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Poly(A)-specific ribonuclease PARN (EC 3.1.13.4) (Polyadenylate-specific ribonuclease) (AtPARN) (Protein ABA hypersensitive germination 2)

 PARN_ARATH              Reviewed;         689 AA.
Q9LG26; Q33CQ7; Q33CQ8; Q33CQ9; Q4W7J2;
01-MAR-2005, integrated into UniProtKB/Swiss-Prot.
01-MAR-2005, sequence version 2.
23-MAY-2018, entry version 103.
RecName: Full=Poly(A)-specific ribonuclease PARN;
EC=3.1.13.4;
AltName: Full=Polyadenylate-specific ribonuclease;
Short=AtPARN;
AltName: Full=Protein ABA hypersensitive germination 2;
Name=PARN; Synonyms=AHG2; OrderedLocusNames=At1g55870;
ORFNames=F14J16.11;
Arabidopsis thaliana (Mouse-ear cress).
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; eudicotyledons; Gunneridae;
Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae;
Arabidopsis.
NCBI_TaxID=3702;
[1]
NUCLEOTIDE SEQUENCE [MRNA] (ISOFORMS 1; 2 AND 3), AND FUNCTION.
STRAIN=cv. Columbia;
PubMed=16359390; DOI=10.1111/j.1365-313X.2005.02589.x;
Nishimura N., Kitahata N., Seki M., Narusaka Y., Narusaka M.,
Kuromori T., Asami T., Shinozaki K., Hirayama T.;
"Analysis of ABA hypersensitive germination2 revealed the pivotal
functions of PARN in stress response in Arabidopsis.";
Plant J. 44:972-984(2005).
[2]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=cv. Columbia;
PubMed=11130712; DOI=10.1038/35048500;
Theologis A., Ecker J.R., Palm C.J., Federspiel N.A., Kaul S.,
White O., Alonso J., Altafi H., Araujo R., Bowman C.L., Brooks S.Y.,
Buehler E., Chan A., Chao Q., Chen H., Cheuk R.F., Chin C.W.,
Chung M.K., Conn L., Conway A.B., Conway A.R., Creasy T.H., Dewar K.,
Dunn P., Etgu P., Feldblyum T.V., Feng J.-D., Fong B., Fujii C.Y.,
Gill J.E., Goldsmith A.D., Haas B., Hansen N.F., Hughes B., Huizar L.,
Hunter J.L., Jenkins J., Johnson-Hopson C., Khan S., Khaykin E.,
Kim C.J., Koo H.L., Kremenetskaia I., Kurtz D.B., Kwan A., Lam B.,
Langin-Hooper S., Lee A., Lee J.M., Lenz C.A., Li J.H., Li Y.-P.,
Lin X., Liu S.X., Liu Z.A., Luros J.S., Maiti R., Marziali A.,
Militscher J., Miranda M., Nguyen M., Nierman W.C., Osborne B.I.,
Pai G., Peterson J., Pham P.K., Rizzo M., Rooney T., Rowley D.,
Sakano H., Salzberg S.L., Schwartz J.R., Shinn P., Southwick A.M.,
Sun H., Tallon L.J., Tambunga G., Toriumi M.J., Town C.D.,
Utterback T., Van Aken S., Vaysberg M., Vysotskaia V.S., Walker M.,
Wu D., Yu G., Fraser C.M., Venter J.C., Davis R.W.;
"Sequence and analysis of chromosome 1 of the plant Arabidopsis
thaliana.";
Nature 408:816-820(2000).
[3]
GENOME REANNOTATION.
STRAIN=cv. Columbia;
PubMed=27862469; DOI=10.1111/tpj.13415;
Cheng C.Y., Krishnakumar V., Chan A.P., Thibaud-Nissen F., Schobel S.,
Town C.D.;
"Araport11: a complete reannotation of the Arabidopsis thaliana
reference genome.";
Plant J. 89:789-804(2017).
[4]
FUNCTION, SUBCELLULAR LOCATION, AND TISSUE SPECIFICITY.
PubMed=15019988; DOI=10.1016/j.gene.2003.11.028;
Chiba Y., Johnson M.A., Lidder P., Vogel J.T., van Erp H., Green P.J.;
"AtPARN is an essential poly(A) ribonuclease in Arabidopsis.";
Gene 328:95-102(2004).
[5]
FUNCTION, SUBCELLULAR LOCATION, TISSUE SPECIFICITY, AND MUTAGENESIS OF
66-ASP--GLU-68.
PubMed=15247430; DOI=10.1261/rna.7540204;
Reverdatto S.V., Dutko J.A., Chekanova J.A., Hamilton D.A.,
Belostotsky D.A.;
"mRNA deadenylation by PARN is essential for embryogenesis in higher
plants.";
RNA 10:1200-1214(2004).
-!- 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. Essential for early
development, possibly by participating in silencing certain
maternal mRNAs translationally. May have a pivotal role in stress
response. {ECO:0000269|PubMed:15019988,
ECO:0000269|PubMed:15247430, ECO:0000269|PubMed:16359390}.
-!- CATALYTIC ACTIVITY: Exonucleolytic cleavage of poly(A) to 5'-AMP.
-!- COFACTOR:
Name=a divalent metal cation; Xref=ChEBI:CHEBI:60240;
Evidence={ECO:0000250|UniProtKB:O95453};
-!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:15019988}.
Cytoplasm {ECO:0000269|PubMed:15019988,
ECO:0000269|PubMed:15247430}. Note=Only cytoplasmic.
{ECO:0000269|PubMed:15247430}.
-!- ALTERNATIVE PRODUCTS:
Event=Alternative splicing; Named isoforms=3;
Name=1;
IsoId=Q9LG26-1; Sequence=Displayed;
Name=2;
IsoId=Q9LG26-2; Sequence=VSP_037056;
Note=May be due to a competing acceptor splice site.;
Name=3;
IsoId=Q9LG26-3; Sequence=VSP_037055;
Note=May be due to intron retention. No experimental
confirmation available.;
-!- TISSUE SPECIFICITY: Widely expressed. Expressed in roots, stems,
leaves and flowers. {ECO:0000269|PubMed:15019988,
ECO:0000269|PubMed:15247430}.
-!- SIMILARITY: Belongs to the CAF1 family. {ECO:0000305}.
-!- SEQUENCE CAUTION:
Sequence=AAF79314.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
Sequence=BAE47488.1; Type=Erroneous translation; Note=Wrong choice of frame.; Evidence={ECO:0000305};
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EMBL; AB194966; BAD98514.1; -; mRNA.
EMBL; AB223028; BAE47489.1; -; mRNA.
EMBL; AB223029; BAE47490.1; -; mRNA.
EMBL; AB223027; BAE47488.1; ALT_SEQ; mRNA.
EMBL; AC002304; AAF79314.1; ALT_SEQ; Genomic_DNA.
EMBL; CP002684; AEE33311.1; -; Genomic_DNA.
EMBL; CP002684; ANM60396.1; -; Genomic_DNA.
RefSeq; NP_001322686.1; NM_001333742.1. [Q9LG26-3]
RefSeq; NP_175983.5; NM_104464.7. [Q9LG26-1]
UniGene; At.49981; -.
ProteinModelPortal; Q9LG26; -.
SMR; Q9LG26; -.
STRING; 3702.AT1G55870.1; -.
PaxDb; Q9LG26; -.
PRIDE; Q9LG26; -.
EnsemblPlants; AT1G55870.1; AT1G55870.1; AT1G55870. [Q9LG26-1]
EnsemblPlants; AT1G55870.4; AT1G55870.4; AT1G55870. [Q9LG26-3]
GeneID; 842037; -.
Gramene; AT1G55870.1; AT1G55870.1; AT1G55870. [Q9LG26-1]
Gramene; AT1G55870.4; AT1G55870.4; AT1G55870. [Q9LG26-3]
KEGG; ath:AT1G55870; -.
Araport; AT1G55870; -.
TAIR; locus:2012100; AT1G55870.
eggNOG; KOG1990; Eukaryota.
eggNOG; ENOG410XS9D; LUCA.
HOGENOM; HOG000078691; -.
InParanoid; Q9LG26; -.
KO; K01148; -.
OMA; FFVFPRQ; -.
OrthoDB; EOG0936052S; -.
PhylomeDB; Q9LG26; -.
BRENDA; 3.1.13.4; 399.
Reactome; R-ATH-450604; KSRP (KHSRP) binds and destabilizes mRNA.
PRO; PR:Q9LG26; -.
Proteomes; UP000006548; Chromosome 1.
ExpressionAtlas; Q9LG26; baseline and differential.
Genevisible; Q9LG26; AT.
GO; GO:0005739; C:mitochondrion; IDA:TAIR.
GO; GO:0005634; C:nucleus; IEA:UniProtKB-SubCell.
GO; GO:0043169; F:cation binding; ISS:UniProtKB.
GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
GO; GO:0004535; F:poly(A)-specific ribonuclease activity; IEA:UniProtKB-EC.
GO; GO:0003723; F:RNA binding; IEA:UniProtKB-KW.
GO; GO:0006952; P:defense response; IEA:UniProtKB-KW.
GO; GO:0006397; P:mRNA processing; IEA:UniProtKB-KW.
GO; GO:0009737; P:response to abscisic acid; IMP:TAIR.
GO; GO:0006970; P:response to osmotic stress; IMP:TAIR.
GO; GO:0009751; P:response to salicylic acid; IMP:TAIR.
GO; GO:0009651; P:response to salt stress; IMP:TAIR.
Gene3D; 3.30.420.10; -; 2.
InterPro; IPR006941; RNase_CAF1.
InterPro; IPR012337; RNaseH-like_sf.
InterPro; IPR036397; RNaseH_sf.
Pfam; PF04857; CAF1; 1.
SUPFAM; SSF53098; SSF53098; 2.
1: Evidence at protein level;
Alternative splicing; Complete proteome; Cytoplasm; Exonuclease;
Hydrolase; Metal-binding; mRNA processing; Nuclease; Nucleus;
Plant defense; Reference proteome; RNA-binding.
CHAIN 1 689 Poly(A)-specific ribonuclease PARN.
/FTId=PRO_0000212856.
METAL 66 66 Divalent metal cation. {ECO:0000305}.
METAL 68 68 Divalent metal cation. {ECO:0000305}.
METAL 354 354 Divalent metal cation.
{ECO:0000250|UniProtKB:O95453}.
METAL 459 459 Divalent metal cation.
{ECO:0000250|UniProtKB:O95453}.
VAR_SEQ 1 184 Missing (in isoform 3).
{ECO:0000303|PubMed:16359390}.
/FTId=VSP_037055.
VAR_SEQ 1 149 Missing (in isoform 2).
{ECO:0000303|PubMed:16359390}.
/FTId=VSP_037056.
MUTAGEN 66 68 DLE->ALA: Loss of function.
{ECO:0000269|PubMed:15247430}.
SEQUENCE 689 AA; 78010 MW; E6E1782F7ABBF731 CRC64;
MRRHKRWPLR SLVCSFSSSA AETVTTSTAA SATAAFPLKH VTRSNFETTL NDLRSLVKAA
DFVAIDLEMT GVTSAPWRDS LEFDRYDVRY LKVKDSAEKF AVVQFGVCPF RWDSRTQSFV
SYPHNFFVFP RQELTFDPPA HEFLCQTTSM DFLAKYQFDF NTCIHEGISY LSRREEEEAS
KRLKMLHGED GIDSSGETEE LKLVRLADVL FAARMEKLLN EWRSGLLHGG NASSEFPRIS
NGSNQSMETV FHHMRPALSL KGFTSHQLRV LNSVLRKHFG DLVYIHSNDK SSSSRDIVVY
TDSDSDKENL MKEAKDERKR LAERKIQSAI GFRQVIDLLA SEKKLIVGHN CFLDIAHVYS
KFVGPLPSTA EKFVASINSH FPYIVDTKIL LNVNPMLHQR MKKSSTSLSS AFSSLCPQIE
FSSRSSDSFL QQRVNIDVEI DNVRCSNWNA GGKHEAGYDA FMTGCIFAQA CNHLGFDFKQ
HSQLDDFAQN EKLEKYINRL YLSWTRGDII DLRTGHSNAD NWRVSKFKYE NIVLIWNFPR
KLKARGIKEC ICKAFGSASV TSVYHVDDSA VFVLFKNSEL VWDFLALKRQ LESSDGPVSV
LHPLSKILEG GNTGAADYEA YKEICSSHVS EVMFSDQAET VGVKSRTRPN AQCETETREE
NTVTVTHKAS DLIDAFLANR VEVETATSN


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