RNE_ARATH
ID RNE_ARATH Reviewed; 1001 AA.
AC F4IV66; F4IV67; F4IV69; Q8GZQ4; Q8RWB3; Q9M498; Q9SI08;
DT 06-MAR-2013, integrated into UniProtKB/Swiss-Prot.
DT 28-JUN-2011, sequence version 1.
DT 03-AUG-2022, entry version 70.
DE RecName: Full=Ribonuclease E/G-like protein, chloroplastic;
DE Short=RNase E/G-like protein;
DE EC=3.1.26.-;
DE AltName: Full=RNase E;
DE Flags: Precursor;
GN Name=RNE; Synonyms=RNEE/G; OrderedLocusNames=At2g04270; ORFNames=T23O15.10;
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 [MRNA] (ISOFORM 2).
RA Walter M., Kudla J.;
RT "Molecular characterization of an Arabidopsis RNase E-like
RT endoribonuclease.";
RL Submitted (NOV-2001) to the EMBL/GenBank/DDBJ databases.
RN [2]
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., Moffat K.S.,
RA Cronin L.A., Shen M., Pai G., Van Aken S., Umayam L., Tallon L.J.,
RA Gill J.E., Adams M.D., Carrera A.J., Creasy T.H., Goodman H.M.,
RA Somerville C.R., Copenhaver G.P., Preuss D., Nierman W.C., White O.,
RA Eisen J.A., Salzberg S.L., Fraser C.M., Venter J.C.;
RT "Sequence and analysis of chromosome 2 of the plant Arabidopsis thaliana.";
RL Nature 402:761-768(1999).
RN [3]
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 [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 4).
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 [5]
RP NUCLEOTIDE SEQUENCE [MRNA] OF 45-619 (ISOFORM 5), FUNCTION, SUBCELLULAR
RP LOCATION, TISSUE SPECIFICITY, ALTERNATIVE SPLICING, AND DISRUPTION
RP PHENOTYPE.
RX PubMed=18515828; DOI=10.1093/jxb/ern126;
RA Mudd E.A., Sullivan S., Gisby M.F., Mironov A., Kwon C.S., Chung W.I.,
RA Day A.;
RT "A 125 kDa RNase E/G-like protein is present in plastids and is essential
RT for chloroplast development and autotrophic growth in Arabidopsis.";
RL J. Exp. Bot. 59:2597-2610(2008).
RN [6]
RP FUNCTION, MUTAGENESIS OF LYS-551 AND LYS-557, SUBUNIT, 3D-STRUCTURE
RP MODELING, AND SUBCELLULAR LOCATION.
RX PubMed=18441049; DOI=10.1261/rna.907608;
RA Schein A., Sheffy-Levin S., Glaser F., Schuster G.;
RT "The RNase E/G-type endoribonuclease of higher plants is located in the
RT chloroplast and cleaves RNA similarly to the E. coli enzyme.";
RL RNA 14:1057-1068(2008).
RN [7]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RX PubMed=21105931; DOI=10.1111/j.1365-313x.2010.04377.x;
RA Walter M., Piepenburg K., Schottler M.A., Petersen K., Kahlau S.,
RA Tiller N., Drechsel O., Weingartner M., Kudla J., Bock R.;
RT "Knockout of the plastid RNase E leads to defective RNA processing and
RT chloroplast ribosome deficiency.";
RL Plant J. 64:851-863(2010).
RN [8]
RP MUTAGENESIS OF 693-VAL--GLN-698, SUBCELLULAR LOCATION, INTERACTION WITH
RP RHON1, AND DISRUPTION PHENOTYPE.
RC STRAIN=cv. Columbia;
RX PubMed=22735703; DOI=10.1093/nar/gks613;
RA Stoppel R., Manavski N., Schein A., Schuster G., Teubner M.,
RA Schmitz-Linneweber C., Meurer J.;
RT "RHON1 is a novel ribonucleic acid-binding protein that supports RNase E
RT function in the Arabidopsis chloroplast.";
RL Nucleic Acids Res. 40:8593-8606(2012).
CC -!- FUNCTION: Involved in intercistronic processing of primary transcripts
CC from chloroplast operons. The endonucleolytic activity of the enzyme
CC depends on the number of phosphates at the 5' end, is inhibited by
CC structured RNA, and preferentially cleaves A/U-rich sequences.
CC {ECO:0000269|PubMed:18441049, ECO:0000269|PubMed:18515828,
CC ECO:0000269|PubMed:21105931}.
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000250|UniProtKB:P21513};
CC Note=Binds 1 Mg(2+) ion per subunit. {ECO:0000250|UniProtKB:P21513};
CC -!- COFACTOR:
CC Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
CC Evidence={ECO:0000250|UniProtKB:P21513};
CC Note=Binds 2 Zn(2+) ions per homotetramer. Zinc ions are bound between
CC subunits. {ECO:0000250|UniProtKB:P21513};
CC -!- SUBUNIT: Part of a chloroplastic degradosome-like complex. Interacts
CC with RHON1 (PubMed:18441049, PubMed:22735703). A homotetramer formed by
CC a dimer of dimers (By similarity). {ECO:0000250|UniProtKB:P21513,
CC ECO:0000269|PubMed:18441049, ECO:0000269|PubMed:22735703}.
CC -!- SUBCELLULAR LOCATION: Plastid, chloroplast stroma
CC {ECO:0000269|PubMed:18441049, ECO:0000269|PubMed:18515828,
CC ECO:0000269|PubMed:22735703}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=5;
CC Name=1;
CC IsoId=F4IV66-1; Sequence=Displayed;
CC Name=2;
CC IsoId=F4IV66-2; Sequence=VSP_045664;
CC Name=3;
CC IsoId=F4IV66-3; Sequence=VSP_045663, VSP_045665;
CC Name=4;
CC IsoId=F4IV66-4; Sequence=VSP_045662;
CC Name=5;
CC IsoId=F4IV66-5; Sequence=VSP_045662, VSP_045666, VSP_045667;
CC -!- TISSUE SPECIFICITY: Expressed in cotyledons, rosette and cauline
CC leaves. {ECO:0000269|PubMed:18515828}.
CC -!- DISRUPTION PHENOTYPE: Reduced photosynthetic activity and retarded
CC growth. Increased number and decreased size of chloroplasts. Loss of
CC autotrophic growth. Pale cotyledons when grown on sucrose-complemented
CC medium. {ECO:0000269|PubMed:18515828, ECO:0000269|PubMed:21105931,
CC ECO:0000269|PubMed:22735703}.
CC -!- SIMILARITY: Belongs to the RNase E/G family. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAD27911.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AF450479; AAN76770.1; -; mRNA.
DR EMBL; AC007213; AAD27911.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002685; AEC05813.1; -; Genomic_DNA.
DR EMBL; CP002685; AEC05814.1; -; Genomic_DNA.
DR EMBL; CP002685; AEC05815.1; -; Genomic_DNA.
DR EMBL; CP002685; AEC05816.1; -; Genomic_DNA.
DR EMBL; CP002685; AEC05817.1; -; Genomic_DNA.
DR EMBL; CP002685; ANM63269.1; -; Genomic_DNA.
DR EMBL; CP002685; ANM63270.1; -; Genomic_DNA.
DR EMBL; CP002685; ANM63271.1; -; Genomic_DNA.
DR EMBL; AY093213; AAM13212.1; -; mRNA.
DR EMBL; BT008793; AAP68232.1; -; mRNA.
DR EMBL; AJ252122; CAB76425.1; -; mRNA.
DR PIR; F84455; F84455.
DR RefSeq; NP_001189510.1; NM_001202581.2. [F4IV66-1]
DR RefSeq; NP_001318196.1; NM_001335223.1. [F4IV66-4]
DR RefSeq; NP_001325370.1; NM_001335226.1. [F4IV66-4]
DR RefSeq; NP_001325371.1; NM_001335224.1. [F4IV66-3]
DR RefSeq; NP_178508.2; NM_126460.4. [F4IV66-4]
DR RefSeq; NP_850987.1; NM_180656.2. [F4IV66-2]
DR RefSeq; NP_850988.1; NM_180657.2. [F4IV66-3]
DR RefSeq; NP_850989.1; NM_180658.2. [F4IV66-5]
DR AlphaFoldDB; F4IV66; -.
DR SMR; F4IV66; -.
DR STRING; 3702.AT2G04270.5; -.
DR PaxDb; F4IV66; -.
DR PRIDE; F4IV66; -.
DR ProteomicsDB; 227998; -. [F4IV66-1]
DR EnsemblPlants; AT2G04270.1; AT2G04270.1; AT2G04270. [F4IV66-2]
DR EnsemblPlants; AT2G04270.2; AT2G04270.2; AT2G04270. [F4IV66-3]
DR EnsemblPlants; AT2G04270.3; AT2G04270.3; AT2G04270. [F4IV66-5]
DR EnsemblPlants; AT2G04270.4; AT2G04270.4; AT2G04270. [F4IV66-4]
DR EnsemblPlants; AT2G04270.5; AT2G04270.5; AT2G04270. [F4IV66-1]
DR EnsemblPlants; AT2G04270.6; AT2G04270.6; AT2G04270. [F4IV66-3]
DR EnsemblPlants; AT2G04270.8; AT2G04270.8; AT2G04270. [F4IV66-4]
DR EnsemblPlants; AT2G04270.9; AT2G04270.9; AT2G04270. [F4IV66-4]
DR GeneID; 814965; -.
DR Gramene; AT2G04270.1; AT2G04270.1; AT2G04270. [F4IV66-2]
DR Gramene; AT2G04270.2; AT2G04270.2; AT2G04270. [F4IV66-3]
DR Gramene; AT2G04270.3; AT2G04270.3; AT2G04270. [F4IV66-5]
DR Gramene; AT2G04270.4; AT2G04270.4; AT2G04270. [F4IV66-4]
DR Gramene; AT2G04270.5; AT2G04270.5; AT2G04270. [F4IV66-1]
DR Gramene; AT2G04270.6; AT2G04270.6; AT2G04270. [F4IV66-3]
DR Gramene; AT2G04270.8; AT2G04270.8; AT2G04270. [F4IV66-4]
DR Gramene; AT2G04270.9; AT2G04270.9; AT2G04270. [F4IV66-4]
DR KEGG; ath:AT2G04270; -.
DR Araport; AT2G04270; -.
DR TAIR; locus:2059775; AT2G04270.
DR eggNOG; ENOG502QPXM; Eukaryota.
DR InParanoid; F4IV66; -.
DR OMA; GQNPTIE; -.
DR OrthoDB; 722846at2759; -.
DR PRO; PR:F4IV66; -.
DR Proteomes; UP000006548; Chromosome 2.
DR ExpressionAtlas; F4IV66; baseline and differential.
DR Genevisible; F4IV66; AT.
DR GO; GO:0009507; C:chloroplast; IDA:TAIR.
DR GO; GO:0009570; C:chloroplast stroma; IEA:UniProtKB-SubCell.
DR GO; GO:0005737; C:cytoplasm; IBA:GO_Central.
DR GO; GO:0004521; F:endoribonuclease activity; IDA:TAIR.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0004540; F:ribonuclease activity; IBA:GO_Central.
DR GO; GO:0003723; F:RNA binding; IEA:UniProtKB-KW.
DR GO; GO:2001070; F:starch binding; IEA:InterPro.
DR GO; GO:0010239; P:chloroplast mRNA processing; IMP:TAIR.
DR GO; GO:0009658; P:chloroplast organization; IMP:TAIR.
DR GO; GO:1901259; P:chloroplast rRNA processing; IMP:TAIR.
DR GO; GO:0006364; P:rRNA processing; IBA:GO_Central.
DR Gene3D; 2.40.50.140; -; 1.
DR Gene3D; 2.60.40.10; -; 1.
DR InterPro; IPR013784; Carb-bd-like_fold.
DR InterPro; IPR002044; CBM_fam20.
DR InterPro; IPR013783; Ig-like_fold.
DR InterPro; IPR012340; NA-bd_OB-fold.
DR InterPro; IPR019307; RNA-bd_AU-1/RNase_E/G.
DR InterPro; IPR004659; RNase_E/G.
DR PANTHER; PTHR30001; PTHR30001; 1.
DR Pfam; PF00686; CBM_20; 1.
DR Pfam; PF10150; RNase_E_G; 1.
DR SMART; SM01065; CBM_2; 1.
DR SUPFAM; SSF49452; SSF49452; 1.
DR SUPFAM; SSF50249; SSF50249; 1.
DR TIGRFAMs; TIGR00757; RNaseEG; 1.
DR PROSITE; PS51166; CBM20; 1.
PE 1: Evidence at protein level;
KW Alternative splicing; Chloroplast; Coiled coil; Endonuclease; Hydrolase;
KW Magnesium; Metal-binding; mRNA processing; Nuclease; Plastid;
KW Reference proteome; RNA-binding; Transit peptide; Zinc.
FT TRANSIT 1..48
FT /note="Chloroplast"
FT /evidence="ECO:0000255"
FT CHAIN 49..1001
FT /note="Ribonuclease E/G-like protein, chloroplastic"
FT /id="PRO_0000421383"
FT DOMAIN 76..185
FT /note="CBM20"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00594"
FT COILED 769..789
FT /evidence="ECO:0000255"
FT BINDING 755
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250|UniProtKB:P21513"
FT BINDING 800
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250|UniProtKB:P21513"
FT BINDING 858
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="ligand shared between dimeric partners"
FT /evidence="ECO:0000250|UniProtKB:P21513"
FT BINDING 861
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="ligand shared between dimeric partners"
FT /evidence="ECO:0000250|UniProtKB:P21513"
FT VAR_SEQ 1..288
FT /note="Missing (in isoform 4 and isoform 5)"
FT /evidence="ECO:0000303|PubMed:14593172,
FT ECO:0000303|PubMed:18515828"
FT /id="VSP_045662"
FT VAR_SEQ 1..130
FT /note="Missing (in isoform 3)"
FT /evidence="ECO:0000305"
FT /id="VSP_045663"
FT VAR_SEQ 62..71
FT /note="PLRFLLSVFS -> VSAQQ (in isoform 2)"
FT /evidence="ECO:0000303|Ref.1"
FT /id="VSP_045664"
FT VAR_SEQ 131..139
FT /note="VKIASGVNF -> MIMNGKLKS (in isoform 3)"
FT /evidence="ECO:0000305"
FT /id="VSP_045665"
FT VAR_SEQ 886..907
FT /note="AKMEKRGDLENPKSWPRFILRV -> VSVIISILFCYFSFQPNEEHLE (in
FT isoform 5)"
FT /evidence="ECO:0000303|PubMed:18515828"
FT /id="VSP_045666"
FT VAR_SEQ 908..1001
FT /note="Missing (in isoform 5)"
FT /evidence="ECO:0000303|PubMed:18515828"
FT /id="VSP_045667"
FT MUTAGEN 551
FT /note="K->A: Loss of endonucleolytic activity; when
FT associated with A-557."
FT /evidence="ECO:0000269|PubMed:18441049"
FT MUTAGEN 557
FT /note="K->A: Loss of endonucleolytic activity; when
FT associated with A-551."
FT /evidence="ECO:0000269|PubMed:18441049"
FT MUTAGEN 693..698
FT /note="Missing: In rne-2; loss of endonucleolytic
FT activity."
FT /evidence="ECO:0000269|PubMed:22735703"
SQ 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
