CCR4C_ARATH
ID CCR4C_ARATH Reviewed; 448 AA.
AC Q9LS39; A8MSA8; Q8RWF7;
DT 25-NOV-2008, integrated into UniProtKB/Swiss-Prot.
DT 25-NOV-2008, sequence version 2.
DT 03-AUG-2022, entry version 99.
DE RecName: Full=Carbon catabolite repressor protein 4 homolog 3;
DE Short=CCR4 homolog 3;
DE EC=3.1.13.4;
GN Name=CCR4-3; OrderedLocusNames=At3g18500; ORFNames=MYF24.23;
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 [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=10819329; DOI=10.1093/dnares/7.2.131;
RA Sato S., Nakamura Y., Kaneko T., Katoh T., Asamizu E., Tabata S.;
RT "Structural analysis of Arabidopsis thaliana chromosome 3. I. Sequence
RT features of the regions of 4,504,864 bp covered by sixty P1 and TAC
RT clones.";
RL DNA Res. 7:131-135(2000).
RN [2]
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 [3]
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 [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 2 AND 3).
RC STRAIN=cv. Columbia;
RX PubMed=14993207; DOI=10.1101/gr.1515604;
RA Castelli V., Aury J.-M., Jaillon O., Wincker P., Clepet C., Menard M.,
RA Cruaud C., Quetier F., Scarpelli C., Schaechter V., Temple G., Caboche M.,
RA Weissenbach J., Salanoubat M.;
RT "Whole genome sequence comparisons and 'full-length' cDNA sequences: a
RT combined approach to evaluate and improve Arabidopsis genome annotation.";
RL Genome Res. 14:406-413(2004).
CC -!- FUNCTION: Acts as catalytic component of the CCR4-NOT core complex,
CC which in the nucleus seems to be a general transcription factor, and in
CC the cytoplasm the major mRNA deadenylase involved in mRNA turnover.
CC {ECO:0000250}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=Exonucleolytic cleavage of poly(A) to 5'-AMP.; EC=3.1.13.4;
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420; Evidence={ECO:0000250};
CC -!- SUBUNIT: Component of the CCR4-NOT complex, at least composed of CRR4
CC and CAF1 proteins. {ECO:0000250}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000250}. Cytoplasm {ECO:0000250}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=4;
CC Name=1;
CC IsoId=Q9LS39-1; Sequence=Displayed;
CC Name=2;
CC IsoId=Q9LS39-2; Sequence=VSP_035824;
CC Name=3;
CC IsoId=Q9LS39-3; Sequence=VSP_035825, VSP_035826;
CC Name=4;
CC IsoId=Q9LS39-4; Sequence=VSP_035823, VSP_035825, VSP_035826;
CC -!- SIMILARITY: Belongs to the CCR4/nocturin family. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=BAB01117.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC Sequence=BX822235; Type=Miscellaneous discrepancy; Note=Sequencing errors.; Evidence={ECO:0000305};
CC Sequence=BX823421; Type=Miscellaneous discrepancy; Note=Sequencing errors.; Evidence={ECO:0000305};
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DR EMBL; AB026658; BAB01117.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002686; AEE76105.1; -; Genomic_DNA.
DR EMBL; CP002686; AEE76106.1; -; Genomic_DNA.
DR EMBL; AY093122; AAM13121.1; -; mRNA.
DR EMBL; BT003387; AAO30050.1; -; mRNA.
DR EMBL; BX822235; -; NOT_ANNOTATED_CDS; mRNA.
DR EMBL; BX823421; -; NOT_ANNOTATED_CDS; mRNA.
DR RefSeq; NP_001078178.1; NM_001084709.1. [Q9LS39-1]
DR RefSeq; NP_001326135.1; NM_001338338.1.
DR RefSeq; NP_188479.3; NM_112735.4. [Q9LS39-2]
DR AlphaFoldDB; Q9LS39; -.
DR SMR; Q9LS39; -.
DR STRING; 3702.AT3G18500.3; -.
DR PaxDb; Q9LS39; -.
DR PRIDE; Q9LS39; -.
DR EnsemblPlants; AT3G18500.1; AT3G18500.1; AT3G18500. [Q9LS39-2]
DR EnsemblPlants; AT3G18500.2; AT3G18500.2; AT3G18500. [Q9LS39-1]
DR GeneID; 821380; -.
DR Gramene; AT3G18500.1; AT3G18500.1; AT3G18500. [Q9LS39-2]
DR Gramene; AT3G18500.2; AT3G18500.2; AT3G18500. [Q9LS39-1]
DR KEGG; ath:AT3G18500; -.
DR Araport; AT3G18500; -.
DR eggNOG; KOG2338; Eukaryota.
DR HOGENOM; CLU_016428_0_0_1; -.
DR InParanoid; Q9LS39; -.
DR PhylomeDB; Q9LS39; -.
DR PRO; PR:Q9LS39; -.
DR Proteomes; UP000006548; Chromosome 3.
DR ExpressionAtlas; Q9LS39; baseline and differential.
DR Genevisible; Q9LS39; AT.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0005634; C:nucleus; IEA:UniProtKB-SubCell.
DR GO; GO:0000175; F:3'-5'-exoribonuclease activity; IBA:GO_Central.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0004535; F:poly(A)-specific ribonuclease activity; IEA:UniProtKB-EC.
DR GO; GO:0003723; F:RNA binding; IEA:UniProtKB-KW.
DR Gene3D; 3.60.10.10; -; 1.
DR InterPro; IPR036691; Endo/exonu/phosph_ase_sf.
DR InterPro; IPR005135; Endo/exonuclease/phosphatase.
DR Pfam; PF03372; Exo_endo_phos; 1.
DR SUPFAM; SSF56219; SSF56219; 1.
PE 2: Evidence at transcript level;
KW Alternative splicing; Cytoplasm; Exonuclease; Hydrolase; Magnesium;
KW Metal-binding; Nuclease; Nucleus; Reference proteome; Repeat; RNA-binding;
KW Transcription; Transcription regulation.
FT CHAIN 1..448
FT /note="Carbon catabolite repressor protein 4 homolog 3"
FT /id="PRO_0000355046"
FT REGION 50..92
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 162
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250|UniProtKB:O95551"
FT VAR_SEQ 105..106
FT /note="Missing (in isoform 4)"
FT /evidence="ECO:0000303|PubMed:14593172"
FT /id="VSP_035823"
FT VAR_SEQ 162..183
FT /note="Missing (in isoform 2)"
FT /evidence="ECO:0000303|PubMed:14993207"
FT /id="VSP_035824"
FT VAR_SEQ 184..264
FT /note="RRTGDNVDGCAMFWKADRFGVLERENIEFSQFGMRDNVAQLAVLELRKSNKS
FT RKILLGNIHVLYNPNQGDVKLGQVRSLCS -> KDYKYKLCNGSGELEITSMVAQCFGR
FT LTGLEFWRGKTLSLASLVCGIMLHSLLFLSSGSLISQERYCWVTFTCFIIQIKEM (in
FT isoform 3 and isoform 4)"
FT /evidence="ECO:0000303|PubMed:14593172,
FT ECO:0000303|PubMed:14993207"
FT /id="VSP_035825"
FT VAR_SEQ 265..448
FT /note="Missing (in isoform 3 and isoform 4)"
FT /evidence="ECO:0000303|PubMed:14593172,
FT ECO:0000303|PubMed:14993207"
FT /id="VSP_035826"
SQ SEQUENCE 448 AA; 50322 MW; AA328C57A2E598E5 CRC64;
MRCVNRVDCS WSRPSEAYRI LPSGGHLSSG FHQCPLSSLS FRSSFVCCSS STSGPSDSNP
ESSSNRSYSR RWQNPLPRRQ HPDQIPSSQI ARDWIDSDTT PVSQALERFT VVSYNILGDG
NSSYHRELYS NVSVPYLKWG YRKRLICEEL IRLNPDIISM QEVDKYFDLF SMMEKAGYAG
SYKRRTGDNV DGCAMFWKAD RFGVLERENI EFSQFGMRDN VAQLAVLELR KSNKSRKILL
GNIHVLYNPN QGDVKLGQVR SLCSKAHLLS KKWGDIPIVL CGDFNSTPKS PLYNFLASSE
LNVMEHDKKE LSGQKNCRPT KVLETGSKSS NTITFSFCSS WTKEEIRVAT GQENSYWAAH
PLKLNSSYAS VKGSANTRDS VGEPLATSYH SKFLGTVDYL WYSDGLLPAR VLDTLPIDVL
CKTKGLPCQE LGSDHLALVS EFVFEPDG
