XRN3_ARATH
ID XRN3_ARATH Reviewed; 1020 AA.
AC Q9FQ03; Q8L7A3; Q9LR05;
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 3 {ECO:0000305};
DE Short=AtXRN3 {ECO:0000303|PubMed:11106401};
DE EC=3.1.13.- {ECO:0000269|PubMed:11106401};
DE AltName: Full=Protein EXORIBONUCLEASE 3 {ECO:0000305};
GN Name=XRN3 {ECO:0000303|PubMed:11106401}; OrderedLocusNames=At1g75660;
GN ORFNames=F10A5.15;
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] (ISOFORM 1), FUNCTION, CATALYTIC ACTIVITY,
RP TISSUE 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=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 NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
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 FUNCTION, AND DISRUPTION PHENOTYPE.
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 [6]
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. Required for proper development
CC (PubMed:17993620). Involved in pre-rRNA processing. Involved with XRN2
CC in the 5'-end exonucleolytic processing of 5.8S and 25S rRNAs.
CC Contributes with XRN2 to polyadenylation-dependent nuclear RNA
CC surveillance. Involved in the degradation of aberrant polyadenylated
CC pre-rRNA through 5'-end processing (PubMed:20338880).
CC {ECO:0000269|PubMed:11106401, ECO:0000269|PubMed:17993620,
CC ECO:0000269|PubMed:20338880}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:11106401}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1;
CC IsoId=Q9FQ03-1; Sequence=Displayed;
CC Name=2;
CC IsoId=Q9FQ03-2; Sequence=VSP_035194, VSP_035195;
CC -!- TISSUE SPECIFICITY: Expressed in roots, leaves, stems and flowers.
CC {ECO:0000269|PubMed:11106401}.
CC -!- DISRUPTION PHENOTYPE: Embryonic lethality.
CC {ECO:0000269|PubMed:17993620}.
CC -!- SIMILARITY: Belongs to the 5'-3' exonuclease family. XRN2/RAT1
CC subfamily. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAF87130.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AF286719; AAG40732.1; -; mRNA.
DR EMBL; AC006434; AAF87130.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002684; AEE35742.1; -; Genomic_DNA.
DR EMBL; AY136383; AAM97049.1; -; mRNA.
DR EMBL; BT000175; AAN15494.1; -; mRNA.
DR PIR; D96786; D96786.
DR RefSeq; NP_565114.1; NM_106217.3. [Q9FQ03-1]
DR AlphaFoldDB; Q9FQ03; -.
DR SMR; Q9FQ03; -.
DR STRING; 3702.AT1G75660.1; -.
DR iPTMnet; Q9FQ03; -.
DR PaxDb; Q9FQ03; -.
DR PRIDE; Q9FQ03; -.
DR ProteomicsDB; 242405; -. [Q9FQ03-1]
DR EnsemblPlants; AT1G75660.1; AT1G75660.1; AT1G75660. [Q9FQ03-1]
DR GeneID; 843900; -.
DR Gramene; AT1G75660.1; AT1G75660.1; AT1G75660. [Q9FQ03-1]
DR KEGG; ath:AT1G75660; -.
DR Araport; AT1G75660; -.
DR TAIR; locus:2005614; AT1G75660.
DR eggNOG; KOG2044; Eukaryota.
DR HOGENOM; CLU_006038_1_0_1; -.
DR OMA; CLHYYVH; -.
DR OrthoDB; 685597at2759; -.
DR PhylomeDB; Q9FQ03; -.
DR PRO; PR:Q9FQ03; -.
DR Proteomes; UP000006548; Chromosome 1.
DR ExpressionAtlas; Q9FQ03; baseline and differential.
DR Genevisible; Q9FQ03; AT.
DR GO; GO:0005634; C:nucleus; IDA:TAIR.
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:TAIR.
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; Coiled coil; Exonuclease; Hydrolase; Metal-binding;
KW mRNA processing; Nuclease; Nucleus; Reference proteome; rRNA processing;
KW Zinc; Zinc-finger.
FT CHAIN 1..1020
FT /note="5'-3' exoribonuclease 3"
FT /id="PRO_0000348955"
FT ZN_FING 262..279
FT /note="CCHC-type"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00047"
FT REGION 113..144
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 411..440
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 452..483
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 831..859
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 875..897
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 911..1020
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COILED 487..523
FT /evidence="ECO:0000255"
FT COMPBIAS 117..144
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 411..436
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 453..469
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 836..855
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 938..988
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1002..1020
FT /note="Basic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT VAR_SEQ 746..763
FT /note="SDGMNGYLTPCSGETHPP -> RFVKRNPICLFYDFVVNE (in isoform
FT 2)"
FT /evidence="ECO:0000303|PubMed:14593172"
FT /id="VSP_035194"
FT VAR_SEQ 764..1020
FT /note="Missing (in isoform 2)"
FT /evidence="ECO:0000303|PubMed:14593172"
FT /id="VSP_035195"
SQ SEQUENCE 1020 AA; 116826 MW; E383AB94A0A758D3 CRC64;
MGVPSFYRWL AEKYPLLVAD VIEEEPVEIE GIKIPVDTSK PNPNNLEYDN LYLDMNGIIH
PCFHPEDRPS PTTFEEVFQC MFDYIDRLFV MVRPRKLLYM AIDGVAPRAK MNQQRSRRFR
SAKDASDAAA EEERLREEFE REGRRLPPKV DSQVFDSNVI TPGTEFMGVL SIALQYYVHL
RLNHDVGWKN IKVILSDANV PGEGEHKIMS YIRLQRNLPG FDPNTRHCLY GLDADLIMLG
LATHEVHFSI LREVVYTPGQ QERCFLCGQM GHFASNCEGK PKKRAGESDE KGDGNDFVKK
PYQFLHIWVL REYLELEMRI PNPPFEIDLE RIVDDFIFIC FFVGNDFLPH MPTLEIREGA
INLLMAVYKK EFRSFDGYLT DGCKPNLKRV EQFIQAVGSF EDKIFQKRAM QHQRQAERVK
RDKAGKATKR MDDEAPTVQP DLVPVARFSG SRLASAPTPS PFQSNDGRSA PHQKVRRLSP
GSSVGAAIVD VENSLESDER ENKEELKTKL KELIREKSDA FNSDTTEEDK VKLGQPGWRE
RYYEEKFSVV TPEEMERVRK DVVLKYTEGL CWVMHYYMEG VCSWQWFYPY HYAPFASDLK
DLGEMDIKFE LGTPFKPFNQ LLGVFPAASS HALPERYRTL MTDPNSPIID FYPTDFEVDM
NGKRFSWQGI AKLPFIDERR LLEAVSEVEF TLTDEEKRRN SRMCDMLFIA TSHRLAELVF
SLDNHCRQLS ARERVDFKVK IKPKLSDGMN GYLTPCSGET HPPVFRSPME GMEDILTNQV
ICCIYRLPDA HEHITRPPPG VIFPKKTVDI GDLKPPPALW HEDNGRRPMH NNHGMHNNHG
MHNNQGRQNP PGSVSGRHLG NAAHRLVSNS LQMGTDRYQT PTDVPAPGYG YNPPQYVPPI
PYQHGGYMAP PGAQGYAQPA PYQNRGGYQP RGPSGRFPSE PYQSQSREGQ HASRGGGYSG
NHQNQHQQQQ WHGQGGSEQN NPRGYNGQHH HQQGGDHDRR GRGRGSHHHH DQGGNPRHRY
