EXOS5_ORYSJ
ID EXOS5_ORYSJ Reviewed; 238 AA.
AC Q84T68; A0A0P0W6B3;
DT 03-MAY-2011, integrated into UniProtKB/Swiss-Prot.
DT 15-FEB-2005, sequence version 2.
DT 03-AUG-2022, entry version 114.
DE RecName: Full=Exosome complex exonuclease RRP46 homolog;
DE EC=3.1.13.-;
DE AltName: Full=Exosome component 5;
DE AltName: Full=Ribosomal RNA-processing protein 46;
DE Short=oRrp46;
GN Name=RRP46; OrderedLocusNames=Os03g0854200, LOC_Os03g63720;
OS Oryza sativa subsp. japonica (Rice).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; Liliopsida; Poales; Poaceae; BOP clade;
OC Oryzoideae; Oryzeae; Oryzinae; Oryza; Oryza sativa.
OX NCBI_TaxID=39947;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=16109971; DOI=10.1101/gr.3869505;
RG The rice chromosome 3 sequencing consortium;
RA Buell C.R., Yuan Q., Ouyang S., Liu J., Zhu W., Wang A., Maiti R., Haas B.,
RA Wortman J., Pertea M., Jones K.M., Kim M., Overton L., Tsitrin T.,
RA Fadrosh D., Bera J., Weaver B., Jin S., Johri S., Reardon M., Webb K.,
RA Hill J., Moffat K., Tallon L., Van Aken S., Lewis M., Utterback T.,
RA Feldblyum T., Zismann V., Iobst S., Hsiao J., de Vazeille A.R.,
RA Salzberg S.L., White O., Fraser C.M., Yu Y., Kim H., Rambo T., Currie J.,
RA Collura K., Kernodle-Thompson S., Wei F., Kudrna K., Ammiraju J.S.S.,
RA Luo M., Goicoechea J.L., Wing R.A., Henry D., Oates R., Palmer M.,
RA Pries G., Saski C., Simmons J., Soderlund C., Nelson W., de la Bastide M.,
RA Spiegel L., Nascimento L., Huang E., Preston R., Zutavern T., Palmer L.,
RA O'Shaughnessy A., Dike S., McCombie W.R., Minx P., Cordum H., Wilson R.,
RA Jin W., Lee H.R., Jiang J., Jackson S.;
RT "Sequence, annotation, and analysis of synteny between rice chromosome 3
RT and diverged grass species.";
RL Genome Res. 15:1284-1291(2005).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=16100779; DOI=10.1038/nature03895;
RG International rice genome sequencing project (IRGSP);
RT "The map-based sequence of the rice genome.";
RL Nature 436:793-800(2005).
RN [3]
RP GENOME REANNOTATION.
RC STRAIN=cv. Nipponbare;
RX PubMed=18089549; DOI=10.1093/nar/gkm978;
RG The rice annotation project (RAP);
RT "The rice annotation project database (RAP-DB): 2008 update.";
RL Nucleic Acids Res. 36:D1028-D1033(2008).
RN [4]
RP GENOME REANNOTATION.
RC STRAIN=cv. Nipponbare;
RX PubMed=24280374; DOI=10.1186/1939-8433-6-4;
RA Kawahara Y., de la Bastide M., Hamilton J.P., Kanamori H., McCombie W.R.,
RA Ouyang S., Schwartz D.C., Tanaka T., Wu J., Zhou S., Childs K.L.,
RA Davidson R.M., Lin H., Quesada-Ocampo L., Vaillancourt B., Sakai H.,
RA Lee S.S., Kim J., Numa H., Itoh T., Buell C.R., Matsumoto T.;
RT "Improvement of the Oryza sativa Nipponbare reference genome using next
RT generation sequence and optical map data.";
RL Rice 6:4-4(2013).
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=12869764; DOI=10.1126/science.1081288;
RG The rice full-length cDNA consortium;
RT "Collection, mapping, and annotation of over 28,000 cDNA clones from
RT japonica rice.";
RL Science 301:376-379(2003).
RN [6]
RP X-RAY CRYSTALLOGRAPHY (1.98 ANGSTROMS), FUNCTION, SUBUNIT, AND MUTAGENESIS
RP OF 75-LYS-GLN-76 AND GLU-160.
RX PubMed=20660080; DOI=10.1261/rna.2180810;
RA Yang C.C., Wang Y.T., Hsiao Y.Y., Doudeva L.G., Kuo P.H., Chow S.Y.,
RA Yuan H.S.;
RT "Structural and biochemical characterization of CRN-5 and Rrp46: an exosome
RT component participating in apoptotic DNA degradation.";
RL RNA 16:1748-1759(2010).
CC -!- FUNCTION: Probable component of the exosome 3'->5' exoribonuclease
CC complex, a complex that degrades inherently unstable mRNAs containing
CC AU-rich elements (AREs) within their 3'-untranslated regions. May form
CC a homodimer separately from exosome complexes and function in DNA
CC cleavage process. Binds double-stranded DNA (dsDNA) and single-stranded
CC RNA (ssRNA), and possesses hydrolytic DNase and phosphorolytic RNase
CC activities in vitro. {ECO:0000269|PubMed:20660080}.
CC -!- SUBUNIT: Homodimer or monomer when reduced or oxidized, respectively.
CC Component of the exosome core complex (Probable).
CC {ECO:0000305|PubMed:20660080}.
CC -!- SUBCELLULAR LOCATION: Nucleus, nucleolus {ECO:0000305}.
CC -!- SIMILARITY: Belongs to the RNase PH family. {ECO:0000305}.
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DR EMBL; AC120506; AAO66540.2; -; Genomic_DNA.
DR EMBL; DP000009; ABF99960.1; -; Genomic_DNA.
DR EMBL; AP008209; BAF13850.1; -; Genomic_DNA.
DR EMBL; AP014959; BAS87423.1; -; Genomic_DNA.
DR EMBL; AK069107; BAG91256.1; -; mRNA.
DR RefSeq; XP_015630424.1; XM_015774938.1.
DR PDB; 3HKM; X-ray; 1.98 A; A/B/C=1-238.
DR PDBsum; 3HKM; -.
DR AlphaFoldDB; Q84T68; -.
DR SMR; Q84T68; -.
DR STRING; 4530.OS03T0854200-01; -.
DR PaxDb; Q84T68; -.
DR PRIDE; Q84T68; -.
DR EnsemblPlants; Os03t0854200-01; Os03t0854200-01; Os03g0854200.
DR GeneID; 4334824; -.
DR Gramene; Os03t0854200-01; Os03t0854200-01; Os03g0854200.
DR KEGG; osa:4334824; -.
DR eggNOG; KOG1069; Eukaryota.
DR HOGENOM; CLU_063514_2_3_1; -.
DR InParanoid; Q84T68; -.
DR OMA; CIINEQG; -.
DR OrthoDB; 1129417at2759; -.
DR EvolutionaryTrace; Q84T68; -.
DR Proteomes; UP000000763; Chromosome 3.
DR Proteomes; UP000059680; Chromosome 3.
DR Genevisible; Q84T68; OS.
DR GO; GO:0000177; C:cytoplasmic exosome (RNase complex); IBA:GO_Central.
DR GO; GO:0000176; C:nuclear exosome (RNase complex); IBA:GO_Central.
DR GO; GO:0005730; C:nucleolus; IBA:GO_Central.
DR GO; GO:0004536; F:deoxyribonuclease activity; IDA:UniProtKB.
DR GO; GO:0003690; F:double-stranded DNA binding; IDA:UniProtKB.
DR GO; GO:0004527; F:exonuclease activity; IEA:UniProtKB-KW.
DR GO; GO:0042802; F:identical protein binding; IPI:UniProtKB.
DR GO; GO:0004540; F:ribonuclease activity; IDA:UniProtKB.
DR GO; GO:0003727; F:single-stranded RNA binding; IDA:UniProtKB.
DR GO; GO:0071028; P:nuclear mRNA surveillance; 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:0016075; P:rRNA catabolic process; IBA:GO_Central.
DR GO; GO:0006364; P:rRNA processing; IEA:UniProtKB-KW.
DR GO; GO:0034475; P:U4 snRNA 3'-end processing; IBA:GO_Central.
DR Gene3D; 3.30.230.70; -; 1.
DR InterPro; IPR001247; ExoRNase_PH_dom1.
DR InterPro; IPR036345; ExoRNase_PH_dom2_sf.
DR InterPro; IPR027408; PNPase/RNase_PH_dom_sf.
DR InterPro; IPR020568; Ribosomal_S5_D2-typ_fold.
DR Pfam; PF01138; RNase_PH; 1.
DR SUPFAM; SSF54211; SSF54211; 1.
DR SUPFAM; SSF55666; SSF55666; 1.
PE 1: Evidence at protein level;
KW 3D-structure; DNA-binding; Exonuclease; Exosome; Hydrolase; Nuclease;
KW Nucleus; Reference proteome; RNA-binding; rRNA processing.
FT CHAIN 1..238
FT /note="Exosome complex exonuclease RRP46 homolog"
FT /id="PRO_0000407329"
FT REGION 174..194
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 180..194
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MUTAGEN 75..76
FT /note="KQ->EE: Loss of dsDNA- and ssRNA-binding. Loss of
FT DNase and RNase activities."
FT /evidence="ECO:0000269|PubMed:20660080"
FT MUTAGEN 160
FT /note="E->Q: Strongly reduces DNase activity."
FT /evidence="ECO:0000269|PubMed:20660080"
FT STRAND 17..21
FT /evidence="ECO:0007829|PDB:3HKM"
FT STRAND 25..35
FT /evidence="ECO:0007829|PDB:3HKM"
FT STRAND 38..44
FT /evidence="ECO:0007829|PDB:3HKM"
FT STRAND 57..59
FT /evidence="ECO:0007829|PDB:3HKM"
FT STRAND 61..67
FT /evidence="ECO:0007829|PDB:3HKM"
FT STRAND 69..71
FT /evidence="ECO:0007829|PDB:3HKM"
FT HELIX 77..91
FT /evidence="ECO:0007829|PDB:3HKM"
FT STRAND 99..110
FT /evidence="ECO:0007829|PDB:3HKM"
FT HELIX 115..130
FT /evidence="ECO:0007829|PDB:3HKM"
FT STRAND 134..145
FT /evidence="ECO:0007829|PDB:3HKM"
FT STRAND 151..154
FT /evidence="ECO:0007829|PDB:3HKM"
FT HELIX 157..160
FT /evidence="ECO:0007829|PDB:3HKM"
FT STRAND 164..173
FT /evidence="ECO:0007829|PDB:3HKM"
FT STRAND 197..201
FT /evidence="ECO:0007829|PDB:3HKM"
FT HELIX 205..227
FT /evidence="ECO:0007829|PDB:3HKM"
FT TURN 228..230
FT /evidence="ECO:0007829|PDB:3HKM"
SQ 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
