RICE2_ARATH
ID RICE2_ARATH Reviewed; 206 AA.
AC Q9FNG3;
DT 30-AUG-2005, integrated into UniProtKB/Swiss-Prot.
DT 01-MAR-2001, sequence version 1.
DT 03-AUG-2022, entry version 125.
DE RecName: Full=Protein RISC-INTERACTING CLEARING 3'-5' EXORIBONUCLEASE 2 {ECO:0000303|PubMed:28463111};
DE EC=3.1.13.1 {ECO:0000269|PubMed:28463111};
DE AltName: Full=DnaQ-like 3'-5' exonuclease domain-containing protein {ECO:0000303|PubMed:23616405};
DE Short=AtDECP {ECO:0000303|PubMed:23616405};
GN Name=RICE2 {ECO:0000303|PubMed:28463111};
GN Synonyms=DECP {ECO:0000303|PubMed:23616405};
GN OrderedLocusNames=At5g06450 {ECO:0000312|Araport:AT5G06450};
GN ORFNames=MHF15.3 {ECO:0000312|EMBL:BAB08967.1};
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=9405937; DOI=10.1093/dnares/4.4.291;
RA Kotani H., Nakamura Y., Sato S., Kaneko T., Asamizu E., Miyajima N.,
RA Tabata S.;
RT "Structural analysis of Arabidopsis thaliana chromosome 5. II. Sequence
RT features of the regions of 1,044,062 bp covered by thirteen physically
RT assigned P1 clones.";
RL DNA Res. 4:291-300(1997).
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 FUNCTION, DISRUPTION PHENOTYPE, CATALYTIC ACTIVITY, INTERACTION WITH AGO1
RP AND AGO10, SUBUNIT, 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).
RN [5]
RP X-RAY CRYSTALLOGRAPHY (2.10 ANGSTROMS) OF 2-206, AND SUBUNIT.
RX PubMed=17850744; DOI=10.1016/j.str.2007.06.019;
RA Levin E.J., Kondrashov D.A., Wesenberg G.E., Phillips G.N. Jr.;
RT "Ensemble refinement of protein crystal structures: validation and
RT application.";
RL Structure 15:1040-1052(2007).
RN [6]
RP X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS) OF 2-206, AND SUBUNIT.
RX PubMed=23616405; DOI=10.1002/prot.24315;
RA Smith D.W., Han M.R., Park J.S., Kim K.R., Yeom T., Lee J.Y., Kim D.J.,
RA Bingman C.A., Kim H.-J., Jo K., Han B.W., Phillips G.N. Jr.;
RT "Crystal structure of the protein from Arabidopsis thaliana gene At5g06450,
RT a putative DnaQ-like exonuclease domain-containing protein with
RT homohexameric assembly.";
RL Proteins 81:1669-1675(2013).
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 (By similarity).
CC {ECO:0000250|UniProtKB:Q9SF21, 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, PubMed:23616405,
CC PubMed:17850744). Component of AGO1 and AGO10-centered RNA-induced
CC silencing complexes (RISC) (PubMed:28463111). Interacts with and acts
CC as a cofactor of AGO1 and AGO10 (PubMed:28463111).
CC {ECO:0000269|PubMed:17850744, ECO:0000269|PubMed:23616405,
CC ECO:0000269|PubMed:28463111}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000250|UniProtKB:Q9SF21}.
CC -!- TISSUE SPECIFICITY: Restricted to shoot and root apical meristems,
CC trichomes, and vascular veins. {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; AB006700; BAB08967.1; -; Genomic_DNA.
DR EMBL; CP002688; AED91019.1; -; Genomic_DNA.
DR EMBL; AY080689; AAL86312.1; -; mRNA.
DR EMBL; AY117335; AAM51410.1; -; mRNA.
DR RefSeq; NP_196263.1; NM_120728.6.
DR PDB; 1VK0; X-ray; 2.10 A; A/B/C/D/E/F=2-206.
DR PDB; 2Q3S; X-ray; 2.10 A; A/B/C/D/E/F=2-206.
DR PDBsum; 1VK0; -.
DR PDBsum; 2Q3S; -.
DR AlphaFoldDB; Q9FNG3; -.
DR SMR; Q9FNG3; -.
DR BioGRID; 15812; 1.
DR STRING; 3702.AT5G06450.1; -.
DR PaxDb; Q9FNG3; -.
DR PRIDE; Q9FNG3; -.
DR ProteomicsDB; 243074; -.
DR DNASU; 830533; -.
DR EnsemblPlants; AT5G06450.1; AT5G06450.1; AT5G06450.
DR GeneID; 830533; -.
DR Gramene; AT5G06450.1; AT5G06450.1; AT5G06450.
DR KEGG; ath:AT5G06450; -.
DR Araport; AT5G06450; -.
DR TAIR; locus:2164255; AT5G06450.
DR eggNOG; ENOG502RRGJ; Eukaryota.
DR HOGENOM; CLU_1373971_0_0_1; -.
DR InParanoid; Q9FNG3; -.
DR OMA; PFHDNLK; -.
DR OrthoDB; 1295758at2759; -.
DR PhylomeDB; Q9FNG3; -.
DR EvolutionaryTrace; Q9FNG3; -.
DR PRO; PR:Q9FNG3; -.
DR Proteomes; UP000006548; Chromosome 5.
DR ExpressionAtlas; Q9FNG3; baseline and differential.
DR GO; GO:0005737; C:cytoplasm; IDA: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..206
FT /note="Protein RISC-INTERACTING CLEARING 3'-5'
FT EXORIBONUCLEASE 2"
FT /id="PRO_0000220619"
FT REGION 35..71
FT /note="Oligomerization"
FT /evidence="ECO:0000269|PubMed:17850744,
FT ECO:0000269|PubMed:23616405, ECO:0007744|PDB:1VK0,
FT ECO:0007744|PDB:2Q3S"
FT REGION 107..132
FT /note="Oligomerization"
FT /evidence="ECO:0000269|PubMed:17850744,
FT ECO:0000269|PubMed:23616405, ECO:0007744|PDB:1VK0,
FT ECO:0007744|PDB:2Q3S"
FT REGION 171..178
FT /note="Oligomerization"
FT /evidence="ECO:0000269|PubMed:17850744,
FT ECO:0000269|PubMed:23616405, ECO:0007744|PDB:1VK0,
FT ECO:0007744|PDB:2Q3S"
FT STRAND 8..10
FT /evidence="ECO:0007829|PDB:1VK0"
FT STRAND 16..23
FT /evidence="ECO:0007829|PDB:1VK0"
FT HELIX 31..44
FT /evidence="ECO:0007829|PDB:1VK0"
FT STRAND 48..56
FT /evidence="ECO:0007829|PDB:1VK0"
FT HELIX 67..70
FT /evidence="ECO:0007829|PDB:1VK0"
FT STRAND 72..79
FT /evidence="ECO:0007829|PDB:1VK0"
FT STRAND 81..88
FT /evidence="ECO:0007829|PDB:1VK0"
FT HELIX 95..97
FT /evidence="ECO:0007829|PDB:1VK0"
FT HELIX 98..104
FT /evidence="ECO:0007829|PDB:1VK0"
FT STRAND 107..115
FT /evidence="ECO:0007829|PDB:1VK0"
FT HELIX 117..127
FT /evidence="ECO:0007829|PDB:1VK0"
FT STRAND 132..136
FT /evidence="ECO:0007829|PDB:1VK0"
FT HELIX 137..145
FT /evidence="ECO:0007829|PDB:1VK0"
FT HELIX 148..152
FT /evidence="ECO:0007829|PDB:1VK0"
FT HELIX 155..163
FT /evidence="ECO:0007829|PDB:1VK0"
FT HELIX 168..175
FT /evidence="ECO:0007829|PDB:1VK0"
FT HELIX 176..179
FT /evidence="ECO:0007829|PDB:1VK0"
FT HELIX 182..205
FT /evidence="ECO:0007829|PDB:1VK0"
SQ SEQUENCE 206 AA; 23215 MW; 75A7D8480079E47A CRC64;
MASFDGPKFK MTDGSYVQTK TIDVGSSTDI SPYLSLIRED SILNGNRAVI FDVYWDVGFP
ETETKTKTSG WSLSSVKLST RNLCLFLRLP KPFHDNLKDL YRFFASKFVT FVGVQIEEDL
DLLRENHGLV IRNAINVGKL AAEARGTLVL EFLGTRELAH RVLWSDLGQL DSIEAKWEKA
GPEEQLEAAA IEGWLIVNVW DQLSDE
