RICE1_ARATH
ID RICE1_ARATH Reviewed; 200 AA.
AC Q9SF21; A0A178VAY5;
DT 08-MAY-2019, integrated into UniProtKB/Swiss-Prot.
DT 01-MAY-2000, sequence version 1.
DT 25-MAY-2022, entry version 150.
DE RecName: Full=Protein RISC-INTERACTING CLEARING 3'-5' EXORIBONUCLEASE 1 {ECO:0000303|PubMed:28463111};
DE EC=3.1.13.1 {ECO:0000269|PubMed:28463111};
GN Name=RICE1 {ECO:0000303|PubMed:28463111};
GN OrderedLocusNames=At3g11770 {ECO:0000312|Araport:AT3G11770};
GN ORFNames=F26K24.6 {ECO:0000312|EMBL:AAF23193.1};
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;
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 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 (JUL-2006) to the EMBL/GenBank/DDBJ databases.
RN [5]
RP X-RAY CRYSTALLOGRAPHY (2.94 ANGSTROMS), FUNCTION, MUTAGENESIS OF ARG-47;
RP ASP-52; TYR-54; ASP-114; LYS-119 AND GLU-187, DISRUPTION PHENOTYPE,
RP INTERACTION WITH AGO1 AND AGO10, SUBUNIT, IDENTIFICATION BY MASS
RP SPECTROMETRY, SUBCELLULAR LOCATION, AND TISSUE SPECIFICITY.
RC STRAIN=cv. Columbia, and cv. Landsberg erecta;
RX PubMed=28463111; DOI=10.7554/elife.24466;
RA Zhang Z., Hu F., Sung M.W., Shu C., Castillo-Gonzalez C., Koiwa H.,
RA Tang G., Dickman M., Li P., Zhang X.;
RT "RISC-interacting clearing 3'- 5' exoribonucleases (RICEs) degrade
RT uridylated cleavage fragments to maintain functional RISC in Arabidopsis
RT thaliana.";
RL Elife 6:E24466-E24466(2017).
CC -!- FUNCTION: 3'-to-5' exoribonuclease (RNase) specifically targeting
CC single-stranded RNAs (PubMed:28463111). Triggers miRNA accumulation in
CC RNA-induced silencing complex (RISC), composed of miRNAs and AGO
CC proteins, by degrading uridylated cleavage fragments (PubMed:28463111).
CC Required during plant growth and development (PubMed:28463111).
CC {ECO:0000269|PubMed:28463111}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=Exonucleolytic cleavage in the 3'- to 5'-direction to yield
CC nucleoside 5'-phosphates.; EC=3.1.13.1;
CC Evidence={ECO:0000269|PubMed:28463111};
CC -!- SUBUNIT: Homohexamer with DnaQ-like exonuclease fold in a ring-shaped
CC structure with a central cavity (PubMed:28463111). Component of AGO1
CC and AGO10-centered RNA-induced silencing complexes (RISC)
CC (PubMed:28463111). Interacts with and acts as a cofactor of AGO1 and
CC AGO10 (PubMed:28463111). {ECO:0000269|PubMed:28463111}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:28463111}.
CC -!- TISSUE SPECIFICITY: Ubiquitously expressed throughout development in
CC germinating seeds, cotyledons, leaves and roots of young seedlings and
CC adult plants, stems and inflorescence. {ECO:0000269|PubMed:28463111}.
CC -!- DISRUPTION PHENOTYPE: Little effect on miRNAs levels (PubMed:28463111).
CC Plants lacking both RICE1 and RICE2 have reduced miRNAs levels and
CC lower miRNA retained by AGO1, thus leading to the up-regulation of
CC targeted mRNA transcripts (PubMed:28463111).
CC {ECO:0000269|PubMed:28463111}.
CC -!- SIMILARITY: Belongs to the RICE family. {ECO:0000305}.
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DR EMBL; AC016795; AAF23193.1; -; Genomic_DNA.
DR EMBL; CP002686; AEE75095.1; -; Genomic_DNA.
DR EMBL; BT003106; AAO24538.1; -; mRNA.
DR EMBL; AK228135; BAF00092.1; -; mRNA.
DR RefSeq; NP_187783.1; NM_112010.6.
DR PDB; 5V5F; X-ray; 2.94 A; A/B/C=1-200.
DR PDBsum; 5V5F; -.
DR AlphaFoldDB; Q9SF21; -.
DR SMR; Q9SF21; -.
DR STRING; 3702.AT3G11770.1; -.
DR PaxDb; Q9SF21; -.
DR PRIDE; Q9SF21; -.
DR ProteomicsDB; 181475; -.
DR EnsemblPlants; AT3G11770.1; AT3G11770.1; AT3G11770.
DR GeneID; 820351; -.
DR Gramene; AT3G11770.1; AT3G11770.1; AT3G11770.
DR KEGG; ath:AT3G11770; -.
DR Araport; AT3G11770; -.
DR TAIR; locus:2081526; AT3G11770.
DR eggNOG; ENOG502RRGJ; Eukaryota.
DR HOGENOM; CLU_1373971_0_0_1; -.
DR InParanoid; Q9SF21; -.
DR OMA; TKSEWRL; -.
DR OrthoDB; 1295758at2759; -.
DR PhylomeDB; Q9SF21; -.
DR PRO; PR:Q9SF21; -.
DR Proteomes; UP000006548; Chromosome 3.
DR ExpressionAtlas; Q9SF21; baseline and differential.
DR GO; GO:0005737; C:cytoplasm; IDA:TAIR.
DR GO; GO:0005829; C:cytosol; HDA:TAIR.
DR GO; GO:0005634; C:nucleus; IBA:GO_Central.
DR GO; GO:0000325; C:plant-type vacuole; HDA:TAIR.
DR GO; GO:0008408; F:3'-5' exonuclease activity; IBA:GO_Central.
DR GO; GO:0008859; F:exoribonuclease II activity; IEA:UniProtKB-EC.
DR GO; GO:0003676; F:nucleic acid binding; IEA:InterPro.
DR GO; GO:0043621; F:protein self-association; IDA:UniProtKB.
DR GO; GO:1905172; F:RISC complex binding; IDA:UniProtKB.
DR GO; GO:0008310; F:single-stranded DNA 3'-5' exodeoxyribonuclease activity; IDA:TAIR.
DR GO; GO:0031047; P:gene silencing by RNA; IEA:UniProtKB-KW.
DR GO; GO:2000630; P:positive regulation of miRNA metabolic process; IMP:TAIR.
DR Gene3D; 3.30.420.10; -; 1.
DR InterPro; IPR012337; RNaseH-like_sf.
DR InterPro; IPR036397; RNaseH_sf.
DR SUPFAM; SSF53098; SSF53098; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Cytoplasm; Hydrolase; Nuclease; Reference proteome;
KW RNA-mediated gene silencing.
FT CHAIN 1..200
FT /note="Protein RISC-INTERACTING CLEARING 3'-5'
FT EXORIBONUCLEASE 1"
FT /id="PRO_0000447255"
FT REGION 35..66
FT /note="Oligomerization"
FT /evidence="ECO:0000269|PubMed:28463111,
FT ECO:0007744|PDB:5V5F"
FT REGION 102..127
FT /note="Oligomerization"
FT /evidence="ECO:0000269|PubMed:28463111,
FT ECO:0007744|PDB:5V5F"
FT REGION 166..173
FT /note="Oligomerization"
FT /evidence="ECO:0000269|PubMed:28463111,
FT ECO:0007744|PDB:5V5F"
FT MUTAGEN 47
FT /note="R->E: Impaired oligomerization."
FT /evidence="ECO:0000269|PubMed:28463111"
FT MUTAGEN 52
FT /note="D->A: Normal oligomerization but impaired
FT exoribonuclease activity. Pleiotropic developmental defects
FT including spoon-shaped cotyledons, twisted true leaves and
FT infertile flowers associated with reduced miRNAs and trans-
FT acting siRNA levels. Lower miRNA retained by AGO1, but
FT accumulation of extended uridylated 5' RNA fragments
FT generated by RISC cleavage."
FT /evidence="ECO:0000269|PubMed:28463111"
FT MUTAGEN 54
FT /note="Y->S: Normal oligomerization but impaired
FT exoribonuclease activity. Pleiotropic developmental defects
FT including spoon-shaped cotyledons, twisted true leaves and
FT infertile flowers associated with reduced miRNAs and trans-
FT acting siRNA levels."
FT /evidence="ECO:0000269|PubMed:28463111"
FT MUTAGEN 114
FT /note="D->E: Impaired oligomerization."
FT /evidence="ECO:0000269|PubMed:28463111"
FT MUTAGEN 119
FT /note="K->E: Normal oligomerization."
FT /evidence="ECO:0000269|PubMed:28463111"
FT MUTAGEN 187
FT /note="E->A: Normal oligomerization but impaired
FT exoribonuclease activity."
FT /evidence="ECO:0000269|PubMed:28463111"
FT STRAND 6..10
FT /evidence="ECO:0007829|PDB:5V5F"
FT STRAND 16..23
FT /evidence="ECO:0007829|PDB:5V5F"
FT HELIX 31..44
FT /evidence="ECO:0007829|PDB:5V5F"
FT STRAND 48..58
FT /evidence="ECO:0007829|PDB:5V5F"
FT TURN 60..62
FT /evidence="ECO:0007829|PDB:5V5F"
FT STRAND 65..74
FT /evidence="ECO:0007829|PDB:5V5F"
FT STRAND 76..83
FT /evidence="ECO:0007829|PDB:5V5F"
FT HELIX 90..92
FT /evidence="ECO:0007829|PDB:5V5F"
FT HELIX 93..99
FT /evidence="ECO:0007829|PDB:5V5F"
FT STRAND 102..110
FT /evidence="ECO:0007829|PDB:5V5F"
FT HELIX 112..122
FT /evidence="ECO:0007829|PDB:5V5F"
FT STRAND 127..131
FT /evidence="ECO:0007829|PDB:5V5F"
FT HELIX 132..140
FT /evidence="ECO:0007829|PDB:5V5F"
FT HELIX 143..147
FT /evidence="ECO:0007829|PDB:5V5F"
FT HELIX 150..158
FT /evidence="ECO:0007829|PDB:5V5F"
FT HELIX 163..170
FT /evidence="ECO:0007829|PDB:5V5F"
FT HELIX 172..174
FT /evidence="ECO:0007829|PDB:5V5F"
FT HELIX 177..199
FT /evidence="ECO:0007829|PDB:5V5F"
SQ SEQUENCE 200 AA; 22956 MW; EAD785D0F3B5AD48 CRC64;
MASFDGQGFM MVDNSWVQTK AIDVESTTDI SPYLSKILED SVWNGNRSIV FDVYWDVKSV
STKSEWRLCS VKFSTKNFCL FLRLPNPFCD NLKDLYRFFA SKFVTFVGVQ IQEDLALLKE
NHGIVIRSSL EIGKLAAKAR GTPIVEFLGT RELAHKILWY DMSRLDSIQS KWDEASSNDR
LEAAAIEGWL IFNVYDQLQQ
