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Q8VDG3

- PARN_MOUSE

UniProt

Q8VDG3 - PARN_MOUSE

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Protein
Poly(A)-specific ribonuclease PARN
Gene
Parn
Organism
Mus musculus (Mouse)
Status
Reviewed - Annotation score: 5 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.

Catalytic activityi

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

Cofactori

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

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi28 – 281Divalent metal cation; catalytic By similarity
Metal bindingi30 – 301Divalent metal cation; catalytic By similarity
Metal bindingi285 – 2851Divalent metal cation; catalytic By similarity
Sitei319 – 3191Interaction with poly(A) By similarity
Metal bindingi375 – 3751Divalent metal cation; catalytic By similarity

GO - Molecular functioni

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

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
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.

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 PARN
PRO_0000212852Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei213 – 2131N6-acetyllysine By similarity
Modified residuei492 – 4921N6-acetyllysine By similarity
Modified residuei543 – 5431Phosphoserine; by MAPKAPK2 By similarity
Modified residuei605 – 6051Phosphoserine By similarity
Modified residuei609 – 6091Phosphoserine By similarity
Modified residuei613 – 6131Phosphoserine By 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.

Protein-protein interaction databases

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

Structurei

Secondary structure

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.

Miscellaneous databases

EvolutionaryTraceiQ8VDG3.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini171 – 23868R3H
Add
BLAST

Sequence similaritiesi

Belongs to the CAF1 family.
Contains 1 R3H domain.

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

Sequence conflict

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti36 – 361D → N in BAB23382. 1 Publication
Sequence conflicti36 – 361D → N in BAC32249. 1 Publication
Sequence conflicti511 – 5111E → K in BAB23382. 1 Publication
Sequence conflicti511 – 5111E → K in BAC32249. 1 Publication
Sequence conflicti549 – 5491V → M in BAB23382. 1 Publication
Sequence conflicti549 – 5491V → M in BAC32249. 1 Publication

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

« 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: September 3, 2014
This is version 106 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

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