Entry euk:RP44A_ARATH

ID   RP44A_ARATH             Reviewed;         933 AA.
AC   Q9SHL7; Q93ZK2;
DT   20-JAN-2016, integrated into UniProtKB/Swiss-Prot.
DT   01-JUN-2002, sequence version 2.
DT   12-APR-2017, entry version 112.
DE   RecName: Full=Exosome complex exonuclease RRP44 homolog A {ECO:0000305};
DE            Short=RRP44 homolog A {ECO:0000305};
DE            EC=3.1.13.-;
DE            EC=3.1.26.-;
DE   AltName: Full=Protein EMBRYO DEFECTIVE 2763 {ECO:0000305};
DE   AltName: Full=Ribosomal RNA-processing protein 44A {ECO:0000305};
DE            Short=AtRRP44A {ECO:0000303|PubMed:24244451};
GN   Name=RRP44A {ECO:0000303|PubMed:24244451};
GN   Synonyms=EMB2763 {ECO:0000312|EMBL:AEC06638.1};
GN   OrderedLocusNames=At2g17510 {ECO:0000312|Araport:AT2G17510};
OS   Arabidopsis thaliana (Mouse-ear cress).
OC   Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC   Spermatophyta; Magnoliophyta; eudicotyledons; Gunneridae;
OC   Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae;
OC   Arabidopsis.
OX   NCBI_TaxID=3702;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=cv. Columbia;
RX   PubMed=10617197; DOI=10.1038/45471;
RA   Lin X., Kaul S., Rounsley S.D., Shea T.P., Benito M.-I., Town C.D.,
RA   Fujii C.Y., Mason T.M., Bowman C.L., Barnstead M.E., Feldblyum T.V.,
RA   Buell C.R., Ketchum K.A., Lee J.J., Ronning C.M., Koo H.L.,
RA   Moffat K.S., Cronin L.A., Shen M., Pai G., Van Aken S., Umayam L.,
RA   Tallon L.J., Gill J.E., Adams M.D., Carrera A.J., Creasy T.H.,
RA   Goodman H.M., Somerville C.R., Copenhaver G.P., Preuss D.,
RA   Nierman W.C., White O., Eisen J.A., Salzberg S.L., Fraser C.M.,
RA   Venter J.C.;
RT   "Sequence and analysis of chromosome 2 of the plant Arabidopsis
RT   thaliana.";
RL   Nature 402:761-768(1999).
RN   [2]
RP   GENOME REANNOTATION.
RC   STRAIN=cv. Columbia;
RG   The Arabidopsis Information Portal (Araport);
RL   Submitted (MAY-2016) to the EMBL/GenBank/DDBJ databases.
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.,
RA   Southwick A.M., Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F.,
RA   Karlin-Newmann G., Liu S.X., Lam B., Sakano H., Wu T., Yu G.,
RA   Miranda M., Quach H.L., Tripp M., Chang C.H., Lee J.M., Toriumi M.J.,
RA   Chan M.M., Tang C.C., Onodera C.S., Deng J.M., Akiyama K., Ansari Y.,
RA   Arakawa T., Banh J., Banno F., Bowser L., Brooks S.Y., Carninci P.,
RA   Chao Q., Choy N., Enju A., Goldsmith A.D., Gurjal M., Hansen N.F.,
RA   Hayashizaki Y., Johnson-Hopson C., Hsuan V.W., Iida K., Karnes M.,
RA   Khan S., Koesema E., Ishida J., Jiang P.X., Jones T., Kawai J.,
RA   Kamiya A., Meyers C., Nakajima M., Narusaka M., Seki M., Sakurai T.,
RA   Satou M., Tamse R., Vaysberg M., Wallender E.K., Wong C., Yamamura Y.,
RA   Yuan S., Shinozaki K., Davis R.W., Theologis A., Ecker J.R.;
RT   "Empirical analysis of transcriptional activity in the Arabidopsis
RT   genome.";
RL   Science 302:842-846(2003).
RN   [4]
RP   FUNCTION, SUBCELLULAR LOCATION, AND DISRUPTION PHENOTYPE.
RX   PubMed=20798041; DOI=10.1073/pnas.1007060107;
RA   Zhang W., Murphy C., Sieburth L.E.;
RT   "Conserved RNaseII domain protein functions in cytoplasmic mRNA decay
RT   and suppresses Arabidopsis decapping mutant phenotypes.";
RL   Proc. Natl. Acad. Sci. U.S.A. 107:15981-15985(2010).
RN   [5]
RP   FUNCTION, AND DISRUPTION PHENOTYPE.
RX   PubMed=24244451; DOI=10.1371/journal.pone.0079219;
RA   Kumakura N., Otsuki H., Tsuzuki M., Takeda A., Watanabe Y.;
RT   "Arabidopsis AtRRP44A is the functional homolog of Rrp44/Dis3, an
RT   exosome component, is essential for viability and is required for RNA
RT   processing and degradation.";
RL   PLoS ONE 8:E79219-E79219(2013).
CC   -!- FUNCTION: Catalytic component of the RNA exosome complex which has
CC       3'->5' exoribonuclease activity and participates in a multitude of
CC       cellular RNA processing and degradation events. Required for 5.8S
CC       rRNA intermediate processing and the degradation of 5' external
CC       transcribed spacer (5' ETS), a maturation by-product of rRNA
CC       synthesis. Is not involved in the degradation of turnip crinkle
CC       virus (TCV) RNA and significant virus resistance
CC       (PubMed:24244451). Required for normal development of female
CC       gametophytes and early embryogenesis (PubMed:20798041,
CC       PubMed:24244451). {ECO:0000269|PubMed:20798041,
CC       ECO:0000269|PubMed:24244451}.
CC   -!- COFACTOR:
CC       Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC         Evidence={ECO:0000250|UniProtKB:Q08162};
CC   -!- SUBUNIT: Probable component of the RNA exosome complex.
CC       {ECO:0000250|UniProtKB:Q08162}.
CC   -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:20798041}.
CC   -!- ALTERNATIVE PRODUCTS:
CC       Event=Alternative splicing; Named isoforms=1;
CC         Comment=A number of isoforms are produced. According to EST
CC         sequences. {ECO:0000305};
CC       Name=1;
CC         IsoId=Q9SHL7-1; Sequence=Displayed;
CC   -!- DISRUPTION PHENOTYPE: Aborted development of female gametophytes.
CC       {ECO:0000269|PubMed:20798041, ECO:0000269|PubMed:24244451}.
CC   -!- SIMILARITY: Belongs to the RNR ribonuclease family. {ECO:0000305}.
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DR   EMBL; AC007584; AAD32908.2; -; Genomic_DNA.
DR   EMBL; CP002685; AEC06638.1; -; Genomic_DNA.
DR   EMBL; AY057479; AAL09713.1; -; mRNA.
DR   EMBL; AY090298; AAL90959.1; -; mRNA.
DR   PIR; A84553; A84553.
DR   RefSeq; NP_565418.1; NM_127305.3. [Q9SHL7-1]
DR   UniGene; At.14584; -.
DR   UniGene; At.40137; -.
DR   ProteinModelPortal; Q9SHL7; -.
DR   SMR; Q9SHL7; -.
DR   STRING; 3702.AT2G17510.2; -.
DR   iPTMnet; Q9SHL7; -.
DR   PaxDb; Q9SHL7; -.
DR   EnsemblPlants; AT2G17510.1; AT2G17510.1; AT2G17510. [Q9SHL7-1]
DR   GeneID; 816257; -.
DR   Gramene; AT2G17510.1; AT2G17510.1; AT2G17510.
DR   KEGG; ath:AT2G17510; -.
DR   Araport; AT2G17510; -.
DR   eggNOG; KOG2102; Eukaryota.
DR   eggNOG; COG0557; LUCA.
DR   HOGENOM; HOG000191945; -.
DR   KO; K12585; -.
DR   PhylomeDB; Q9SHL7; -.
DR   Reactome; R-ATH-429958; mRNA decay by 3' to 5' exoribonuclease.
DR   Reactome; R-ATH-450604; KSRP (KHSRP) binds and destabilizes mRNA.
DR   PRO; PR:Q9SHL7; -.
DR   Proteomes; UP000006548; Chromosome 2.
DR   ExpressionAtlas; Q9SHL7; baseline and differential.
DR   GO; GO:0000178; C:exosome (RNase complex); IEA:UniProtKB-KW.
DR   GO; GO:0005634; C:nucleus; IEA:UniProtKB-SubCell.
DR   GO; GO:0004519; F:endonuclease activity; IEA:UniProtKB-KW.
DR   GO; GO:0004527; F:exonuclease activity; IEA:UniProtKB-KW.
DR   GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR   GO; GO:0003723; F:RNA binding; IEA:UniProtKB-KW.
DR   GO; GO:0006364; P:rRNA processing; IEA:UniProtKB-KW.
DR   Gene3D; 3.40.50.1010; -; 1.
DR   InterPro; IPR012340; NA-bd_OB-fold.
DR   InterPro; IPR002716; PIN_dom.
DR   InterPro; IPR029060; PIN_domain-like.
DR   InterPro; IPR022966; RNase_II/R_CS.
DR   InterPro; IPR033771; Rrp44_CSD1.
DR   InterPro; IPR033770; RRP44_S1.
DR   Pfam; PF13638; PIN_4; 1.
DR   Pfam; PF17216; Rrp44_CSD1; 1.
DR   Pfam; PF17215; Rrp44_S1; 1.
DR   SMART; SM00670; PINc; 1.
DR   SUPFAM; SSF50249; SSF50249; 4.
DR   SUPFAM; SSF88723; SSF88723; 1.
DR   PROSITE; PS01175; RIBONUCLEASE_II; 1.
PE   2: Evidence at transcript level;
KW   Alternative splicing; Complete proteome; Endonuclease; Exonuclease;
KW   Exosome; Hydrolase; Magnesium; Metal-binding; Nuclease; Nucleus;
KW   Reference proteome; RNA-binding; rRNA processing.
FT   CHAIN         1    933       Exosome complex exonuclease RRP44 homolog
FT                                A.
FT                                /FTId=PRO_0000435321.
FT   DOMAIN       50    163       PINc. {ECO:0000255}.
FT   METAL       481    481       Magnesium.
FT                                {ECO:0000250|UniProtKB:Q08162}.
FT   METAL       490    490       Magnesium.
FT                                {ECO:0000250|UniProtKB:Q08162}.
CC   --------------------------------------------------------------------------
CC   The following FT lines are automated annotations from the MyHits database.
CC   --------------------------------------------------------------------------
FT   MYHIT       767    791       ipat:RIBONUCLEASE_II [T]
FT   MYHIT       849    919       ipfam:Rrp44_S1 [T]
FT   MYHIT        52    175       ipfam:PIN_4 [T]
FT   MYHIT        50    163       ismart:PINc [T]
FT   MYHIT       217    321       ipfam:Rrp44_CSD1 [T]
SQ   SEQUENCE   933 AA;  104996 MW;  B2A38DB8BEF3DCE3 CRC64;
     MLQSKVFNKK TRGGRIQKQV REVYLRDDIY CGAFSCKSCD SSAARLSSSK IIVVDTNVVL
     HQIDLLENKA IDTVVVLSVV LDEVKNRNRS VYNRIRLLCS NPARQFYVFS NHVHKDTYVQ
     AMEKESANDH NDRAIRVATL WYQKHLGDTS QVLLVTNDRE NKRKATEEGI SAETIEAYVK
     SLGQPELLDL LAQPTNEDIT MEDADDSRPS KRKLIYQEHK PMSEITAGLH RGIYHQGKLR
     VNRFNPYEAY VGSESIGEEI IIYGRSNMNR AFDGDIVAVE LLPRDQWQDE KALSIAEEDD
     EEDDTVHLAP DNVDDAPRTS NLSHETSGDK NAAPVRPSGR VVGVIRRNWH SYCGSLEPMS
     LPAGSGGTAH ALFVSKDRRI PKIRINTRQL QNLLDMRIVV AVDSWDRQSR YPSGHYVRPI
     GKIGDKETET EVVLIENDVD YSPFSSQVLA CLPPLPWSVS SEDVSNPVRQ DLRHLLVFSV
     DPPGCKDIDD ALHCTSLPNG NFELGVHIAD VTNFVHPGTP LDDEASKRGT SVYLVERRID
     MLPKPLTEDI CSLRADVERL AFSVIWEMSP DAEIISTRFT KSIIKSSAAL SYIEAQARMD
     DSRLTDSLTT DLRNMNTLAK IMRQRRIDRG ALTLASAEVK FDIDPENHDP LNIGMYQILE
     ANQMVEEFML AANVSVAGQI LKLFPSCSLL RRHPTPTREM LEPLLRTAAA IGLTLDVSSS
     KALADSLDRA VGEDPYFNKL IRILATRCMT QAVYFCSGDL SPPEYHHYGL AAPLYTHFTS
     PIRRYADVFV HRLLAASLGI YKLPTVFQDR PQLTSVADNL NYRHRNAQMA GRASVELYVL
     IYFRTRPTDE EARVVKIRSN GFIVFVPKYG IEGPVYLTGK GEKGAGDWYV DEEKQKIVKM
     DGSLSYSVLQ TVKIHMEVVE PQPNRPKLQL TLL
//