Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
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)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi28 – 281Divalent metal cation; catalyticBy similarity
Metal bindingi30 – 301Divalent metal cation; catalyticBy similarity
Metal bindingi285 – 2851Divalent metal cation; catalyticBy similarity
Sitei319 – 3191Interaction with poly(A)By similarity
Metal bindingi375 – 3751Divalent metal cation; catalyticBy similarity

GO - Molecular functioni

  1. metal ion binding Source: UniProtKB-KW
  2. nucleotide binding Source: InterPro
  3. poly(A) RNA binding Source: MGI
  4. poly(A)-specific ribonuclease activity Source: UniProtKB-EC
  5. protein kinase binding Source: MGI

GO - Biological processi

  1. nuclear-transcribed mRNA catabolic process, nonsense-mediated decay Source: MGI
  2. nuclear-transcribed mRNA poly(A) tail shortening Source: MGI
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

ReactomeiREACT_198696. KSRP destabilizes mRNA.
REACT_244119. Deadenylation of mRNA.

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
ProteomesiUP000000589: Chromosome 16

Organism-specific databases

MGIiMGI:1921358. Parn.

Subcellular locationi

Nucleus. Cytoplasm. Nucleusnucleolus
Note: Some nuclear fraction is nucleolar.

GO - Cellular componenti

  1. cytoplasm Source: UniProtKB-SubCell
  2. nucleolus Source: UniProtKB-SubCell
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 624624Poly(A)-specific ribonuclease PARNPRO_0000212852Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei213 – 2131N6-acetyllysineBy similarity
Modified residuei492 – 4921N6-acetyllysineBy similarity
Modified residuei543 – 5431Phosphoserine; by MAPKAPK2By similarity
Modified residuei605 – 6051PhosphoserineBy similarity
Modified residuei609 – 6091PhosphoserineBy similarity
Modified residuei613 – 6131PhosphoserineBy similarity

Post-translational modificationi

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

Keywords - PTMi

Acetylation, Phosphoprotein

Proteomic databases

MaxQBiQ8VDG3.
PaxDbiQ8VDG3.
PRIDEiQ8VDG3.

PTM databases

PhosphoSiteiQ8VDG3.

Expressioni

Gene expression databases

BgeeiQ8VDG3.
GenevestigatoriQ8VDG3.

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

Protein-protein interaction databases

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

Structurei

Secondary structure

624
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi1 – 33Combined sources
Helixi5 – 2117Combined sources
Beta strandi23 – 3210Combined sources
Helixi50 – 6112Combined sources
Beta strandi66 – 7611Combined sources
Beta strandi78 – 814Combined sources
Beta strandi83 – 9210Combined sources
Beta strandi98 – 1014Combined sources
Beta strandi105 – 1095Combined sources
Helixi110 – 1178Combined sources
Turni118 – 1203Combined sources
Helixi123 – 1275Combined sources
Helixi136 – 14510Combined sources
Helixi169 – 18618Combined sources
Beta strandi192 – 1943Combined sources
Helixi201 – 21313Combined sources
Beta strandi214 – 22310Combined sources
Beta strandi226 – 2283Combined sources
Beta strandi230 – 2367Combined sources
Turni239 – 2413Combined sources
Helixi254 – 2607Combined sources
Helixi264 – 27310Combined sources
Beta strandi276 – 2816Combined sources
Helixi283 – 29311Combined sources
Helixi301 – 31111Combined sources
Beta strandi315 – 3173Combined sources
Helixi318 – 3214Combined sources
Helixi327 – 3304Combined sources
Helixi336 – 3427Combined sources
Beta strandi353 – 3553Combined sources
Helixi372 – 39019Combined sources
Beta strandi406 – 4083Combined sources
Helixi409 – 4113Combined sources
Beta strandi419 – 4224Combined sources
Beta strandi425 – 4306Combined sources
Helixi437 – 4393Combined sources
Beta strandi440 – 4445Combined sources
Helixi451 – 4577Combined sources
Helixi458 – 4614Combined sources
Beta strandi465 – 4684Combined sources
Beta strandi470 – 4778Combined sources
Helixi481 – 49111Combined sources
Beta strandi496 – 5016Combined sources
Helixi502 – 5098Combined sources

3D structure databases

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

Miscellaneous databases

EvolutionaryTraceiQ8VDG3.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini171 – 23868R3HPROSITE-ProRule annotationAdd
BLAST

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiNOG145331.
GeneTreeiENSGT00530000063673.
HOGENOMiHOG000007285.
HOVERGENiHBG053512.
InParanoidiQ8VDG3.
KOiK01148.
OrthoDBiEOG7GN2MD.
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_ss-bd.
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.
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)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti36 – 361D → N in BAB23382. (PubMed:16141072)Curated
Sequence conflicti36 – 361D → N in BAC32249. (PubMed:16141072)Curated
Sequence conflicti511 – 5111E → K in BAB23382. (PubMed:16141072)Curated
Sequence conflicti511 – 5111E → K in BAC32249. (PubMed:16141072)Curated
Sequence conflicti549 – 5491V → M in BAB23382. (PubMed:16141072)Curated
Sequence conflicti549 – 5491V → M in BAC32249. (PubMed:16141072)Curated

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

EnsembliENSMUST00000058884; ENSMUSP00000055969; ENSMUSG00000022685.
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
EntryMethodResolution (Å)ChainPositionsPDBsum
1UG8NMR-A169-242[»]
1WHVNMR-A430-516[»]
2ROKNMR-A430-516[»]
3D45X-ray3.00A/B1-505[»]
ProteinModelPortaliQ8VDG3.
SMRiQ8VDG3. Positions 1-505.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

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

PTM databases

PhosphoSiteiQ8VDG3.

Proteomic databases

MaxQBiQ8VDG3.
PaxDbiQ8VDG3.
PRIDEiQ8VDG3.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSMUST00000058884; ENSMUSP00000055969; ENSMUSG00000022685.
GeneIDi74108.
KEGGimmu:74108.

Organism-specific databases

CTDi5073.
MGIiMGI:1921358. Parn.

Phylogenomic databases

eggNOGiNOG145331.
GeneTreeiENSGT00530000063673.
HOGENOMiHOG000007285.
HOVERGENiHBG053512.
InParanoidiQ8VDG3.
KOiK01148.
OrthoDBiEOG7GN2MD.
PhylomeDBiQ8VDG3.
TreeFamiTF314502.

Enzyme and pathway databases

ReactomeiREACT_198696. KSRP destabilizes mRNA.
REACT_244119. Deadenylation of mRNA.

Miscellaneous databases

ChiTaRSiParn. mouse.
EvolutionaryTraceiQ8VDG3.
NextBioi339800.
PROiQ8VDG3.
SOURCEiSearch...

Gene expression databases

BgeeiQ8VDG3.
GenevestigatoriQ8VDG3.

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_ss-bd.
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.
SSF82708. SSF82708. 1 hit.
PROSITEiPS51061. R3H. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "The transcriptional landscape of the mammalian genome."
    Carninci P., Kasukawa T., Katayama S., Gough J., Frith M.C., Maeda N., Oyama R., Ravasi T., Lenhard B., Wells C., Kodzius R., Shimokawa K., Bajic V.B., Brenner S.E., Batalov S., Forrest A.R., Zavolan M., Davis M.J.
    , Wilming L.G., Aidinis V., Allen J.E., Ambesi-Impiombato A., Apweiler R., Aturaliya R.N., Bailey T.L., Bansal M., Baxter L., Beisel K.W., Bersano T., Bono H., Chalk A.M., Chiu K.P., Choudhary V., Christoffels A., Clutterbuck D.R., Crowe M.L., Dalla E., Dalrymple B.P., de Bono B., Della Gatta G., di Bernardo D., Down T., Engstrom P., Fagiolini M., Faulkner G., Fletcher C.F., Fukushima T., Furuno M., Futaki S., Gariboldi M., Georgii-Hemming P., Gingeras T.R., Gojobori T., Green R.E., Gustincich S., Harbers M., Hayashi Y., Hensch T.K., Hirokawa N., Hill D., Huminiecki L., Iacono M., Ikeo K., Iwama A., Ishikawa T., Jakt M., Kanapin A., Katoh M., Kawasawa Y., Kelso J., Kitamura H., Kitano H., Kollias G., Krishnan S.P., Kruger A., Kummerfeld S.K., Kurochkin I.V., Lareau L.F., Lazarevic D., Lipovich L., Liu J., Liuni S., McWilliam S., Madan Babu M., Madera M., Marchionni L., Matsuda H., Matsuzawa S., Miki H., Mignone F., Miyake S., Morris K., Mottagui-Tabar S., Mulder N., Nakano N., Nakauchi H., Ng P., Nilsson R., Nishiguchi S., Nishikawa S., Nori F., Ohara O., Okazaki Y., Orlando V., Pang K.C., Pavan W.J., Pavesi G., Pesole G., Petrovsky N., Piazza S., Reed J., Reid J.F., Ring B.Z., Ringwald M., Rost B., Ruan Y., Salzberg S.L., Sandelin A., Schneider C., Schoenbach C., Sekiguchi K., Semple C.A., Seno S., Sessa L., Sheng Y., Shibata Y., Shimada H., Shimada K., Silva D., Sinclair B., Sperling S., Stupka E., Sugiura K., Sultana R., Takenaka Y., Taki K., Tammoja K., Tan S.L., Tang S., Taylor M.S., Tegner J., Teichmann S.A., Ueda H.R., van Nimwegen E., Verardo R., Wei C.L., Yagi K., Yamanishi H., Zabarovsky E., Zhu S., Zimmer A., Hide W., Bult C., Grimmond S.M., Teasdale R.D., Liu E.T., Brusic V., Quackenbush J., Wahlestedt C., Mattick J.S., Hume D.A., Kai C., Sasaki D., Tomaru Y., Fukuda S., Kanamori-Katayama M., Suzuki M., Aoki J., Arakawa T., Iida J., Imamura K., Itoh M., Kato T., Kawaji H., Kawagashira N., Kawashima T., Kojima M., Kondo S., Konno H., Nakano K., Ninomiya N., Nishio T., Okada M., Plessy C., Shibata K., Shiraki T., Suzuki S., Tagami M., Waki K., Watahiki A., Okamura-Oho Y., Suzuki H., Kawai J., Hayashizaki Y.
    Science 309:1559-1563(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Strain: C57BL/6J.
    Tissue: Hippocampus.
  2. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
    The MGC Project Team
    Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Strain: Czech II.
    Tissue: Mammary tumor.
  3. Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Liver.
  4. "NMR structure of the R3H domain from poly(A)-specific ribonuclease."
    RIKEN structural genomics initiative (RSGI)
    Submitted (AUG-2004) to the PDB data bank
    Cited for: STRUCTURE BY NMR OF 162-248 AND 430-516.

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: February 4, 2015
This is version 111 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

External Data

Dasty 3

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 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.