PARN_MOUSE
ID PARN_MOUSE Reviewed; 624 AA.
AC Q8VDG3; Q8C7N6; Q9DC46;
DT 01-MAR-2005, integrated into UniProtKB/Swiss-Prot.
DT 01-MAR-2002, sequence version 1.
DT 03-AUG-2022, entry version 155.
DE RecName: Full=Poly(A)-specific ribonuclease PARN;
DE EC=3.1.13.4;
DE AltName: Full=Polyadenylate-specific ribonuclease;
GN Name=Parn;
OS Mus musculus (Mouse).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae;
OC Murinae; Mus; Mus.
OX NCBI_TaxID=10090;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=C57BL/6J; TISSUE=Hippocampus;
RX PubMed=16141072; DOI=10.1126/science.1112014;
RA Carninci P., Kasukawa T., Katayama S., Gough J., Frith M.C., Maeda N.,
RA Oyama R., Ravasi T., Lenhard B., Wells C., Kodzius R., Shimokawa K.,
RA Bajic V.B., Brenner S.E., Batalov S., Forrest A.R., Zavolan M., Davis M.J.,
RA Wilming L.G., Aidinis V., Allen J.E., Ambesi-Impiombato A., Apweiler R.,
RA Aturaliya R.N., Bailey T.L., Bansal M., Baxter L., Beisel K.W., Bersano T.,
RA Bono H., Chalk A.M., Chiu K.P., Choudhary V., Christoffels A.,
RA Clutterbuck D.R., Crowe M.L., Dalla E., Dalrymple B.P., de Bono B.,
RA Della Gatta G., di Bernardo D., Down T., Engstrom P., Fagiolini M.,
RA Faulkner G., Fletcher C.F., Fukushima T., Furuno M., Futaki S.,
RA Gariboldi M., Georgii-Hemming P., Gingeras T.R., Gojobori T., Green R.E.,
RA Gustincich S., Harbers M., Hayashi Y., Hensch T.K., Hirokawa N., Hill D.,
RA Huminiecki L., Iacono M., Ikeo K., Iwama A., Ishikawa T., Jakt M.,
RA Kanapin A., Katoh M., Kawasawa Y., Kelso J., Kitamura H., Kitano H.,
RA Kollias G., Krishnan S.P., Kruger A., Kummerfeld S.K., Kurochkin I.V.,
RA Lareau L.F., Lazarevic D., Lipovich L., Liu J., Liuni S., McWilliam S.,
RA Madan Babu M., Madera M., Marchionni L., Matsuda H., Matsuzawa S., Miki H.,
RA Mignone F., Miyake S., Morris K., Mottagui-Tabar S., Mulder N., Nakano N.,
RA Nakauchi H., Ng P., Nilsson R., Nishiguchi S., Nishikawa S., Nori F.,
RA Ohara O., Okazaki Y., Orlando V., Pang K.C., Pavan W.J., Pavesi G.,
RA Pesole G., Petrovsky N., Piazza S., Reed J., Reid J.F., Ring B.Z.,
RA Ringwald M., Rost B., Ruan Y., Salzberg S.L., Sandelin A., Schneider C.,
RA Schoenbach C., Sekiguchi K., Semple C.A., Seno S., Sessa L., Sheng Y.,
RA Shibata Y., Shimada H., Shimada K., Silva D., Sinclair B., Sperling S.,
RA Stupka E., Sugiura K., Sultana R., Takenaka Y., Taki K., Tammoja K.,
RA Tan S.L., Tang S., Taylor M.S., Tegner J., Teichmann S.A., Ueda H.R.,
RA van Nimwegen E., Verardo R., Wei C.L., Yagi K., Yamanishi H.,
RA Zabarovsky E., Zhu S., Zimmer A., Hide W., Bult C., Grimmond S.M.,
RA Teasdale R.D., Liu E.T., Brusic V., Quackenbush J., Wahlestedt C.,
RA Mattick J.S., Hume D.A., Kai C., Sasaki D., Tomaru Y., Fukuda S.,
RA Kanamori-Katayama M., Suzuki M., Aoki J., Arakawa T., Iida J., Imamura K.,
RA Itoh M., Kato T., Kawaji H., Kawagashira N., Kawashima T., Kojima M.,
RA Kondo S., Konno H., Nakano K., Ninomiya N., Nishio T., Okada M., Plessy C.,
RA Shibata K., Shiraki T., Suzuki S., Tagami M., Waki K., Watahiki A.,
RA Okamura-Oho Y., Suzuki H., Kawai J., Hayashizaki Y.;
RT "The transcriptional landscape of the mammalian genome.";
RL Science 309:1559-1563(2005).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=Czech II; TISSUE=Mammary tumor;
RX PubMed=15489334; DOI=10.1101/gr.2596504;
RG The MGC Project Team;
RT "The status, quality, and expansion of the NIH full-length cDNA project:
RT the Mammalian Gene Collection (MGC).";
RL Genome Res. 14:2121-2127(2004).
RN [3]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC TISSUE=Liver;
RX PubMed=17242355; DOI=10.1073/pnas.0609836104;
RA Villen J., Beausoleil S.A., Gerber S.A., Gygi S.P.;
RT "Large-scale phosphorylation analysis of mouse liver.";
RL Proc. Natl. Acad. Sci. U.S.A. 104:1488-1493(2007).
RN [4]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-569; SER-573 AND SER-575, AND
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC TISSUE=Brain, Brown adipose tissue, Heart, Kidney, Liver, Lung, Pancreas,
RC Spleen, and Testis;
RX PubMed=21183079; DOI=10.1016/j.cell.2010.12.001;
RA Huttlin E.L., Jedrychowski M.P., Elias J.E., Goswami T., Rad R.,
RA Beausoleil S.A., Villen J., Haas W., Sowa M.E., Gygi S.P.;
RT "A tissue-specific atlas of mouse protein phosphorylation and expression.";
RL Cell 143:1174-1189(2010).
RN [5]
RP STRUCTURE BY NMR OF 162-248 AND 430-516.
RG RIKEN structural genomics initiative (RSGI);
RT "NMR structure of the R3H domain from poly(A)-specific ribonuclease.";
RL Submitted (AUG-2004) to the PDB data bank.
CC -!- FUNCTION: 3'-exoribonuclease that has a preference for poly(A) tails of
CC mRNAs, thereby efficiently degrading poly(A) tails. Exonucleolytic
CC degradation of the poly(A) tail is often the first step in the decay of
CC eukaryotic mRNAs and is also used to silence certain maternal mRNAs
CC translationally during oocyte maturation and early embryonic
CC development. Interacts with both the 3'-end poly(A) tail and the 5'-end
CC cap structure during degradation, the interaction with the cap
CC structure being required for an efficient degradation of poly(A) tails.
CC Involved in nonsense-mediated mRNA decay, a critical process of
CC selective degradation of mRNAs that contain premature stop codons. Also
CC involved in degradation of inherently unstable mRNAs that contain AU-
CC rich elements (AREs) in their 3'-UTR, possibly via its interaction with
CC KHSRP. Probably mediates the removal of poly(A) tails of AREs mRNAs,
CC which constitutes the first step of destabilization (By similarity).
CC Also able to recognize poly(A) tails of microRNAs such as MIR21 and
CC H/ACA box snoRNAs (small nucleolar RNAs) leading to leading to
CC microRNAs degradation or snoRNA increased stability (By similarity).
CC {ECO:0000250|UniProtKB:O95453}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=Exonucleolytic cleavage of poly(A) to 5'-AMP.; EC=3.1.13.4;
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000250|UniProtKB:O95453};
CC Note=Divalent metal cations. Mg(2+) is the most probable.
CC {ECO:0000250|UniProtKB:O95453};
CC -!- SUBUNIT: Homodimer. Found in a mRNA decay complex with RENT1, RENT2 and
CC RENT3B. Interacts with KHSRP. Interacts with CELF1/CUGBP1. Interacts
CC with ZC3HAV1 in an RNA-independent manner. Interacts with DHX36.
CC {ECO:0000250|UniProtKB:O95453}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000250|UniProtKB:O95453}. Cytoplasm
CC {ECO:0000250|UniProtKB:O95453}. Nucleus, nucleolus
CC {ECO:0000250|UniProtKB:O95453}. Note=Some nuclear fraction is
CC nucleolar. {ECO:0000250|UniProtKB:O95453}.
CC -!- PTM: Phosphorylation by MAPKAPK2, preventing GADD45A mRNA degradation
CC after genotoxic stress. {ECO:0000250|UniProtKB:O95453}.
CC -!- SIMILARITY: Belongs to the CAF1 family. {ECO:0000305}.
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DR EMBL; AK004572; BAB23382.1; -; mRNA.
DR EMBL; AK045181; BAC32249.1; -; mRNA.
DR EMBL; BC021899; AAH21899.1; -; mRNA.
DR CCDS; CCDS37259.1; -.
DR RefSeq; NP_083037.1; NM_028761.3.
DR PDB; 1UG8; NMR; -; A=169-242.
DR PDB; 1WHV; NMR; -; A=430-516.
DR PDB; 2ROK; NMR; -; A=430-516.
DR PDB; 3D45; X-ray; 3.00 A; A/B=1-505.
DR PDBsum; 1UG8; -.
DR PDBsum; 1WHV; -.
DR PDBsum; 2ROK; -.
DR PDBsum; 3D45; -.
DR AlphaFoldDB; Q8VDG3; -.
DR SMR; Q8VDG3; -.
DR BioGRID; 216499; 3.
DR DIP; DIP-48330N; -.
DR IntAct; Q8VDG3; 1.
DR STRING; 10090.ENSMUSP00000055969; -.
DR iPTMnet; Q8VDG3; -.
DR PhosphoSitePlus; Q8VDG3; -.
DR EPD; Q8VDG3; -.
DR jPOST; Q8VDG3; -.
DR MaxQB; Q8VDG3; -.
DR PaxDb; Q8VDG3; -.
DR PeptideAtlas; Q8VDG3; -.
DR PRIDE; Q8VDG3; -.
DR ProteomicsDB; 288063; -.
DR DNASU; 74108; -.
DR GeneID; 74108; -.
DR KEGG; mmu:74108; -.
DR CTD; 5073; -.
DR MGI; MGI:1921358; Parn.
DR eggNOG; KOG1990; Eukaryota.
DR InParanoid; Q8VDG3; -.
DR OrthoDB; 1402758at2759; -.
DR PhylomeDB; Q8VDG3; -.
DR TreeFam; TF314502; -.
DR BRENDA; 3.1.13.4; 3474.
DR Reactome; R-MMU-429947; Deadenylation of mRNA.
DR Reactome; R-MMU-450604; KSRP (KHSRP) binds and destabilizes mRNA.
DR BioGRID-ORCS; 74108; 24 hits in 77 CRISPR screens.
DR ChiTaRS; Parn; mouse.
DR EvolutionaryTrace; Q8VDG3; -.
DR PRO; PR:Q8VDG3; -.
DR Proteomes; UP000000589; Unplaced.
DR RNAct; Q8VDG3; protein.
DR GO; GO:0005737; C:cytoplasm; IBA:GO_Central.
DR GO; GO:0016607; C:nuclear speck; ISO:MGI.
DR GO; GO:0005730; C:nucleolus; ISO:MGI.
DR GO; GO:0000175; F:3'-5'-exoribonuclease activity; IBA:GO_Central.
DR GO; GO:0043169; F:cation binding; ISS:UniProtKB.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0004535; F:poly(A)-specific ribonuclease activity; ISS:UniProtKB.
DR GO; GO:0019901; F:protein kinase binding; ISO:MGI.
DR GO; GO:0003723; F:RNA binding; ISS:UniProtKB.
DR GO; GO:0000495; P:box H/ACA RNA 3'-end processing; ISS:UniProtKB.
DR GO; GO:0010587; P:miRNA catabolic process; ISS:UniProtKB.
DR GO; GO:0110008; P:ncRNA deadenylation; ISO:MGI.
DR GO; GO:0000184; P:nuclear-transcribed mRNA catabolic process, nonsense-mediated decay; IEA:UniProtKB-KW.
DR GO; GO:0000289; P:nuclear-transcribed mRNA poly(A) tail shortening; IDA:MGI.
DR GO; GO:0071051; P:polyadenylation-dependent snoRNA 3'-end processing; ISS:UniProtKB.
DR GO; GO:0051973; P:positive regulation of telomerase activity; ISO:MGI.
DR GO; GO:0032212; P:positive regulation of telomere maintenance via telomerase; ISO:MGI.
DR GO; GO:1904872; P:regulation of telomerase RNA localization to Cajal body; ISO:MGI.
DR GO; GO:0090503; P:RNA phosphodiester bond hydrolysis, exonucleolytic; ISO:MGI.
DR GO; GO:0090669; P:telomerase RNA stabilization; ISO:MGI.
DR CDD; cd02637; R3H_PARN; 1.
DR Gene3D; 3.30.420.10; -; 2.
DR Gene3D; 3.30.70.330; -; 1.
DR InterPro; IPR012677; Nucleotide-bd_a/b_plait_sf.
DR InterPro; IPR034042; PARN_R3H.
DR InterPro; IPR014789; PolyA-riboNase_RNA-binding.
DR InterPro; IPR001374; R3H_dom.
DR InterPro; IPR036867; R3H_dom_sf.
DR InterPro; IPR035979; RBD_domain_sf.
DR InterPro; IPR006941; RNase_CAF1.
DR InterPro; IPR012337; RNaseH-like_sf.
DR InterPro; IPR036397; RNaseH_sf.
DR Pfam; PF04857; CAF1; 1.
DR Pfam; PF01424; R3H; 1.
DR Pfam; PF08675; RNA_bind; 1.
DR SUPFAM; SSF53098; SSF53098; 1.
DR SUPFAM; SSF54928; SSF54928; 1.
DR SUPFAM; SSF82708; SSF82708; 1.
DR PROSITE; PS51061; R3H; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Acetylation; Cytoplasm; Exonuclease; Hydrolase; Magnesium;
KW Metal-binding; Nonsense-mediated mRNA decay; Nuclease; Nucleus;
KW Phosphoprotein; Reference proteome; RNA-binding.
FT CHAIN 1..624
FT /note="Poly(A)-specific ribonuclease PARN"
FT /id="PRO_0000212852"
FT DOMAIN 171..238
FT /note="R3H"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00382"
FT REGION 551..612
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 28
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250|UniProtKB:O95453"
FT BINDING 30
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250|UniProtKB:O95453"
FT BINDING 285
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250|UniProtKB:O95453"
FT BINDING 375
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250|UniProtKB:O95453"
FT SITE 319
FT /note="Interaction with poly(A)"
FT /evidence="ECO:0000250|UniProtKB:O95453"
FT MOD_RES 213
FT /note="N6-acetyllysine"
FT /evidence="ECO:0000250|UniProtKB:O95453"
FT MOD_RES 492
FT /note="N6-acetyllysine"
FT /evidence="ECO:0000250|UniProtKB:O95453"
FT MOD_RES 523
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:O95453"
FT MOD_RES 543
FT /note="Phosphoserine; by MAPKAPK2"
FT /evidence="ECO:0000250|UniProtKB:O95453"
FT MOD_RES 569
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:21183079"
FT MOD_RES 573
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:21183079"
FT MOD_RES 575
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:21183079"
FT MOD_RES 605
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:O95453"
FT MOD_RES 609
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:O95453"
FT MOD_RES 613
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:O95453"
FT CONFLICT 36
FT /note="D -> N (in Ref. 1; BAB23382/BAC32249)"
FT /evidence="ECO:0000305"
FT CONFLICT 511
FT /note="E -> K (in Ref. 1; BAB23382/BAC32249)"
FT /evidence="ECO:0000305"
FT CONFLICT 549
FT /note="V -> M (in Ref. 1; BAB23382/BAC32249)"
FT /evidence="ECO:0000305"
FT STRAND 1..3
FT /evidence="ECO:0007829|PDB:3D45"
FT HELIX 5..21
FT /evidence="ECO:0007829|PDB:3D45"
FT STRAND 23..32
FT /evidence="ECO:0007829|PDB:3D45"
FT HELIX 40..43
FT /evidence="ECO:0007829|PDB:3D45"
FT HELIX 50..61
FT /evidence="ECO:0007829|PDB:3D45"
FT STRAND 66..76
FT /evidence="ECO:0007829|PDB:3D45"
FT STRAND 78..81
FT /evidence="ECO:0007829|PDB:3D45"
FT STRAND 83..92
FT /evidence="ECO:0007829|PDB:3D45"
FT STRAND 98..101
FT /evidence="ECO:0007829|PDB:3D45"
FT STRAND 105..109
FT /evidence="ECO:0007829|PDB:3D45"
FT HELIX 110..117
FT /evidence="ECO:0007829|PDB:3D45"
FT TURN 118..120
FT /evidence="ECO:0007829|PDB:3D45"
FT HELIX 123..127
FT /evidence="ECO:0007829|PDB:3D45"
FT HELIX 136..145
FT /evidence="ECO:0007829|PDB:3D45"
FT HELIX 169..186
FT /evidence="ECO:0007829|PDB:1UG8"
FT STRAND 192..194
FT /evidence="ECO:0007829|PDB:1UG8"
FT HELIX 201..213
FT /evidence="ECO:0007829|PDB:1UG8"
FT STRAND 214..223
FT /evidence="ECO:0007829|PDB:1UG8"
FT STRAND 226..228
FT /evidence="ECO:0007829|PDB:1UG8"
FT STRAND 230..236
FT /evidence="ECO:0007829|PDB:1UG8"
FT TURN 239..241
FT /evidence="ECO:0007829|PDB:1UG8"
FT HELIX 254..260
FT /evidence="ECO:0007829|PDB:3D45"
FT HELIX 264..273
FT /evidence="ECO:0007829|PDB:3D45"
FT STRAND 276..281
FT /evidence="ECO:0007829|PDB:3D45"
FT HELIX 283..293
FT /evidence="ECO:0007829|PDB:3D45"
FT HELIX 301..311
FT /evidence="ECO:0007829|PDB:3D45"
FT STRAND 315..317
FT /evidence="ECO:0007829|PDB:3D45"
FT HELIX 318..321
FT /evidence="ECO:0007829|PDB:3D45"
FT HELIX 327..330
FT /evidence="ECO:0007829|PDB:3D45"
FT HELIX 336..342
FT /evidence="ECO:0007829|PDB:3D45"
FT STRAND 353..355
FT /evidence="ECO:0007829|PDB:3D45"
FT HELIX 372..390
FT /evidence="ECO:0007829|PDB:3D45"
FT STRAND 406..408
FT /evidence="ECO:0007829|PDB:3D45"
FT HELIX 409..411
FT /evidence="ECO:0007829|PDB:3D45"
FT STRAND 419..422
FT /evidence="ECO:0007829|PDB:3D45"
FT STRAND 425..430
FT /evidence="ECO:0007829|PDB:3D45"
FT HELIX 437..439
FT /evidence="ECO:0007829|PDB:3D45"
FT STRAND 440..444
FT /evidence="ECO:0007829|PDB:3D45"
FT HELIX 451..457
FT /evidence="ECO:0007829|PDB:3D45"
FT HELIX 458..461
FT /evidence="ECO:0007829|PDB:3D45"
FT STRAND 465..468
FT /evidence="ECO:0007829|PDB:3D45"
FT STRAND 470..477
FT /evidence="ECO:0007829|PDB:3D45"
FT HELIX 481..491
FT /evidence="ECO:0007829|PDB:3D45"
FT STRAND 496..501
FT /evidence="ECO:0007829|PDB:1WHV"
FT HELIX 502..509
FT /evidence="ECO:0007829|PDB:1WHV"
SQ SEQUENCE 624 AA; 71559 MW; D729BFAABA2EB40A CRC64;
MEIIRSNFKI NLHKVYQAIE EADFFAIDGE FSGISDGPSV TALTSGFDTP EERYQKLKKH
SMDFLLFQFG LCAFKYDHTD SKHVTKSFNF YVFPKPFSRS SPDVKFVCQS SSIDFLASQG
FDFNKVFCSG IPYLNQEEER QLREQFDEKR SQANGAGALA KCPVTIPEDQ KKFIDQVIEK
IEDFLQSEEK RSLELDPCTG FQRKLIYQTL SWKYPKGIHV ETLETDKKER HIVISKVDEE
ERKRREQEKY TKEQEELNDA VGFSRVIHAI ANSGKLVVGH NMLLDVMHTI HQFYCPLPAD
LNEFKEMAIC VFPRLLDTKL MASTQPFKDI INNTSLAELE KRLKETPFDP PKVESAEGFP
SYDTASEQLH EAGYDAYITG LCFISMANYL GSLLSPPKMC VSARSKLIEP FFNKLFLMRV
MDIPYLNLEG PDLQPKRDHV LHVTFPKEWK TSDLYQLFSA FGNIQISWID DTSAFVSLSQ
PEQVQIAVNT SKYAESYRIQ TYAEYVGKKQ EGKQVKRKWT EDSWKEVDRK RPHMQGPCYH
SNSFTAAGVL GKRTLSPDPR EAALEDRESE EVSDSELEQT DSCTDPLPEG RKKSKKLKRM
KKELSLAGSV SDSPAVLFEV PDTW
