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Exosome complex exonuclease RRP46 homolog (EC 3.1.13.-) (Exosome component 5) (Ribosomal RNA-processing protein 46) (oRrp46)

 EXOS5_ORYSJ             Reviewed;         238 AA.
Q84T68; A0A0P0W6B3;
03-MAY-2011, integrated into UniProtKB/Swiss-Prot.
15-FEB-2005, sequence version 2.
07-NOV-2018, entry version 98.
RecName: Full=Exosome complex exonuclease RRP46 homolog;
EC=3.1.13.-;
AltName: Full=Exosome component 5;
AltName: Full=Ribosomal RNA-processing protein 46;
Short=oRrp46;
Name=RRP46; OrderedLocusNames=Os03g0854200, LOC_Os03g63720;
Oryza sativa subsp. japonica (Rice).
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BOP clade;
Oryzoideae; Oryzeae; Oryzinae; Oryza; Oryza sativa.
NCBI_TaxID=39947;
[1]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=cv. Nipponbare;
PubMed=16109971; DOI=10.1101/gr.3869505;
The rice chromosome 3 sequencing consortium;
Buell C.R., Yuan Q., Ouyang S., Liu J., Zhu W., Wang A., Maiti R.,
Haas B., Wortman J., Pertea M., Jones K.M., Kim M., Overton L.,
Tsitrin T., Fadrosh D., Bera J., Weaver B., Jin S., Johri S.,
Reardon M., Webb K., Hill J., Moffat K., Tallon L., Van Aken S.,
Lewis M., Utterback T., Feldblyum T., Zismann V., Iobst S., Hsiao J.,
de Vazeille A.R., Salzberg S.L., White O., Fraser C.M., Yu Y., Kim H.,
Rambo T., Currie J., Collura K., Kernodle-Thompson S., Wei F.,
Kudrna K., Ammiraju J.S.S., Luo M., Goicoechea J.L., Wing R.A.,
Henry D., Oates R., Palmer M., Pries G., Saski C., Simmons J.,
Soderlund C., Nelson W., de la Bastide M., Spiegel L., Nascimento L.,
Huang E., Preston R., Zutavern T., Palmer L., O'Shaughnessy A.,
Dike S., McCombie W.R., Minx P., Cordum H., Wilson R., Jin W.,
Lee H.R., Jiang J., Jackson S.;
"Sequence, annotation, and analysis of synteny between rice chromosome
3 and diverged grass species.";
Genome Res. 15:1284-1291(2005).
[2]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=cv. Nipponbare;
PubMed=16100779; DOI=10.1038/nature03895;
International rice genome sequencing project (IRGSP);
"The map-based sequence of the rice genome.";
Nature 436:793-800(2005).
[3]
GENOME REANNOTATION.
STRAIN=cv. Nipponbare;
PubMed=18089549; DOI=10.1093/nar/gkm978;
The rice annotation project (RAP);
"The rice annotation project database (RAP-DB): 2008 update.";
Nucleic Acids Res. 36:D1028-D1033(2008).
[4]
GENOME REANNOTATION.
STRAIN=cv. Nipponbare;
PubMed=24280374; DOI=10.1186/1939-8433-6-4;
Kawahara Y., de la Bastide M., Hamilton J.P., Kanamori H.,
McCombie W.R., Ouyang S., Schwartz D.C., Tanaka T., Wu J., Zhou S.,
Childs K.L., Davidson R.M., Lin H., Quesada-Ocampo L.,
Vaillancourt B., Sakai H., Lee S.S., Kim J., Numa H., Itoh T.,
Buell C.R., Matsumoto T.;
"Improvement of the Oryza sativa Nipponbare reference genome using
next generation sequence and optical map data.";
Rice 6:4-4(2013).
[5]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
STRAIN=cv. Nipponbare;
PubMed=12869764; DOI=10.1126/science.1081288;
The rice full-length cDNA consortium;
"Collection, mapping, and annotation of over 28,000 cDNA clones from
japonica rice.";
Science 301:376-379(2003).
[6]
X-RAY CRYSTALLOGRAPHY (1.98 ANGSTROMS), FUNCTION, SUBUNIT, AND
MUTAGENESIS OF 75-LYS-GLN-76 AND GLU-160.
PubMed=20660080; DOI=10.1261/rna.2180810;
Yang C.C., Wang Y.T., Hsiao Y.Y., Doudeva L.G., Kuo P.H., Chow S.Y.,
Yuan H.S.;
"Structural and biochemical characterization of CRN-5 and Rrp46: an
exosome component participating in apoptotic DNA degradation.";
RNA 16:1748-1759(2010).
-!- FUNCTION: Probable component of the exosome 3'->5' exoribonuclease
complex, a complex that degrades inherently unstable mRNAs
containing AU-rich elements (AREs) within their 3'-untranslated
regions. May form a homodimer separately from exosome complexes
and function in DNA cleavage process. Binds double-stranded DNA
(dsDNA) and single-stranded RNA (ssRNA), and possesses hydrolytic
DNase and phosphorolytic RNase activities in vitro.
{ECO:0000269|PubMed:20660080}.
-!- SUBUNIT: Homodimer or monomer when reduced or oxidized,
respectively. Component of the exosome core complex (Probable).
{ECO:0000305|PubMed:20660080}.
-!- SUBCELLULAR LOCATION: Nucleus, nucleolus {ECO:0000305}.
-!- SIMILARITY: Belongs to the RNase PH family. {ECO:0000305}.
-----------------------------------------------------------------------
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EMBL; AC120506; AAO66540.2; -; Genomic_DNA.
EMBL; DP000009; ABF99960.1; -; Genomic_DNA.
EMBL; AP008209; BAF13850.1; -; Genomic_DNA.
EMBL; AP014959; BAS87423.1; -; Genomic_DNA.
EMBL; AK069107; BAG91256.1; -; mRNA.
RefSeq; XP_015630424.1; XM_015774938.1.
UniGene; Os.47503; -.
PDB; 3HKM; X-ray; 1.98 A; A/B/C=1-238.
PDBsum; 3HKM; -.
ProteinModelPortal; Q84T68; -.
SMR; Q84T68; -.
STRING; 39947.LOC_Os03g63720.1; -.
PaxDb; Q84T68; -.
EnsemblPlants; Os03t0854200-01; Os03t0854200-01; Os03g0854200.
GeneID; 4334824; -.
Gramene; Os03t0854200-01; Os03t0854200-01; Os03g0854200.
KEGG; osa:4334824; -.
eggNOG; KOG1069; Eukaryota.
eggNOG; COG0689; LUCA.
InParanoid; Q84T68; -.
KO; K12590; -.
OMA; CNYRPKA; -.
OrthoDB; EOG09360KHD; -.
Reactome; R-OSA-429958; mRNA decay by 3' to 5' exoribonuclease.
Reactome; R-OSA-6791226; Major pathway of rRNA processing in the nucleolus and cytosol.
EvolutionaryTrace; Q84T68; -.
Proteomes; UP000059680; Chromosome 3.
ExpressionAtlas; Q84T68; differential.
Genevisible; Q84T68; OS.
GO; GO:0000177; C:cytoplasmic exosome (RNase complex); IBA:GO_Central.
GO; GO:0000176; C:nuclear exosome (RNase complex); IBA:GO_Central.
GO; GO:0005730; C:nucleolus; IBA:GO_Central.
GO; GO:0004536; F:deoxyribonuclease activity; IDA:UniProtKB.
GO; GO:0003690; F:double-stranded DNA binding; IDA:UniProtKB.
GO; GO:0004527; F:exonuclease activity; IEA:UniProtKB-KW.
GO; GO:0042802; F:identical protein binding; IPI:UniProtKB.
GO; GO:0004540; F:ribonuclease activity; IDA:UniProtKB.
GO; GO:0003727; F:single-stranded RNA binding; IDA:UniProtKB.
GO; GO:0071028; P:nuclear mRNA surveillance; IBA:GO_Central.
GO; GO:0034427; P:nuclear-transcribed mRNA catabolic process, exonucleolytic, 3'-5'; IBA:GO_Central.
GO; GO:0071051; P:polyadenylation-dependent snoRNA 3'-end processing; IBA:GO_Central.
GO; GO:0016075; P:rRNA catabolic process; IBA:GO_Central.
GO; GO:0006364; P:rRNA processing; IEA:UniProtKB-KW.
GO; GO:0034475; P:U4 snRNA 3'-end processing; IBA:GO_Central.
Gene3D; 3.30.230.70; -; 1.
InterPro; IPR001247; ExoRNase_PH_dom1.
InterPro; IPR036345; ExoRNase_PH_dom2_sf.
InterPro; IPR027408; PNPase/RNase_PH_dom_sf.
InterPro; IPR020568; Ribosomal_S5_D2-typ_fold.
Pfam; PF01138; RNase_PH; 1.
SUPFAM; SSF54211; SSF54211; 1.
SUPFAM; SSF55666; SSF55666; 1.
1: Evidence at protein level;
3D-structure; Complete proteome; DNA-binding; Exonuclease; Exosome;
Hydrolase; Nuclease; Nucleus; Reference proteome; RNA-binding;
rRNA processing.
CHAIN 1 238 Exosome complex exonuclease RRP46
homolog.
/FTId=PRO_0000407329.
MUTAGEN 75 76 KQ->EE: Loss of dsDNA- and ssRNA-binding.
Loss of DNase and RNase activities.
{ECO:0000269|PubMed:20660080}.
MUTAGEN 160 160 E->Q: Strongly reduces DNase activity.
{ECO:0000269|PubMed:20660080}.
STRAND 17 21 {ECO:0000244|PDB:3HKM}.
STRAND 25 35 {ECO:0000244|PDB:3HKM}.
STRAND 38 44 {ECO:0000244|PDB:3HKM}.
STRAND 57 59 {ECO:0000244|PDB:3HKM}.
STRAND 61 67 {ECO:0000244|PDB:3HKM}.
STRAND 69 71 {ECO:0000244|PDB:3HKM}.
HELIX 77 91 {ECO:0000244|PDB:3HKM}.
STRAND 99 110 {ECO:0000244|PDB:3HKM}.
HELIX 115 130 {ECO:0000244|PDB:3HKM}.
STRAND 134 145 {ECO:0000244|PDB:3HKM}.
STRAND 151 154 {ECO:0000244|PDB:3HKM}.
HELIX 157 160 {ECO:0000244|PDB:3HKM}.
STRAND 164 173 {ECO:0000244|PDB:3HKM}.
STRAND 197 201 {ECO:0000244|PDB:3HKM}.
HELIX 205 227 {ECO:0000244|PDB:3HKM}.
TURN 228 230 {ECO:0000244|PDB:3HKM}.
SEQUENCE 238 AA; 25909 MW; E3B010A4FEC3DED0 CRC64;
MEESRADGRN PNQLRPFSCT RNPLDRAHGS ARWAQGDTIV LAAVYGPKPG TRKGENPEKA
SIEVVWKPMT GQIGKQEKEY EMTLKRTLQS ICLLTVHPNT TTSVILQVVG NDGSLLPCAI
NACCAALVFA GIPLKHLAVA IGCGVLEDGE VILDTNKAEE QQLKSFAHLV FPNSRKSASS
KEPNQKEEDS ERGLITSITH GVMSEEDYFS CIERGLAASS RISDFMRTTL QKQAPGDV


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