CAF1F_ARATH
ID CAF1F_ARATH Reviewed; 274 AA.
AC Q9SAI2;
DT 05-MAY-2009, integrated into UniProtKB/Swiss-Prot.
DT 01-MAY-2000, sequence version 1.
DT 03-AUG-2022, entry version 128.
DE RecName: Full=Probable CCR4-associated factor 1 homolog 6;
DE EC=3.1.13.4;
GN Name=CAF1-6; OrderedLocusNames=At1g80780; ORFNames=F23A5.13;
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].
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 TISSUE SPECIFICITY.
RX PubMed=15010618; DOI=10.1023/b:plan.0000019063.18097.62;
RA Hu W., Wang Y., Bowers C., Ma H.;
RT "Isolation, sequence analysis, and expression studies of florally expressed
RT cDNAs in Arabidopsis.";
RL Plant Mol. Biol. 53:545-563(2003).
CC -!- FUNCTION: Ubiquitous transcription factor required for a diverse set of
CC processes. It is a component of the CCR4 complex involved in the
CC control of gene expression (By similarity). {ECO:0000250}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=Exonucleolytic cleavage of poly(A) to 5'-AMP.; EC=3.1.13.4;
CC -!- COFACTOR:
CC Name=a divalent metal cation; Xref=ChEBI:CHEBI:60240;
CC Evidence={ECO:0000250};
CC -!- SUBUNIT: Component of the CCR4-NOT complex, at least composed of CRR4
CC and CAF1 proteins. {ECO:0000250}.
CC -!- INTERACTION:
CC Q9SAI2; Q42381: HLS1; NbExp=4; IntAct=EBI-4465274, EBI-15207218;
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000250}. Cytoplasm {ECO:0000250}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=1;
CC Comment=A number of isoforms are produced. According to EST
CC sequences.;
CC Name=1;
CC IsoId=Q9SAI2-1; Sequence=Displayed;
CC -!- TISSUE SPECIFICITY: Expressed in flowers.
CC {ECO:0000269|PubMed:15010618}.
CC -!- SIMILARITY: Belongs to the CAF1 family. {ECO:0000305}.
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DR EMBL; AC011713; AAF14666.1; -; Genomic_DNA.
DR EMBL; CP002684; AEE36448.1; -; Genomic_DNA.
DR EMBL; CP002684; AEE36449.1; -; Genomic_DNA.
DR EMBL; AY070420; AAL49916.1; -; mRNA.
DR EMBL; AY096747; AAM20381.1; -; mRNA.
DR PIR; D96840; D96840.
DR RefSeq; NP_178193.1; NM_106726.5. [Q9SAI2-1]
DR RefSeq; NP_849915.1; NM_179584.3. [Q9SAI2-1]
DR AlphaFoldDB; Q9SAI2; -.
DR SMR; Q9SAI2; -.
DR BioGRID; 29635; 2.
DR IntAct; Q9SAI2; 2.
DR STRING; 3702.AT1G80780.3; -.
DR PaxDb; Q9SAI2; -.
DR PRIDE; Q9SAI2; -.
DR DNASU; 844417; -.
DR EnsemblPlants; AT1G80780.1; AT1G80780.1; AT1G80780. [Q9SAI2-1]
DR EnsemblPlants; AT1G80780.2; AT1G80780.2; AT1G80780. [Q9SAI2-1]
DR GeneID; 844417; -.
DR Gramene; AT1G80780.1; AT1G80780.1; AT1G80780. [Q9SAI2-1]
DR Gramene; AT1G80780.2; AT1G80780.2; AT1G80780. [Q9SAI2-1]
DR KEGG; ath:AT1G80780; -.
DR Araport; AT1G80780; -.
DR eggNOG; KOG0304; Eukaryota.
DR HOGENOM; CLU_027974_0_1_1; -.
DR InParanoid; Q9SAI2; -.
DR OMA; MYFPTIY; -.
DR PhylomeDB; Q9SAI2; -.
DR PRO; PR:Q9SAI2; -.
DR Proteomes; UP000006548; Chromosome 1.
DR ExpressionAtlas; Q9SAI2; baseline and differential.
DR Genevisible; Q9SAI2; AT.
DR GO; GO:0030015; C:CCR4-NOT core complex; IBA:GO_Central.
DR GO; GO:0005634; C:nucleus; IEA:UniProtKB-SubCell.
DR GO; GO:0000932; C:P-body; IBA:GO_Central.
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:0003723; F:RNA binding; IEA:UniProtKB-KW.
DR GO; GO:0043928; P:exonucleolytic catabolism of deadenylated mRNA; IBA:GO_Central.
DR Gene3D; 3.30.420.10; -; 1.
DR InterPro; IPR039637; CNOT7/CNOT8/Pop2.
DR InterPro; IPR006941; RNase_CAF1.
DR InterPro; IPR012337; RNaseH-like_sf.
DR InterPro; IPR036397; RNaseH_sf.
DR PANTHER; PTHR10797; PTHR10797; 1.
DR Pfam; PF04857; CAF1; 2.
DR SUPFAM; SSF53098; SSF53098; 1.
PE 1: Evidence at protein level;
KW Alternative splicing; Cytoplasm; Exonuclease; Hydrolase; Metal-binding;
KW Nuclease; Nucleus; Reference proteome; RNA-binding; Transcription;
KW Transcription regulation.
FT CHAIN 1..274
FT /note="Probable CCR4-associated factor 1 homolog 6"
FT /id="PRO_0000371556"
FT BINDING 40
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250"
FT BINDING 42
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250"
FT BINDING 166
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250"
FT BINDING 235
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250"
SQ SEQUENCE 274 AA; 31201 MW; 6D59588003C6C9CC CRC64;
MSLFLKDDSI QIREVWNDNL QEEMDLIRDV VDDFPYVAMD TEFPGIVVRP VGTFKSNADY
HYETLKTNVN ILKMIQLGLT FSNEQGNLPT CGTDKYCIWQ FNFREFDLDS DIFALDSIEL
LKQSGIDLAK NTLDGIDSKR FAELLMSSGI VLNENVHWVT FHSGYDFGYL LKLLTCQNLP
DSQTDFFKLI NVYFPTVYDI KHLMKFCNSL HGGLNKLAEL LEVERVGICH QAGSDSLLTS
CTFRKLKENF FVGPLHKYSG VLYGLGVENG QVAI
