RRP4_ARATH
ID RRP4_ARATH Reviewed; 322 AA.
AC Q9ZVT7;
DT 20-JAN-2016, integrated into UniProtKB/Swiss-Prot.
DT 01-MAY-1999, sequence version 1.
DT 03-AUG-2022, entry version 144.
DE RecName: Full=Exosome complex component RRP4 homolog {ECO:0000305};
DE AltName: Full=Ribosomal RNA-processing protein 4 {ECO:0000305};
DE Short=AtRRP4 {ECO:0000303|PubMed:11809881};
DE Short=AtRrp4p {ECO:0000303|PubMed:11809881};
GN Name=RRP4 {ECO:0000305};
GN OrderedLocusNames=At1g03360 {ECO:0000312|Araport:AT1G03360};
GN ORFNames=F15K9.4 {ECO:0000312|EMBL:AAC72108.1};
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=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 [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 (SEP-2004) to the EMBL/GenBank/DDBJ databases.
RN [5]
RP FUNCTION, SUBUNIT, INTERACTION WITH RPP41, TISSUE SPECIFICITY, AND DOMAIN.
RX PubMed=11809881; DOI=10.1093/nar/30.3.695;
RA Chekanova J.A., Dutko J.A., Mian I.S., Belostotsky D.A.;
RT "Arabidopsis thaliana exosome subunit AtRrp4p is a hydrolytic 3'-->5'
RT exonuclease containing S1 and KH RNA-binding domains.";
RL Nucleic Acids Res. 30:695-700(2002).
RN [6]
RP SUBUNIT, AND DISRUPTION PHENOTYPE.
RX PubMed=18160042; DOI=10.1016/j.cell.2007.10.056;
RA Chekanova J.A., Gregory B.D., Reverdatto S.V., Chen H., Kumar R.,
RA Hooker T., Yazaki J., Li P., Skiba N., Peng Q., Alonso J., Brukhin V.,
RA Grossniklaus U., Ecker J.R., Belostotsky D.A.;
RT "Genome-wide high-resolution mapping of exosome substrates reveals hidden
RT features in the Arabidopsis transcriptome.";
RL Cell 131:1340-1353(2007).
CC -!- FUNCTION: Non-catalytic component of the RNA exosome complex which has
CC 3'->5' exoribonuclease activity and participates in a multitude of
CC cellular RNA processing, maturation and degradation events. In vitro,
CC is an active and distributive 3'->5' exonuclease requiring a free 3'-OH
CC on the substrate and releasing nucleoside 5'-monophosphates
CC (PubMed:11809881). Required for normal embryo development
CC (PubMed:18160042). {ECO:0000269|PubMed:11809881,
CC ECO:0000269|PubMed:18160042}.
CC -!- SUBUNIT: Component of the RNA exosome complex (PubMed:11809881,
CC PubMed:18160042). Interacts with RPP41 (PubMed:11809881).
CC {ECO:0000269|PubMed:11809881, ECO:0000269|PubMed:18160042}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000250|UniProtKB:Q13868}.
CC Nucleus, nucleolus {ECO:0000250|UniProtKB:Q13868}. Nucleus
CC {ECO:0000250|UniProtKB:Q13868}.
CC -!- TISSUE SPECIFICITY: Expressed in roots, stems, rosette and cauline
CC leaves, flowers and siliques. {ECO:0000269|PubMed:11809881}.
CC -!- DOMAIN: The two RNA-binding domains (S1 motif and KH domain) are
CC separated by a conserved linker of five amino acids (KYGKL) and can
CC bind RNA independently. Both domains are also needed for RNA
CC degradation and interaction with RRP41, another exosome subunit.
CC -!- DISRUPTION PHENOTYPE: Embryonic lethality due to embryo developmental
CC arrest at early globular stage. {ECO:0000269|PubMed:18160042}.
CC -!- SIMILARITY: Belongs to the RRP4 family. {ECO:0000305}.
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DR EMBL; AC005278; AAC72108.1; -; Genomic_DNA.
DR EMBL; CP002684; AEE27563.1; -; Genomic_DNA.
DR EMBL; BT010533; AAQ65156.1; -; mRNA.
DR EMBL; AK176232; BAD43995.1; -; mRNA.
DR PIR; C86165; C86165.
DR RefSeq; NP_171835.1; NM_100218.5.
DR AlphaFoldDB; Q9ZVT7; -.
DR SMR; Q9ZVT7; -.
DR IntAct; Q9ZVT7; 8.
DR STRING; 3702.AT1G03360.1; -.
DR PaxDb; Q9ZVT7; -.
DR PRIDE; Q9ZVT7; -.
DR ProteomicsDB; 226848; -.
DR EnsemblPlants; AT1G03360.1; AT1G03360.1; AT1G03360.
DR GeneID; 839521; -.
DR Gramene; AT1G03360.1; AT1G03360.1; AT1G03360.
DR KEGG; ath:AT1G03360; -.
DR Araport; AT1G03360; -.
DR TAIR; locus:2014535; AT1G03360.
DR eggNOG; KOG3013; Eukaryota.
DR HOGENOM; CLU_034114_3_0_1; -.
DR InParanoid; Q9ZVT7; -.
DR OMA; MNMPDGV; -.
DR OrthoDB; 1121868at2759; -.
DR PhylomeDB; Q9ZVT7; -.
DR PRO; PR:Q9ZVT7; -.
DR Proteomes; UP000006548; Chromosome 1.
DR ExpressionAtlas; Q9ZVT7; baseline and differential.
DR GO; GO:0005737; C:cytoplasm; IDA:TAIR.
DR GO; GO:0000177; C:cytoplasmic exosome (RNase complex); IBA:GO_Central.
DR GO; GO:0000178; C:exosome (RNase complex); IBA:GO_Central.
DR GO; GO:0000176; C:nuclear exosome (RNase complex); IBA:GO_Central.
DR GO; GO:0005730; C:nucleolus; IDA:TAIR.
DR GO; GO:0005654; C:nucleoplasm; IDA:TAIR.
DR GO; GO:0003723; F:RNA binding; IBA:GO_Central.
DR GO; GO:0071034; P:CUT catabolic process; IBA:GO_Central.
DR GO; GO:0043928; P:exonucleolytic catabolism of deadenylated mRNA; IBA:GO_Central.
DR GO; GO:0000467; P:exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA); IBA:GO_Central.
DR GO; GO:0000460; P:maturation of 5.8S rRNA; IMP:TAIR.
DR GO; GO:0060149; P:negative regulation of post-transcriptional gene silencing; IMP:TAIR.
DR GO; GO:0071035; P:nuclear polyadenylation-dependent rRNA catabolic process; IBA:GO_Central.
DR GO; GO:0071038; P:nuclear polyadenylation-dependent tRNA catabolic process; IBA:GO_Central.
DR GO; GO:0034427; P:nuclear-transcribed mRNA catabolic process, exonucleolytic, 3'-5'; IBA:GO_Central.
DR GO; GO:0071051; P:polyadenylation-dependent snoRNA 3'-end processing; IBA:GO_Central.
DR GO; GO:0034475; P:U4 snRNA 3'-end processing; IBA:GO_Central.
DR Gene3D; 2.40.50.140; -; 1.
DR InterPro; IPR026699; Exosome_RNA_bind1/RRP40/RRP4.
DR InterPro; IPR004088; KH_dom_type_1.
DR InterPro; IPR036612; KH_dom_type_1_sf.
DR InterPro; IPR012340; NA-bd_OB-fold.
DR InterPro; IPR022967; S1_dom.
DR PANTHER; PTHR21321; PTHR21321; 1.
DR Pfam; PF15985; KH_6; 1.
DR SMART; SM00316; S1; 1.
DR SUPFAM; SSF50249; SSF50249; 1.
DR SUPFAM; SSF54791; SSF54791; 1.
PE 1: Evidence at protein level;
KW Cytoplasm; Exosome; Nucleus; Reference proteome; RNA-binding;
KW rRNA processing.
FT CHAIN 1..322
FT /note="Exosome complex component RRP4 homolog"
FT /id="PRO_0000435317"
FT DOMAIN 94..172
FT /note="S1 motif"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00180"
FT DOMAIN 182..237
FT /note="KH"
FT /evidence="ECO:0000255"
SQ SEQUENCE 322 AA; 36574 MW; A6B87D8C0BF17786 CRC64;
MVMRKLQLPL SQTQKVRFER AIERLQSLSS SANSDASVIV TDSIPVNHDD AFLKGHGTSE
VDGELLATVC GVVERVDKLV YVRTLRARYK PEVGDIVVGR VIEVAQKRWR VELNFNQDGV
LMLSSMNMPD GIQRRRTSVD ELNMRNIFVE HDVVCAEVRN FQHDGSLQLQ ARSQKYGKLE
KGQLLKVDPY LVKRSKHHFH YVESLGIDLI IGCNGFIWVG EHVEVRDPMA IDDQKDEEMI
SSSSTGKEQS HIPLETRQTI CRIGNAIRVL SNLGFTVTLE VIMETVNLSN SKNIDIHDML
GSEFHVVVAE NEAERRRTKR KK
