POP2_YEAST
ID POP2_YEAST Reviewed; 433 AA.
AC P39008; D6W1M7;
DT 01-FEB-1995, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-1996, sequence version 2.
DT 03-AUG-2022, entry version 192.
DE RecName: Full=Poly(A) ribonuclease POP2;
DE EC=3.1.13.4;
DE AltName: Full=CCR4-associated factor 1;
GN Name=POP2; Synonyms=CAF1; OrderedLocusNames=YNR052C; ORFNames=N3470;
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].
RC STRAIN=ATCC 204508 / S288c, and ATCC 204626 / S288c / A364A;
RX PubMed=1475183; DOI=10.1093/nar/20.23.6227;
RA Sakai A., Chibazakura T., Shimizu Y., Hishinuma F.;
RT "Molecular analysis of POP2 gene, a gene required for glucose-derepression
RT of gene expression in Saccharomyces cerevisiae.";
RL Nucleic Acids Res. 20:6227-6233(1992).
RN [2]
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 [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 NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 213-433.
RA Cusick M.E.;
RL Submitted (MAR-1992) to the EMBL/GenBank/DDBJ databases.
RN [6]
RP CHARACTERIZATION.
RX PubMed=7791755; DOI=10.1128/mcb.15.7.3487;
RA Draper M.P., Salvadore C., Denis C.L.;
RT "Identification of a mouse protein whose homolog in Saccharomyces
RT cerevisiae is a component of the CCR4 transcriptional regulatory complex.";
RL Mol. Cell. Biol. 15:3487-3495(1995).
RN [7]
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 [8]
RP INTERACTION WITH NOT1.
RX PubMed=10490603; DOI=10.1128/mcb.19.10.6642;
RA Bai Y., Salvadore C., Chiang Y.C., Collart M.A., Liu H.Y., Denis C.L.;
RT "The CCR4 and CAF1 proteins of the CCR4-NOT complex are physically and
RT functionally separated from NOT2, NOT4, and NOT5.";
RL Mol. Cell. Biol. 19:6642-6651(1999).
RN [9]
RP FUNCTION IN MRNA DEADENYLATION, AND SUBCELLULAR LOCATION.
RX PubMed=11239395; DOI=10.1016/s0092-8674(01)00225-2;
RA Tucker M., Valencia-Sanchez M.A., Staples R.R., Chen J., Denis C.L.,
RA Parker R.;
RT "The transcription factor associated Ccr4 and Caf1 proteins are components
RT of the major cytoplasmic mRNA deadenylase in Saccharomyces cerevisiae.";
RL Cell 104:377-386(2001).
RN [10]
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 [11]
RP FUNCTION IN MRNA DEADENYLATION.
RX PubMed=11410650; DOI=10.1093/nar/29.12.2448;
RA Daugeron M.-C., Mauxion F., Seraphin B.;
RT "The yeast POP2 gene encodes a nuclease involved in mRNA deadenylation.";
RL Nucleic Acids Res. 29:2448-2455(2001).
RN [12]
RP PHOSPHORYLATION AT THR-97, AND MUTAGENESIS OF THR-97.
RX PubMed=11358866; DOI=10.1101/gad.884001;
RA Moriya H., Shimizu-Yoshida Y., Omori A., Iwashita S., Katoh M., Sakai A.;
RT "Yak1p, a DYRK family kinase, translocates to the nucleus and
RT phosphorylates yeast Pop2p in response to a glucose signal.";
RL Genes Dev. 15:1217-1228(2001).
RN [13]
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 [14]
RP ACETYLATION [LARGE SCALE ANALYSIS] AT MET-1, AND IDENTIFICATION BY MASS
RP SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=22814378; DOI=10.1073/pnas.1210303109;
RA Van Damme P., Lasa M., Polevoda B., Gazquez C., Elosegui-Artola A.,
RA Kim D.S., De Juan-Pardo E., Demeyer K., Hole K., Larrea E., Timmerman E.,
RA Prieto J., Arnesen T., Sherman F., Gevaert K., Aldabe R.;
RT "N-terminal acetylome analyses and functional insights of the N-terminal
RT acetyltransferase NatB.";
RL Proc. Natl. Acad. Sci. U.S.A. 109:12449-12454(2012).
RN [15]
RP X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) OF 147-433 IN COMPLEX WITH METAL
RP IONS, FUNCTION IN MRNA DEADENYLATION, AND MUTAGENESIS OF SER-188 AND
RP GLU-190.
RX PubMed=14618157; DOI=10.1038/sj.embor.7400020;
RA Thore S., Mauxion F., Seraphin B., Suck D.;
RT "X-ray structure and activity of the yeast Pop2 protein: a nuclease subunit
RT of the mRNA deadenylase complex.";
RL EMBO Rep. 4:1150-1155(2003).
CC -!- FUNCTION: Acts as probably catalytic component of the CCR4-NOT core
CC complex, which in the nucleus seems to be a general transcription
CC factor, and in the cytoplasm the major mRNA deadenylase involved in
CC mRNA turnover. In vitro, POP2 has 3'-exoribonuclease activity with a
CC preference for poly(A) RNAs, but also degrades poly(U) and poly(C)
CC RNAs. Is part of a glucose-sensing system involved in growth control in
CC response to glucose availability. {ECO:0000269|PubMed:11239395,
CC ECO:0000269|PubMed:11410650, ECO:0000269|PubMed:14618157,
CC ECO:0000269|PubMed:9463387}.
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;
CC Note=Divalent metal cations. Mg(2+) is the most probable.;
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:10490603, ECO:0000269|PubMed:11733989,
CC ECO:0000269|PubMed:14618157, ECO:0000269|PubMed:9463387}.
CC -!- INTERACTION:
CC P39008; P53829: CAF40; NbExp=7; IntAct=EBI-13629, EBI-28306;
CC P39008; P31384: CCR4; NbExp=10; IntAct=EBI-13629, EBI-4396;
CC P39008; P25655: CDC39; NbExp=10; IntAct=EBI-13629, EBI-12139;
CC P39008; P39517: DHH1; NbExp=3; IntAct=EBI-13629, EBI-158;
CC P39008; P40484: MOB1; NbExp=2; IntAct=EBI-13629, EBI-11119;
CC P39008; P34909: MOT2; NbExp=3; IntAct=EBI-13629, EBI-12174;
CC P39008; P39016: MPT5; NbExp=4; IntAct=EBI-13629, EBI-2052996;
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:11239395}. Nucleus
CC {ECO:0000269|PubMed:11239395}.
CC -!- MISCELLANEOUS: Present with 1520 molecules/cell in log phase SD medium.
CC {ECO:0000269|PubMed:14562106}.
CC -!- SIMILARITY: Belongs to the CAF1 family. {ECO:0000305}.
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DR EMBL; D12807; BAA02246.1; -; Genomic_DNA.
DR EMBL; D12808; BAA02247.1; -; Genomic_DNA.
DR EMBL; Z71667; CAA96333.1; -; Genomic_DNA.
DR EMBL; AY692792; AAT92811.1; -; Genomic_DNA.
DR EMBL; M88607; AAA34832.1; -; Genomic_DNA.
DR EMBL; BK006947; DAA10593.1; -; Genomic_DNA.
DR PIR; S63383; S63383.
DR RefSeq; NP_014450.3; NM_001183229.3.
DR PDB; 1UOC; X-ray; 2.30 A; A/B=147-433.
DR PDB; 4B8A; X-ray; 2.40 A; B=151-433.
DR PDB; 4B8C; X-ray; 3.41 A; A/C/E/F=146-433.
DR PDBsum; 1UOC; -.
DR PDBsum; 4B8A; -.
DR PDBsum; 4B8C; -.
DR AlphaFoldDB; P39008; -.
DR SMR; P39008; -.
DR BioGRID; 35877; 265.
DR ComplexPortal; CPX-1800; CCR4-NOT mRNA deadenylase complex.
DR DIP; DIP-1957N; -.
DR IntAct; P39008; 41.
DR MINT; P39008; -.
DR STRING; 4932.YNR052C; -.
DR iPTMnet; P39008; -.
DR MaxQB; P39008; -.
DR PaxDb; P39008; -.
DR PRIDE; P39008; -.
DR EnsemblFungi; YNR052C_mRNA; YNR052C; YNR052C.
DR GeneID; 855788; -.
DR KEGG; sce:YNR052C; -.
DR SGD; S000005335; POP2.
DR VEuPathDB; FungiDB:YNR052C; -.
DR eggNOG; KOG0304; Eukaryota.
DR GeneTree; ENSGT00390000000080; -.
DR HOGENOM; CLU_027974_3_1_1; -.
DR InParanoid; P39008; -.
DR OMA; VIWQFNF; -.
DR BioCyc; YEAST:G3O-33358-MON; -.
DR EvolutionaryTrace; P39008; -.
DR PRO; PR:P39008; -.
DR Proteomes; UP000002311; Chromosome XIV.
DR RNAct; P39008; protein.
DR GO; GO:0030015; C:CCR4-NOT core complex; IDA:SGD.
DR GO; GO:0005737; C:cytoplasm; IDA:SGD.
DR GO; GO:0043332; C:mating projection tip; HDA:SGD.
DR GO; GO:0005634; C:nucleus; IEA:UniProtKB-SubCell.
DR GO; GO:0000932; C:P-body; IDA:SGD.
DR GO; GO:0000175; F:3'-5'-exoribonuclease activity; IDA:SGD.
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 GO; GO:0000289; P:nuclear-transcribed mRNA poly(A) tail shortening; IDA:SGD.
DR GO; GO:0032968; P:positive regulation of transcription elongation from RNA polymerase II promoter; IDA:SGD.
DR GO; GO:0006368; P:transcription elongation from RNA polymerase II promoter; IMP:SGD.
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; 1.
DR SUPFAM; SSF53098; SSF53098; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Acetylation; Activator; Cytoplasm; Exonuclease; Hydrolase;
KW Magnesium; Metal-binding; Nuclease; Nucleus; Phosphoprotein;
KW Reference proteome; Repressor; RNA-binding; Transcription;
KW Transcription regulation.
FT CHAIN 1..433
FT /note="Poly(A) ribonuclease POP2"
FT /id="PRO_0000212849"
FT REGION 78..98
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 188
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255"
FT BINDING 190
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255"
FT BINDING 310
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255"
FT BINDING 394
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255"
FT MOD_RES 1
FT /note="N-acetylmethionine"
FT /evidence="ECO:0007744|PubMed:22814378"
FT MOD_RES 97
FT /note="Phosphothreonine; by YAK1"
FT /evidence="ECO:0000269|PubMed:11358866"
FT VARIANT 41
FT /note="K -> Q (in strain: A364A)"
FT VARIANT 91
FT /note="Q -> QQQQQQQQQQQQQQQQQQ (in strain: A364A)"
FT VARIANT 118..122
FT /note="Missing (in strain: A364A)"
FT VARIANT 278
FT /note="L -> S (in strain: A364A)"
FT VARIANT 412
FT /note="K -> M"
FT MUTAGEN 97
FT /note="T->A: No cell-cycle stop in response to glucose
FT deprivation."
FT /evidence="ECO:0000269|PubMed:11358866"
FT MUTAGEN 188
FT /note="S->A: Abolishes poly(A) RNA degradation; when
FT associated with A-190."
FT /evidence="ECO:0000269|PubMed:14618157"
FT MUTAGEN 190
FT /note="E->A: Abolishes poly(A) RNA degradation; when
FT associated with A-188."
FT /evidence="ECO:0000269|PubMed:14618157"
FT HELIX 155..158
FT /evidence="ECO:0007829|PDB:1UOC"
FT STRAND 161..163
FT /evidence="ECO:0007829|PDB:1UOC"
FT TURN 165..167
FT /evidence="ECO:0007829|PDB:1UOC"
FT HELIX 168..178
FT /evidence="ECO:0007829|PDB:1UOC"
FT TURN 179..181
FT /evidence="ECO:0007829|PDB:1UOC"
FT STRAND 184..192
FT /evidence="ECO:0007829|PDB:1UOC"
FT STRAND 197..200
FT /evidence="ECO:0007829|PDB:4B8C"
FT HELIX 205..217
FT /evidence="ECO:0007829|PDB:1UOC"
FT STRAND 221..230
FT /evidence="ECO:0007829|PDB:1UOC"
FT STRAND 238..240
FT /evidence="ECO:0007829|PDB:1UOC"
FT STRAND 242..248
FT /evidence="ECO:0007829|PDB:1UOC"
FT TURN 252..254
FT /evidence="ECO:0007829|PDB:4B8A"
FT HELIX 259..267
FT /evidence="ECO:0007829|PDB:1UOC"
FT HELIX 272..278
FT /evidence="ECO:0007829|PDB:1UOC"
FT HELIX 282..290
FT /evidence="ECO:0007829|PDB:1UOC"
FT STRAND 292..296
FT /evidence="ECO:0007829|PDB:4B8A"
FT STRAND 300..306
FT /evidence="ECO:0007829|PDB:1UOC"
FT HELIX 309..318
FT /evidence="ECO:0007829|PDB:1UOC"
FT HELIX 327..337
FT /evidence="ECO:0007829|PDB:1UOC"
FT STRAND 339..343
FT /evidence="ECO:0007829|PDB:1UOC"
FT HELIX 344..351
FT /evidence="ECO:0007829|PDB:1UOC"
FT HELIX 353..355
FT /evidence="ECO:0007829|PDB:4B8A"
FT HELIX 373..379
FT /evidence="ECO:0007829|PDB:1UOC"
FT HELIX 386..389
FT /evidence="ECO:0007829|PDB:1UOC"
FT HELIX 391..408
FT /evidence="ECO:0007829|PDB:1UOC"
FT TURN 409..411
FT /evidence="ECO:0007829|PDB:1UOC"
FT HELIX 419..422
FT /evidence="ECO:0007829|PDB:1UOC"
SQ SEQUENCE 433 AA; 49682 MW; F3CAF97106A65933 CRC64;
MQSMNVQPRV LAVGGEQFFS QRQASEQHQQ QNMGPQVYSP KVNRARMFPQ GMPVNTINGS
VNQEMNNAYL LKQKNEPLLT QQQQQQQQQQ QPFNIGTPVS VASLPPGLNV LQQQQQQQQQ
QQQQQQGVGL NRPLASQLPK HLTNQSMPPI FLPPPNYLFV RDVWKSNLYS EFAVIRQLVS
QYNHVSISTE FVGTLARPIG TFRSKVDYHY QTMRANVDFL NPIQLGLSLS DANGNKPDNG
PSTWQFNFEF DPKKEIMSTE SLELLRKSGI NFEKHENLGI DVFEFSQLLM DSGLMMDDSV
TWITYHAAYD LGFLINILMN DSMPNNKEDF EWWVHQYMPN FYDLNLVYKI IQEFKNPQLQ
QSSQQQQQQQ YSLTTLADEL GLPRFSIFTT TGGQSLLMLL SFCQLSKLSM HKFPNGTDFA
KYQGVIYGID GDQ
