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Q8VDG3

- PARN_MOUSE

UniProt

Q8VDG3 - PARN_MOUSE

Protein

Poly(A)-specific ribonuclease PARN

Gene

Parn

Organism
Mus musculus (Mouse)
Status
Reviewed - Annotation score: 4 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 107 (01 Oct 2014)
      Sequence version 1 (01 Mar 2002)
      Previous versions | rss
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    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

    Divalent metal cations. Mg2+ is the most probable By similarity.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)-specific ribonuclease activity Source: UniProtKB-EC
    4. protein binding Source: MGI
    5. RNA binding Source: UniProtKB-KW

    GO - Biological processi

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

    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.

    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

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

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    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

    MEIIRSNFKI NLHKVYQAIE EADFFAIDGE FSGISDGPSV TALTSGFDTP    50
    EERYQKLKKH SMDFLLFQFG LCAFKYDHTD SKHVTKSFNF YVFPKPFSRS 100
    SPDVKFVCQS SSIDFLASQG FDFNKVFCSG IPYLNQEEER QLREQFDEKR 150
    SQANGAGALA KCPVTIPEDQ KKFIDQVIEK IEDFLQSEEK RSLELDPCTG 200
    FQRKLIYQTL SWKYPKGIHV ETLETDKKER HIVISKVDEE ERKRREQEKY 250
    TKEQEELNDA VGFSRVIHAI ANSGKLVVGH NMLLDVMHTI HQFYCPLPAD 300
    LNEFKEMAIC VFPRLLDTKL MASTQPFKDI INNTSLAELE KRLKETPFDP 350
    PKVESAEGFP SYDTASEQLH EAGYDAYITG LCFISMANYL GSLLSPPKMC 400
    VSARSKLIEP FFNKLFLMRV MDIPYLNLEG PDLQPKRDHV LHVTFPKEWK 450
    TSDLYQLFSA FGNIQISWID DTSAFVSLSQ PEQVQIAVNT SKYAESYRIQ 500
    TYAEYVGKKQ EGKQVKRKWT EDSWKEVDRK RPHMQGPCYH SNSFTAAGVL 550
    GKRTLSPDPR EAALEDRESE EVSDSELEQT DSCTDPLPEG RKKSKKLKRM 600
    KKELSLAGSV SDSPAVLFEV PDTW 624
    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:
    EMBL
    GenBank
    DDBJ
    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:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AK004572 mRNA. Translation: BAB23382.1 .
    AK045181 mRNA. Translation: BAC32249.1 .
    BC021899 mRNA. Translation: AAH21899.1 .
    CCDSi CCDS37259.1.
    RefSeqi NP_083037.1. NM_028761.3.
    UniGenei Mm.182350.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1UG8 NMR - A 169-242 [» ]
    1WHV NMR - A 430-516 [» ]
    2ROK NMR - A 430-516 [» ]
    3D45 X-ray 3.00 A/B 1-505 [» ]
    ProteinModelPortali Q8VDG3.
    SMRi Q8VDG3. Positions 1-505.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    DIPi DIP-48330N.
    IntActi Q8VDG3. 1 interaction.
    MINTi MINT-4106622.
    STRINGi 10090.ENSMUSP00000055969.

    PTM databases

    PhosphoSitei Q8VDG3.

    Proteomic databases

    MaxQBi Q8VDG3.
    PaxDbi Q8VDG3.
    PRIDEi Q8VDG3.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    Ensembli ENSMUST00000058884 ; ENSMUSP00000055969 ; ENSMUSG00000022685 .
    GeneIDi 74108.
    KEGGi mmu:74108.

    Organism-specific databases

    CTDi 5073.
    MGIi MGI:1921358. Parn.

    Phylogenomic databases

    eggNOGi NOG145331.
    GeneTreei ENSGT00530000063673.
    HOGENOMi HOG000007285.
    HOVERGENi HBG053512.
    InParanoidi Q8VDG3.
    KOi K01148.
    OrthoDBi EOG7GN2MD.
    PhylomeDBi Q8VDG3.
    TreeFami TF314502.

    Enzyme and pathway databases

    Reactomei REACT_198696. KSRP destabilizes mRNA.

    Miscellaneous databases

    ChiTaRSi PARN. mouse.
    EvolutionaryTracei Q8VDG3.
    NextBioi 339800.
    PROi Q8VDG3.
    SOURCEi Search...

    Gene expression databases

    Bgeei Q8VDG3.
    Genevestigatori Q8VDG3.

    Family and domain databases

    Gene3Di 3.30.1370.50. 1 hit.
    3.30.420.10. 2 hits.
    3.30.70.330. 1 hit.
    InterProi IPR012677. Nucleotide-bd_a/b_plait.
    IPR014789. PolyA-riboNase_RNA_binding.
    IPR001374. R3H_ss-bd.
    IPR006941. RNase_CAF1.
    IPR012337. RNaseH-like_dom.
    [Graphical view ]
    Pfami PF04857. CAF1. 1 hit.
    PF01424. R3H. 1 hit.
    PF08675. RNA_bind. 1 hit.
    [Graphical view ]
    SUPFAMi SSF53098. SSF53098. 2 hits.
    SSF82708. SSF82708. 1 hit.
    PROSITEi PS51061. R3H. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    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: October 1, 2014
    This is version 107 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