ID CSL4_YEAST Reviewed; 292 AA.
AC P53859; D6W0W0;
DT 01-OCT-1996, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-1996, sequence version 1.
DT 27-MAR-2024, entry version 191.
DE RecName: Full=Exosome complex component CSL4;
DE AltName: Full=CEP1 synthetic lethal protein 4;
GN Name=CSL4; Synonyms=SKI4; OrderedLocusNames=YNL232W; ORFNames=N1154;
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=8896273;
RX DOI=10.1002/(sici)1097-0061(199609)12:10b<1071::aid-yea4>3.0.co;2-s;
RA Pandolfo D., de Antoni A., Lanfranchi G., Valle G.;
RT "The DNA sequence of cosmid 14-5 from chromosome XIV reveals 21 open
RT reading frames including a novel gene encoding a globin-like domain.";
RL Yeast 12:1071-1076(1996).
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 GENE NAME.
RX PubMed=9584087; DOI=10.1093/genetics/149.1.73;
RA Baker R.E., Harris K., Zhang K.;
RT "Mutations synthetically lethal with cep1 target S. cerevisiae kinetochore
RT components.";
RL Genetics 149:73-85(1998).
RN [5]
RP FUNCTION, AND IDENTIFICATION IN THE RNA EXOSOME COMPLEX BY MASS
RP SPECTROMETRY.
RX PubMed=10465791; DOI=10.1101/gad.13.16.2148;
RA Allmang C., Petfalski E., Podtelejnikov A., Mann M., Tollervey D.,
RA Mitchell P.;
RT "The yeast exosome and human PM-Scl are related complexes of 3'-->5'
RT exonucleases.";
RL Genes Dev. 13:2148-2158(1999).
RN [6]
RP SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
RX PubMed=14562095; DOI=10.1038/nature02026;
RA Huh W.-K., Falvo J.V., Gerke L.C., Carroll A.S., Howson R.W.,
RA Weissman J.S., O'Shea E.K.;
RT "Global analysis of protein localization in budding yeast.";
RL Nature 425:686-691(2003).
RN [7]
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 [8]
RP RECONSTITUTION OF THE RNA EXOSOME COMPLEX, AND LACK OF EXONUCLEASE
RP ACTIVITY.
RX PubMed=17174896; DOI=10.1016/j.cell.2006.10.037;
RA Liu Q., Greimann J.C., Lima C.D.;
RT "Reconstitution, activities, and structure of the eukaryotic RNA exosome.";
RL Cell 127:1223-1237(2006).
RN [9]
RP ERRATUM OF PUBMED:17174896.
RA Liu Q., Greimann J.C., Lima C.D.;
RL Cell 131:188-189(2007).
RN [10]
RP IDENTIFICATION BY MASS SPECTROMETRY, FUNCTION OF THE RNA EXOSOME COMPLEX,
RP AND SUBUNIT.
RX PubMed=17173052; DOI=10.1038/nsmb1184;
RA Dziembowski A., Lorentzen E., Conti E., Seraphin B.;
RT "A single subunit, Dis3, is essentially responsible for yeast exosome core
RT activity.";
RL Nat. Struct. Mol. Biol. 14:15-22(2007).
RN [11]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-94, 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 [12]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-94, AND IDENTIFICATION BY
RP 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 [13]
RP FUNCTION IN MRNA DEGRADATION.
RX PubMed=19060898; DOI=10.1038/nsmb.1528;
RA Schaeffer D., Tsanova B., Barbas A., Reis F.P., Dastidar E.G.,
RA Sanchez-Rotunno M., Arraiano C.M., van Hoof A.;
RT "The exosome contains domains with specific endoribonuclease,
RT exoribonuclease and cytoplasmic mRNA decay activities.";
RL Nat. Struct. Mol. Biol. 16:56-62(2009).
CC -!- FUNCTION: Non-catalytic component of the RNA exosome complex which has
CC 3'->5' exoribonuclease activity and participates in a multitude of
CC cellular RNA processing and degradation events. In the nucleus, the RNA
CC exosome complex is involved in proper maturation of stable RNA species
CC such as rRNA, snRNA and snoRNA, in the elimination of RNA processing
CC by-products and non-coding 'pervasive' transcripts, such as antisense
CC RNA species and cryptic unstable transcripts (CUTs), and of mRNAs with
CC processing defects, thereby limiting or excluding their export to the
CC cytoplasm. In the cytoplasm, the RNA exosome complex is involved in
CC general mRNA turnover and in RNA surveillance pathways, preventing
CC translation of aberrant mRNAs. The catalytic inactive RNA exosome core
CC complex of 9 subunits (Exo-9) is proposed to play a pivotal role in the
CC binding and presentation of RNA for ribonucleolysis, and to serve as a
CC scaffold for the association with catalytic subunits and accessory
CC proteins or complexes. {ECO:0000269|PubMed:10465791,
CC ECO:0000269|PubMed:17173052, ECO:0000269|PubMed:19060898}.
CC -!- SUBUNIT: Component of the RNA exosome complex. Specifically part of the
CC catalytically inactive RNA exosome core (Exo-9) complex which
CC associates with catalytic subunits DIS3 and RRP6 in cytoplasmic- and
CC nuclear-specific RNA exosome complex forms. Exo-9 is formed by a
CC hexameric ring of RNase PH domain-containing subunits and peripheral S1
CC domain-containing components CSL4, RRP4 and RRP40 located on the top of
CC the ring structure. {ECO:0000269|PubMed:10465791,
CC ECO:0000269|PubMed:17173052}.
CC -!- INTERACTION:
CC P53859; P48240: MTR3; NbExp=16; IntAct=EBI-1731, EBI-1749;
CC P53859; P38792: RRP4; NbExp=15; IntAct=EBI-1731, EBI-1757;
CC P53859; Q08285: RRP40; NbExp=14; IntAct=EBI-1731, EBI-1831;
CC P53859; Q12277: RRP42; NbExp=16; IntAct=EBI-1731, EBI-1765;
CC P53859; P25359: RRP43; NbExp=15; IntAct=EBI-1731, EBI-1773;
CC P53859; Q05636: RRP45; NbExp=15; IntAct=EBI-1731, EBI-1810;
CC P53859; P53256: RRP46; NbExp=16; IntAct=EBI-1731, EBI-1842;
CC P53859; P46948: SKI6; NbExp=17; IntAct=EBI-1731, EBI-1788;
CC P53859; Q08491: SKI7; NbExp=4; IntAct=EBI-1731, EBI-1389;
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:14562095}. Nucleus,
CC nucleolus {ECO:0000269|PubMed:14562095}.
CC -!- MISCELLANEOUS: Present with 5550 molecules/cell in log phase SD medium.
CC {ECO:0000269|PubMed:14562106}.
CC -!- SIMILARITY: Belongs to the CSL4 family. {ECO:0000305}.
CC -!- CAUTION: According to PubMed:17173052 and PubMed:17174896, only
CC DIS3/RRP44 subunit of the exosome core has exonuclease activity.
CC {ECO:0000305}.
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DR EMBL; Z69381; CAA93366.1; -; Genomic_DNA.
DR EMBL; Z71508; CAA96137.1; -; Genomic_DNA.
DR EMBL; BK006947; DAA10326.1; -; Genomic_DNA.
DR PIR; S63198; S63198.
DR RefSeq; NP_014167.1; NM_001183070.1.
DR PDB; 4IFD; X-ray; 2.80 A; I=1-292.
DR PDB; 4OO1; X-ray; 3.30 A; I=1-292.
DR PDB; 5C0W; X-ray; 4.60 A; I=1-292.
DR PDB; 5C0X; X-ray; 3.81 A; I=1-292.
DR PDB; 5G06; EM; 4.20 A; I=1-292.
DR PDB; 5JEA; X-ray; 2.65 A; I=1-292.
DR PDB; 5K36; X-ray; 3.10 A; I=1-292.
DR PDB; 5OKZ; X-ray; 3.20 A; I/S/c/m=1-292.
DR PDB; 5VZJ; X-ray; 3.30 A; I=1-292.
DR PDB; 6FSZ; EM; 4.60 A; II=1-292.
DR PDB; 6LQS; EM; 3.80 A; C4=1-292.
DR PDB; 7AJT; EM; 4.60 A; EJ=1-292.
DR PDB; 7AJU; EM; 3.80 A; EJ=1-292.
DR PDB; 7D4I; EM; 4.00 A; C4=1-292.
DR PDBsum; 4IFD; -.
DR PDBsum; 4OO1; -.
DR PDBsum; 5C0W; -.
DR PDBsum; 5C0X; -.
DR PDBsum; 5G06; -.
DR PDBsum; 5JEA; -.
DR PDBsum; 5K36; -.
DR PDBsum; 5OKZ; -.
DR PDBsum; 5VZJ; -.
DR PDBsum; 6FSZ; -.
DR PDBsum; 6LQS; -.
DR PDBsum; 7AJT; -.
DR PDBsum; 7AJU; -.
DR PDBsum; 7D4I; -.
DR AlphaFoldDB; P53859; -.
DR EMDB; EMD-0952; -.
DR EMDB; EMD-11807; -.
DR EMDB; EMD-11808; -.
DR EMDB; EMD-30574; -.
DR EMDB; EMD-4301; -.
DR SMR; P53859; -.
DR BioGRID; 35606; 502.
DR ComplexPortal; CPX-599; Nuclear/nucleolar exosome complex, DIS3-RRP6 variant.
DR ComplexPortal; CPX-603; Cytoplasmic exosome complex, DIS3 variant.
DR DIP; DIP-6785N; -.
DR IntAct; P53859; 19.
DR MINT; P53859; -.
DR STRING; 4932.YNL232W; -.
DR iPTMnet; P53859; -.
DR MaxQB; P53859; -.
DR PaxDb; 4932-YNL232W; -.
DR PeptideAtlas; P53859; -.
DR EnsemblFungi; YNL232W_mRNA; YNL232W; YNL232W.
DR GeneID; 855489; -.
DR KEGG; sce:YNL232W; -.
DR AGR; SGD:S000005176; -.
DR SGD; S000005176; CSL4.
DR VEuPathDB; FungiDB:YNL232W; -.
DR eggNOG; KOG3409; Eukaryota.
DR GeneTree; ENSGT00390000015287; -.
DR HOGENOM; CLU_067135_0_0_1; -.
DR InParanoid; P53859; -.
DR OMA; LMYPIDW; -.
DR OrthoDB; 297439at2759; -.
DR BioCyc; YEAST:G3O-33232-MONOMER; -.
DR Reactome; R-SCE-429958; mRNA decay by 3' to 5' exoribonuclease.
DR Reactome; R-SCE-450385; Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA.
DR Reactome; R-SCE-450513; Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA.
DR Reactome; R-SCE-6791226; Major pathway of rRNA processing in the nucleolus and cytosol.
DR BioGRID-ORCS; 855489; 1 hit in 10 CRISPR screens.
DR PRO; PR:P53859; -.
DR Proteomes; UP000002311; Chromosome XIV.
DR RNAct; P53859; Protein.
DR GO; GO:0005737; C:cytoplasm; IDA:SGD.
DR GO; GO:0000177; C:cytoplasmic exosome (RNase complex); IDA:SGD.
DR GO; GO:0000178; C:exosome (RNase complex); IPI:ComplexPortal.
DR GO; GO:0000176; C:nuclear exosome (RNase complex); IDA:SGD.
DR GO; GO:0005730; C:nucleolus; IDA:ComplexPortal.
DR GO; GO:0005634; C:nucleus; IDA:SGD.
DR GO; GO:0003723; F:RNA binding; IEA:UniProtKB-KW.
DR GO; GO:0000467; P:exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA); IMP:SGD.
DR GO; GO:0006397; P:mRNA processing; IMP:SGD.
DR GO; GO:0071035; P:nuclear polyadenylation-dependent rRNA catabolic process; IMP:SGD.
DR GO; GO:0071038; P:nuclear polyadenylation-dependent tRNA catabolic process; IDA:SGD.
DR GO; GO:0034427; P:nuclear-transcribed mRNA catabolic process, exonucleolytic, 3'-5'; IMP:SGD.
DR GO; GO:0070481; P:nuclear-transcribed mRNA catabolic process, non-stop decay; IMP:SGD.
DR GO; GO:0006401; P:RNA catabolic process; IDA:ComplexPortal.
DR GO; GO:0006396; P:RNA processing; IDA:ComplexPortal.
DR CDD; cd05791; S1_CSL4; 1.
DR Gene3D; 2.40.50.880; -; 1.
DR Gene3D; 2.40.50.140; Nucleic acid-binding proteins; 1.
DR InterPro; IPR039771; Csl4.
DR InterPro; IPR048626; CSL4_N.
DR InterPro; IPR019495; EXOSC1_C.
DR InterPro; IPR012340; NA-bd_OB-fold.
DR PANTHER; PTHR12686; 3'-5' EXORIBONUCLEASE CSL4-RELATED; 1.
DR PANTHER; PTHR12686:SF8; EXOSOME COMPLEX COMPONENT CSL4; 1.
DR Pfam; PF21551; CSL4_N; 1.
DR Pfam; PF10447; EXOSC1; 1.
DR SUPFAM; SSF50249; Nucleic acid-binding proteins; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Cytoplasm; Exosome; Nucleus; Phosphoprotein;
KW Reference proteome; RNA-binding; rRNA processing.
FT CHAIN 1..292
FT /note="Exosome complex component CSL4"
FT /id="PRO_0000079403"
FT REGION 67..98
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 67..95
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOD_RES 94
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:17287358,
FT ECO:0007744|PubMed:18407956"
FT STRAND 9..11
FT /evidence="ECO:0007829|PDB:5JEA"
FT STRAND 15..23
FT /evidence="ECO:0007829|PDB:5JEA"
FT STRAND 32..37
FT /evidence="ECO:0007829|PDB:5JEA"
FT STRAND 41..48
FT /evidence="ECO:0007829|PDB:5JEA"
FT STRAND 51..58
FT /evidence="ECO:0007829|PDB:5JEA"
FT STRAND 60..67
FT /evidence="ECO:0007829|PDB:5JEA"
FT STRAND 106..112
FT /evidence="ECO:0007829|PDB:5JEA"
FT HELIX 115..120
FT /evidence="ECO:0007829|PDB:5K36"
FT TURN 121..123
FT /evidence="ECO:0007829|PDB:5K36"
FT HELIX 124..130
FT /evidence="ECO:0007829|PDB:5K36"
FT STRAND 138..146
FT /evidence="ECO:0007829|PDB:5JEA"
FT STRAND 148..160
FT /evidence="ECO:0007829|PDB:5JEA"
FT STRAND 162..165
FT /evidence="ECO:0007829|PDB:5JEA"
FT HELIX 183..186
FT /evidence="ECO:0007829|PDB:5JEA"
FT TURN 190..192
FT /evidence="ECO:0007829|PDB:5JEA"
FT TURN 195..198
FT /evidence="ECO:0007829|PDB:4IFD"
FT STRAND 202..206
FT /evidence="ECO:0007829|PDB:5JEA"
FT HELIX 207..209
FT /evidence="ECO:0007829|PDB:5JEA"
FT STRAND 212..214
FT /evidence="ECO:0007829|PDB:5JEA"
FT HELIX 215..217
FT /evidence="ECO:0007829|PDB:5JEA"
FT HELIX 220..222
FT /evidence="ECO:0007829|PDB:5JEA"
FT STRAND 229..236
FT /evidence="ECO:0007829|PDB:5JEA"
FT STRAND 240..246
FT /evidence="ECO:0007829|PDB:5JEA"
FT STRAND 249..251
FT /evidence="ECO:0007829|PDB:5VZJ"
FT STRAND 253..256
FT /evidence="ECO:0007829|PDB:5JEA"
FT TURN 259..263
FT /evidence="ECO:0007829|PDB:5JEA"
FT STRAND 268..271
FT /evidence="ECO:0007829|PDB:5JEA"
FT STRAND 274..276
FT /evidence="ECO:0007829|PDB:5JEA"
FT TURN 278..280
FT /evidence="ECO:0007829|PDB:5JEA"
FT STRAND 283..285
FT /evidence="ECO:0007829|PDB:4IFD"
SQ SEQUENCE 292 AA; 31583 MW; 52D3416EA183583B CRC64;
MACNFQFPEI AYPGKLICPQ YGTENKDGED IIFNYVPGPG TKLIQYEHNG RTLEAITATL
VGTVRCEEEK KTDQEEEREG TDQSTEEEKS VDASPNDVTR RTVKNILVSV LPGTEKGRKT
NKYANNDFAN NLPKEGDIVL TRVTRLSLQR ANVEILAVED KPSPIDSGIG SNGSGIVAAG
GGSGAATFSV SQASSDLGET FRGIIRSQDV RSTDRDRVKV IECFKPGDIV RAQVLSLGDG
TNYYLTTARN DLGVVFARAA NGAGGLMYAT DWQMMTSPVT GATEKRKCAK PF
//
