ID   SDN3_ARATH              Reviewed;         782 AA.
AC   Q8RXK2; Q9FH89;
DT   25-NOV-2008, integrated into UniProtKB/Swiss-Prot.
DT   01-JUN-2002, sequence version 1.
DT   25-MAY-2022, entry version 124.
DE   RecName: Full=Small RNA degrading nuclease 3;
DE            EC=3.1.-.-;
GN   Name=SDN3; OrderedLocusNames=At5g67240; ORFNames=K21H1.20;
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 [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   [2]
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   [3]
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   [4]
RP   IDENTIFICATION BY MASS SPECTROMETRY, AND SUBUNIT.
RX   PubMed=17560376; DOI=10.1016/j.molcel.2007.05.007;
RA   Baeckstroem S., Elfving N., Nilsson R., Wingsle G., Bjoerklund S.;
RT   "Purification of a plant mediator from Arabidopsis thaliana identifies PFT1
RT   as the Med25 subunit.";
RL   Mol. Cell 26:717-729(2007).
RN   [5]
RP   IDENTIFICATION, AND DISRUPTION PHENOTYPE.
RX   PubMed=18787168; DOI=10.1126/science.1163728;
RA   Ramachandran V., Chen X.;
RT   "Degradation of microRNAs by a family of exoribonucleases in Arabidopsis.";
RL   Science 321:1490-1492(2008).
CC   -!- FUNCTION: 3'-5' exonuclease degrading single-stranded small RNAs.
CC   -!- SUBUNIT: Associated with the Mediator complex.
CC       {ECO:0000269|PubMed:17560376}.
CC   -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000305}.
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=Q8RXK2-1; Sequence=Displayed;
CC   -!- DISRUPTION PHENOTYPE: No visible phenotype; due to the redundancy with
CC       other SDN ribonucleases. Simultaneous knockdown of SDN1, SDN2 and SDN3
CC       results in elevated miRNA levels and pleiotropic developmental defects.
CC       {ECO:0000269|PubMed:18787168}.
CC   -!- SIMILARITY: Belongs to the REXO1/REXO3 family. {ECO:0000305}.
CC   -!- SEQUENCE CAUTION:
CC       Sequence=BAB10958.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR   EMBL; AB020742; BAB10958.1; ALT_SEQ; Genomic_DNA.
DR   EMBL; CP002688; AED98317.1; -; Genomic_DNA.
DR   EMBL; AY080843; AAL87318.1; -; mRNA.
DR   EMBL; BT001977; AAN71976.1; -; mRNA.
DR   RefSeq; NP_201525.2; NM_126124.4. [Q8RXK2-1]
DR   AlphaFoldDB; Q8RXK2; -.
DR   SMR; Q8RXK2; -.
DR   IntAct; Q8RXK2; 1.
DR   STRING; 3702.AT5G67240.1; -.
DR   iPTMnet; Q8RXK2; -.
DR   PaxDb; Q8RXK2; -.
DR   PRIDE; Q8RXK2; -.
DR   ProteomicsDB; 232969; -. [Q8RXK2-1]
DR   EnsemblPlants; AT5G67240.1; AT5G67240.1; AT5G67240. [Q8RXK2-1]
DR   GeneID; 836859; -.
DR   Gramene; AT5G67240.1; AT5G67240.1; AT5G67240. [Q8RXK2-1]
DR   KEGG; ath:AT5G67240; -.
DR   Araport; AT5G67240; -.
DR   TAIR; locus:2155563; AT5G67240.
DR   eggNOG; KOG2248; Eukaryota.
DR   InParanoid; Q8RXK2; -.
DR   PhylomeDB; Q8RXK2; -.
DR   PRO; PR:Q8RXK2; -.
DR   Proteomes; UP000006548; Chromosome 5.
DR   ExpressionAtlas; Q8RXK2; baseline and differential.
DR   Genevisible; Q8RXK2; AT.
DR   GO; GO:0016592; C:mediator complex; IDA:UniProtKB.
DR   GO; GO:0005634; C:nucleus; IBA:GO_Central.
DR   GO; GO:0004527; F:exonuclease activity; IBA:GO_Central.
DR   GO; GO:0003723; F:RNA binding; IEA:UniProtKB-KW.
DR   CDD; cd06145; REX1_like; 1.
DR   Gene3D; 3.30.420.10; -; 1.
DR   Gene3D; 3.30.70.330; -; 1.
DR   InterPro; IPR013520; Exonuclease_RNaseT/DNA_pol3.
DR   InterPro; IPR012677; Nucleotide-bd_a/b_plait_sf.
DR   InterPro; IPR035979; RBD_domain_sf.
DR   InterPro; IPR034922; REX1-like_exo.
DR   InterPro; IPR012337; RNaseH-like_sf.
DR   InterPro; IPR036397; RNaseH_sf.
DR   SMART; SM00479; EXOIII; 1.
DR   SUPFAM; SSF53098; SSF53098; 1.
DR   SUPFAM; SSF54928; SSF54928; 1.
PE   1: Evidence at protein level;
KW   Alternative splicing; Coiled coil; Exonuclease; Hydrolase; Nuclease;
KW   Nucleus; Reference proteome; Repeat; RNA-binding; Transcription;
KW   Transcription regulation.
FT   CHAIN           1..782
FT                   /note="Small RNA degrading nuclease 3"
FT                   /id="PRO_0000355086"
FT   DOMAIN          145..296
FT                   /note="Exonuclease"
FT   DOMAIN          331..410
FT                   /note="RRM 1"
FT   DOMAIN          469..549
FT                   /note="RRM 2"
FT   DOMAIN          608..688
FT                   /note="RRM 3"
FT   REGION          426..464
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   REGION          563..605
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COILED          577..605
FT                   /evidence="ECO:0000255"
FT   COILED          709..779
FT                   /evidence="ECO:0000255"
FT   COMPBIAS        429..464
FT                   /note="Basic and acidic residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
SQ   SEQUENCE   782 AA;  87465 MW;  427EDB62E043DBC5 CRC64;
     MEHKLATAEK KLLVDLVKLV QKRGLEGENG GWKEFLNVYD KKLGSSLSDP ARRSNDVLVA
     FLLTFKKKED LQLIARVMQC GANRELIEKF KQETPDKETP EQRLVRLTIT HDDYPGNYTF
     PSYAEDWYVT ELGKKKSKVI KSTRMLSIDC EMVTCEDGSQ ALVRVGAVDR DLKVVLDKFV
     KPDKPVIDYK TDITGVTAED LERATLSVAD IQKKLRRFLS VGTILVGHGL HNDLQVLRID
     HARVIDTSYV FEFVDAPKTQ RPSLNNLCKS VLGQEVRMDG AAHNCVHDAA AAMKLVLAAV
     EKGAATLIQP TEEMMVAEKR RQEARQEAGK AQLFLHKIPH DVPSEELHGV LSGNFTLVVK
     PPKTGGYSTA VVDFSSPEEA NEAFENVEGD VAKDKSGLPQ KKAVLKLSSG LAVSLFVRKM
     VQDDSPCEIS TSERARAEEN NVSSKRQKTE DETEETKEAT VNQREADKTK LFLHKIPHDV
     PSQELHGVLN GDFTLDVKPP KRKGGYYNAV VDFNSPEEAN EAFENVEGDV VKDKTGLPQK
     MVVFKLSSGS GVSLYVRKMV HDDSPGEIST TKRARTEESN MSSKRQKTED ESEETKEANA
     KQREADKTKL LLHKIPLNVP SQELKVVITG QFTLEVMPPK RKGRYYNAVV TFNSPEEANK
     AFEKVKGEAV KEKGGLAQKM VAFKLSSGSG ACLYVRKMVQ DESEETKEAN ANHCEDDHLK
     EMEELKEKLK AMEFAISCEG HSKEIEELKQ KLNAKEHQIQ AQDKIIANLK MKLEKKQSKS
     RS