ID   NOT3_YEAST              Reviewed;         836 AA.
AC   P06102; D6VVP4; Q6B233;
DT   01-JAN-1988, integrated into UniProtKB/Swiss-Prot.
DT   01-FEB-1995, sequence version 2.
DT   27-MAR-2024, entry version 208.
DE   RecName: Full=General negative regulator of transcription subunit 3;
GN   Name=NOT3; OrderedLocusNames=YIL038C;
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 [GENOMIC DNA].
RX   PubMed=3018676; DOI=10.1093/nar/14.16.6681;
RA   Ferguson J., Ho J.-Y., Peterson T.A., Reed S.I.;
RT   "Nucleotide sequence of the yeast cell division cycle start genes CDC28,
RT   CDC36, CDC37, and CDC39, and a structural analysis of the predicted
RT   products.";
RL   Nucleic Acids Res. 14:6681-6697(1986).
RN   [2]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=ATCC 204508 / S288c;
RX   PubMed=9169870;
RA   Churcher C.M., Bowman S., Badcock K., Bankier A.T., Brown D.,
RA   Chillingworth T., Connor R., Devlin K., Gentles S., Hamlin N., Harris D.E.,
RA   Horsnell T., Hunt S., Jagels K., Jones M., Lye G., Moule S., Odell C.,
RA   Pearson D., Rajandream M.A., Rice P., Rowley N., Skelton J., Smith V.,
RA   Walsh S.V., Whitehead S., Barrell B.G.;
RT   "The nucleotide sequence of Saccharomyces cerevisiae chromosome IX.";
RL   Nature 387:84-87(1997).
RN   [3]
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   [4]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC   STRAIN=ATCC 204508 / S288c;
RX   PubMed=17322287; DOI=10.1101/gr.6037607;
RA   Hu Y., Rolfs A., Bhullar B., Murthy T.V.S., Zhu C., Berger M.F.,
RA   Camargo A.A., Kelley F., McCarron S., Jepson D., Richardson A., Raphael J.,
RA   Moreira D., Taycher E., Zuo D., Mohr S., Kane M.F., Williamson J.,
RA   Simpson A.J.G., Bulyk M.L., Harlow E., Marsischky G., Kolodner R.D.,
RA   LaBaer J.;
RT   "Approaching a complete repository of sequence-verified protein-encoding
RT   clones for Saccharomyces cerevisiae.";
RL   Genome Res. 17:536-543(2007).
RN   [5]
RP   CHARACTERIZATION.
RX   PubMed=7926748; DOI=10.1101/gad.8.5.525;
RA   Collart M.A., Struhl K.;
RT   "NOT1(CDC39), NOT2(CDC36), NOT3, and NOT4 encode a global-negative
RT   regulator of transcription that differentially affects TATA-element
RT   utilization.";
RL   Genes Dev. 8:525-537(1994).
RN   [6]
RP   IDENTIFICATION IN THE CCR4-NOT CORE COMPLEX, AND FUNCTION OF THE CCR4-NOT
RP   CORE COMPLEX IN TRANSCRIPTIONAL REGULATION.
RX   PubMed=9463387; DOI=10.1093/emboj/17.4.1096;
RA   Liu H.Y., Badarinarayana V., Audino D.C., Rappsilber J., Mann M.,
RA   Denis C.L.;
RT   "The NOT proteins are part of the CCR4 transcriptional complex and affect
RT   gene expression both positively and negatively.";
RL   EMBO J. 17:1096-1106(1998).
RN   [7]
RP   IDENTIFICATION IN THE CCR4-NOT CORE COMPLEX.
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   [8]
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).
RN   [9]
RP   PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-450 AND SER-657, AND
RP   IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC   STRAIN=ADR376;
RX   PubMed=17330950; DOI=10.1021/pr060559j;
RA   Li X., Gerber S.A., Rudner A.D., Beausoleil S.A., Haas W., Villen J.,
RA   Elias J.E., Gygi S.P.;
RT   "Large-scale phosphorylation analysis of alpha-factor-arrested
RT   Saccharomyces cerevisiae.";
RL   J. Proteome Res. 6:1190-1197(2007).
RN   [10]
RP   PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-322, AND IDENTIFICATION BY
RP   MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX   PubMed=17287358; DOI=10.1073/pnas.0607084104;
RA   Chi A., Huttenhower C., Geer L.Y., Coon J.J., Syka J.E.P., Bai D.L.,
RA   Shabanowitz J., Burke D.J., Troyanskaya O.G., Hunt D.F.;
RT   "Analysis of phosphorylation sites on proteins from Saccharomyces
RT   cerevisiae by electron transfer dissociation (ETD) mass spectrometry.";
RL   Proc. Natl. Acad. Sci. U.S.A. 104:2193-2198(2007).
RN   [11]
RP   PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-450; SER-565 AND SER-657, AND
RP   IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX   PubMed=18407956; DOI=10.1074/mcp.m700468-mcp200;
RA   Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H.;
RT   "A multidimensional chromatography technology for in-depth phosphoproteome
RT   analysis.";
RL   Mol. Cell. Proteomics 7:1389-1396(2008).
RN   [12]
RP   PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-303; SER-307; SER-446;
RP   SER-450; SER-565; SER-569 AND THR-571, AND IDENTIFICATION BY MASS
RP   SPECTROMETRY [LARGE SCALE ANALYSIS].
RX   PubMed=19779198; DOI=10.1126/science.1172867;
RA   Holt L.J., Tuch B.B., Villen J., Johnson A.D., Gygi S.P., Morgan D.O.;
RT   "Global analysis of Cdk1 substrate phosphorylation sites provides insights
RT   into evolution.";
RL   Science 325:1682-1686(2009).
RN   [13]
RP   UBIQUITINATION [LARGE SCALE ANALYSIS] AT LYS-535, AND IDENTIFICATION BY
RP   MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX   PubMed=22106047; DOI=10.1002/pmic.201100166;
RA   Starita L.M., Lo R.S., Eng J.K., von Haller P.D., Fields S.;
RT   "Sites of ubiquitin attachment in Saccharomyces cerevisiae.";
RL   Proteomics 12:236-240(2012).
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. The NOT
CC       protein subcomplex negatively regulates the basal and activated
CC       transcription of many genes. Preferentially affects TC-type TATA
CC       element-dependent transcription. Could directly or indirectly inhibit
CC       component(s) of the general transcription machinery.
CC       {ECO:0000269|PubMed:9463387}.
CC   -!- SUBUNIT: Forms a NOT protein complex that comprises NOT1, NOT2, NOT3,
CC       NOT4 and NOT5. Subunit of the 1.0 MDa CCR4-NOT core complex that
CC       contains CCR4, CAF1, NOT1, NOT2, NOT3, NOT4, NOT5, CAF40 and CAF130.
CC       The core complex probably is part of a less characterized 1.9 MDa CCR4-
CC       NOT complex. {ECO:0000269|PubMed:11733989, ECO:0000269|PubMed:9463387}.
CC   -!- INTERACTION:
CC       P06102; P53829: CAF40; NbExp=3; IntAct=EBI-12165, EBI-28306;
CC       P06102; P06100: CDC36; NbExp=2; IntAct=EBI-12165, EBI-12153;
CC       P06102; P25655: CDC39; NbExp=3; IntAct=EBI-12165, EBI-12139;
CC   -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000305}. Nucleus.
CC   -!- MISCELLANEOUS: Present with 2490 molecules/cell in log phase SD medium.
CC       {ECO:0000269|PubMed:14562106}.
CC   -!- SIMILARITY: Belongs to the CNOT2/3/5 family. {ECO:0000305}.
CC   -!- CAUTION: Was originally thought to be CDC39 (which is in fact NOT1).
CC       {ECO:0000305|PubMed:3018676}.
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DR   EMBL; Z46861; CAA86913.1; -; Genomic_DNA.
DR   EMBL; X04289; CAA27837.1; -; Genomic_DNA.
DR   EMBL; AY692897; AAT92916.1; -; Genomic_DNA.
DR   EMBL; BK006942; DAA08510.1; -; Genomic_DNA.
DR   PIR; S49940; S49940.
DR   RefSeq; NP_012226.3; NM_001179388.3.
DR   AlphaFoldDB; P06102; -.
DR   SMR; P06102; -.
DR   BioGRID; 34952; 261.
DR   ComplexPortal; CPX-1800; CCR4-NOT mRNA deadenylase complex.
DR   DIP; DIP-2256N; -.
DR   IntAct; P06102; 45.
DR   MINT; P06102; -.
DR   STRING; 4932.YIL038C; -.
DR   GlyGen; P06102; 4 sites, 1 O-linked glycan (4 sites).
DR   iPTMnet; P06102; -.
DR   MaxQB; P06102; -.
DR   PaxDb; 4932-YIL038C; -.
DR   PeptideAtlas; P06102; -.
DR   TopDownProteomics; P06102; -.
DR   EnsemblFungi; YIL038C_mRNA; YIL038C; YIL038C.
DR   GeneID; 854773; -.
DR   KEGG; sce:YIL038C; -.
DR   AGR; SGD:S000001300; -.
DR   SGD; S000001300; NOT3.
DR   VEuPathDB; FungiDB:YIL038C; -.
DR   eggNOG; KOG2150; Eukaryota.
DR   HOGENOM; CLU_020483_0_0_1; -.
DR   InParanoid; P06102; -.
DR   OMA; YKPQTPY; -.
DR   OrthoDB; 10289at2759; -.
DR   BioCyc; YEAST:G3O-31310-MONOMER; -.
DR   BioGRID-ORCS; 854773; 0 hits in 10 CRISPR screens.
DR   PRO; PR:P06102; -.
DR   Proteomes; UP000002311; Chromosome IX.
DR   RNAct; P06102; Protein.
DR   GO; GO:0030015; C:CCR4-NOT core complex; IPI:SGD.
DR   GO; GO:0005737; C:cytoplasm; IDA:SGD.
DR   GO; GO:0005634; C:nucleus; IEA:UniProtKB-SubCell.
DR   GO; GO:0000932; C:P-body; IBA:GO_Central.
DR   GO; GO:0000290; P:deadenylation-dependent decapping of nuclear-transcribed mRNA; IMP:SGD.
DR   GO; GO:0000289; P:nuclear-transcribed mRNA poly(A) tail shortening; IDA:SGD.
DR   GO; GO:0032968; P:positive regulation of transcription elongation by RNA polymerase II; IDA:SGD.
DR   GO; GO:0016567; P:protein ubiquitination; IMP:SGD.
DR   Gene3D; 2.30.30.1020; CCR4-NOT complex subunit 2/3/5, C-terminal domain; 1.
DR   InterPro; IPR038635; CCR4-NOT_su2/3/5_C_sf.
DR   InterPro; IPR012270; CCR4-NOT_su3/5.
DR   InterPro; IPR040168; Not2/3/5.
DR   InterPro; IPR007282; NOT2/3/5_C.
DR   InterPro; IPR007207; Not_N.
DR   PANTHER; PTHR23326; CCR4 NOT-RELATED; 1.
DR   PANTHER; PTHR23326:SF16; GENERAL NEGATIVE REGULATOR OF TRANSCRIPTION SUBUNIT 3; 1.
DR   Pfam; PF04153; NOT2_3_5_C; 1.
DR   Pfam; PF04065; Not3; 1.
DR   PIRSF; PIRSF005290; NOT_su_3_5; 1.
PE   1: Evidence at protein level;
KW   Activator; Coiled coil; Cytoplasm; Isopeptide bond; Nucleus;
KW   Phosphoprotein; Reference proteome; Repressor; Transcription;
KW   Transcription regulation; Ubl conjugation.
FT   CHAIN           1..836
FT                   /note="General negative regulator of transcription subunit
FT                   3"
FT                   /id="PRO_0000198337"
FT   REGION          252..284
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   REGION          296..391
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   REGION          410..471
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   REGION          513..532
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   REGION          537..583
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COILED          36..68
FT                   /evidence="ECO:0000255"
FT   COILED          119..195
FT                   /evidence="ECO:0000255"
FT   COILED          255..292
FT                   /evidence="ECO:0000255"
FT   COILED          803..831
FT                   /evidence="ECO:0000255"
FT   COMPBIAS        265..284
FT                   /note="Basic and acidic residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        341..387
FT                   /note="Polar residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        414..471
FT                   /note="Polar residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   MOD_RES         303
FT                   /note="Phosphoserine"
FT                   /evidence="ECO:0007744|PubMed:19779198"
FT   MOD_RES         307
FT                   /note="Phosphoserine"
FT                   /evidence="ECO:0007744|PubMed:19779198"
FT   MOD_RES         322
FT                   /note="Phosphoserine"
FT                   /evidence="ECO:0007744|PubMed:17287358"
FT   MOD_RES         446
FT                   /note="Phosphoserine"
FT                   /evidence="ECO:0007744|PubMed:19779198"
FT   MOD_RES         450
FT                   /note="Phosphoserine"
FT                   /evidence="ECO:0007744|PubMed:17330950,
FT                   ECO:0007744|PubMed:18407956, ECO:0007744|PubMed:19779198"
FT   MOD_RES         565
FT                   /note="Phosphoserine"
FT                   /evidence="ECO:0007744|PubMed:18407956,
FT                   ECO:0007744|PubMed:19779198"
FT   MOD_RES         569
FT                   /note="Phosphoserine"
FT                   /evidence="ECO:0007744|PubMed:19779198"
FT   MOD_RES         571
FT                   /note="Phosphothreonine"
FT                   /evidence="ECO:0007744|PubMed:19779198"
FT   MOD_RES         657
FT                   /note="Phosphoserine"
FT                   /evidence="ECO:0007744|PubMed:17330950,
FT                   ECO:0007744|PubMed:18407956"
FT   CROSSLNK        535
FT                   /note="Glycyl lysine isopeptide (Lys-Gly) (interchain with
FT                   G-Cter in ubiquitin)"
FT                   /evidence="ECO:0007744|PubMed:22106047"
FT   CONFLICT        106
FT                   /note="I -> N (in Ref. 1; CAA86913)"
FT                   /evidence="ECO:0000305"
FT   CONFLICT        593
FT                   /note="K -> R (in Ref. 4; AAT92916)"
FT                   /evidence="ECO:0000305"
FT   CONFLICT        725
FT                   /note="Y -> C (in Ref. 1; CAA86913)"
FT                   /evidence="ECO:0000305"
FT   CONFLICT        827..836
FT                   /note="KQLKQGKISV -> ETIETGKN (in Ref. 1; CAA86913)"
FT                   /evidence="ECO:0000305"
SQ   SEQUENCE   836 AA;  94403 MW;  69B76694FCC6846F CRC64;
     MAHRKLQQEV DRVFKKINEG LEIFNSYYER HESCTNNPSQ KDKLESDLKR EVKKLQRLRE
     QIKSWQSSPD IKDKDSLLDY RRSVEIAMEK YKAVEKASKE KAYSNISLKK SETLDPQERE
     RRDISEYLSQ MIDELERQYD SLQVEIDKLL LLNKKKKTSS TTNDEKKEQY KRFQARYRWH
     QQQMELALRL LANEELDPQD VKNVQDDINY FVESNQDPDF VEDETIYDGL NLQSNEAIAH
     EVAQYFASQN AEDNNTSDAN ESLQDISKLS KKEQRKLERE AKKAAKLAAK NATGAAIPVA
     GPSSTPSPVI PVADASKETE RSPSSSPIHN ATKPEEAVKT SIKSPRSSAD NLLPSLQKSP
     SSATPETPTN VHTHIHQTPN GITGATTLKP ATLPAKPAGE LKWAVAASQA VEKDRKVTSA
     SSTISNTSTK TPTTAAATTT SSNANSRIGS ALNTPKLSTS SLSLQPDNTG ASSSAATAAA
     VLAAGAAAVH QNNQAFYRNM SSSHHPLVSL ATNPKSEHEV ATTVNQNGPE NTTKKVMEQK
     EEESPEERNK LQVPTFGVFD DDFESDRDSE TEPEEEEQPS TPKYLSLEQR EAKTNEIKKE
     FVSDFETLLL PSGVQEFIMS SELYNSQIES KITYKRSRDM CEISRLVEVP QGVNPPSPLD
     AFRSTQQWDV MRCSLRDIII GSERLKEDSS SIYAKILENF RTLEMFSLFY NYYFAITPLE
     REIAYKILNE RDWKVSKDGT MWFLRQGEVK FFNEICEVGD YKIFKLDDWT VIDKINFRLD
     YSFLQPPVDT ASEVRDVSVD NNNVNDQSNV TLEQQKQEIS HGKQLLKQLK QGKISV
//