XRN2_ARATH
ID XRN2_ARATH Reviewed; 1012 AA.
AC Q9FQ02; Q56WR6; Q570J7; Q9AST0; Q9FH70; Q9FH71;
DT 02-SEP-2008, integrated into UniProtKB/Swiss-Prot.
DT 01-MAR-2001, sequence version 1.
DT 03-AUG-2022, entry version 124.
DE RecName: Full=5'-3' exoribonuclease 2 {ECO:0000305};
DE Short=AtXRN2 {ECO:0000303|PubMed:11106401};
DE EC=3.1.13.- {ECO:0000269|PubMed:11106401};
DE AltName: Full=Protein EXORIBONUCLEASE 2 {ECO:0000305};
GN Name=XRN2 {ECO:0000303|PubMed:11106401};
GN OrderedLocusNames=At5g42540/At5g42550; ORFNames=K16E1.1/K16E1.2;
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], FUNCTION, CATALYTIC ACTIVITY, TISSUE
RP SPECIFICITY, AND SUBCELLULAR LOCATION.
RX PubMed=11106401; DOI=10.1073/pnas.97.25.13985;
RA Kastenmayer J.P., Green P.J.;
RT "Novel features of the XRN-family in Arabidopsis: evidence that AtXRN4, one
RT of several orthologs of nuclear Xrn2p/Rat1p, functions in the cytoplasm.";
RL Proc. Natl. Acad. Sci. U.S.A. 97:13985-13990(2000).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=10718197; DOI=10.1093/dnares/7.1.31;
RA Sato S., Nakamura Y., Kaneko T., Katoh T., Asamizu E., Kotani H.,
RA Tabata S.;
RT "Structural analysis of Arabidopsis thaliana chromosome 5. X. Sequence
RT features of the regions of 3,076,755 bp covered by sixty P1 and TAC
RT clones.";
RL DNA Res. 7:31-63(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 NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Columbia;
RX PubMed=14593172; DOI=10.1126/science.1088305;
RA Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M.,
RA Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G.,
RA Liu S.X., Lam B., Sakano H., Wu T., Yu G., Miranda M., Quach H.L.,
RA Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C.,
RA Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J.,
RA Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A.,
RA Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C.,
RA Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X.,
RA Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M.,
RA Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K.,
RA Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A.,
RA Ecker J.R.;
RT "Empirical analysis of transcriptional activity in the Arabidopsis
RT genome.";
RL Science 302:842-846(2003).
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Columbia;
RA Totoki Y., Seki M., Ishida J., Nakajima M., Enju A., Kamiya A.,
RA Narusaka M., Shin-i T., Nakagawa M., Sakamoto N., Oishi K., Kohara Y.,
RA Kobayashi M., Toyoda A., Sakaki Y., Sakurai T., Iida K., Akiyama K.,
RA Satou M., Toyoda T., Konagaya A., Carninci P., Kawai J., Hayashizaki Y.,
RA Shinozaki K.;
RT "Large-scale analysis of RIKEN Arabidopsis full-length (RAFL) cDNAs.";
RL Submitted (MAR-2005) to the EMBL/GenBank/DDBJ databases.
RN [6]
RP FUNCTION.
RX PubMed=17993620; DOI=10.1105/tpc.107.055319;
RA Gy I., Gasciolli V., Lauressergues D., Morel J.-B., Gombert J., Proux F.,
RA Proux C., Vaucheret H., Mallory A.C.;
RT "Arabidopsis FIERY1, XRN2, and XRN3 are endogenous RNA silencing
RT suppressors.";
RL Plant Cell 19:3451-3461(2007).
RN [7]
RP FUNCTION.
RX PubMed=20338880; DOI=10.1093/nar/gkq172;
RA Zakrzewska-Placzek M., Souret F.F., Sobczyk G.J., Green P.J., Kufel J.;
RT "Arabidopsis thaliana XRN2 is required for primary cleavage in the pre-
RT ribosomal RNA.";
RL Nucleic Acids Res. 38:4487-4502(2010).
CC -!- FUNCTION: Possesses 5'->3' exoribonuclease activity (PubMed:11106401).
CC Acts as an endogenous post-transcriptional gene silencing (PTGS)
CC suppressor. Degrades miRNA-derived loops, excised during miRNA
CC maturation in the nucleus (PubMed:17993620). Involved in pre-rRNA
CC processing. Involved in the primary exonucleolytic shortening of the 5'
CC external transcribed spacer (5'ETS), required for endonucleolytic
CC processing at site P by the U3 snoRNP complex. Involved with XRN3 in
CC the 5'-end processing of 5.8S and 25S rRNAs. Contributes with XRN3 to
CC polyadenylation-dependent nuclear RNA surveillance. Involved in the
CC degradation of aberrant polyadenylated pre-rRNA through 5'-end
CC processing (PubMed:20338880). {ECO:0000269|PubMed:11106401,
CC ECO:0000269|PubMed:17993620, ECO:0000269|PubMed:20338880}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:11106401}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=1;
CC Comment=A number of isoforms are produced. According to EST
CC sequences.;
CC Name=1;
CC IsoId=Q9FQ02-1; Sequence=Displayed;
CC -!- TISSUE SPECIFICITY: Expressed in roots, leaves, stems and flowers.
CC {ECO:0000269|PubMed:11106401}.
CC -!- SIMILARITY: Belongs to the 5'-3' exonuclease family. XRN2/RAT1
CC subfamily. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAK32883.1; Type=Erroneous termination; Note=Truncated C-terminus.; Evidence={ECO:0000305};
CC Sequence=BAB09325.1; Type=Erroneous gene model prediction; Note=Was originally thought to correspond to two different genes At5g42540 and At5g42550.; Evidence={ECO:0000305};
CC Sequence=BAB09326.1; Type=Erroneous gene model prediction; Note=Was originally thought to correspond to two different genes At5g42540 and At5g42550.; Evidence={ECO:0000305};
CC Sequence=BAD94484.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305};
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DR EMBL; AF286720; AAG40733.1; -; mRNA.
DR EMBL; AB022210; BAB09325.1; ALT_SEQ; Genomic_DNA.
DR EMBL; AB022210; BAB09326.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002688; AED94824.1; -; Genomic_DNA.
DR EMBL; AF367296; AAK32883.1; ALT_SEQ; mRNA.
DR EMBL; AY091687; AAM10286.1; -; mRNA.
DR EMBL; AK176100; BAD43863.1; -; mRNA.
DR EMBL; AK220711; BAD93823.1; -; mRNA.
DR EMBL; AK220893; BAD94308.1; -; mRNA.
DR EMBL; AK221968; BAD94484.1; ALT_INIT; mRNA.
DR RefSeq; NP_199069.1; NM_123619.4. [Q9FQ02-1]
DR AlphaFoldDB; Q9FQ02; -.
DR SMR; Q9FQ02; -.
DR STRING; 3702.AT5G42540.2; -.
DR iPTMnet; Q9FQ02; -.
DR PaxDb; Q9FQ02; -.
DR PRIDE; Q9FQ02; -.
DR ProteomicsDB; 242382; -. [Q9FQ02-1]
DR EnsemblPlants; AT5G42540.1; AT5G42540.1; AT5G42540. [Q9FQ02-1]
DR GeneID; 834261; -.
DR Gramene; AT5G42540.1; AT5G42540.1; AT5G42540. [Q9FQ02-1]
DR KEGG; ath:AT5G42540; -.
DR Araport; AT5G42540; -.
DR eggNOG; KOG2044; Eukaryota.
DR HOGENOM; CLU_006038_1_0_1; -.
DR OMA; YKANRRE; -.
DR PhylomeDB; Q9FQ02; -.
DR PRO; PR:Q9FQ02; -.
DR Proteomes; UP000006548; Chromosome 5.
DR ExpressionAtlas; Q9FQ02; baseline and differential.
DR Genevisible; Q9FQ02; AT.
DR GO; GO:0005634; C:nucleus; IDA:UniProtKB.
DR GO; GO:0004534; F:5'-3' exoribonuclease activity; IDA:UniProtKB.
DR GO; GO:0003723; F:RNA binding; IBA:GO_Central.
DR GO; GO:0008270; F:zinc ion binding; IEA:InterPro.
DR GO; GO:0010587; P:miRNA catabolic process; IMP:UniProtKB.
DR GO; GO:0006397; P:mRNA processing; IEA:UniProtKB-KW.
DR GO; GO:0060149; P:negative regulation of post-transcriptional gene silencing; IMP:UniProtKB.
DR GO; GO:0071035; P:nuclear polyadenylation-dependent rRNA catabolic process; IMP:UniProtKB.
DR GO; GO:0000956; P:nuclear-transcribed mRNA catabolic process; IBA:GO_Central.
DR GO; GO:0000967; P:rRNA 5'-end processing; IMP:UniProtKB.
DR InterPro; IPR027073; 5_3_exoribonuclease.
DR InterPro; IPR004859; Put_53exo.
DR InterPro; IPR041412; Xrn1_helical.
DR InterPro; IPR017151; Xrn2/3/4.
DR InterPro; IPR001878; Znf_CCHC.
DR InterPro; IPR036875; Znf_CCHC_sf.
DR PANTHER; PTHR12341; PTHR12341; 1.
DR Pfam; PF17846; XRN_M; 1.
DR Pfam; PF03159; XRN_N; 1.
DR Pfam; PF00098; zf-CCHC; 1.
DR PIRSF; PIRSF037239; Exonuclease_Xrn2; 1.
DR SMART; SM00343; ZnF_C2HC; 1.
DR SUPFAM; SSF57756; SSF57756; 1.
DR PROSITE; PS50158; ZF_CCHC; 1.
PE 1: Evidence at protein level;
KW Alternative splicing; Exonuclease; Hydrolase; Metal-binding;
KW mRNA processing; Nuclease; Nucleus; Reference proteome; rRNA processing;
KW Zinc; Zinc-finger.
FT CHAIN 1..1012
FT /note="5'-3' exoribonuclease 2"
FT /id="PRO_0000348954"
FT ZN_FING 264..281
FT /note="CCHC-type"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00047"
FT REGION 411..439
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 888..976
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 990..1012
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 413..434
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 895..912
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 914..935
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 946..967
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT CONFLICT 390
FT /note="V -> D (in Ref. 5; BAD93823)"
FT /evidence="ECO:0000305"
FT CONFLICT 414
FT /note="R -> S (in Ref. 5; BAD93823)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 1012 AA; 116385 MW; 9BC6DDC74755265A CRC64;
MGVPSFYRWL IQRYPLTIQE VIEEEPLEVN GGGVTIPIDS SKPNPNGYEY DNLYLDMNGI
IHPCFHPEDK PSPTTFTEVF QCMFDYIDRL FVMVRPRKLL FMAIDGVAPR AKMNQQRARR
FRAAKDAAEA AAEEEQLREE FEREGKKLPP KVDSQVFDSN VITPGTEFMA TLSFALRYYI
HVRLNSDPGW KNIKVILSDA NVPGEGEHKI MSYIRCNKNH PGYNPNTHHC LYGLDADLIM
LSLATHEIHF SILREVVFFP GEEGKCFLCG QEGHRAADCE GKIKRKTGEM LDNTEADVVV
KKPYEFVNIW ILREYLEHDM QIPGAKKNLD RLIDDFIFIC FFVGNDFLPH MPTLEIREGA
IELLMSVYKN KFRSAKKYLT DSSKLNLRNV ERFIKAVGMY ENQIFQKRAQ VQQRQSERFR
RDKARDKARD NARDNAQASR QFSGKLVQLD SLDEVSDSLH SSPSRKYLRL SLDDNIGVAN
VETENSLKAE ELDNEEDLKF KLKKLLRDKG DGFRSGNGEQ DKVKLNKVGW RERYYEEKFA
AKSVEEMEQI RRDVVLKYTE GLCWIMHYYY HGVCSWNWFY PYHYAPFASD LKGLEKLDIK
FELGSPFKPF NQLLAVLPSA SAHALPECYR SLMTNPDSPI ADFYPADFEI DMNGKRYSWQ
GISKLPFVEE KRLLEAAAQV EKSLTNEEIR RNSALFDMLF VVASHPLGEL IRSLNSRTNN
LSNEERATII EKIDPGLSDG MNGYIASCGG DSQPSCFCST VEGMEDVLTN QVICAIYKLP
EDIRGSEITH QIPRLAIPKK TISLVDLKSG GLLWHEDGDK RRAPPKVIKI KRYNPEGSIS
GGRLGKASHR LVLQTINAQP DYMNINSEPA LCPNTVFQNE RVPKKIPTFK DNGIQWISPP
PSQITPKKMN SPQRQKAWKK DETPQSREKS KKLKSSLKVN PLKMKKTKSP QREFTREKKK
ENITPQRKLT KAQRQVKHIR MMEEAKMIKQ RKKEKYLRKK AKYAQGAPPK TA
