Any feedback?
Information on EC 3.1.13.4 - poly(A)-specific ribonuclease and Organism(s) Mus musculus and UniProt Accession O35710
for references in articles please use BRENDA:EC3.1.13.4Please wait a moment until all data is loaded. This message will disappear when all data is loaded.
EC Tree
3.1.13.4 poly(A)-specific ribonucleaseSpecify your search results
Word Map
- 3.1.13.4
-
deadenylation
-
polya-specific
-
rna-binding
-
decapping
-
polyadenylation
-
polya-binding
- nocturnin
-
au-rich
-
mirna-mediated
-
telomere
-
trim
-
argonaute
- eif4e
-
pirnas
-
pumilio
- tristetraprolin
-
cap-binding
- congenita
-
exonucleolytic
-
p-bodies
-
dyskeratosis
-
oligoadenylation
-
pabps
- diagnostics
-
miriscs
- poly-a
-
are-binding
-
microrna-mediated
- medicine
-
eif4e-binding
The taxonomic range for the selected organisms is: Mus musculus
The expected taxonomic range for this enzyme is: Eukaryota, Bacteria, Archaea
The expected taxonomic range for this enzyme is: Eukaryota, Bacteria, Archaea
Synonyms
deadenylase, ccr4-not complex, parn, poly(a)-specific ribonuclease, rnase as, pnldc1, cytoplasmic deadenylase, poly(a) nuclease, 3'-exoribonuclease, poly(a) ribonuclease, 
more
topSYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
2',3'-exoribonuclease
-
-
-
-
3'-exoribonuclease
-
-
-
-
nuclease, polyadenylate-specific exoribo-
-
-
-
-
PAB1P-dependent poly(A)-nuclease
-
-
-
-
PARN
poly(A)-specific 3'-exoribonuclease
-
-
-
-
poly(A)-specific mRNA exoribonuclease
-
-
-
-
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
hydrolysis of phosphoric ester
-
-
-
-
CAS REGISTRY NUMBER
COMMENTARY
110541-21-4
-
215797-47-0
-
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
mRNA-poly(A) + H2O
?
the enzyme is involved in the removal of polyA tails from mRNAs
-
-
?
additional information
?
-
PARN is a divalent metal ion-dependent 3'-exonuclease that specifically catalyzes the 3'-5'-degradation of the single-stranded poly(A) tail of mRNA with a free 3'-hydroxyl group
-
-
?
additional information
?
-
-
PARN is a divalent metal ion-dependent 3'-exonuclease that specifically catalyzes the 3'-5'-degradation of the single-stranded poly(A) tail of mRNA with a free 3'-hydroxyl group
-
-
?
additional information
?
-
PARN is one of the major mammalian 3'-specific exoribonucleases involved in the degradation of the mRNA poly(A)-tail and it is also involved in the regulation of translation in early embryonic development, it is the key enzyme involved in the deadenylation of mRNA in a cap-dependent manner
-
-
?
additional information
?
-
-
PARN is one of the major mammalian 3'-specific exoribonucleases involved in the degradation of the mRNA poly(A)-tail and it is also involved in the regulation of translation in early embryonic development, it is the key enzyme involved in the deadenylation of mRNA in a cap-dependent manner
-
-
?
additional information
?
-
-
PARN protein levels are not appreciably altered by lipopolysaccharide stimulation in RAW264.7 macrophage cells
-
-
?
additional information
?
-
the interaction between PARN and the 7-methylguanosine cap of mRNA plays a key role in stimulating the rate of deadenylation
-
-
?
additional information
?
-
-
the interaction between PARN and the 7-methylguanosine cap of mRNA plays a key role in stimulating the rate of deadenylation
-
-
?
additional information
?
-
usage of synthetic oligoRNA substrates: N9A15, A12, U12, C12, G12 and dA12. Activity modulation experiments in the presence of m7G(5')ppp(5')G cap analogue. The recombinant enzyme exhibits specific deadenylation activity in vitro, with very high specificity for recognition of poly(A) or poly(dA)
-
-
?
additional information
?
-
-
usage of synthetic oligoRNA substrates: N9A15, A12, U12, C12, G12 and dA12. Activity modulation experiments in the presence of m7G(5')ppp(5')G cap analogue. The recombinant enzyme exhibits specific deadenylation activity in vitro, with very high specificity for recognition of poly(A) or poly(dA)
-
-
?
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
mRNA-poly(A) + H2O
?
the enzyme is involved in the removal of polyA tails from mRNAs
-
-
?
additional information
?
-
PARN is a divalent metal ion-dependent 3'-exonuclease that specifically catalyzes the 3'-5'-degradation of the single-stranded poly(A) tail of mRNA with a free 3'-hydroxyl group
-
-
?
additional information
?
-
-
PARN is a divalent metal ion-dependent 3'-exonuclease that specifically catalyzes the 3'-5'-degradation of the single-stranded poly(A) tail of mRNA with a free 3'-hydroxyl group
-
-
?
additional information
?
-
PARN is one of the major mammalian 3'-specific exoribonucleases involved in the degradation of the mRNA poly(A)-tail and it is also involved in the regulation of translation in early embryonic development, it is the key enzyme involved in the deadenylation of mRNA in a cap-dependent manner
-
-
?
additional information
?
-
-
PARN is one of the major mammalian 3'-specific exoribonucleases involved in the degradation of the mRNA poly(A)-tail and it is also involved in the regulation of translation in early embryonic development, it is the key enzyme involved in the deadenylation of mRNA in a cap-dependent manner
-
-
?
additional information
?
-
-
PARN protein levels are not appreciably altered by lipopolysaccharide stimulation in RAW264.7 macrophage cells
-
-
?
additional information
?
-
the interaction between PARN and the 7-methylguanosine cap of mRNA plays a key role in stimulating the rate of deadenylation
-
-
?
additional information
?
-
-
the interaction between PARN and the 7-methylguanosine cap of mRNA plays a key role in stimulating the rate of deadenylation
-
-
?
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
additional information
additional information
PARN is a divalent metal ion-dependent 3'-exonuclease
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
neomycin
-
antibiotic neomycin B inhibits approximately 80% of PARN activity at a concentration of 10 microg/ml
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
additional information
PARN interacts with the 7-methylguanosine cap, which enhances its deadenylation activity
-
additional information
-
PARN interacts with the 7-methylguanosine cap, which enhances its deadenylation activity
-
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
additional information
additional information
10-mer poly(A) oligonucöleotide can not bind to the cap-binding site on PARN RNA-recognition motif
additional information
-
10-mer poly(A) oligonucöleotide can not bind to the cap-binding site on PARN RNA-recognition motif
additional information
Kd value of 45 microM for the interaction between PARN RNA-recognition motif and 7-methylguanosine
additional information
-
Kd value of 45 microM for the interaction between PARN RNA-recognition motif and 7-methylguanosine
additional information
PARN RRM has stronger affinity for the 7-methylguanosine than for the GpppG and GpppA cap analogs
additional information
-
PARN RRM has stronger affinity for the 7-methylguanosine than for the GpppG and GpppA cap analogs
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SOURCE
differentiated cells express PNLDC1 only after demethylation
additional information
additional information
PNLDC1 is present in stem and germ cells and fades during embryogenesis and early differentiation. Pnldc1 is highly expressed in mouse embryonic stem cells (E14) and testes, whereas expression in skin, late embryos and ovaries is almost undetectable (albeit slightly higher in ovaries than other organs)
additional information
-
PNLDC1 is present in stem and germ cells and fades during embryogenesis and early differentiation. Pnldc1 is highly expressed in mouse embryonic stem cells (E14) and testes, whereas expression in skin, late embryos and ovaries is almost undetectable (albeit slightly higher in ovaries than other organs)
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY
GeneOntology No.
LITERATURE
SOURCE
PNLDC1 is localized predominantly in the endoplasmic reticulum
additional information
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
malfunction
physiological function
physiological function
malfunction
mice lacking the Noc gene display resistance to diet-induced obesity and hepatic steatosis, due in part to reduced lipid trafficking in the small intestine
malfunction
Noc knock-out (Noc-/-) mice exhibit no obvious abnormalities in development or reproduction, however, they exhibit striking metabolic phenotypes when fed a High-Fat Diet (HFD). This diet causes wild-type mice to become obese, but the Noc-/- mice remain lean although they do not exhibit increased activity or reduced food intake
physiological function
PARN, nocturnin and Angel are three of the multiple deadenylases that have been described in eukaryotic cells. While each of these enzymes appears to target poly(A) tails for shortening and influence RNA gene expression levels and quality control, the enzymes differ in terms of enzymatic mechanisms, regulation and biological impact. Nocturnin functions in adipogenesis and lipid metabolism
physiological function
the enzyme is involved in the removal of polyA tails from mRNAs. Noc is a potential key post-transcriptional mediator in the circadian control of many metabolic processes. It appears to play important roles in other tissues and has been implicated in lipid metabolism, adipogenesis, glucose homeostasis, inflammation and osteogenesis
physiological function
PNLDC1 is a deadenylase that is excluded from the nucleus and most likely, its function occurs mainly in the endoplasmic reticulum. Pnldc1 is present in early mouse development
physiological function
PARN, nocturnin and Angel are three of the multiple deadenylases that have been described in eukaryotic cells. While each of these enzymes appears to target poly(A) tails for shortening and influence RNA gene expression levels and quality control, the enzymes differ in terms of enzymatic mechanisms, regulation and biological impact. PARN plays a role in early development, DNA damage and possibly cancer
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). NOCT_MOUSE
429
0
48301
Swiss-Prot
Secretory Pathway (Reliability: 2)
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
recombinant His-tagged enzyme from Escherichia coli by nickel affinity chromatography
The wild type and mutant forms of the cap-binding domain of PARN are overexpressed in Escherichia coli BL21(DE3) cells, harvested by centrifugation and suspended in 20 mM Tris-HCl buffer containing 1 M NaCl, 30 mM imidazole, 1 mM 1,4-DL-dithiothreitol, 0.1 mg/ml lysozyme, DNaseI and protease inhibitor cocktail, and lyse with a sonicator. Cell debris and inclusion bodies are removed by centrifugation. The supernatant is loaded on a Ni2+-NTA-agarose column and the proteins are eluted with 20 mM Tris-HCl, 1 M NaCl and 200 mM imidazole.
Unlabeled and [15N], [13C]-labeled PARN cap-binding domains used for NMR experiments are synthesized by the cell-free protein expression system. After reaction, proteins are isolated by Ni2+-affinity chromatography before removing of the His6-tag. Subsequent cation-exchange chromatography yields the purified cap-binding domain.
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
gene PNLDC1, recombinant expression of EGFP-tagged enzyme in HEK-293 cells, mouse PNLDC1 has one predicted isoform, recombinant expression of His-tagged enzyme in Escherichia coli
The DNA fragment encoding the cap-binding domain of PARN (residues 430-516) is amplified from a cDNA clone by PCR and is subcloned into pCR2.1. The cap-binding domain is expressed with a His6-tail, a protease cleavage site, a (Gly-Gly-Ser)2-Gly sequence at the N-terminus and a Ser-Gly-Pro-Ser-Ser-Gly sequence at the C-terminus. Deletion mutants of PARN that contain the cap-binding domain and its N- and/or C-terminal flanking regions, encoding residues 420-506, 420-516, 420-536, 430-506, 430-516 and 430-536, are amplified by PCR and subcloned into pET15b. Selected point mutations are introduced into the cap-binding domain (residues 430-516) using a site-directed mutagenesis kit. The wild type and mutant forms of the cap-binding domain of PARN are overexpressed in Escherichia coli.
EXPRESSION
ORGANISM
UNIPROT
LITERATURE
nocturin deadenylase shows rhythmic expression under circadian control. It is rapidly induced in response to serum shock, LPS and other stimuli
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Schrder, H.C.; Bachmann, M.; Messer, R.; Muller, W.E.G.
Nucleotide-specific ribonucleases from eucaryotes. Their possible role during poly(A)(+)mRNA maturation and degradation
Prog. Mol. Subcell. Biol.
9
53-103
1985
Bos taurus, Mus musculus
-
Bachmann, M.; Schrder, H.C.; Messer, R.; Muller, W.E.
Base-specific ribonucleases potentially involved in heterogeneous nuclear RNA processing and poly(A) metabolism
FEBS Lett.
171
25-30
1984
Bos taurus, Mus musculus
Yamashita, A.; Chang, T.C.; Yamashita, Y.; Zhu, W.; Zhong, Z.; Chen, C.Y.; Shyu, A.B.
Concerted action of poly(A) nucleases and decapping enzyme in mammalian mRNA turnover
Nat. Struct. Mol. Biol.
12
1054-1063
2005
Mus musculus
Rowlett, R.M.; Chrestensen, C.A.; Schroeder, M.J.; Harp, M.G.; Pelo, J.W.; Shabanowitz, J.; DeRose, R.; Hunt, D.F.; Sturgill, T.W.; Worthington, M.T.
Inhibition of tristetraprolin deadenylation by poly(A) binding protein
Am. J. Physiol. Gastrointest. Liver Physiol.
295
G421-G430
2008
Mus musculus
Nagata, T.; Suzuki, S.; Endo, R.; Shirouzu, M.; Terada, T.; Inoue, M.; Kigawa, T.; Kobayashi, N.; Guentert, P.; Tanaka, A.; Hayashizaki, Y.; Muto, Y.; Yokoyama, S.
The RRM domain of poly(A)-specific ribonuclease has a noncanonical binding site for mRNA cap analog recognition
Nucleic Acids Res.
36
4754-4767
2008
Mus musculus (Q8VDG3), Mus musculus
Anastasakis, D.; Skeparnias, I.; Shaukat, A.N.; Grafanaki, K.; Kanellou, A.; Taraviras, S.; Papachristou, D.J.; Papakyriakou, A.; Stathopoulos, C.
Mammalian PNLDC1 is a novel poly(A) specific exonuclease with discrete expression during early development
Nucleic Acids Res.
44
8908-8920
2016
Homo sapiens (Q8NA58), Homo sapiens, Mus musculus (B2RXZ1), Mus musculus
Godwin, A.; Kojima, S.; Green, C.; Wilusz, J.
Kiss your tail goodbye The role of PARN, Nocturnin, and Angel deadenylases in mRNA biology
Biochim. Biophys. Acta
1829
571-579
2013
Mus musculus (O35710), Mus musculus (Q8VDG3), Homo sapiens (O95453)
EXTERNAL LINKS (specific for EC-Number 3.1.13.4)
Use of this online version of BRENDA is free under the CC BY 4.0 license. See terms of use for full details.
Release 2023.1 (January 2023)
Legal
Curated at
Member of
