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Protein

Poly(A)-specific ribonuclease PARN

Gene

PARN

Organism
Bos taurus (Bovine)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

3'-exoribonuclease that has a preference for poly(A) tails of mRNAs, thereby efficiently degrading poly(A) tails. Exonucleolytic degradation of the poly(A) tail is often the first step in the decay of eukaryotic mRNAs and is also used to silence certain maternal mRNAs translationally during oocyte maturation and early embryonic development. Involved in nonsense-mediated mRNA decay, a critical process of selective degradation of mRNAs that contain premature stop codons. Also involved in degradation of inherently unstable mRNAs that contain AU-rich elements (AREs) in their 3'-UTR, possibly via its interaction with KHSRP. Probably mediates the removal of poly(A) tails of AREs mRNAs, which constitutes the first step of destabilization (By similarity). Interacts with both the 3'-end poly(A) tail and the 5'-end cap structure during degradation, the interaction with the cap structure being required for an efficient degradation of poly(A) tails.By similarity2 Publications

Catalytic activityi

Exonucleolytic cleavage of poly(A) to 5'-AMP.1 Publication

Cofactori

Mg2+By similarityNote: Divalent metal cations. Mg2+ is the most probable.By similarity

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi28 – 281Divalent metal cation; catalyticCurated
Metal bindingi30 – 301Divalent metal cation; catalyticCurated
Metal bindingi292 – 2921Divalent metal cation; catalyticCurated
Metal bindingi382 – 3821Divalent metal cation; catalyticCurated

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Exonuclease, Hydrolase, Nuclease

Keywords - Biological processi

Nonsense-mediated mRNA decay

Keywords - Ligandi

Magnesium, Metal-binding, RNA-binding

Enzyme and pathway databases

ReactomeiR-BTA-429947. Deadenylation of mRNA.
R-BTA-450604. KSRP (KHSRP) binds and destabilizes mRNA.

Names & Taxonomyi

Protein namesi
Recommended name:
Poly(A)-specific ribonuclease PARN (EC:3.1.13.4)
Alternative name(s):
Deadenylating nuclease
Deadenylation nuclease
Polyadenylate-specific ribonuclease
Gene namesi
Name:PARN
Synonyms:DAN
OrganismiBos taurus (Bovine)
Taxonomic identifieri9913 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaLaurasiatheriaCetartiodactylaRuminantiaPecoraBovidaeBovinaeBos
Proteomesi
  • UP000009136 Componenti: Chromosome 25

Subcellular locationi

  • Nucleus By similarity
  • Cytoplasm By similarity

  • Note: Some nuclear fraction is nucleolar.By similarity

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 638638Poly(A)-specific ribonuclease PARNPRO_0000212850Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei163 – 1631PhosphoserineBy similarity
Modified residuei220 – 2201N6-acetyllysineBy similarity
Modified residuei499 – 4991N6-acetyllysineBy similarity
Modified residuei557 – 5571Phosphoserine; by MAPKAPK2By similarity
Modified residuei583 – 5831PhosphoserineBy similarity
Modified residuei587 – 5871PhosphoserineBy similarity
Modified residuei619 – 6191PhosphoserineBy similarity
Modified residuei623 – 6231PhosphoserineBy similarity
Modified residuei627 – 6271PhosphoserineBy similarity

Post-translational modificationi

Phosphorylation by MAPKAPK2, preventing GADD45A mRNA degradation after genotoxic stress.By similarity

Keywords - PTMi

Acetylation, Phosphoprotein

Proteomic databases

PaxDbiP69341.
PRIDEiP69341.

Interactioni

Subunit structurei

Homodimer. Interacts with KHSRP and CELF1/CUGBP1. Found in a mRNA decay complex with RENT1, RENT2 and RENT3B. Interacts with ZC3HAV1 in an RNA-independent manner (By similarity).By similarity

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sitei326 – 3261Interaction with poly(A)By similarity

Protein-protein interaction databases

STRINGi9913.ENSBTAP00000024087.

Structurei

3D structure databases

ProteinModelPortaliP69341.
SMRiP69341. Positions 1-430, 438-512.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini178 – 24568R3HPROSITE-ProRule annotationAdd
BLAST

Sequence similaritiesi

Belongs to the CAF1 family.Curated
Contains 1 R3H domain.PROSITE-ProRule annotation

Phylogenomic databases

eggNOGiKOG1990. Eukaryota.
ENOG410XS9D. LUCA.
GeneTreeiENSGT00530000063673.
HOGENOMiHOG000007285.
HOVERGENiHBG053512.
InParanoidiP69341.
KOiK01148.
OMAiEDGWKEA.
OrthoDBiEOG7GN2MD.
TreeFamiTF314502.

Family and domain databases

Gene3Di3.30.1370.50. 1 hit.
3.30.420.10. 2 hits.
3.30.70.330. 1 hit.
InterProiIPR012677. Nucleotide-bd_a/b_plait.
IPR014789. PolyA-riboNase_RNA_binding.
IPR001374. R3H_dom.
IPR006941. RNase_CAF1.
IPR012337. RNaseH-like_dom.
[Graphical view]
PfamiPF04857. CAF1. 1 hit.
PF01424. R3H. 1 hit.
PF08675. RNA_bind. 1 hit.
[Graphical view]
SUPFAMiSSF53098. SSF53098. 2 hits.
SSF54928. SSF54928. 1 hit.
SSF82708. SSF82708. 1 hit.
PROSITEiPS51061. R3H. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P69341-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MEIIRSNFKS NLHKVYQAIE EADFFAIDGE FSGISDGPSV TALTNGFDTP
60 70 80 90 100
EERYQKLKKH SMDFLLFQFG LCTFKYDYTD SKYITKSFNF YVFPKPFNRS
110 120 130 140 150
SPDVKFVCQS SSIDFLASQG FDFNKVFRNG IPYLNQEEER QLREQYDEKR
160 170 180 190 200
SQSNGAGALS YTSPNTSKCP VTIPDDQKKF IDQVVEKIED LLQSEENKNL
210 220 230 240 250
DLEPCTGFQR KLIYQTLSWK YPKGIHVETL ETEKKERYIV ISKVDEEERK
260 270 280 290 300
RREQQKHAKE QEELNDAVGF SRVIHAIANS GKLVIGHNML LDVMHTVHQF
310 320 330 340 350
YCPLPADLNE FKEMTTCVFP RLLDTKLMAS TQPFKDIINN TSLAELEKRL
360 370 380 390 400
KETPFNPPKV ESAEGFPSYD TASEQLHEAG YDAYITGLCF ISMANYLGSF
410 420 430 440 450
LSPPKSHVSA RSKLIEPFFN KLFLMRVMDI PYLNLEGPDL QPKRDHVLHV
460 470 480 490 500
TFPKEWKTSD LYQLFSAFGN IQISWIDDTS AFVSLSQPEQ VPIAVNTSKY
510 520 530 540 550
AESYRIQTYA DYVGKKREEK QMKRKWTEDS WKEVEPKRLN TQCGSYSLQN
560 570 580 590 600
HHYHANSLTA TSTVGKRNLS PSRAEAGLEA RASGEISDTE LEQTDPCAEP
610 620 630
LSEGRKKAKK LKRMKKDLSP TGSISDSSAK LFEVPDTW
Length:638
Mass (Da):73,182
Last modified:February 10, 2009 - v2
Checksum:iD183F2632C55BFEE
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti505 – 5051R → W AA sequence (PubMed:9736620).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BC150015 mRNA. Translation: AAI50016.1.
RefSeqiNP_001094588.1. NM_001101118.2.
UniGeneiBt.15863.

Genome annotation databases

EnsembliENSBTAT00000024087; ENSBTAP00000024087; ENSBTAG00000018097.
GeneIDi524155.
KEGGibta:524155.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BC150015 mRNA. Translation: AAI50016.1.
RefSeqiNP_001094588.1. NM_001101118.2.
UniGeneiBt.15863.

3D structure databases

ProteinModelPortaliP69341.
SMRiP69341. Positions 1-430, 438-512.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi9913.ENSBTAP00000024087.

Proteomic databases

PaxDbiP69341.
PRIDEiP69341.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSBTAT00000024087; ENSBTAP00000024087; ENSBTAG00000018097.
GeneIDi524155.
KEGGibta:524155.

Organism-specific databases

CTDi5073.

Phylogenomic databases

eggNOGiKOG1990. Eukaryota.
ENOG410XS9D. LUCA.
GeneTreeiENSGT00530000063673.
HOGENOMiHOG000007285.
HOVERGENiHBG053512.
InParanoidiP69341.
KOiK01148.
OMAiEDGWKEA.
OrthoDBiEOG7GN2MD.
TreeFamiTF314502.

Enzyme and pathway databases

ReactomeiR-BTA-429947. Deadenylation of mRNA.
R-BTA-450604. KSRP (KHSRP) binds and destabilizes mRNA.

Miscellaneous databases

NextBioi20873902.

Family and domain databases

Gene3Di3.30.1370.50. 1 hit.
3.30.420.10. 2 hits.
3.30.70.330. 1 hit.
InterProiIPR012677. Nucleotide-bd_a/b_plait.
IPR014789. PolyA-riboNase_RNA_binding.
IPR001374. R3H_dom.
IPR006941. RNase_CAF1.
IPR012337. RNaseH-like_dom.
[Graphical view]
PfamiPF04857. CAF1. 1 hit.
PF01424. R3H. 1 hit.
PF08675. RNA_bind. 1 hit.
[Graphical view]
SUPFAMiSSF53098. SSF53098. 2 hits.
SSF54928. SSF54928. 1 hit.
SSF82708. SSF82708. 1 hit.
PROSITEiPS51061. R3H. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. NIH - Mammalian Gene Collection (MGC) project
    Submitted (JUL-2007) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Strain: Hereford.
    Tissue: Thymus.
  2. "The deadenylating nuclease (DAN) is involved in poly(A) tail removal during the meiotic maturation of Xenopus oocytes."
    Koerner C.G., Wormington M., Muckenthaler M., Schneider S., Dehlin E., Wahle E.
    EMBO J. 17:5427-5437(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: PROTEIN SEQUENCE OF 86-105; 259-267; 421-429 AND 499-514, FUNCTION.
  3. "Poly(A) tail shortening by a mammalian poly(A)-specific 3'-exoribonuclease."
    Koerner C.G., Wahle E.
    J. Biol. Chem. 272:10448-10456(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: ENZYME ACTIVITY.
  4. Cited for: FUNCTION.

Entry informationi

Entry nameiPARN_BOVIN
AccessioniPrimary (citable) accession number: P69341
Secondary accession number(s): A6QQW2
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 1, 2005
Last sequence update: February 10, 2009
Last modified: January 20, 2016
This is version 76 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.