PfRNase II, RC-RNase 2, ribonuclease 2, ribonuclease II, ribonuclease Q, Ribonuclease R, RNase, RNase 2, RNase A, RNase II, RNase R, RNase-2, RNaseR, Rnb, RNR, RNR1, Rrp44, XRN2
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General Information
General Information on EC 3.1.13.1 - exoribonuclease II
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evolution
malfunction
metabolism
physiological function
additional information
RC-RNase 2, a cytotoxic ribonuclease isolated from oocytes of bullfrog Rana catesbeiana, consists of 105 residues linked with 4 disulfide bridges and belongs to the bovine pancreatic ribonuclease (RNase A) superfamily. Among the RC-RNases, the base preference for RNase 2 is UpG but CpG for RCRNase 4, while RC-RNase possesses the base specificity of both UpG and CpG. RC-RNase 2 or 4 has much lower catalytic activity but only 3fold less cytotoxicity than RC-RNase. The differences of side-chain conformations of subsite residues among RNase A, RC-RNase, RC-RNase 4 and rRNase 2 are related to their distinct catalytic activities and base preferences. Chemical shift perturbations of three RC-RNases with various substrate analogues, overview
evolution
RNase II is another 3'-5' hydrolytic exoribonuclease from the RNase II family of exoribonucleases
evolution
RNase R is another 3'-5' hydrolytic exoribonuclease from the RNase II family of exoribonucleases
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instead of A-site cleavage, translational pausing in DELTARNase II cells produces transcripts that are truncated +12 and +28 nucleotides downstream of the A-site codon. Deletion of RNase R has little effect on A-site cleavage. Polynucleotide phosphorylase overexpression restores A-site cleavage activity to DELTARNase II cells
malfunction
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a specific subclass of var genes called upsA are strongly up-regulated in parasites that expressed a defective PfRNase II (C-terminally tagged with the FKBP destabilization domain) compared to wild-type parasites. Different combinations of up to 3 distinct upsA var genes, together with an upsC var gene, were upregulated simultaneously in single parasite clones
malfunction
RNase II thermolability of the rnb500 phenotype is due to the Cys284Tyr mutation within the RNB domain, which abolishes activity by increasing protein kinetic instability at the nonpermissive temperature. In vivo and in vitro investigation of RNase II mutation(s) that confer the rnb500 phenotype
malfunction
RNase R mutants form more biofilms than wild-type cells
malfunction
Escherichia coli SK5689
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RNase II thermolability of the rnb500 phenotype is due to the Cys284Tyr mutation within the RNB domain, which abolishes activity by increasing protein kinetic instability at the nonpermissive temperature. In vivo and in vitro investigation of RNase II mutation(s) that confer the rnb500 phenotype
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exoribonuclease-mediated gene silencing, mechanism and a more general regulatory role of ribonucleases in dynamic gene expression in Plasmodium falciparum, overview
metabolism
NF-kappaB-repressing factor phosphorylation regulates transcription elongation via its interactions with 5'->3' exoribonuclease 2 and negative elongation factor. Interleukin-1 has a more drastic effect on NELF-E or XRN2 binding to NKRF than the M1 mutation
metabolism
role for RNase II Lys501 acetylation in modulating cell growth during stress conditions
metabolism
the enzyme is involved in cell motility and biofilm formation
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plays an important role in RelE-independent A-site cleavage
physiological function
major hydrolytic exoribonuclease RNase II is associated with the degradosome components endoribonuclease E, RNA helicase B, polynucleotide phosphorylase and enolase. Formation of the RNase II-degradosome complex requires the degradosomal proteins RNA helicase B and polynucleotide phosphorylase as well as a C-terminal domain of endoribonuclease E that contains binding sites for the other degradosomal proteins
physiological function
mutants lacking both ribonuclease RNR1 and polynucleotide phosphorylase exhibit embryo lethality. Combination of a RNR1 null mutation with weak polynucleotide phosphorylase mutant alleles leads to chlorotic plants which display a global reduction in RNA abundance. The enzymes catalyze a two-step maturation of mRNA 3' ends, with RNR1 polishing 3' termini created by polynucleotide phosphorylase. The bulky quaternary structure of polynucleotide phosphorylase compared with RNR1 may explain this activity split between the two enzymes. The RNR1 single mutant overaccumulates most mRNA species when compared with the wild type. The excess mRNAs in RNR1 are often present in non-polysomal fractions, and mostly show a substantial increase in stability
physiological function
RNase II self-interaction and the ability of the protein to assemble into organized cellular structures requires the membrane binding domain. The ability of RNase II to maintain cell viability in the absence of exoribonuclease polynucleotide phosphorylase is markedly diminished when the RNase II cellular structures are lost due to changes in the amphipathicity of the amino-terminal helix
physiological function
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although genes represent monocistronic units that are expressed in a life cycle stage-specific manner, posttranscriptional regulation via translational repression of mRNA has been observed in parasite stages that transition from the vertebrate host to the Anopheles vector. In Plasmodium falciparum stages that infect human erythrocytes, a subgroup of genes that have been thought to be transcriptionally silent are actually transcribed but degraded immediately by an RNase II that is recruited to these gene loci. This cryptic RNA is not detectable in steady-state RNA but has been detected using nuclear run-on techniques and in mutant RNase II parasites. Nascent RNA degradation controls virulence genes expressed in a monoallelic fashion and noncoding RNAs (ncRNAs), but also a number of housekeeping-like of genes. PfRNase II is recruited to certain gene loci and accelerates the decay of mRNAs and ncRNA. PfRNase II is highly enriched at the promoters and introns of silenced upsA gene loci, and transcription analysis revealed that any nascent transcripts from these genes are only short-lived, cryptic mRNAs. Exoribonuclease-mediated gene silencing, mechanism, overview
physiological function
cytotoxic ribonucleases with antitumor activity are found in the oocytes and early embryos of frogs
physiological function
interactions between NKRF, 5'->3' exoribonuclease 2 (XRN2) and the negative elongation factor (NELF)-E in HeLa cells. Interleukin IL-1 stimulation leads to decrease in NKRF amino acids 421-429 phosphorylation and dissociation of NELF-E and XRN2 by concomitant resumption of transcription elongation of a synthetic reporter or the endogenous NKRF target gene, interleukin IL-8. 5'->3' exoribonuclease 2 (XRN2) is implicated in inhibition of transcription elongation via the termination of initiated transcripts in many RNA Pol II-dependent promoters
physiological function
RNase II is a 3' to 5' processive exoribonuclease and is the major hydrolytic enzyme in Escherichia coli accounting for about 90% of the total activity. Acetylation of residue Lys501 in RNase II, reversibly controlled by the acetyltransferase Pka and the deacetylase CobB, affects binding of the substrate and decreases the catalytic activity of RNase II. As a consequence, the steady-state level of target RNAs of RNase II may be altered in the cells. Under conditions of slowed growth, the acetylation level of RNase II is elevated and the activity of RNase II decreases, emphasizing the importance of this regulatory process
physiological function
the RNA steady-state levels in the cell are a balance between synthesis and degradation rates. Although transcription is important, RNA processing and turnover are also key factors in the regulation of gene expression. In Escherichia coli there are three main exoribonucleases (RNase II, RNase R and PNPase) involved in RNA degradation. RNase II, RNase R and PNPase significantly impair the motility of the cells
physiological function
the RNA steady-state levels in the cell are a balance between synthesis and degradation rates. Although transcription is important, RNA processing and turnover are also key factors in the regulation of gene expression. In Escherichia coli there are three main exoribonucleases (RNase II, RNase R and PNPase) involved in RNA degradation. RNase R is a critical enzyme involved in RNA and protein quality control, namely in the degradation of defective tRNAs and rRNAs and is involved in RNA degradation during trans-translation. RNase R is involved in virulence, it affects virulence by altering the motility of the pathogens. RNase II, RNase R and PNPase significantly impair the motility of the cells
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stability of RNAse II-RNA interactions and effects on the enzyme reaction mechanism processing and degrading RNA molecules, analysis by surface plasmon resonance and electrophoretic mobility shift Assay, overview
additional information
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RNase II of Plasmodium falciparum is a non-canonical exoribonuclease that contains a putative RNase II domain (termed PfRNase II). Loss of PfRNase II affects the strict gene counting mechanism that controls monoallelic var gene expression
additional information
solution structure of recombinant RC-RNase 2 by heteronuclear NMR technique, overview. The substrate-related residues in the base specificity among native RC-RNases are derived using the chemical shift perturbation on ligand binding
additional information
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solution structure of recombinant RC-RNase 2 by heteronuclear NMR technique, overview. The substrate-related residues in the base specificity among native RC-RNases are derived using the chemical shift perturbation on ligand binding