LOCUS RNE_ARATH 1001 aa linear PLN 27-NOV-2024
DEFINITION RecName: Full=Ribonuclease E/G-like protein, chloroplastic;
Short=RNase E/G-like protein; AltName: Full=RNase E; Flags:
Precursor.
ACCESSION F4IV66
VERSION F4IV66.1
DBSOURCE UniProtKB: locus RNE_ARATH, accession F4IV66;
class: standard.
extra accessions:F4IV67,F4IV69,Q8GZQ4,Q8RWB3,Q9M498,Q9SI08
created: Mar 6, 2013.
sequence updated: Jun 28, 2011.
annotation updated: Nov 27, 2024.
xrefs: AF450479.1, AAN76770.1, AC007213.6, AAD27911.1, CP002685.1,
AEC05813.1, AEC05814.1, AEC05815.1, AEC05816.1, AEC05817.1,
ANM63269.1, ANM63270.1, ANM63271.1, AY093213.1, AAM13212.1,
BT008793.1, AAP68232.1, AJ252122.1, CAB76425.1, F84455,
NP_001189510.1, NP_001318196.1, NP_001325370.1, NP_001325371.1,
NP_178508.2, NP_850987.1, NP_850988.1, NP_850989.1
xrefs (non-sequence databases): AlphaFoldDB:F4IV66, SMR:F4IV66,
STRING:3702.F4IV66, PaxDb:3702-AT2G04270.5, ProteomicsDB:227998,
EnsemblPlants:AT2G04270.1, EnsemblPlants:AT2G04270.1,
EnsemblPlants:AT2G04270, EnsemblPlants:AT2G04270.2,
EnsemblPlants:AT2G04270.2, EnsemblPlants:AT2G04270.3,
EnsemblPlants:AT2G04270.3, EnsemblPlants:AT2G04270.4,
EnsemblPlants:AT2G04270.4, EnsemblPlants:AT2G04270.5,
EnsemblPlants:AT2G04270.5, EnsemblPlants:AT2G04270.6,
EnsemblPlants:AT2G04270.6, EnsemblPlants:AT2G04270.8,
EnsemblPlants:AT2G04270.8, EnsemblPlants:AT2G04270.9,
EnsemblPlants:AT2G04270.9, GeneID:814965, Gramene:AT2G04270.1,
Gramene:AT2G04270.2, Gramene:AT2G04270.3, Gramene:AT2G04270.4,
Gramene:AT2G04270.5, Gramene:AT2G04270.6, Gramene:AT2G04270.8,
Gramene:AT2G04270.9, KEGG:ath:AT2G04270, Araport:AT2G04270,
TAIR:AT2G04270, eggNOG:ENOG502QPXM, InParanoid:F4IV66, OMA:CERVELH,
OrthoDB:1206148at2759, PRO:PR:F4IV66, Proteomes:UP000006548,
ExpressionAtlas:F4IV66, GO:0009507, GO:0009570, GO:0046872,
GO:0003723, GO:0004521, GO:2001070, GO:0010239, GO:0009658,
GO:1901259, FunFam:2.60.40.10:FF:001568, Gene3D:2.60.40.10,
Gene3D:2.40.50.140, Gene3D:3.40.1260.20, InterPro:IPR013784,
InterPro:IPR002044, InterPro:IPR013783, InterPro:IPR012340,
InterPro:IPR019307, InterPro:IPR004659, NCBIfam:TIGR00757,
PANTHER:PTHR30001, PANTHER:PTHR30001:SF1, Pfam:PF00686,
Pfam:PF10150, SMART:SM01065, SUPFAM:SSF50249, SUPFAM:SSF49452,
PROSITE:PS51166
KEYWORDS Alternative splicing; Chloroplast; Coiled coil; Endonuclease;
Hydrolase; Magnesium; Metal-binding; mRNA processing; Nuclease;
Plastid; Reference proteome; RNA-binding; Transit peptide; Zinc.
SOURCE Arabidopsis thaliana (thale cress)
ORGANISM Arabidopsis thaliana
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae;
Pentapetalae; rosids; malvids; Brassicales; Brassicaceae;
Camelineae; Arabidopsis.
REFERENCE 1 (residues 1 to 1001)
AUTHORS Walter,M. and Kudla,J.
TITLE Direct Submission
JOURNAL Submitted (??-NOV-2001) to the EMBL/GenBank/DDBJ databases
REMARK NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 2).
REFERENCE 2 (residues 1 to 1001)
AUTHORS Lin,X., Kaul,S., Rounsley,S., Shea,T.P., Benito,M.I., Town,C.D.,
Fujii,C.Y., Mason,T., Bowman,C.L., Barnstead,M., Feldblyum,T.V.,
Buell,C.R., Ketchum,K.A., Lee,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. and
Venter,J.C.
TITLE Sequence and analysis of chromosome 2 of the plant Arabidopsis
thaliana
JOURNAL Nature 402 (6763), 761-768 (1999)
PUBMED 10617197
REMARK NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].;
STRAIN=cv. Columbia
REFERENCE 3 (residues 1 to 1001)
AUTHORS Cheng,C.Y., Krishnakumar,V., Chan,A.P., Thibaud-Nissen,F.,
Schobel,S. and Town,C.D.
TITLE Araport11: a complete reannotation of the Arabidopsis thaliana
reference genome
JOURNAL Plant J 89 (4), 789-804 (2017)
PUBMED 27862469
REMARK GENOME REANNOTATION.;
STRAIN=cv. Columbia
REFERENCE 4 (residues 1 to 1001)
AUTHORS Yamada,K., Lim,J., Dale,J.M., Chen,H., Shinn,P., Palm,C.J.,
Southwick,A.M., Wu,H.C., Kim,C., Nguyen,M., Pham,P., Cheuk,R.,
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.,
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.,
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. and Ecker,J.R.
TITLE Empirical analysis of transcriptional activity in the Arabidopsis
genome
JOURNAL Science 302 (5646), 842-846 (2003)
PUBMED 14593172
REMARK NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 4).;
STRAIN=cv. Columbia
REFERENCE 5 (residues 1 to 1001)
AUTHORS Mudd,E.A., Sullivan,S., Gisby,M.F., Mironov,A., Kwon,C.S.,
Chung,W.I. and Day,A.
TITLE A 125 kDa RNase E/G-like protein is present in plastids and is
essential for chloroplast development and autotrophic growth in
Arabidopsis
JOURNAL J Exp Bot 59 (10), 2597-2610 (2008)
PUBMED 18515828
REMARK NUCLEOTIDE SEQUENCE [MRNA] OF 45-619 (ISOFORM 5), FUNCTION,
SUBCELLULAR LOCATION, TISSUE SPECIFICITY, ALTERNATIVE SPLICING, AND
DISRUPTION PHENOTYPE.
REFERENCE 6 (residues 1 to 1001)
AUTHORS Schein,A., Sheffy-Levin,S., Glaser,F. and Schuster,G.
TITLE The RNase E/G-type endoribonuclease of higher plants is located in
the chloroplast and cleaves RNA similarly to the E. coli enzyme
JOURNAL RNA 14 (6), 1057-1068 (2008)
PUBMED 18441049
REMARK FUNCTION, MUTAGENESIS OF LYS-551 AND LYS-557, SUBUNIT, 3D-STRUCTURE
MODELING, AND SUBCELLULAR LOCATION.
REFERENCE 7 (residues 1 to 1001)
AUTHORS Walter,M., Piepenburg,K., Schottler,M.A., Petersen,K., Kahlau,S.,
Tiller,N., Drechsel,O., Weingartner,M., Kudla,J. and Bock,R.
TITLE Knockout of the plastid RNase E leads to defective RNA processing
and chloroplast ribosome deficiency
JOURNAL Plant J 64 (5), 851-863 (2010)
PUBMED 21105931
REMARK FUNCTION, AND DISRUPTION PHENOTYPE.
REFERENCE 8 (residues 1 to 1001)
AUTHORS Stoppel,R., Manavski,N., Schein,A., Schuster,G., Teubner,M.,
Schmitz-Linneweber,C. and Meurer,J.
TITLE RHON1 is a novel ribonucleic acid-binding protein that supports
RNase E function in the Arabidopsis chloroplast
JOURNAL Nucleic Acids Res 40 (17), 8593-8606 (2012)
PUBMED 22735703
REMARK MUTAGENESIS OF 693-VAL--GLN-698, SUBCELLULAR LOCATION, INTERACTION
WITH RHON1, AND DISRUPTION PHENOTYPE.;
STRAIN=cv. Columbia
COMMENT On or before Mar 13, 2013 this sequence version replaced
gi:75151654, gi:75158660, gi:75184260, gi:75206015.
[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}.
[COFACTOR] Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
Evidence={ECO:0000250|UniProtKB:P21513}; Note=Binds 1 Mg(2+) ion
per subunit. {ECO:0000250|UniProtKB:P21513}.
[COFACTOR] Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
Evidence={ECO:0000250|UniProtKB:P21513}; Note=Binds 2 Zn(2+) ions
per homotetramer. Zinc ions are bound between subunits.
{ECO:0000250|UniProtKB:P21513}.
[SUBUNIT] Part of a chloroplastic degradosome-like complex.
Interacts with RHON1 (PubMed:18441049, PubMed:22735703). A
homotetramer formed by a dimer of dimers (By similarity).
{ECO:0000250|UniProtKB:P21513, 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; Name=2;
IsoId=F4IV66-2; Sequence=VSP_045664; Name=3; IsoId=F4IV66-3;
Sequence=VSP_045663, VSP_045665; Name=4; IsoId=F4IV66-4;
Sequence=VSP_045662; Name=5; IsoId=F4IV66-5; Sequence=VSP_045662,
VSP_045666, VSP_045667.
[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}.
FEATURES Location/Qualifiers
source 1..1001
/organism="Arabidopsis thaliana"
/db_xref="taxon:3702"
gene 1..1001
/gene="RNE"
/locus_tag="At2g04270"
/gene_synonym="RNEE/G"
/gene_synonym="T23O15.10"
Protein 1..1001
/product="Ribonuclease E/G-like protein, chloroplastic"
/EC_number="3.1.26.-"
/note="RNase E/G-like protein"
/UniProtKB_evidence="Evidence at protein level"
Region 1..288
/region_name="Splicing variant"
/note="Missing (in isoform 4 and isoform 5).
/evidence=ECO:0000303|PubMed:14593172,
ECO:0000303|PubMed:18515828. /id=VSP_045662."
Region 1..130
/region_name="Splicing variant"
/note="Missing (in isoform 3). /evidence=ECO:0000305.
/id=VSP_045663."
Region 1..48
/region_name="Transit peptide"
/note="Chloroplast. /evidence=ECO:0000255."
Region 49..1001
/region_name="Mature chain"
/note="Ribonuclease E/G-like protein, chloroplastic.
/id=PRO_0000421383."
Region 62..71
/region_name="Splicing variant"
/note="PLRFLLSVFS -> VSAQQ (in isoform 2).
/evidence=ECO:0000303|Ref.1. /id=VSP_045664."
Region 76..185
/region_name="Domain"
/note="CBM20.
/evidence=ECO:0000255|PROSITE-ProRule:PRU00594."
Region 82..177
/region_name="CBM20"
/note="The family 20 carbohydrate-binding module (CBM20),
also known as the starch-binding domain, is found in a
large number of starch degrading enzymes including
alpha-amylase, beta-amylase, glucoamylase, and CGTase
(cyclodextrin glucanotransferase). CBM20 is...; cl15347"
/db_xref="CDD:449530"
Site order(92..97,120,127)
/site_type="other"
/note="starch-binding site 2 [chemical binding]"
/db_xref="CDD:99883"
Site order(110,142,157..158,162)
/site_type="other"
/note="starch-binding site 1 [chemical binding]"
/db_xref="CDD:99883"
Region 131..139
/region_name="Splicing variant"
/note="VKIASGVNF -> MIMNGKLKS (in isoform 3).
/evidence=ECO:0000305. /id=VSP_045665."
Region 336..956
/region_name="CafA"
/note="Ribonuclease G or E [Translation, ribosomal
structure and biogenesis]; COG1530"
/db_xref="CDD:441139"
Site 551
/site_type="mutagenized"
/note="K->A: Loss of endonucleolytic activity; when
associated with A-557.
/evidence=ECO:0000269|PubMed:18441049."
Site 557
/site_type="mutagenized"
/note="K->A: Loss of endonucleolytic activity; when
associated with A-551.
/evidence=ECO:0000269|PubMed:18441049."
Site 693..698
/site_type="mutagenized"
/note="Missing: In rne-2; loss of endonucleolytic
activity. /evidence=ECO:0000269|PubMed:22735703."
Region 769..789
/region_name="Coiled-coil region"
/note="/evidence=ECO:0000255."
Region 886..907
/region_name="Splicing variant"
/note="AKMEKRGDLENPKSWPRFILRV -> VSVIISILFCYFSFQPNEEHLE
(in isoform 5). /evidence=ECO:0000303|PubMed:18515828.
/id=VSP_045666."
Region 908..1001
/region_name="Splicing variant"
/note="Missing (in isoform 5).
/evidence=ECO:0000303|PubMed:18515828. /id=VSP_045667."
ORIGIN
1 mdvtevpwrr lpqfsvssra swlvssgfpl ssymfshver gktfrltlcf gvsrlrprsa
61 iplrfllsvf seqppsrlkg lcevvwivea dlaanehlyv tgdpstlgsw epdcaismyp
121 tendneweak vkiasgvnfr ynyllkagyg sssdviwrpg pqfslsvpss vnqdrkiiir
181 dswmsmsiss ksqesygwgs widdaylfpn cvtpaqsede ctsadsaiev prthlndkqv
241 gaesflcdel aafssensnl salfsdnyqp ieepwliqes itlqhernmq tdseqdvesc
301 ddnennlntd eqnhqltetl lpdggffqse siattilins sictvqriav leggklvell
361 lepvktnvqc dsvylgvitk fvphmggafv nigsarhsfm diksnrepfi fppfcdgskk
421 qaadgspils mndipaphei ehasydfeas slldidsndp gesfhdddde hendeyhvsd
481 hlaglvngtv vnhgavevgs enghipmerg hsadsldsna svakaskvms skdnkwiqvr
541 kgtkiivqvv keglgtkgpt ltaypklrsr fwvlltrckr igvskkisgv ertrlkviak
601 tlqpqgfglt vrtvaaghsl eelqkdldgl lltwknitde aksaalaade gvegaipall
661 hramgqtlsv vqdyfndkve kmvvdsprty hevthylqdm apdlcnrvel hdkgiplfdl
721 yeieeeiegi lskrvplsng gslvieqtea lvsidvnggh gmfgqgnsqe kailevnlaa
781 arqiareirl rdiggiivvd fidmadesnk rlvyeevkka verdrslvkv selsrhglme
841 itrkrvrpsv tfmisepcsc chatgrveal ettfskieqe icrqlakmek rgdlenpksw
901 prfilrvdsh mssflttgkr trlailsssl kvwillkvar hftrgtfevk pfmdektvne
961 rqhqvaisll kkadaiadss gkkkltlipi kkektsgkqr r
//