PARN_ARATH
ID PARN_ARATH Reviewed; 689 AA.
AC Q9LG26; Q33CQ7; Q33CQ8; Q33CQ9; Q4W7J2;
DT 01-MAR-2005, integrated into UniProtKB/Swiss-Prot.
DT 01-MAR-2005, sequence version 2.
DT 03-AUG-2022, entry version 122.
DE RecName: Full=Poly(A)-specific ribonuclease PARN;
DE EC=3.1.13.4;
DE AltName: Full=Polyadenylate-specific ribonuclease;
DE Short=AtPARN;
DE AltName: Full=Protein ABA hypersensitive germination 2;
GN Name=PARN; Synonyms=AHG2; OrderedLocusNames=At1g55870; ORFNames=F14J16.11;
OS Arabidopsis thaliana (Mouse-ear cress).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis.
OX NCBI_TaxID=3702;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA] (ISOFORMS 1; 2 AND 3), AND FUNCTION.
RC STRAIN=cv. Columbia;
RX PubMed=16359390; DOI=10.1111/j.1365-313x.2005.02589.x;
RA Nishimura N., Kitahata N., Seki M., Narusaka Y., Narusaka M., Kuromori T.,
RA Asami T., Shinozaki K., Hirayama T.;
RT "Analysis of ABA hypersensitive germination2 revealed the pivotal functions
RT of PARN in stress response in Arabidopsis.";
RL Plant J. 44:972-984(2005).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=11130712; DOI=10.1038/35048500;
RA Theologis A., Ecker J.R., Palm C.J., Federspiel N.A., Kaul S., White O.,
RA Alonso J., Altafi H., Araujo R., Bowman C.L., Brooks S.Y., Buehler E.,
RA Chan A., Chao Q., Chen H., Cheuk R.F., Chin C.W., Chung M.K., Conn L.,
RA Conway A.B., Conway A.R., Creasy T.H., Dewar K., Dunn P., Etgu P.,
RA Feldblyum T.V., Feng J.-D., Fong B., Fujii C.Y., Gill J.E., Goldsmith A.D.,
RA Haas B., Hansen N.F., Hughes B., Huizar L., Hunter J.L., Jenkins J.,
RA Johnson-Hopson C., Khan S., Khaykin E., Kim C.J., Koo H.L.,
RA Kremenetskaia I., Kurtz D.B., Kwan A., Lam B., Langin-Hooper S., Lee A.,
RA Lee J.M., Lenz C.A., Li J.H., Li Y.-P., Lin X., Liu S.X., Liu Z.A.,
RA Luros J.S., Maiti R., Marziali A., Militscher J., Miranda M., Nguyen M.,
RA Nierman W.C., Osborne B.I., Pai G., Peterson J., Pham P.K., Rizzo M.,
RA Rooney T., Rowley D., Sakano H., Salzberg S.L., Schwartz J.R., Shinn P.,
RA Southwick A.M., Sun H., Tallon L.J., Tambunga G., Toriumi M.J., Town C.D.,
RA Utterback T., Van Aken S., Vaysberg M., Vysotskaia V.S., Walker M., Wu D.,
RA Yu G., Fraser C.M., Venter J.C., Davis R.W.;
RT "Sequence and analysis of chromosome 1 of the plant Arabidopsis thaliana.";
RL Nature 408:816-820(2000).
RN [3]
RP GENOME REANNOTATION.
RC STRAIN=cv. Columbia;
RX PubMed=27862469; DOI=10.1111/tpj.13415;
RA Cheng C.Y., Krishnakumar V., Chan A.P., Thibaud-Nissen F., Schobel S.,
RA Town C.D.;
RT "Araport11: a complete reannotation of the Arabidopsis thaliana reference
RT genome.";
RL Plant J. 89:789-804(2017).
RN [4]
RP FUNCTION, SUBCELLULAR LOCATION, AND TISSUE SPECIFICITY.
RX PubMed=15019988; DOI=10.1016/j.gene.2003.11.028;
RA Chiba Y., Johnson M.A., Lidder P., Vogel J.T., van Erp H., Green P.J.;
RT "AtPARN is an essential poly(A) ribonuclease in Arabidopsis.";
RL Gene 328:95-102(2004).
RN [5]
RP FUNCTION, SUBCELLULAR LOCATION, TISSUE SPECIFICITY, AND MUTAGENESIS OF
RP 66-ASP--GLU-68.
RX PubMed=15247430; DOI=10.1261/rna.7540204;
RA Reverdatto S.V., Dutko J.A., Chekanova J.A., Hamilton D.A.,
RA Belostotsky D.A.;
RT "mRNA deadenylation by PARN is essential for embryogenesis in higher
RT plants.";
RL RNA 10:1200-1214(2004).
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. Essential for early development, possibly by
CC participating in silencing certain maternal mRNAs translationally. May
CC have a pivotal role in stress response. {ECO:0000269|PubMed:15019988,
CC ECO:0000269|PubMed:15247430, ECO:0000269|PubMed:16359390}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=Exonucleolytic cleavage of poly(A) to 5'-AMP.; EC=3.1.13.4;
CC -!- COFACTOR:
CC Name=a divalent metal cation; Xref=ChEBI:CHEBI:60240;
CC Evidence={ECO:0000250|UniProtKB:O95453};
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:15019988}. Cytoplasm
CC {ECO:0000269|PubMed:15019988, ECO:0000269|PubMed:15247430}. Note=Only
CC cytoplasmic. {ECO:0000269|PubMed:15247430}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=3;
CC Name=1;
CC IsoId=Q9LG26-1; Sequence=Displayed;
CC Name=2;
CC IsoId=Q9LG26-2; Sequence=VSP_037056;
CC Name=3;
CC IsoId=Q9LG26-3; Sequence=VSP_037055;
CC -!- TISSUE SPECIFICITY: Widely expressed. Expressed in roots, stems, leaves
CC and flowers. {ECO:0000269|PubMed:15019988,
CC ECO:0000269|PubMed:15247430}.
CC -!- MISCELLANEOUS: [Isoform 2]: May be due to a competing acceptor splice
CC site. {ECO:0000305}.
CC -!- MISCELLANEOUS: [Isoform 3]: May be due to intron retention.
CC {ECO:0000305}.
CC -!- SIMILARITY: Belongs to the CAF1 family. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAF79314.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC Sequence=BAE47488.1; Type=Erroneous translation; Note=Wrong choice of frame.; Evidence={ECO:0000305};
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DR EMBL; AB194966; BAD98514.1; -; mRNA.
DR EMBL; AB223028; BAE47489.1; -; mRNA.
DR EMBL; AB223029; BAE47490.1; -; mRNA.
DR EMBL; AB223027; BAE47488.1; ALT_SEQ; mRNA.
DR EMBL; AC002304; AAF79314.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002684; AEE33311.1; -; Genomic_DNA.
DR EMBL; CP002684; ANM60396.1; -; Genomic_DNA.
DR RefSeq; NP_001322686.1; NM_001333742.1. [Q9LG26-3]
DR RefSeq; NP_175983.5; NM_104464.7. [Q9LG26-1]
DR AlphaFoldDB; Q9LG26; -.
DR SMR; Q9LG26; -.
DR STRING; 3702.AT1G55870.1; -.
DR PaxDb; Q9LG26; -.
DR PRIDE; Q9LG26; -.
DR ProteomicsDB; 236707; -. [Q9LG26-1]
DR EnsemblPlants; AT1G55870.1; AT1G55870.1; AT1G55870. [Q9LG26-1]
DR EnsemblPlants; AT1G55870.4; AT1G55870.4; AT1G55870. [Q9LG26-3]
DR GeneID; 842037; -.
DR Gramene; AT1G55870.1; AT1G55870.1; AT1G55870. [Q9LG26-1]
DR Gramene; AT1G55870.4; AT1G55870.4; AT1G55870. [Q9LG26-3]
DR KEGG; ath:AT1G55870; -.
DR Araport; AT1G55870; -.
DR TAIR; locus:2012100; AT1G55870.
DR eggNOG; KOG1990; Eukaryota.
DR HOGENOM; CLU_020384_1_0_1; -.
DR InParanoid; Q9LG26; -.
DR OMA; QFQTIFF; -.
DR OrthoDB; 1402758at2759; -.
DR PhylomeDB; Q9LG26; -.
DR BRENDA; 3.1.13.4; 399.
DR PRO; PR:Q9LG26; -.
DR Proteomes; UP000006548; Chromosome 1.
DR ExpressionAtlas; Q9LG26; baseline and differential.
DR Genevisible; Q9LG26; AT.
DR GO; GO:0005737; C:cytoplasm; IBA:GO_Central.
DR GO; GO:0005739; C:mitochondrion; IDA:TAIR.
DR GO; GO:0005634; C:nucleus; IEA:UniProtKB-SubCell.
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; IEA:UniProtKB-EC.
DR GO; GO:0003723; F:RNA binding; IBA:GO_Central.
DR GO; GO:0006952; P:defense response; IEA:UniProtKB-KW.
DR GO; GO:0006397; P:mRNA processing; IEA:UniProtKB-KW.
DR GO; GO:0009737; P:response to abscisic acid; IMP:TAIR.
DR GO; GO:0006970; P:response to osmotic stress; IMP:TAIR.
DR GO; GO:0009751; P:response to salicylic acid; IMP:TAIR.
DR GO; GO:0009651; P:response to salt stress; IMP:TAIR.
DR Gene3D; 3.30.420.10; -; 2.
DR InterPro; IPR006941; RNase_CAF1.
DR InterPro; IPR012337; RNaseH-like_sf.
DR InterPro; IPR036397; RNaseH_sf.
DR Pfam; PF04857; CAF1; 1.
DR SUPFAM; SSF53098; SSF53098; 1.
PE 1: Evidence at protein level;
KW Alternative splicing; Cytoplasm; Exonuclease; Hydrolase; Metal-binding;
KW mRNA processing; Nuclease; Nucleus; Plant defense; Reference proteome;
KW RNA-binding.
FT CHAIN 1..689
FT /note="Poly(A)-specific ribonuclease PARN"
FT /id="PRO_0000212856"
FT BINDING 66
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000305"
FT BINDING 68
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000305"
FT BINDING 354
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000250|UniProtKB:O95453"
FT BINDING 459
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000250|UniProtKB:O95453"
FT VAR_SEQ 1..184
FT /note="Missing (in isoform 3)"
FT /evidence="ECO:0000303|PubMed:16359390"
FT /id="VSP_037055"
FT VAR_SEQ 1..149
FT /note="Missing (in isoform 2)"
FT /evidence="ECO:0000303|PubMed:16359390"
FT /id="VSP_037056"
FT MUTAGEN 66..68
FT /note="DLE->ALA: Loss of function."
FT /evidence="ECO:0000269|PubMed:15247430"
SQ 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
