CCR4D_ARATH
ID CCR4D_ARATH Reviewed; 417 AA.
AC A8MS41; Q304C9; Q3ED42; Q3ED43; Q84JM1; Q9C559;
DT 25-NOV-2008, integrated into UniProtKB/Swiss-Prot.
DT 04-DEC-2007, sequence version 1.
DT 03-AUG-2022, entry version 90.
DE RecName: Full=Carbon catabolite repressor protein 4 homolog 4 {ECO:0000305};
DE Short=CCR4 homolog 4 {ECO:0000305};
DE EC=3.1.13.4 {ECO:0000269|PubMed:26619288};
DE AltName: Full=Protein HESPERIN {ECO:0000303|PubMed:26619288};
DE Short=AtHESP {ECO:0000303|PubMed:26619288};
DE Short=AtHesperin {ECO:0000303|PubMed:26619288};
GN Name=CCR4-4 {ECO:0000305}; Synonyms=HESP {ECO:0000303|PubMed:26619288};
GN OrderedLocusNames=At1g31500 {ECO:0000312|Araport:AT1G31500};
GN ORFNames=F27M3_27 {ECO:0000312|EMBL:AAG60143.1},
GN T8E3.7 {ECO:0000312|EMBL:AAG51276.1};
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=11130712; DOI=10.1038/35048500;
RA Theologis A., Ecker J.R., Palm C.J., Federspiel N.A., Kaul S., White O.,
RA Alonso J., Altafi H., Araujo R., Bowman C.L., Brooks S.Y., Buehler E.,
RA Chan A., Chao Q., Chen H., Cheuk R.F., Chin C.W., Chung M.K., Conn L.,
RA Conway A.B., Conway A.R., Creasy T.H., Dewar K., Dunn P., Etgu P.,
RA Feldblyum T.V., Feng J.-D., Fong B., Fujii C.Y., Gill J.E., Goldsmith A.D.,
RA Haas B., Hansen N.F., Hughes B., Huizar L., Hunter J.L., Jenkins J.,
RA Johnson-Hopson C., Khan S., Khaykin E., Kim C.J., Koo H.L.,
RA Kremenetskaia I., Kurtz D.B., Kwan A., Lam B., Langin-Hooper S., Lee A.,
RA Lee J.M., Lenz C.A., Li J.H., Li Y.-P., Lin X., Liu S.X., Liu Z.A.,
RA Luros J.S., Maiti R., Marziali A., Militscher J., Miranda M., Nguyen M.,
RA Nierman W.C., Osborne B.I., Pai G., Peterson J., Pham P.K., Rizzo M.,
RA Rooney T., Rowley D., Sakano H., Salzberg S.L., Schwartz J.R., Shinn P.,
RA Southwick A.M., Sun H., Tallon L.J., Tambunga G., Toriumi M.J., Town C.D.,
RA Utterback T., Van Aken S., Vaysberg M., Vysotskaia V.S., Walker M., Wu D.,
RA Yu G., Fraser C.M., Venter J.C., Davis R.W.;
RT "Sequence and analysis of chromosome 1 of the plant Arabidopsis thaliana.";
RL Nature 408:816-820(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; 5 AND 6).
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).
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 4).
RC STRAIN=cv. Columbia;
RA Totoki Y., Seki M., Ishida J., Nakajima M., Enju A., Kamiya A.,
RA Narusaka M., Shin-i T., Nakagawa M., Sakamoto N., Oishi K., Kohara Y.,
RA Kobayashi M., Toyoda A., Sakaki Y., Sakurai T., Iida K., Akiyama K.,
RA Satou M., Toyoda T., Konagaya A., Carninci P., Kawai J., Hayashizaki Y.,
RA Shinozaki K.;
RT "Large-scale analysis of RIKEN Arabidopsis full-length (RAFL) cDNAs.";
RL Submitted (JUL-2006) to the EMBL/GenBank/DDBJ databases.
RN [6]
RP ACETYLATION [LARGE SCALE ANALYSIS] AT SER-2 (ISOFORM 3), CLEAVAGE OF
RP INITIATOR METHIONINE [LARGE SCALE ANALYSIS] (ISOFORM 3), AND IDENTIFICATION
RP BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=22223895; DOI=10.1074/mcp.m111.015131;
RA Bienvenut W.V., Sumpton D., Martinez A., Lilla S., Espagne C., Meinnel T.,
RA Giglione C.;
RT "Comparative large-scale characterisation of plant vs. mammal proteins
RT reveals similar and idiosyncratic N-alpha acetylation features.";
RL Mol. Cell. Proteomics 11:M111.015131-M111.015131(2012).
RN [7]
RP FUNCTION, CATALYTIC ACTIVITY, COFACTOR, SUBUNIT, INDUCTION, AND DISRUPTION
RP PHENOTYPE.
RX PubMed=26619288; DOI=10.1080/15476286.2015.1119363;
RA Delis C., Krokida A., Tomatsidou A., Tsikou D., Beta R.A., Tsioumpekou M.,
RA Moustaka J., Stravodimos G., Leonidas D.D., Balatsos N.A.,
RA Papadopoulou K.K.;
RT "AtHESPERIN: a novel regulator of circadian rhythms with poly(A)-degrading
RT activity in plants.";
RL RNA Biol. 13:68-82(2016).
RN [8]
RP SUBCELLULAR LOCATION.
RX PubMed=31093672; DOI=10.1093/pcp/pcz089;
RA Arae T., Morita K., Imahori R., Suzuki Y., Yasuda S., Sato T.,
RA Yamaguchi J., Chiba Y.;
RT "Identification of Arabidopsis CCR4-NOT Complexes with Pumilio RNA-Binding
RT Proteins, APUM5 and APUM2.";
RL Plant Cell Physiol. 60:2015-2025(2019).
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 (By
CC similarity). Transcriptional regulator of circadian rhythms with
CC poly(A)-degrading activity that affects the expression and rhythmicity
CC of the clock core oscillator genes TOC1 and CCA1 (PubMed:26619288).
CC Deadenylation may be a mechanism involved in the regulation of the
CC circadian clock (PubMed:26619288). May play a negative role in response
CC against oxidative stress (PubMed:26619288). Possesses magnesium-
CC dependent poly(A)-specific exoribonuclease activity in vitro and is
CC almost inactive with poly(U), poly(C) and poly(G) as substrates
CC (PubMed:26619288). {ECO:0000250|UniProtKB:P31384,
CC ECO:0000269|PubMed:26619288}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=Exonucleolytic cleavage of poly(A) to 5'-AMP.; EC=3.1.13.4;
CC Evidence={ECO:0000269|PubMed:26619288};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000269|PubMed:26619288};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC pH dependence:
CC Optimum pH is 6.5. {ECO:0000269|PubMed:26619288};
CC Temperature dependence:
CC Optimum temperature is 25 degrees Celsius.
CC {ECO:0000269|PubMed:26619288};
CC -!- SUBUNIT: Component of the CCR4-NOT complex, at least composed of CRR4
CC and CAF1 proteins (By similarity). Forms homooligomers
CC (PubMed:26619288). {ECO:0000250|UniProtKB:P31384,
CC ECO:0000269|PubMed:26619288}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000250|UniProtKB:P31384}. Cytoplasm
CC {ECO:0000269|PubMed:31093672}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=6;
CC Name=1;
CC IsoId=A8MS41-1; Sequence=Displayed;
CC Name=2;
CC IsoId=A8MS41-2; Sequence=VSP_035829, VSP_035830;
CC Name=3;
CC IsoId=A8MS41-3; Sequence=VSP_035828, VSP_035830;
CC Name=4;
CC IsoId=A8MS41-4; Sequence=VSP_035827, VSP_035831;
CC Name=5;
CC IsoId=A8MS41-5; Sequence=VSP_035830, VSP_035832;
CC Name=6;
CC IsoId=A8MS41-6; Sequence=VSP_035830;
CC -!- INDUCTION: Expressed with a high amplitude circadian rhythm showing a
CC peak in the late day, just before night. {ECO:0000269|PubMed:26619288}.
CC -!- DISRUPTION PHENOTYPE: No visible phenotype under normal growth
CC conditions. {ECO:0000269|PubMed:26619288}.
CC -!- MISCELLANEOUS: Plants overexpressing CCR4-4 exhibit retarded growth
CC phenotype and severe reduction in root length that is attenuated over
CC time. {ECO:0000269|PubMed:26619288}.
CC -!- MISCELLANEOUS: [Isoform 4]: May be due to intron retention.
CC {ECO:0000305}.
CC -!- MISCELLANEOUS: [Isoform 5]: May be due to intron retention.
CC {ECO:0000305}.
CC -!- SIMILARITY: Belongs to the CCR4/nocturin family. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAG51276.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC Sequence=AAG60143.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC Sequence=BX815872; Type=Miscellaneous discrepancy; Note=Sequencing errors.; Evidence={ECO:0000305};
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DR EMBL; AC027135; AAG51276.1; ALT_SEQ; Genomic_DNA.
DR EMBL; AC074360; AAG60143.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002684; AEE31362.1; -; Genomic_DNA.
DR EMBL; CP002684; AEE31363.1; -; Genomic_DNA.
DR EMBL; CP002684; AEE31364.1; -; Genomic_DNA.
DR EMBL; CP002684; AEE31365.1; -; Genomic_DNA.
DR EMBL; CP002684; ANM61087.1; -; Genomic_DNA.
DR EMBL; BT005746; AAO64154.1; -; mRNA.
DR EMBL; BT006109; AAP04094.1; -; mRNA.
DR EMBL; BX813786; -; NOT_ANNOTATED_CDS; mRNA.
DR EMBL; BX815872; -; NOT_ANNOTATED_CDS; mRNA.
DR EMBL; BX814736; -; NOT_ANNOTATED_CDS; mRNA.
DR EMBL; AK228566; BAF00485.1; -; mRNA.
DR RefSeq; NP_001077640.1; NM_001084171.2. [A8MS41-1]
DR RefSeq; NP_001323327.1; NM_001332964.1. [A8MS41-6]
DR RefSeq; NP_174435.2; NM_102889.5. [A8MS41-2]
DR RefSeq; NP_973943.2; NM_202214.3. [A8MS41-3]
DR RefSeq; NP_973944.1; NM_202215.3. [A8MS41-5]
DR AlphaFoldDB; A8MS41; -.
DR SMR; A8MS41; -.
DR STRING; 3702.AT1G31500.4; -.
DR PaxDb; A8MS41; -.
DR PRIDE; A8MS41; -.
DR EnsemblPlants; AT1G31500.1; AT1G31500.1; AT1G31500. [A8MS41-2]
DR EnsemblPlants; AT1G31500.2; AT1G31500.2; AT1G31500. [A8MS41-3]
DR EnsemblPlants; AT1G31500.3; AT1G31500.3; AT1G31500. [A8MS41-5]
DR EnsemblPlants; AT1G31500.4; AT1G31500.4; AT1G31500. [A8MS41-1]
DR EnsemblPlants; AT1G31500.5; AT1G31500.5; AT1G31500. [A8MS41-6]
DR GeneID; 840040; -.
DR Gramene; AT1G31500.1; AT1G31500.1; AT1G31500. [A8MS41-2]
DR Gramene; AT1G31500.2; AT1G31500.2; AT1G31500. [A8MS41-3]
DR Gramene; AT1G31500.3; AT1G31500.3; AT1G31500. [A8MS41-5]
DR Gramene; AT1G31500.4; AT1G31500.4; AT1G31500. [A8MS41-1]
DR Gramene; AT1G31500.5; AT1G31500.5; AT1G31500. [A8MS41-6]
DR KEGG; ath:AT1G31500; -.
DR Araport; AT1G31500; -.
DR TAIR; locus:2028611; AT1G31500.
DR eggNOG; KOG0620; Eukaryota.
DR InParanoid; A8MS41; -.
DR OMA; FRLKRDC; -.
DR PhylomeDB; A8MS41; -.
DR PRO; PR:A8MS41; -.
DR Proteomes; UP000006548; Chromosome 1.
DR ExpressionAtlas; A8MS41; baseline and differential.
DR Genevisible; A8MS41; AT.
DR GO; GO:0009507; C:chloroplast; IDA:TAIR.
DR GO; GO:0005737; C:cytoplasm; IDA:TAIR.
DR GO; GO:0005634; C:nucleus; IEA:UniProtKB-SubCell.
DR GO; GO:0000175; F:3'-5'-exoribonuclease activity; IBA:GO_Central.
DR GO; GO:0004532; F:exoribonuclease activity; IDA:TAIR.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0004535; F:poly(A)-specific ribonuclease activity; IBA:GO_Central.
DR GO; GO:0043621; F:protein self-association; IDA:TAIR.
DR GO; GO:0003723; F:RNA binding; IEA:UniProtKB-KW.
DR GO; GO:0000289; P:nuclear-transcribed mRNA poly(A) tail shortening; IDA:TAIR.
DR GO; GO:0042752; P:regulation of circadian rhythm; IMP:TAIR.
DR GO; GO:0048511; P:rhythmic process; 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 1: Evidence at protein level;
KW Acetylation; Alternative splicing; Biological rhythms; Cytoplasm;
KW Exonuclease; Hydrolase; Magnesium; Metal-binding; Nuclease; Nucleus;
KW Reference proteome; Repeat; RNA-binding; Transcription;
KW Transcription regulation.
FT CHAIN 1..417
FT /note="Carbon catabolite repressor protein 4 homolog 4"
FT /id="PRO_0000355047"
FT BINDING 143
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250|UniProtKB:O95551"
FT VAR_SEQ 1..96
FT /note="Missing (in isoform 4)"
FT /evidence="ECO:0000303|PubMed:14593172, ECO:0000303|Ref.5"
FT /id="VSP_035827"
FT VAR_SEQ 1..25
FT /note="Missing (in isoform 3)"
FT /evidence="ECO:0000305"
FT /id="VSP_035828"
FT VAR_SEQ 18
FT /note="P -> PSSRVC (in isoform 2)"
FT /evidence="ECO:0000303|PubMed:14993207"
FT /id="VSP_035829"
FT VAR_SEQ 55..88
FT /note="Missing (in isoform 2, isoform 3, isoform 5 and
FT isoform 6)"
FT /evidence="ECO:0000303|PubMed:14993207"
FT /id="VSP_035830"
FT VAR_SEQ 97..119
FT /note="YNILAQVYVKSALLPHSPPACLK -> MVLLKGLWFCSKCDLVFLFLCCR
FT (in isoform 4)"
FT /evidence="ECO:0000303|PubMed:14593172, ECO:0000303|Ref.5"
FT /id="VSP_035831"
FT VAR_SEQ 318..417
FT /note="Missing (in isoform 5)"
FT /evidence="ECO:0000303|PubMed:14993207"
FT /id="VSP_035832"
FT CONFLICT 405
FT /note="H -> Y (in Ref. 4; BX813786)"
FT /evidence="ECO:0000305"
FT INIT_MET A8MS41-3:1
FT /note="Removed"
FT /evidence="ECO:0007744|PubMed:22223895"
FT MOD_RES A8MS41-3:2
FT /note="N-acetylserine"
FT /evidence="ECO:0007744|PubMed:22223895"
SQ SEQUENCE 417 AA; 47085 MW; 60FF5DF67AB9405C CRC64;
MFSSTTLHHL PRPNLLLPRK VISRRMSTNP AIEPKVRKFE SVEGVDIGSR NKSDGFFAIP
LYLSKLVALY NCISLSRIGT SNENFVFSGI RFRLVSYNIL AQVYVKSALL PHSPPACLKW
KARSHAILSV LKNLQADFFC LQEVDEYDSF YRNNMDSLGY SGIYIQRTGQ RKRDGCAIFY
KPSCAELVTK ERIEYNDLVD SIKADSVSCS EQKIETSNEG KDSRKDSRDL NDPLVRLKRD
CVGIMAAFRI NKPFQHIVIV ANTHLYWDPE LADVKLAQAK YLLSRLAQFK TLISDEFECT
PSLLLAGDFN SIPGDMVYSY LVSGNAKPTE TIEEEEAPVP LSSVYEVTRG EPKFTNCTPG
FTNTLDYIFI SPSDFIKPVS ILQLPEPDSP DVVGFLPNHH HPSDHLPIGA EFEIRRE
