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Protein

Poly(A)-specific ribonuclease PARN

Gene

Parn

Organism
Mus musculus (Mouse)
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. 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. 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).By similarity

Catalytic activityi

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

Cofactori

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

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi28Divalent metal cation; catalyticBy similarity1
Metal bindingi30Divalent metal cation; catalyticBy similarity1
Metal bindingi285Divalent metal cation; catalyticBy similarity1
Metal bindingi375Divalent metal cation; catalyticBy similarity1

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

BRENDAi3.1.13.4. 3474.

Names & Taxonomyi

Protein namesi
Recommended name:
Poly(A)-specific ribonuclease PARN (EC:3.1.13.4)
Alternative name(s):
Polyadenylate-specific ribonuclease
Gene namesi
Name:Parn
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
Proteomesi
  • UP000000589 Componenti: Unplaced

Organism-specific databases

MGIiMGI:1921358. Parn.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002128521 – 624Poly(A)-specific ribonuclease PARNAdd BLAST624

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei213N6-acetyllysineBy similarity1
Modified residuei492N6-acetyllysineBy similarity1
Modified residuei523PhosphoserineBy similarity1
Modified residuei543Phosphoserine; by MAPKAPK2By similarity1
Modified residuei569PhosphoserineCombined sources1
Modified residuei573PhosphoserineCombined sources1
Modified residuei575PhosphoserineCombined sources1
Modified residuei605PhosphoserineBy similarity1
Modified residuei609PhosphoserineBy similarity1
Modified residuei613PhosphoserineBy similarity1

Post-translational modificationi

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

Keywords - PTMi

Acetylation, Phosphoprotein

Proteomic databases

EPDiQ8VDG3.
MaxQBiQ8VDG3.
PaxDbiQ8VDG3.
PeptideAtlasiQ8VDG3.
PRIDEiQ8VDG3.

PTM databases

iPTMnetiQ8VDG3.
PhosphoSitePlusiQ8VDG3.

Expressioni

Gene expression databases

BgeeiENSMUSG00000022685.

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)DescriptionActionsGraphical viewLength
Sitei319Interaction with poly(A)By similarity1

GO - Molecular functioni

Protein-protein interaction databases

DIPiDIP-48330N.
IntActiQ8VDG3. 1 interactor.
MINTiMINT-4106622.
STRINGi10090.ENSMUSP00000055969.

Structurei

Secondary structure

1624
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi1 – 3Combined sources3
Helixi5 – 21Combined sources17
Beta strandi23 – 32Combined sources10
Helixi40 – 43Combined sources4
Helixi50 – 61Combined sources12
Beta strandi66 – 76Combined sources11
Beta strandi78 – 81Combined sources4
Beta strandi83 – 92Combined sources10
Beta strandi98 – 101Combined sources4
Beta strandi105 – 109Combined sources5
Helixi110 – 117Combined sources8
Turni118 – 120Combined sources3
Helixi123 – 127Combined sources5
Helixi136 – 145Combined sources10
Helixi169 – 186Combined sources18
Beta strandi192 – 194Combined sources3
Helixi201 – 213Combined sources13
Beta strandi214 – 223Combined sources10
Beta strandi226 – 228Combined sources3
Beta strandi230 – 236Combined sources7
Turni239 – 241Combined sources3
Helixi254 – 260Combined sources7
Helixi264 – 273Combined sources10
Beta strandi276 – 281Combined sources6
Helixi283 – 293Combined sources11
Helixi301 – 311Combined sources11
Beta strandi315 – 317Combined sources3
Helixi318 – 321Combined sources4
Helixi327 – 330Combined sources4
Helixi336 – 342Combined sources7
Beta strandi353 – 355Combined sources3
Helixi372 – 390Combined sources19
Beta strandi406 – 408Combined sources3
Helixi409 – 411Combined sources3
Beta strandi419 – 422Combined sources4
Beta strandi425 – 430Combined sources6
Helixi437 – 439Combined sources3
Beta strandi440 – 444Combined sources5
Helixi451 – 457Combined sources7
Helixi458 – 461Combined sources4
Beta strandi465 – 468Combined sources4
Beta strandi470 – 477Combined sources8
Helixi481 – 491Combined sources11
Beta strandi496 – 501Combined sources6
Helixi502 – 509Combined sources8

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1UG8NMR-A169-242[»]
1WHVNMR-A430-516[»]
2ROKNMR-A430-516[»]
3D45X-ray3.00A/B1-505[»]
ProteinModelPortaliQ8VDG3.
SMRiQ8VDG3.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ8VDG3.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini171 – 238R3HPROSITE-ProRule annotationAdd BLAST68

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiKOG1990. Eukaryota.
ENOG410XS9D. LUCA.
HOGENOMiHOG000007285.
HOVERGENiHBG053512.
InParanoidiQ8VDG3.
KOiK01148.
PhylomeDBiQ8VDG3.
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.

Q8VDG3-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MEIIRSNFKI NLHKVYQAIE EADFFAIDGE FSGISDGPSV TALTSGFDTP
60 70 80 90 100
EERYQKLKKH SMDFLLFQFG LCAFKYDHTD SKHVTKSFNF YVFPKPFSRS
110 120 130 140 150
SPDVKFVCQS SSIDFLASQG FDFNKVFCSG IPYLNQEEER QLREQFDEKR
160 170 180 190 200
SQANGAGALA KCPVTIPEDQ KKFIDQVIEK IEDFLQSEEK RSLELDPCTG
210 220 230 240 250
FQRKLIYQTL SWKYPKGIHV ETLETDKKER HIVISKVDEE ERKRREQEKY
260 270 280 290 300
TKEQEELNDA VGFSRVIHAI ANSGKLVVGH NMLLDVMHTI HQFYCPLPAD
310 320 330 340 350
LNEFKEMAIC VFPRLLDTKL MASTQPFKDI INNTSLAELE KRLKETPFDP
360 370 380 390 400
PKVESAEGFP SYDTASEQLH EAGYDAYITG LCFISMANYL GSLLSPPKMC
410 420 430 440 450
VSARSKLIEP FFNKLFLMRV MDIPYLNLEG PDLQPKRDHV LHVTFPKEWK
460 470 480 490 500
TSDLYQLFSA FGNIQISWID DTSAFVSLSQ PEQVQIAVNT SKYAESYRIQ
510 520 530 540 550
TYAEYVGKKQ EGKQVKRKWT EDSWKEVDRK RPHMQGPCYH SNSFTAAGVL
560 570 580 590 600
GKRTLSPDPR EAALEDRESE EVSDSELEQT DSCTDPLPEG RKKSKKLKRM
610 620
KKELSLAGSV SDSPAVLFEV PDTW
Length:624
Mass (Da):71,559
Last modified:March 1, 2002 - v1
Checksum:iD729BFAABA2EB40A
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti36D → N in BAB23382 (PubMed:16141072).Curated1
Sequence conflicti36D → N in BAC32249 (PubMed:16141072).Curated1
Sequence conflicti511E → K in BAB23382 (PubMed:16141072).Curated1
Sequence conflicti511E → K in BAC32249 (PubMed:16141072).Curated1
Sequence conflicti549V → M in BAB23382 (PubMed:16141072).Curated1
Sequence conflicti549V → M in BAC32249 (PubMed:16141072).Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK004572 mRNA. Translation: BAB23382.1.
AK045181 mRNA. Translation: BAC32249.1.
BC021899 mRNA. Translation: AAH21899.1.
CCDSiCCDS37259.1.
RefSeqiNP_083037.1. NM_028761.3.
UniGeneiMm.182350.

Genome annotation databases

GeneIDi74108.
KEGGimmu:74108.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK004572 mRNA. Translation: BAB23382.1.
AK045181 mRNA. Translation: BAC32249.1.
BC021899 mRNA. Translation: AAH21899.1.
CCDSiCCDS37259.1.
RefSeqiNP_083037.1. NM_028761.3.
UniGeneiMm.182350.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1UG8NMR-A169-242[»]
1WHVNMR-A430-516[»]
2ROKNMR-A430-516[»]
3D45X-ray3.00A/B1-505[»]
ProteinModelPortaliQ8VDG3.
SMRiQ8VDG3.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

DIPiDIP-48330N.
IntActiQ8VDG3. 1 interactor.
MINTiMINT-4106622.
STRINGi10090.ENSMUSP00000055969.

PTM databases

iPTMnetiQ8VDG3.
PhosphoSitePlusiQ8VDG3.

Proteomic databases

EPDiQ8VDG3.
MaxQBiQ8VDG3.
PaxDbiQ8VDG3.
PeptideAtlasiQ8VDG3.
PRIDEiQ8VDG3.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

GeneIDi74108.
KEGGimmu:74108.

Organism-specific databases

CTDi5073.
MGIiMGI:1921358. Parn.

Phylogenomic databases

eggNOGiKOG1990. Eukaryota.
ENOG410XS9D. LUCA.
HOGENOMiHOG000007285.
HOVERGENiHBG053512.
InParanoidiQ8VDG3.
KOiK01148.
PhylomeDBiQ8VDG3.
TreeFamiTF314502.

Enzyme and pathway databases

BRENDAi3.1.13.4. 3474.

Miscellaneous databases

ChiTaRSiParn. mouse.
EvolutionaryTraceiQ8VDG3.
PROiQ8VDG3.
SOURCEiSearch...

Gene expression databases

BgeeiENSMUSG00000022685.

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...

Entry informationi

Entry nameiPARN_MOUSE
AccessioniPrimary (citable) accession number: Q8VDG3
Secondary accession number(s): Q8C7N6, Q9DC46
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 1, 2005
Last sequence update: March 1, 2002
Last modified: November 2, 2016
This is version 125 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. MGD cross-references
    Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. 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.