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Ribonuclease E/G-like protein, chloroplastic (RNase E/G-like protein) (EC 3.1.26.-) (RNase E)

 RNE_ARATH               Reviewed;        1001 AA.
F4IV66; F4IV67; F4IV69; Q8GZQ4; Q8RWB3; Q9M498; Q9SI08;
06-MAR-2013, integrated into UniProtKB/Swiss-Prot.
28-JUN-2011, sequence version 1.
07-NOV-2018, entry version 52.
RecName: Full=Ribonuclease E/G-like protein, chloroplastic;
Short=RNase E/G-like protein;
EC=3.1.26.-;
AltName: Full=RNase E;
Flags: Precursor;
Name=RNE; Synonyms=RNEE/G; OrderedLocusNames=At2g04270;
ORFNames=T23O15.10;
Arabidopsis thaliana (Mouse-ear cress).
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; eudicotyledons; Gunneridae;
Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae;
Arabidopsis.
NCBI_TaxID=3702;
[1]
NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 2).
Walter M., Kudla J.;
"Molecular characterization of an Arabidopsis RNase E-like
endoribonuclease.";
Submitted (NOV-2001) to the EMBL/GenBank/DDBJ databases.
[2]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=cv. Columbia;
PubMed=10617197; DOI=10.1038/45471;
Lin X., Kaul S., Rounsley S.D., Shea T.P., Benito M.-I., Town C.D.,
Fujii C.Y., Mason T.M., Bowman C.L., Barnstead M.E., Feldblyum T.V.,
Buell C.R., Ketchum K.A., Lee J.J., Ronning C.M., Koo H.L.,
Moffat K.S., Cronin L.A., Shen M., Pai G., Van Aken S., Umayam L.,
Tallon L.J., Gill J.E., Adams M.D., Carrera A.J., Creasy T.H.,
Goodman H.M., Somerville C.R., Copenhaver G.P., Preuss D.,
Nierman W.C., White O., Eisen J.A., Salzberg S.L., Fraser C.M.,
Venter J.C.;
"Sequence and analysis of chromosome 2 of the plant Arabidopsis
thaliana.";
Nature 402:761-768(1999).
[3]
GENOME REANNOTATION.
STRAIN=cv. Columbia;
PubMed=27862469; DOI=10.1111/tpj.13415;
Cheng C.Y., Krishnakumar V., Chan A.P., Thibaud-Nissen F., Schobel S.,
Town C.D.;
"Araport11: a complete reannotation of the Arabidopsis thaliana
reference genome.";
Plant J. 89:789-804(2017).
[4]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 4).
STRAIN=cv. Columbia;
PubMed=14593172; DOI=10.1126/science.1088305;
Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J.,
Southwick A.M., Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F.,
Karlin-Newmann G., Liu S.X., Lam B., Sakano H., Wu T., Yu G.,
Miranda M., Quach H.L., Tripp M., Chang C.H., Lee J.M., Toriumi M.J.,
Chan M.M., Tang C.C., Onodera C.S., Deng J.M., Akiyama K., Ansari Y.,
Arakawa T., Banh J., Banno F., Bowser L., Brooks S.Y., Carninci P.,
Chao Q., Choy N., Enju A., Goldsmith A.D., Gurjal M., Hansen N.F.,
Hayashizaki Y., Johnson-Hopson C., Hsuan V.W., Iida K., Karnes M.,
Khan S., Koesema E., Ishida J., Jiang P.X., Jones T., Kawai J.,
Kamiya A., Meyers C., Nakajima M., Narusaka M., Seki M., Sakurai T.,
Satou M., Tamse R., Vaysberg M., Wallender E.K., Wong C., Yamamura Y.,
Yuan S., Shinozaki K., Davis R.W., Theologis A., Ecker J.R.;
"Empirical analysis of transcriptional activity in the Arabidopsis
genome.";
Science 302:842-846(2003).
[5]
NUCLEOTIDE SEQUENCE [MRNA] OF 45-619 (ISOFORM 5), FUNCTION,
SUBCELLULAR LOCATION, TISSUE SPECIFICITY, ALTERNATIVE SPLICING, AND
DISRUPTION PHENOTYPE.
PubMed=18515828; DOI=10.1093/jxb/ern126;
Mudd E.A., Sullivan S., Gisby M.F., Mironov A., Kwon C.S., Chung W.I.,
Day A.;
"A 125 kDa RNase E/G-like protein is present in plastids and is
essential for chloroplast development and autotrophic growth in
Arabidopsis.";
J. Exp. Bot. 59:2597-2610(2008).
[6]
FUNCTION, MUTAGENESIS OF LYS-551 AND LYS-557, SUBUNIT, 3D-STRUCTURE
MODELING, AND SUBCELLULAR LOCATION.
PubMed=18441049; DOI=10.1261/rna.907608;
Schein A., Sheffy-Levin S., Glaser F., Schuster G.;
"The RNase E/G-type endoribonuclease of higher plants is located in
the chloroplast and cleaves RNA similarly to the E. coli enzyme.";
RNA 14:1057-1068(2008).
[7]
FUNCTION, AND DISRUPTION PHENOTYPE.
PubMed=21105931; DOI=10.1111/j.1365-313X.2010.04377.x;
Walter M., Piepenburg K., Schottler M.A., Petersen K., Kahlau S.,
Tiller N., Drechsel O., Weingartner M., Kudla J., Bock R.;
"Knockout of the plastid RNase E leads to defective RNA processing and
chloroplast ribosome deficiency.";
Plant J. 64:851-863(2010).
[8]
MUTAGENESIS OF 693-VAL--GLN-698, SUBCELLULAR LOCATION, INTERACTION
WITH RHON1, AND DISRUPTION PHENOTYPE.
STRAIN=cv. Columbia;
PubMed=22735703; DOI=10.1093/nar/gks613;
Stoppel R., Manavski N., Schein A., Schuster G., Teubner M.,
Schmitz-Linneweber C., Meurer J.;
"RHON1 is a novel ribonucleic acid-binding protein that supports RNase
E function in the Arabidopsis chloroplast.";
Nucleic Acids Res. 40:8593-8606(2012).
-!- FUNCTION: Involved in intercistronic processing of primary
transcripts from chloroplast operons. The endonucleolytic activity
of the enzyme depends on the number of phosphates at the 5' end,
is inhibited by structured RNA, and preferentially cleaves A/U-
rich sequences. {ECO:0000269|PubMed:18441049,
ECO:0000269|PubMed:18515828, ECO:0000269|PubMed:21105931}.
-!- SUBUNIT: Part of a chloroplastic degradosome-like complex.
Interacts with RHON1. {ECO:0000269|PubMed:18441049,
ECO:0000269|PubMed:22735703}.
-!- SUBCELLULAR LOCATION: Plastid, chloroplast stroma
{ECO:0000269|PubMed:18441049, ECO:0000269|PubMed:18515828,
ECO:0000269|PubMed:22735703}.
-!- ALTERNATIVE PRODUCTS:
Event=Alternative splicing; Named isoforms=5;
Name=1;
IsoId=F4IV66-1; Sequence=Displayed;
Note=Derived from EST data. No experimental confirmation
available.;
Name=2;
IsoId=F4IV66-2; Sequence=VSP_045664;
Note=No experimental confirmation available.;
Name=3;
IsoId=F4IV66-3; Sequence=VSP_045663, VSP_045665;
Note=Derived from EST data. No experimental confirmation
available.;
Name=4;
IsoId=F4IV66-4; Sequence=VSP_045662;
Name=5;
IsoId=F4IV66-5; Sequence=VSP_045662, VSP_045666, VSP_045667;
Note=Derived from EST data. No experimental confirmation
available.;
-!- TISSUE SPECIFICITY: Expressed in cotyledons, rosette and cauline
leaves. {ECO:0000269|PubMed:18515828}.
-!- DISRUPTION PHENOTYPE: Reduced photosynthetic activity and retarded
growth. Increased number and decreased size of chloroplasts. Loss
of autotrophic growth. Pale cotyledons when grown on sucrose-
complemented medium. {ECO:0000269|PubMed:18515828,
ECO:0000269|PubMed:21105931, ECO:0000269|PubMed:22735703}.
-!- SIMILARITY: Belongs to the RNase E/G family. {ECO:0000305}.
-!- SEQUENCE CAUTION:
Sequence=AAD27911.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
-----------------------------------------------------------------------
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EMBL; AF450479; AAN76770.1; -; mRNA.
EMBL; AC007213; AAD27911.1; ALT_SEQ; Genomic_DNA.
EMBL; CP002685; AEC05813.1; -; Genomic_DNA.
EMBL; CP002685; AEC05814.1; -; Genomic_DNA.
EMBL; CP002685; AEC05815.1; -; Genomic_DNA.
EMBL; CP002685; AEC05816.1; -; Genomic_DNA.
EMBL; CP002685; AEC05817.1; -; Genomic_DNA.
EMBL; CP002685; ANM63269.1; -; Genomic_DNA.
EMBL; CP002685; ANM63270.1; -; Genomic_DNA.
EMBL; CP002685; ANM63271.1; -; Genomic_DNA.
EMBL; AY093213; AAM13212.1; -; mRNA.
EMBL; BT008793; AAP68232.1; -; mRNA.
EMBL; AJ252122; CAB76425.1; -; mRNA.
PIR; F84455; F84455.
RefSeq; NP_001189510.1; NM_001202581.2. [F4IV66-1]
RefSeq; NP_001318196.1; NM_001335223.1. [F4IV66-4]
RefSeq; NP_001325370.1; NM_001335226.1. [F4IV66-4]
RefSeq; NP_001325371.1; NM_001335224.1. [F4IV66-3]
RefSeq; NP_178508.2; NM_126460.4. [F4IV66-4]
RefSeq; NP_850987.1; NM_180656.2. [F4IV66-2]
RefSeq; NP_850988.1; NM_180657.2. [F4IV66-3]
RefSeq; NP_850989.1; NM_180658.2. [F4IV66-5]
UniGene; At.41329; -.
UniGene; At.70130; -.
ProteinModelPortal; F4IV66; -.
SMR; F4IV66; -.
STRING; 3702.AT2G04270.5; -.
PaxDb; F4IV66; -.
EnsemblPlants; AT2G04270.1; AT2G04270.1; AT2G04270. [F4IV66-2]
EnsemblPlants; AT2G04270.2; AT2G04270.2; AT2G04270. [F4IV66-3]
EnsemblPlants; AT2G04270.3; AT2G04270.3; AT2G04270. [F4IV66-5]
EnsemblPlants; AT2G04270.4; AT2G04270.4; AT2G04270. [F4IV66-4]
EnsemblPlants; AT2G04270.5; AT2G04270.5; AT2G04270. [F4IV66-1]
EnsemblPlants; AT2G04270.6; AT2G04270.6; AT2G04270. [F4IV66-3]
EnsemblPlants; AT2G04270.8; AT2G04270.8; AT2G04270. [F4IV66-4]
EnsemblPlants; AT2G04270.9; AT2G04270.9; AT2G04270. [F4IV66-4]
GeneID; 814965; -.
Gramene; AT2G04270.1; AT2G04270.1; AT2G04270. [F4IV66-2]
Gramene; AT2G04270.2; AT2G04270.2; AT2G04270. [F4IV66-3]
Gramene; AT2G04270.3; AT2G04270.3; AT2G04270. [F4IV66-5]
Gramene; AT2G04270.4; AT2G04270.4; AT2G04270. [F4IV66-4]
Gramene; AT2G04270.5; AT2G04270.5; AT2G04270. [F4IV66-1]
Gramene; AT2G04270.6; AT2G04270.6; AT2G04270. [F4IV66-3]
Gramene; AT2G04270.8; AT2G04270.8; AT2G04270. [F4IV66-4]
Gramene; AT2G04270.9; AT2G04270.9; AT2G04270. [F4IV66-4]
KEGG; ath:AT2G04270; -.
Araport; AT2G04270; -.
TAIR; locus:2059775; AT2G04270.
eggNOG; ENOG410IIHR; Eukaryota.
eggNOG; COG1530; LUCA.
HOGENOM; HOG000029525; -.
InParanoid; F4IV66; -.
OrthoDB; EOG0936028K; -.
PRO; PR:F4IV66; -.
Proteomes; UP000006548; Chromosome 2.
ExpressionAtlas; F4IV66; baseline and differential.
Genevisible; F4IV66; AT.
GO; GO:0009507; C:chloroplast; IDA:TAIR.
GO; GO:0009570; C:chloroplast stroma; IEA:UniProtKB-SubCell.
GO; GO:0004521; F:endoribonuclease activity; IDA:TAIR.
GO; GO:0003723; F:RNA binding; IEA:UniProtKB-KW.
GO; GO:2001070; F:starch binding; IEA:InterPro.
GO; GO:0010239; P:chloroplast mRNA processing; IMP:TAIR.
GO; GO:0009658; P:chloroplast organization; IMP:TAIR.
GO; GO:1901259; P:chloroplast rRNA processing; IMP:TAIR.
GO; GO:0006364; P:rRNA processing; IBA:GO_Central.
Gene3D; 2.60.40.10; -; 1.
InterPro; IPR013784; Carb-bd-like_fold.
InterPro; IPR002044; CBM_fam20.
InterPro; IPR013783; Ig-like_fold.
InterPro; IPR012340; NA-bd_OB-fold.
InterPro; IPR019307; RNA-bd_AU-1/RNase_E/G.
InterPro; IPR004659; RNase_E/G.
Pfam; PF00686; CBM_20; 1.
Pfam; PF10150; RNase_E_G; 1.
SMART; SM01065; CBM_2; 1.
SUPFAM; SSF49452; SSF49452; 1.
SUPFAM; SSF50249; SSF50249; 1.
TIGRFAMs; TIGR00757; RNaseEG; 1.
PROSITE; PS51166; CBM20; 1.
1: Evidence at protein level;
Alternative splicing; Chloroplast; Coiled coil; Complete proteome;
Endonuclease; Hydrolase; Nuclease; Plastid; Reference proteome;
RNA-binding; Transit peptide.
TRANSIT 1 48 Chloroplast. {ECO:0000255}.
CHAIN 49 1001 Ribonuclease E/G-like protein,
chloroplastic.
/FTId=PRO_0000421383.
DOMAIN 76 185 CBM20. {ECO:0000255|PROSITE-
ProRule:PRU00594}.
COILED 769 789 {ECO:0000255}.
COMPBIAS 466 469 Poly-Asp.
VAR_SEQ 1 288 Missing (in isoform 4 and isoform 5).
{ECO:0000303|PubMed:14593172,
ECO:0000303|PubMed:18515828}.
/FTId=VSP_045662.
VAR_SEQ 1 130 Missing (in isoform 3). {ECO:0000305}.
/FTId=VSP_045663.
VAR_SEQ 62 71 PLRFLLSVFS -> VSAQQ (in isoform 2).
{ECO:0000303|Ref.1}.
/FTId=VSP_045664.
VAR_SEQ 131 139 VKIASGVNF -> MIMNGKLKS (in isoform 3).
{ECO:0000305}.
/FTId=VSP_045665.
VAR_SEQ 886 907 AKMEKRGDLENPKSWPRFILRV -> VSVIISILFCYFSFQ
PNEEHLE (in isoform 5).
{ECO:0000303|PubMed:18515828}.
/FTId=VSP_045666.
VAR_SEQ 908 1001 Missing (in isoform 5).
{ECO:0000303|PubMed:18515828}.
/FTId=VSP_045667.
MUTAGEN 551 551 K->A: Loss of endonucleolytic activity;
when associated with A-557.
{ECO:0000269|PubMed:18441049}.
MUTAGEN 557 557 K->A: Loss of endonucleolytic activity;
when associated with A-551.
{ECO:0000269|PubMed:18441049}.
MUTAGEN 693 698 Missing: In rne-2; loss of
endonucleolytic activity.
{ECO:0000269|PubMed:22735703}.
SEQUENCE 1001 AA; 111552 MW; EEC229D611EADB25 CRC64;
MDVTEVPWRR LPQFSVSSRA SWLVSSGFPL SSYMFSHVER GKTFRLTLCF GVSRLRPRSA
IPLRFLLSVF SEQPPSRLKG LCEVVWIVEA DLAANEHLYV TGDPSTLGSW EPDCAISMYP
TENDNEWEAK VKIASGVNFR YNYLLKAGYG SSSDVIWRPG PQFSLSVPSS VNQDRKIIIR
DSWMSMSISS KSQESYGWGS WIDDAYLFPN CVTPAQSEDE CTSADSAIEV PRTHLNDKQV
GAESFLCDEL AAFSSENSNL SALFSDNYQP IEEPWLIQES ITLQHERNMQ TDSEQDVESC
DDNENNLNTD EQNHQLTETL LPDGGFFQSE SIATTILINS SICTVQRIAV LEGGKLVELL
LEPVKTNVQC DSVYLGVITK FVPHMGGAFV NIGSARHSFM DIKSNREPFI FPPFCDGSKK
QAADGSPILS MNDIPAPHEI EHASYDFEAS SLLDIDSNDP GESFHDDDDE HENDEYHVSD
HLAGLVNGTV VNHGAVEVGS ENGHIPMERG HSADSLDSNA SVAKASKVMS SKDNKWIQVR
KGTKIIVQVV KEGLGTKGPT LTAYPKLRSR FWVLLTRCKR IGVSKKISGV ERTRLKVIAK
TLQPQGFGLT VRTVAAGHSL EELQKDLDGL LLTWKNITDE AKSAALAADE GVEGAIPALL
HRAMGQTLSV VQDYFNDKVE KMVVDSPRTY HEVTHYLQDM APDLCNRVEL HDKGIPLFDL
YEIEEEIEGI LSKRVPLSNG GSLVIEQTEA LVSIDVNGGH GMFGQGNSQE KAILEVNLAA
ARQIAREIRL RDIGGIIVVD FIDMADESNK RLVYEEVKKA VERDRSLVKV SELSRHGLME
ITRKRVRPSV TFMISEPCSC CHATGRVEAL ETTFSKIEQE ICRQLAKMEK RGDLENPKSW
PRFILRVDSH MSSFLTTGKR TRLAILSSSL KVWILLKVAR HFTRGTFEVK PFMDEKTVNE
RQHQVAISLL KKADAIADSS GKKKLTLIPI KKEKTSGKQR R


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