ID   CAF40_YEAST             Reviewed;         373 AA.
AC   P53829; D6W0Q5;
DT   01-OCT-1996, integrated into UniProtKB/Swiss-Prot.
DT   01-OCT-1996, sequence version 1.
DT   27-MAR-2024, entry version 174.
DE   RecName: Full=Protein CAF40;
DE   AltName: Full=40 kDa CCR4-associated factor;
GN   Name=CAF40; OrderedLocusNames=YNL288W; ORFNames=N0540;
OS   Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
OC   Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes;
OC   Saccharomycetales; Saccharomycetaceae; Saccharomyces.
OX   NCBI_TaxID=559292;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=ATCC 204508 / S288c;
RX   PubMed=9169873;
RA   Philippsen P., Kleine K., Poehlmann R., Duesterhoeft A., Hamberg K.,
RA   Hegemann J.H., Obermaier B., Urrestarazu L.A., Aert R., Albermann K.,
RA   Altmann R., Andre B., Baladron V., Ballesta J.P.G., Becam A.-M.,
RA   Beinhauer J.D., Boskovic J., Buitrago M.J., Bussereau F., Coster F.,
RA   Crouzet M., D'Angelo M., Dal Pero F., De Antoni A., del Rey F., Doignon F.,
RA   Domdey H., Dubois E., Fiedler T.A., Fleig U., Floeth M., Fritz C.,
RA   Gaillardin C., Garcia-Cantalejo J.M., Glansdorff N., Goffeau A.,
RA   Gueldener U., Herbert C.J., Heumann K., Heuss-Neitzel D., Hilbert H.,
RA   Hinni K., Iraqui Houssaini I., Jacquet M., Jimenez A., Jonniaux J.-L.,
RA   Karpfinger-Hartl L., Lanfranchi G., Lepingle A., Levesque H., Lyck R.,
RA   Maftahi M., Mallet L., Maurer C.T.C., Messenguy F., Mewes H.-W., Moestl D.,
RA   Nasr F., Nicaud J.-M., Niedenthal R.K., Pandolfo D., Pierard A.,
RA   Piravandi E., Planta R.J., Pohl T.M., Purnelle B., Rebischung C.,
RA   Remacha M.A., Revuelta J.L., Rinke M., Saiz J.E., Sartorello F.,
RA   Scherens B., Sen-Gupta M., Soler-Mira A., Urbanus J.H.M., Valle G.,
RA   Van Dyck L., Verhasselt P., Vierendeels F., Vissers S., Voet M.,
RA   Volckaert G., Wach A., Wambutt R., Wedler H., Zollner A., Hani J.;
RT   "The nucleotide sequence of Saccharomyces cerevisiae chromosome XIV and its
RT   evolutionary implications.";
RL   Nature 387:93-98(1997).
RN   [2]
RP   GENOME REANNOTATION.
RC   STRAIN=ATCC 204508 / S288c;
RX   PubMed=24374639; DOI=10.1534/g3.113.008995;
RA   Engel S.R., Dietrich F.S., Fisk D.G., Binkley G., Balakrishnan R.,
RA   Costanzo M.C., Dwight S.S., Hitz B.C., Karra K., Nash R.S., Weng S.,
RA   Wong E.D., Lloyd P., Skrzypek M.S., Miyasato S.R., Simison M., Cherry J.M.;
RT   "The reference genome sequence of Saccharomyces cerevisiae: Then and now.";
RL   G3 (Bethesda) 4:389-398(2014).
RN   [3]
RP   IDENTIFICATION IN THE CCR4-NOT CORE COMPLEX, AND INTERACTION WITH NOT1.
RX   PubMed=11733989; DOI=10.1006/jmbi.2001.5162;
RA   Chen J., Rappsilber J., Chiang Y.C., Russell P., Mann M., Denis C.L.;
RT   "Purification and characterization of the 1.0 MDa CCR4-NOT complex
RT   identifies two novel components of the complex.";
RL   J. Mol. Biol. 314:683-694(2001).
RN   [4]
RP   LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
RX   PubMed=14562106; DOI=10.1038/nature02046;
RA   Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N.,
RA   O'Shea E.K., Weissman J.S.;
RT   "Global analysis of protein expression in yeast.";
RL   Nature 425:737-741(2003).
CC   -!- FUNCTION: Acts as a component of the CCR4-NOT core complex, which in
CC       the nucleus seems to be a general transcription factor, and in the
CC       cytoplasm the major mRNA deadenylase involved in mRNA turnover.
CC   -!- SUBUNIT: Subunit of the 1.0 MDa CCR4-NOT core complex that contains
CC       CCR4, CAF1, NOT1, NOT2, NOT3, NOT4, NOT5, CAF40 and CAF130. In the
CC       complex interacts with NOT1. The core complex probably is part of a
CC       less characterized 1.9 MDa CCR4-NOT complex.
CC       {ECO:0000269|PubMed:11733989}.
CC   -!- INTERACTION:
CC       P53829; P31384: CCR4; NbExp=8; IntAct=EBI-28306, EBI-4396;
CC       P53829; P25655: CDC39; NbExp=10; IntAct=EBI-28306, EBI-12139;
CC       P53829; P34909: MOT2; NbExp=5; IntAct=EBI-28306, EBI-12174;
CC       P53829; P06102: NOT3; NbExp=3; IntAct=EBI-28306, EBI-12165;
CC       P53829; Q12514: NOT5; NbExp=3; IntAct=EBI-28306, EBI-12184;
CC       P53829; P53935: NST1; NbExp=3; IntAct=EBI-28306, EBI-28788;
CC       P53829; P39008: POP2; NbExp=8; IntAct=EBI-28306, EBI-13629;
CC   -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000305}. Nucleus {ECO:0000305}.
CC   -!- MISCELLANEOUS: Present with 18800 molecules/cell in log phase SD
CC       medium. {ECO:0000269|PubMed:14562106}.
CC   -!- SIMILARITY: Belongs to the CNOT9 family. {ECO:0000305}.
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DR   EMBL; Z71564; CAA96205.1; -; Genomic_DNA.
DR   EMBL; BK006947; DAA10271.1; -; Genomic_DNA.
DR   PIR; S63262; S63262.
DR   RefSeq; NP_014111.1; NM_001183126.1.
DR   PDB; 4CV5; X-ray; 3.81 A; B/D=54-373.
DR   PDBsum; 4CV5; -.
DR   AlphaFoldDB; P53829; -.
DR   SMR; P53829; -.
DR   BioGRID; 35549; 249.
DR   ComplexPortal; CPX-1800; CCR4-NOT mRNA deadenylase complex.
DR   DIP; DIP-1995N; -.
DR   IntAct; P53829; 45.
DR   MINT; P53829; -.
DR   STRING; 4932.YNL288W; -.
DR   MaxQB; P53829; -.
DR   PaxDb; 4932-YNL288W; -.
DR   PeptideAtlas; P53829; -.
DR   EnsemblFungi; YNL288W_mRNA; YNL288W; YNL288W.
DR   GeneID; 855428; -.
DR   KEGG; sce:YNL288W; -.
DR   AGR; SGD:S000005232; -.
DR   SGD; S000005232; CAF40.
DR   VEuPathDB; FungiDB:YNL288W; -.
DR   eggNOG; KOG3036; Eukaryota.
DR   GeneTree; ENSGT00390000001225; -.
DR   HOGENOM; CLU_039962_1_0_1; -.
DR   InParanoid; P53829; -.
DR   OMA; DHVTRRW; -.
DR   OrthoDB; 773206at2759; -.
DR   BioCyc; YEAST:G3O-33278-MONOMER; -.
DR   BioGRID-ORCS; 855428; 2 hits in 10 CRISPR screens.
DR   PRO; PR:P53829; -.
DR   Proteomes; UP000002311; Chromosome XIV.
DR   RNAct; P53829; Protein.
DR   GO; GO:0030015; C:CCR4-NOT core complex; IPI:SGD.
DR   GO; GO:0005634; C:nucleus; IEA:UniProtKB-SubCell.
DR   GO; GO:0000932; C:P-body; IBA:GO_Central.
DR   GO; GO:0017148; P:negative regulation of translation; IBA:GO_Central.
DR   GO; GO:0000289; P:nuclear-transcribed mRNA poly(A) tail shortening; NAS:ComplexPortal.
DR   GO; GO:0032968; P:positive regulation of transcription elongation by RNA polymerase II; IDA:SGD.
DR   Gene3D; 1.25.10.10; Leucine-rich Repeat Variant; 1.
DR   InterPro; IPR011989; ARM-like.
DR   InterPro; IPR016024; ARM-type_fold.
DR   InterPro; IPR007216; CNOT9.
DR   PANTHER; PTHR12262:SF0; CCR4-NOT TRANSCRIPTION COMPLEX SUBUNIT 9; 1.
DR   PANTHER; PTHR12262; UNCHARACTERIZED; 1.
DR   Pfam; PF04078; Rcd1; 1.
DR   SUPFAM; SSF48371; ARM repeat; 1.
PE   1: Evidence at protein level;
KW   3D-structure; Activator; Cytoplasm; Nucleus; Reference proteome; Repressor;
KW   Transcription; Transcription regulation.
FT   CHAIN           1..373
FT                   /note="Protein CAF40"
FT                   /id="PRO_0000203375"
FT   REGION          1..91
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        18..91
FT                   /note="Polar residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
SQ   SEQUENCE   373 AA;  41155 MW;  F3DBABE6AD3C7F3C CRC64;
     MFSAQKPIYG NGAGVNMGGG GPSTNNPGSM SMPGVPTSMG PGMNQQIPSG GPMLMGNTPN
     NNNSNENGEN NGNNGNNGGN DANATRNNPN MVNNRGAVHA LDDPNVYHWI CQLTYGPQKE
     QALLELGRKR EQFDDLAVVL WSSFGVMTSL LNEIISVYPM LQPQMLSNNL SNRVCNALVL
     LQCVASHPET KHLFLQAHIP LFLFPFLNTT SRQRTFEYLR LTSLGVIGAL VKNDSQDVIT
     FLLRTDIVPL CLRIMESSSE LSKTVAIFIL QKILLDDVGL QYICATLERF YAVTNVLKDM
     VEHLTVSTPP GRLLKHIIRC YLRLSDDLEA RRLLKIVLPA KLRDNTFTEV LRDDVGSKRC
     LAQLLLTLNE ETS
//