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Q8VDG3 (PARN_MOUSE) Reviewed, UniProtKB/Swiss-Prot

Last modified May 29, 2013. Version 95. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (3) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Poly(A)-specific ribonuclease PARN
EC=3.1.13.4
Alternative name(s):
Polyadenylate-specific ribonuclease
Gene names
Name:Parn
OrganismMus musculus (Mouse) [Reference proteome]
Taxonomic identifier10090 [NCBI]
Taxonomic lineageEukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Glires › Rodentia › Sciurognathi › Muroidea › Muridae › Murinae › Mus › Mus

Protein attributes

Sequence length624 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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 activity

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

Cofactor

Divalent metal cations. Mg2+ is the most probable By similarity. Interacts with ZC3HAV1 in an RNA-independent manner By similarity.

Subunit structure

Homodimer. Interacts with KHSRP and CELF1/CUGBP1. Found in a mRNA decay complex with RENT1, RENT2 and RENT3B By similarity.

Subcellular location

Nucleus. Cytoplasm. Nucleus › nucleolus. Note: Some nuclear fraction is nucleolar.

Post-translational modification

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

Sequence similarities

Belongs to the CAF1 family.

Contains 1 R3H domain.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 624624Poly(A)-specific ribonuclease PARN
PRO_0000212852

Regions

Domain171 – 23868R3H

Sites

Metal binding281Divalent metal cation; catalytic By similarity
Metal binding301Divalent metal cation; catalytic By similarity
Metal binding2851Divalent metal cation; catalytic By similarity
Metal binding3751Divalent metal cation; catalytic By similarity
Site3191Interaction with poly(A) By similarity

Amino acid modifications

Modified residue2131N6-acetyllysine By similarity
Modified residue4921N6-acetyllysine By similarity
Modified residue5431Phosphoserine; by MAPKAPK2 By similarity
Modified residue5731Phosphoserine Ref.3
Modified residue5751Phosphoserine Ref.3
Modified residue6051Phosphoserine By similarity
Modified residue6091Phosphoserine By similarity
Modified residue6131Phosphoserine By similarity

Experimental info

Sequence conflict361D → N in BAB23382. Ref.1
Sequence conflict361D → N in BAC32249. Ref.1
Sequence conflict5111E → K in BAB23382. Ref.1
Sequence conflict5111E → K in BAC32249. Ref.1
Sequence conflict5491V → M in BAB23382. Ref.1
Sequence conflict5491V → M in BAC32249. Ref.1

Secondary structure

1 ................................................................................ 624
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
Q8VDG3 [UniParc].

Last modified March 1, 2002. Version 1.
Checksum: D729BFAABA2EB40A

FASTA62471,559
        10         20         30         40         50         60 
MEIIRSNFKI NLHKVYQAIE EADFFAIDGE FSGISDGPSV TALTSGFDTP EERYQKLKKH 

        70         80         90        100        110        120 
SMDFLLFQFG LCAFKYDHTD SKHVTKSFNF YVFPKPFSRS SPDVKFVCQS SSIDFLASQG 

       130        140        150        160        170        180 
FDFNKVFCSG IPYLNQEEER QLREQFDEKR SQANGAGALA KCPVTIPEDQ KKFIDQVIEK 

       190        200        210        220        230        240 
IEDFLQSEEK RSLELDPCTG FQRKLIYQTL SWKYPKGIHV ETLETDKKER HIVISKVDEE 

       250        260        270        280        290        300 
ERKRREQEKY TKEQEELNDA VGFSRVIHAI ANSGKLVVGH NMLLDVMHTI HQFYCPLPAD 

       310        320        330        340        350        360 
LNEFKEMAIC VFPRLLDTKL MASTQPFKDI INNTSLAELE KRLKETPFDP PKVESAEGFP 

       370        380        390        400        410        420 
SYDTASEQLH EAGYDAYITG LCFISMANYL GSLLSPPKMC VSARSKLIEP FFNKLFLMRV 

       430        440        450        460        470        480 
MDIPYLNLEG PDLQPKRDHV LHVTFPKEWK TSDLYQLFSA FGNIQISWID DTSAFVSLSQ 

       490        500        510        520        530        540 
PEQVQIAVNT SKYAESYRIQ TYAEYVGKKQ EGKQVKRKWT EDSWKEVDRK RPHMQGPCYH 

       550        560        570        580        590        600 
SNSFTAAGVL GKRTLSPDPR EAALEDRESE EVSDSELEQT DSCTDPLPEG RKKSKKLKRM 

       610        620 
KKELSLAGSV SDSPAVLFEV PDTW

« Hide

References

« Hide 'large scale' references
[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. expand/collapse author list , 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]"Large-scale phosphorylation analysis of mouse liver."
Villen J., Beausoleil S.A., Gerber S.A., Gygi S.P.
Proc. Natl. Acad. Sci. U.S.A. 104:1488-1493(2007) [PubMed] [Europe PMC] [Abstract]
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-573 AND SER-575, MASS SPECTROMETRY.
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.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ		AK004572 mRNA. Translation: BAB23382.1.
AK045181 mRNA. Translation: BAC32249.1.
BC021899 mRNA. Translation: AAH21899.1.
IPIIPI00311534.
RefSeqNP_083037.1. NM_028761.3.
UniGeneMm.182350.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1UG8NMR-A169-242[»]
1WHVNMR-A430-516[»]
2ROKNMR-A430-516[»]
3D45X-ray3.00A/B1-505[»]
ProteinModelPortalQ8VDG3.
SMRQ8VDG3. Positions 1-505.
ModBaseSearch...

Protein-protein interaction databases

DIPDIP-48330N.
MINTMINT-4106622.
STRING10090.ENSMUSP00000055969.

PTM databases

PhosphoSiteQ8VDG3.

Proteomic databases

PaxDbQ8VDG3.
PRIDEQ8VDG3.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENSMUST00000058884; ENSMUSP00000055969; ENSMUSG00000022685.
GeneID74108.
KEGGmmu:74108.

Organism-specific databases

CTD5073.
MGIMGI:1921358. Parn.

Phylogenomic databases

eggNOGNOG145331.
GeneTreeENSGT00530000063673.
HOGENOMHOG000007285.
HOVERGENHBG053512.
InParanoidQ8VDG3.
KOK01148.
OrthoDBEOG4JHCFF.

Gene expression databases

BgeeQ8VDG3.
GenevestigatorQ8VDG3.
GermOnlineENSMUSG00000022685. Mus musculus.

Family and domain databases

Gene3D3.30.70.330. 1 hit.
InterProIPR012677. Nucleotide-bd_a/b_plait.
IPR014789. PolyA-riboNase_RNA_binding.
IPR001374. R3H_ss-bd.
IPR006941. RNase_CAF1.
IPR012337. RNaseH-like_dom.
[Graphical view]
PfamPF04857. CAF1. 1 hit.
PF01424. R3H. 1 hit.
PF08675. RNA_bind. 1 hit.
[Graphical view]
SUPFAMSSF53098. RNaseH_fold. 1 hit.
PROSITEPS51061. R3H. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

ChiTaRSPARN. mouse.
EvolutionaryTraceQ8VDG3.
NextBio339800.
SOURCESearch...

Entry information

Entry namePARN_MOUSE
AccessionPrimary (citable) accession number: Q8VDG3
Secondary accession number(s): Q8C7N6, Q9DC46
Entry history
Integrated into UniProtKB/Swiss-Prot: March 1, 2005
Last sequence update: March 1, 2002
Last modified: May 29, 2013
This is version 95 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Relevant documents

MGD cross-references

Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families

to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents