SDN1_ARATH
ID SDN1_ARATH Reviewed; 409 AA.
AC A3KPE8; Q9SN08;
DT 25-NOV-2008, integrated into UniProtKB/Swiss-Prot.
DT 03-APR-2007, sequence version 1.
DT 03-AUG-2022, entry version 93.
DE RecName: Full=Small RNA degrading nuclease 1;
DE EC=3.1.-.-;
GN Name=SDN1; OrderedLocusNames=At3g50100; ORFNames=F3A4.180;
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=11130713; DOI=10.1038/35048706;
RA Salanoubat M., Lemcke K., Rieger M., Ansorge W., Unseld M., Fartmann B.,
RA Valle G., Bloecker H., Perez-Alonso M., Obermaier B., Delseny M.,
RA Boutry M., Grivell L.A., Mache R., Puigdomenech P., De Simone V.,
RA Choisne N., Artiguenave F., Robert C., Brottier P., Wincker P.,
RA Cattolico L., Weissenbach J., Saurin W., Quetier F., Schaefer M.,
RA Mueller-Auer S., Gabel C., Fuchs M., Benes V., Wurmbach E., Drzonek H.,
RA Erfle H., Jordan N., Bangert S., Wiedelmann R., Kranz H., Voss H.,
RA Holland R., Brandt P., Nyakatura G., Vezzi A., D'Angelo M., Pallavicini A.,
RA Toppo S., Simionati B., Conrad A., Hornischer K., Kauer G., Loehnert T.-H.,
RA Nordsiek G., Reichelt J., Scharfe M., Schoen O., Bargues M., Terol J.,
RA Climent J., Navarro P., Collado C., Perez-Perez A., Ottenwaelder B.,
RA Duchemin D., Cooke R., Laudie M., Berger-Llauro C., Purnelle B., Masuy D.,
RA de Haan M., Maarse A.C., Alcaraz J.-P., Cottet A., Casacuberta E.,
RA Monfort A., Argiriou A., Flores M., Liguori R., Vitale D., Mannhaupt G.,
RA Haase D., Schoof H., Rudd S., Zaccaria P., Mewes H.-W., Mayer K.F.X.,
RA Kaul S., Town C.D., Koo H.L., Tallon L.J., Jenkins J., Rooney T., Rizzo M.,
RA Walts A., Utterback T., Fujii C.Y., Shea T.P., Creasy T.H., Haas B.,
RA Maiti R., Wu D., Peterson J., Van Aken S., Pai G., Militscher J.,
RA Sellers P., Gill J.E., Feldblyum T.V., Preuss D., Lin X., Nierman W.C.,
RA Salzberg S.L., White O., Venter J.C., Fraser C.M., Kaneko T., Nakamura Y.,
RA Sato S., Kato T., Asamizu E., Sasamoto S., Kimura T., Idesawa K.,
RA Kawashima K., Kishida Y., Kiyokawa C., Kohara M., Matsumoto M., Matsuno A.,
RA Muraki A., Nakayama S., Nakazaki N., Shinpo S., Takeuchi C., Wada T.,
RA Watanabe A., Yamada M., Yasuda M., Tabata S.;
RT "Sequence and analysis of chromosome 3 of the plant Arabidopsis thaliana.";
RL Nature 408:820-822(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;
RA Bautista V.R., Kim C.J., Chen H., Wu S.Y., De Los Reyes C., Ecker J.R.;
RT "Arabidopsis ORF clones.";
RL Submitted (FEB-2007) to the EMBL/GenBank/DDBJ databases.
RN [4]
RP FUNCTION, 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 {ECO:0000269|PubMed:18787168}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000305}.
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 -!- MISCELLANEOUS: Presence of 2'-O-methyl or 3'poly-U in the small RNA
CC deters the activity of SDN1.
CC -!- SIMILARITY: Belongs to the REXO1/REXO3 family. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=CAB62118.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AL132978; CAB62118.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002686; AEE78626.1; -; Genomic_DNA.
DR EMBL; BT030315; ABO09879.1; -; mRNA.
DR PIR; T45863; T45863.
DR RefSeq; NP_190579.2; NM_114870.4.
DR PDB; 5Z9X; X-ray; 2.80 A; A=1-409.
DR PDB; 5Z9Z; X-ray; 2.05 A; A=309-409.
DR PDBsum; 5Z9X; -.
DR PDBsum; 5Z9Z; -.
DR AlphaFoldDB; A3KPE8; -.
DR SMR; A3KPE8; -.
DR STRING; 3702.AT3G50100.1; -.
DR iPTMnet; A3KPE8; -.
DR PaxDb; A3KPE8; -.
DR PRIDE; A3KPE8; -.
DR ProteomicsDB; 232666; -.
DR EnsemblPlants; AT3G50100.1; AT3G50100.1; AT3G50100.
DR GeneID; 824172; -.
DR Gramene; AT3G50100.1; AT3G50100.1; AT3G50100.
DR KEGG; ath:AT3G50100; -.
DR Araport; AT3G50100; -.
DR TAIR; locus:2083163; AT3G50100.
DR eggNOG; KOG2248; Eukaryota.
DR HOGENOM; CLU_030142_0_0_1; -.
DR InParanoid; A3KPE8; -.
DR OMA; CAFVIFR; -.
DR OrthoDB; 774159at2759; -.
DR PhylomeDB; A3KPE8; -.
DR PRO; PR:A3KPE8; -.
DR Proteomes; UP000006548; Chromosome 3.
DR ExpressionAtlas; A3KPE8; baseline and differential.
DR GO; GO:0005634; C:nucleus; IBA:GO_Central.
DR GO; GO:0008408; F:3'-5' exonuclease activity; IDA:TAIR.
DR GO; GO:0000175; F:3'-5'-exoribonuclease activity; IDA:CACAO.
DR GO; GO:0044748; F:3'-5'-exoribonuclease activity involved in mature miRNA 3'-end processing; IDA:TAIR.
DR GO; GO:0004527; F:exonuclease activity; IBA:GO_Central.
DR GO; GO:0035198; F:miRNA binding; IPI:TAIR.
DR GO; GO:0010587; P:miRNA catabolic process; IDA:TAIR.
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 Pfam; PF00929; RNase_T; 1.
DR SMART; SM00479; EXOIII; 1.
DR SUPFAM; SSF53098; SSF53098; 1.
DR SUPFAM; SSF54928; SSF54928; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Exonuclease; Hydrolase; Nuclease; Nucleus;
KW Reference proteome.
FT CHAIN 1..409
FT /note="Small RNA degrading nuclease 1"
FT /id="PRO_0000355084"
FT DOMAIN 140..291
FT /note="Exonuclease"
FT HELIX 10..23
FT /evidence="ECO:0007829|PDB:5Z9X"
FT HELIX 32..38
FT /evidence="ECO:0007829|PDB:5Z9X"
FT HELIX 54..61
FT /evidence="ECO:0007829|PDB:5Z9X"
FT HELIX 67..86
FT /evidence="ECO:0007829|PDB:5Z9X"
FT HELIX 90..92
FT /evidence="ECO:0007829|PDB:5Z9X"
FT HELIX 95..105
FT /evidence="ECO:0007829|PDB:5Z9X"
FT HELIX 109..112
FT /evidence="ECO:0007829|PDB:5Z9X"
FT HELIX 127..129
FT /evidence="ECO:0007829|PDB:5Z9X"
FT HELIX 132..135
FT /evidence="ECO:0007829|PDB:5Z9X"
FT STRAND 140..150
FT /evidence="ECO:0007829|PDB:5Z9X"
FT STRAND 155..164
FT /evidence="ECO:0007829|PDB:5Z9X"
FT STRAND 169..175
FT /evidence="ECO:0007829|PDB:5Z9X"
FT HELIX 192..197
FT /evidence="ECO:0007829|PDB:5Z9X"
FT HELIX 203..215
FT /evidence="ECO:0007829|PDB:5Z9X"
FT STRAND 219..224
FT /evidence="ECO:0007829|PDB:5Z9X"
FT HELIX 225..232
FT /evidence="ECO:0007829|PDB:5Z9X"
FT STRAND 239..241
FT /evidence="ECO:0007829|PDB:5Z9X"
FT HELIX 242..245
FT /evidence="ECO:0007829|PDB:5Z9X"
FT HELIX 259..266
FT /evidence="ECO:0007829|PDB:5Z9X"
FT HELIX 280..296
FT /evidence="ECO:0007829|PDB:5Z9X"
FT HELIX 309..313
FT /evidence="ECO:0007829|PDB:5Z9Z"
FT STRAND 316..323
FT /evidence="ECO:0007829|PDB:5Z9Z"
FT HELIX 328..334
FT /evidence="ECO:0007829|PDB:5Z9Z"
FT STRAND 337..343
FT /evidence="ECO:0007829|PDB:5Z9Z"
FT STRAND 351..361
FT /evidence="ECO:0007829|PDB:5Z9Z"
FT HELIX 362..371
FT /evidence="ECO:0007829|PDB:5Z9Z"
FT STRAND 374..378
FT /evidence="ECO:0007829|PDB:5Z9Z"
FT STRAND 384..391
FT /evidence="ECO:0007829|PDB:5Z9Z"
FT STRAND 397..405
FT /evidence="ECO:0007829|PDB:5Z9Z"
SQ SEQUENCE 409 AA; 46364 MW; E7750B8B1411415D CRC64;
MELKLATAEK QVLDELVKLL QSRDLRGENG NWKEFLHVYD KNADSPSDPS RRSHEDLVQF
LTTFKKKEDL QLLKCHANHL LIENLKQESQ DEDTPEQMLV RLTVEHPSYS LDYSFKPYSE
DWFVSDVGMK MKKVMESTNM VAVDCEMVLC EDGTEGLVRV GVVDRDLKVI LDEFVKPNKP
VVDYRTDITG ITAEDIENAS LSVVDIQETL QPFLSTGTIL VGHSLNRDLE VLKIDHPKVI
DTALVFKYPN TRKLRRPSLN NLCKSILGYE VRKTGVPHDC VHDASAAMKL ALAVVEKRVD
TTIKPSKEML EVEKAKLFLH KIPNNVPSEE LEQVLSGKFT LDVKQAKTQG RYYCAFALFH
SSEDADQAFE HIDGIEMTDS LGLPQKVVII KLSSGSRASI YVRKMVQDE
