3.1.13.4: poly(A)-specific ribonuclease
This is an abbreviated version!
For detailed information about poly(A)-specific ribonuclease, go to the full flat file.
Word Map on EC 3.1.13.4
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3.1.13.4
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deadenylation
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polya-specific
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rna-binding
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decapping
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polyadenylation
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polya-binding
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nocturnin
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au-rich
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mirna-mediated
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telomere
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trim
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argonaute
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eif4e
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pirnas
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pumilio
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tristetraprolin
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cap-binding
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congenita
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exonucleolytic
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p-bodies
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dyskeratosis
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oligoadenylation
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pabps
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diagnostics
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miriscs
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poly-a
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are-binding
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microrna-mediated
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medicine
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eif4e-binding
- 3.1.13.4
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deadenylation
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polya-specific
-
rna-binding
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decapping
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polyadenylation
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polya-binding
- nocturnin
-
au-rich
-
mirna-mediated
-
telomere
-
trim
-
argonaute
- eif4e
-
pirnas
-
pumilio
- tristetraprolin
-
cap-binding
- congenita
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exonucleolytic
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p-bodies
-
dyskeratosis
-
oligoadenylation
-
pabps
- diagnostics
-
miriscs
- poly-a
-
are-binding
-
microrna-mediated
- medicine
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eif4e-binding
Reaction
exonucleolytic cleavage of poly(A) to 5'-AMP =
Synonyms
2',3'-exoribonuclease, 3'-exoribonuclease, adenosine-specific exonuclease, AHG2, AtPARN, BTG1-binding factor 1, Caf1, CCR4, CCR4 deadenylase complex, CCR4-associated factor 1, Ccr4-Not complex, CCR4-NOT transcription complex subunit 7, Ccr4p/Pop2p/Notp complex, CNOT6L nuclease, cytoplasmic deadenylase, deadenylase, hPAN, HsPNLDC1, MMAR_3223, More, nuclease, polyadenylate-specific exoribo-, PAB1P-dependent poly(A)-nuclease, PAN, PAN2, PAN3, PARN, PARN-1, PARN-like domain-containing protein 1, PF2046, PNLDC1, poly(A) nuclease, poly(A) nuclease complex, poly(A) ribonuclease, poly(A)-selective ribonuclease, poly(A)-specific 3'-5' ribonuclease, poly(A)-specific 3'-exoribonuclease, poly(A)-specific mRNA exoribonuclease, poly(A)-specific ribonuclease, poly(A)-specific RNase, Pop2p deadenylase, RNase AS, RNase H
ECTree
3.1.13.4 poly(A)-specific ribonucleaseAdvanced search results
results (
results (Engineering
Engineering on EC 3.1.13.4 - poly(A)-specific ribonuclease
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PROTEIN VARIANTS 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
D66A/E68A
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site-directed mutagenesis, enzymatically inactive PARN, the mutant embryos are retarded, and culminate in an arrest at the bent-cotyledon stage, some show hyperadenylation of transcripts
D28C
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mutants inactive in presence of Mg2+, but with restored activity in presence of soft divalent metal ions, amino acid interacts with catalytically essential metal ions
D292C
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mutants inactive in presence of Mg2+, but with restored activity in presence of soft divalent metal ions, amino acid interacts with catalytically essential metal ions
D382C
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mutants inactive in presence of Mg2+, but with restored activity in presence of soft divalent metal ions, amino acid interacts with catalytically essential metal ions
D28C
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mutants inactive in presence of Mg2+, but with restored activity in presence of soft divalent metal ions, amino acid interacts with catalytically essential metal ions
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D292C
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mutants inactive in presence of Mg2+, but with restored activity in presence of soft divalent metal ions, amino acid interacts with catalytically essential metal ions
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D382C
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mutants inactive in presence of Mg2+, but with restored activity in presence of soft divalent metal ions, amino acid interacts with catalytically essential metal ions
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D28A
D292A
D382A
D478A
generated by site-directed mutagenesis, Kd value for 7-methylguanosine triphosphate is 20.0 microM
E30A
F484A
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site-directed mutagenesis, active site mutant, not expressable in Escherichia coli
H449A
site-directed mutagenesis, the mutant shows loss of the negative cooperativity between the PARN dimer subunits that is evident for the m7GpppG and m7GTP binding by the wild-type protein
K454A
generated by site-directed mutagenesis, Kd value for 7-methylguanosine triphosphate is 20.03 microM
L197A
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site-directed mutagenesis, active site mutant, not expressable in Escherichia coli
L216A
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site-directed mutagenesis, active site mutant, not expressable in Escherichia coli
L291A
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site-directed mutagenesis, activity and kinetics with RNA substrates compared to the wild-type enzyme
L414A
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site-directed mutagenesis, active site mutant, not expressable in Escherichia coli
M425A
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site-directed mutagenesis, activity and kinetics with RNA substrates compared to the wild-type enzyme
N412A
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site-directed mutagenesis, active site mutant, not expressable in Escherichia coli
P365A
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site-directed mutagenesis, active site mutant, not expressable in Escherichia coli
P365A/F484A
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site-directed mutagenesis, active site mutant, not expressable in Escherichia coli
P365A/N412A/F484A
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site-directed mutagenesis, active site mutant, not expressable in Escherichia coli
T458A
generated by site-directed mutagenesis, Kd value for 7-methylguanosine triphosphate is 30.58 microM
D471A
point mutation is introduced into the cap-binding domain usin site-directed mutagenesis kit, pull-down assay shows no significant impact on the cap-binding activity of PARN
K447A
point mutation is introduced into the cap-binding domain using site-directed mutagenesis kit, pull-down assay shows no significant impact on the cap-binding activity of PARN
K450A
point mutation is introduced into the cap-binding domain using site-directed mutagenesis kit, pull-down assay shows no significant impact on the cap-binding activity of PARN
W468L
point mutation is introduced into the cap-binding domain using site-directed mutagenesis kit, mutation significantly decreases the interaction between PARN RNA-recognition motif and the cap analog, the aromatic ring of W468 is directly responsible for the cap recognition and is a functionally critical residue for the cap-binding activity of PARN RNA-recognition motif
A519V
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site-directed mutagenesis of Pab1p, the mutant shows no resistance to 3-AT in contrast to the wild-type protein, identification of interaction residues and domains with Ppb1p, Pan2p and Pan3p
E556A
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complete loss of activity, E556 is the key Mg2+-binding residue
G444D
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site-directed mutagenesis of Pab1p, the mutant shows no resistance to 3-AT in contrast to the wild-type protein, identification of interaction residues and domains with Ppb1p, Pan2p and Pan3p
G528D
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site-directed mutagenesis of Pab1p, the mutant shows no resistance to 3-AT in contrast to the wild-type protein, identification of interaction residues and domains with Ppb1p, Pan2p and Pan3p
R506G
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site-directed mutagenesis of Pab1p, the mutant shows no resistance to 3-AT in contrast to the wild-type protein, identification of interaction residues and domains with Ppb1p, Pan2p and Pan3p
V451A
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site-directed mutagenesis of Pab1p, the mutant shows no resistance to 3-AT in contrast to the wild-type protein, identification of interaction residues and domains with Ppb1p, Pan2p and Pan3p
Y514C
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site-directed mutagenesis of Pab1p, the mutant shows reduced resistance to 3-AT compared to the wild-type protein, identification of interaction residues and domains with Ppb1p, Pan2p and Pan3p
additional information
D28A
site-directed mutagenesis, structure comparison to the wild-type enzyme, the mutant shows unaltered ellipticity
D28A
site-directed mutagenesis, catalytically inactive mutant, phenotype, overview
D292A
site-directed mutagenesis, structure comparison to the wild-type enzyme, the mutant shows unaltered ellipticity
D382A
site-directed mutagenesis, structure comparison to the wild-type enzyme, the mutant shows slightly decreased ellipticity
E30A
site-directed mutagenesis, structure comparison to the wild-type enzyme, the mutant shows significantly decreased ellipticity
additional information
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construction of embryos lacking PARN, the mutant embryos are retarded, and culminate in an arrest at the bent-cotyledon stage, some show hyperadenylation of transcripts, the phenotype cannot be rescued by expression of the wild-type enzyme in plants, loss of the enzyme affects poly(A) tail length distribution of only a select subset of embryonic transcripts
additional information
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gene silencing by microinjection of specific iRNA, the mutant worms show no phenotype
additional information
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PARN(443-560/W456/W475A) mutant is severely defective in cap binding, has RNA binding properties
additional information
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removal of the R3H domain (mutant p74DR3H) leads to a dramatic decrease in the thermal stability of PARN, while removal of the RRM domain or both of the two RNA-binding domains only results in a minor decrease in PARN stability against thermal inactivation and denaturation
additional information
construction of deletion mutants, i.e. expression of the N-terminal fragment residues 1-540, the N-terminal fragment residues 1-520, the N-terminal fragment residues 1-470, the N-terminal fragment residues 1-446, residues 1-520 with the deletion of the R3H domain, residues 1-446 with the deletion of the R3H domain. N-terminal fragment residues 1-446, residues 1-520 with the deletion of the R3H domain, residues 1-446 with the deletion of the R3H domain display 30.9%, 5.9% and 2.5% of the catalytic efficiency of the N-terminal fragment residues 1-520, respectively
additional information
generation of PARN knockout cells by CRISPR/Cas9-mediated gene knockout. Complementation of PARN activity restores the normal isoform ratio of miR-362-5p in HEK-293T cells
additional information
stable knockdown of the endogenous PARN in the gastric cancer MKN28 and AGS cells. PARN depletion significantly inhibits the proliferation of the two types of gastric cancer cells and promotes cell death, but does not significantly affect cell motility and invasion. The depletion of PARN arrests the gastric cancer cells at the G0/G1 phase by upregulating the expression levels of p53 and p21 but not p27. The mRNA stability of p53 is unaffected by PARN-knockdown in both types of cells. A significant stabilizing effect of PARN-depletion on p21 mRNA is observed in the AGS cells but not in the MKN28 cells
additional information
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stable knockdown of the endogenous PARN in the gastric cancer MKN28 and AGS cells. PARN depletion significantly inhibits the proliferation of the two types of gastric cancer cells and promotes cell death, but does not significantly affect cell motility and invasion. The depletion of PARN arrests the gastric cancer cells at the G0/G1 phase by upregulating the expression levels of p53 and p21 but not p27. The mRNA stability of p53 is unaffected by PARN-knockdown in both types of cells. A significant stabilizing effect of PARN-depletion on p21 mRNA is observed in the AGS cells but not in the MKN28 cells
additional information
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growth of cells transformed with mutant constructs, overview
additional information
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ccr4delta mutant strain, residual deadenylation is solely due to the Pan2p/Pan3p complex, the MFA2pG mRNA in the nonstressed ccr4delta cells is stabilized 2fold compared to the wild-type strain, difference in deadenylation rates with and without stress in the ccr4D strain is not as severe as in wild-type cells
additional information
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construction of a PARN disruption mutant, the mutant shows no phenotype
additional information
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Cells overexpressing gene PARN-1 have increased deadenylase activity, overexpression of gene PARN-1 leads to PARN-1 affecting the steady-state level and decay rates of at least four different procyclic mRNAs. Depletion of all three PARNs, PARN-1, PARN-2, and PARN-3, using RNA interference in procyclic and bloodstream-form parasites, neither growth rates nor gross morphology are affected in PARN-depleted procyclic forms, and growth rates are only slightly reduced to 90% of control rates in PARN-depleted BF parasites. Following depletion of PARN-1 protein using PARN-1-specific antibodies, RNA-A60 degradation is abolished
additional information
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Cells overexpressing gene PARN-1 have increased deadenylase activity, overexpression of gene PARN-1 leads to PARN-1 affecting the steady-state level and decay rates of at least four different procyclic mRNAs. Depletion of all three PARNs, PARN-1, PARN-2, and PARN-3, using RNA interference in procyclic and bloodstream-form parasites, neither growth rates nor gross morphology are affected in PARN-depleted procyclic forms, and growth rates are only slightly reduced to 90% of control rates in PARN-depleted BF parasites. Following depletion of PARN-1 protein using PARN-1-specific antibodies, RNA-A60 degradation is abolished
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