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Exosome complex component CSL4 (CEP1 synthetic lethal protein 4)

 CSL4_YEAST              Reviewed;         292 AA.
P53859; D6W0W0;
01-OCT-1996, integrated into UniProtKB/Swiss-Prot.
01-OCT-1996, sequence version 1.
27-SEP-2017, entry version 151.
RecName: Full=Exosome complex component CSL4;
AltName: Full=CEP1 synthetic lethal protein 4;
Name=CSL4; Synonyms=SKI4; OrderedLocusNames=YNL232W; ORFNames=N1154;
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina;
Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces.
NCBI_TaxID=559292;
[1]
NUCLEOTIDE SEQUENCE [GENOMIC DNA].
PubMed=8896273;
DOI=10.1002/(SICI)1097-0061(199609)12:10B<1071::AID-YEA4>3.3.CO;2-J;
Pandolfo D., de Antoni A., Lanfranchi G., Valle G.;
"The DNA sequence of cosmid 14-5 from chromosome XIV reveals 21 open
reading frames including a novel gene encoding a globin-like domain.";
Yeast 12:1071-1076(1996).
[2]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=ATCC 204508 / S288c;
PubMed=9169873;
Philippsen P., Kleine K., Poehlmann R., Duesterhoeft A., Hamberg K.,
Hegemann J.H., Obermaier B., Urrestarazu L.A., Aert R., Albermann K.,
Altmann R., Andre B., Baladron V., Ballesta J.P.G., Becam A.-M.,
Beinhauer J.D., Boskovic J., Buitrago M.J., Bussereau F., Coster F.,
Crouzet M., D'Angelo M., Dal Pero F., De Antoni A., del Rey F.,
Doignon F., Domdey H., Dubois E., Fiedler T.A., Fleig U., Floeth M.,
Fritz C., Gaillardin C., Garcia-Cantalejo J.M., Glansdorff N.,
Goffeau A., Gueldener U., Herbert C.J., Heumann K., Heuss-Neitzel D.,
Hilbert H., Hinni K., Iraqui Houssaini I., Jacquet M., Jimenez A.,
Jonniaux J.-L., Karpfinger-Hartl L., Lanfranchi G., Lepingle A.,
Levesque H., Lyck R., Maftahi M., Mallet L., Maurer C.T.C.,
Messenguy F., Mewes H.-W., Moestl D., Nasr F., Nicaud J.-M.,
Niedenthal R.K., Pandolfo D., Pierard A., Piravandi E., Planta R.J.,
Pohl T.M., Purnelle B., Rebischung C., Remacha M.A., Revuelta J.L.,
Rinke M., Saiz J.E., Sartorello F., Scherens B., Sen-Gupta M.,
Soler-Mira A., Urbanus J.H.M., Valle G., Van Dyck L., Verhasselt P.,
Vierendeels F., Vissers S., Voet M., Volckaert G., Wach A.,
Wambutt R., Wedler H., Zollner A., Hani J.;
"The nucleotide sequence of Saccharomyces cerevisiae chromosome XIV
and its evolutionary implications.";
Nature 387:93-98(1997).
[3]
GENOME REANNOTATION.
STRAIN=ATCC 204508 / S288c;
PubMed=24374639; DOI=10.1534/g3.113.008995;
Engel S.R., Dietrich F.S., Fisk D.G., Binkley G., Balakrishnan R.,
Costanzo M.C., Dwight S.S., Hitz B.C., Karra K., Nash R.S., Weng S.,
Wong E.D., Lloyd P., Skrzypek M.S., Miyasato S.R., Simison M.,
Cherry J.M.;
"The reference genome sequence of Saccharomyces cerevisiae: Then and
now.";
G3 (Bethesda) 4:389-398(2014).
[4]
GENE NAME.
PubMed=9584087;
Baker R.E., Harris K., Zhang K.;
"Mutations synthetically lethal with cep1 target S. cerevisiae
kinetochore components.";
Genetics 149:73-85(1998).
[5]
FUNCTION, AND IDENTIFICATION IN THE RNA EXOSOME COMPLEX BY MASS
SPECTROMETRY.
PubMed=10465791; DOI=10.1101/gad.13.16.2148;
Allmang C., Petfalski E., Podtelejnikov A., Mann M., Tollervey D.,
Mitchell P.;
"The yeast exosome and human PM-Scl are related complexes of 3'-->5'
exonucleases.";
Genes Dev. 13:2148-2158(1999).
[6]
SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
PubMed=14562095; DOI=10.1038/nature02026;
Huh W.-K., Falvo J.V., Gerke L.C., Carroll A.S., Howson R.W.,
Weissman J.S., O'Shea E.K.;
"Global analysis of protein localization in budding yeast.";
Nature 425:686-691(2003).
[7]
LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
PubMed=14562106; DOI=10.1038/nature02046;
Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A.,
Dephoure N., O'Shea E.K., Weissman J.S.;
"Global analysis of protein expression in yeast.";
Nature 425:737-741(2003).
[8]
RECONSTITUTION OF THE RNA EXOSOME COMPLEX, AND LACK OF EXONUCLEASE
ACTIVITY.
PubMed=17174896; DOI=10.1016/j.cell.2006.10.037;
Liu Q., Greimann J.C., Lima C.D.;
"Reconstitution, activities, and structure of the eukaryotic RNA
exosome.";
Cell 127:1223-1237(2006).
[9]
ERRATUM.
Liu Q., Greimann J.C., Lima C.D.;
Cell 131:188-189(2007).
[10]
IDENTIFICATION BY MASS SPECTROMETRY, FUNCTION OF THE RNA EXOSOME
COMPLEX, AND SUBUNIT.
PubMed=17173052; DOI=10.1038/nsmb1184;
Dziembowski A., Lorentzen E., Conti E., Seraphin B.;
"A single subunit, Dis3, is essentially responsible for yeast exosome
core activity.";
Nat. Struct. Mol. Biol. 14:15-22(2007).
[11]
PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-94, AND IDENTIFICATION
BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
PubMed=17287358; DOI=10.1073/pnas.0607084104;
Chi A., Huttenhower C., Geer L.Y., Coon J.J., Syka J.E.P., Bai D.L.,
Shabanowitz J., Burke D.J., Troyanskaya O.G., Hunt D.F.;
"Analysis of phosphorylation sites on proteins from Saccharomyces
cerevisiae by electron transfer dissociation (ETD) mass
spectrometry.";
Proc. Natl. Acad. Sci. U.S.A. 104:2193-2198(2007).
[12]
PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-94, AND IDENTIFICATION
BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
PubMed=18407956; DOI=10.1074/mcp.M700468-MCP200;
Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H.;
"A multidimensional chromatography technology for in-depth
phosphoproteome analysis.";
Mol. Cell. Proteomics 7:1389-1396(2008).
[13]
FUNCTION IN MRNA DEGRADATION.
PubMed=19060898; DOI=10.1038/nsmb.1528;
Schaeffer D., Tsanova B., Barbas A., Reis F.P., Dastidar E.G.,
Sanchez-Rotunno M., Arraiano C.M., van Hoof A.;
"The exosome contains domains with specific endoribonuclease,
exoribonuclease and cytoplasmic mRNA decay activities.";
Nat. Struct. Mol. Biol. 16:56-62(2009).
-!- FUNCTION: Non-catalytic component of the RNA exosome complex which
has 3'->5' exoribonuclease activity and participates in a
multitude of cellular RNA processing and degradation events. In
the nucleus, the RNA exosome complex is involved in proper
maturation of stable RNA species such as rRNA, snRNA and snoRNA,
in the elimination of RNA processing by-products and non-coding
'pervasive' transcripts, such as antisense RNA species and cryptic
unstable transcripts (CUTs), and of mRNAs with processing defects,
thereby limiting or excluding their export to the cytoplasm. In
the cytoplasm, the RNA exosome complex is involved in general mRNA
turnover and in RNA surveillance pathways, preventing translation
of aberrant mRNAs. The catalytic inactive RNA exosome core complex
of 9 subunits (Exo-9) is proposed to play a pivotal role in the
binding and presentation of RNA for ribonucleolysis, and to serve
as a scaffold for the association with catalytic subunits and
accessory proteins or complexes. {ECO:0000269|PubMed:10465791,
ECO:0000269|PubMed:17173052, ECO:0000269|PubMed:19060898}.
-!- SUBUNIT: Component of the RNA exosome complex. Specifically part
of the catalytically inactive RNA exosome core (Exo-9) complex
which associates with catalytic subunits DIS3 and RRP6 in
cytoplasmic- and nuclear-specific RNA exosome complex forms. Exo-9
is formed by a hexameric ring of RNase PH domain-containing
subunits and peripheral S1 domain-containing components CSL4, RRP4
and RRP40 located on the top of the ring structure.
{ECO:0000269|PubMed:10465791, ECO:0000269|PubMed:17173052}.
-!- INTERACTION:
Q08162:DIS3; NbExp=17; IntAct=EBI-1731, EBI-1740;
P38801:LRP1; NbExp=3; IntAct=EBI-1731, EBI-1909;
P53725:MPP6; NbExp=3; IntAct=EBI-1731, EBI-28479;
P48240:MTR3; NbExp=11; IntAct=EBI-1731, EBI-1749;
P24583:PKC1; NbExp=2; IntAct=EBI-1731, EBI-9860;
P38792:RRP4; NbExp=7; IntAct=EBI-1731, EBI-1757;
Q08285:RRP40; NbExp=5; IntAct=EBI-1731, EBI-1831;
Q12277:RRP42; NbExp=10; IntAct=EBI-1731, EBI-1765;
P25359:RRP43; NbExp=10; IntAct=EBI-1731, EBI-1773;
Q05636:RRP45; NbExp=13; IntAct=EBI-1731, EBI-1810;
P53256:RRP46; NbExp=12; IntAct=EBI-1731, EBI-1842;
Q12149:RRP6; NbExp=7; IntAct=EBI-1731, EBI-1782;
P46948:SKI6; NbExp=10; IntAct=EBI-1731, EBI-1788;
Q08491:SKI7; NbExp=9; IntAct=EBI-1731, EBI-1389;
-!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:14562095}.
Nucleus, nucleolus {ECO:0000269|PubMed:14562095}.
-!- MISCELLANEOUS: Present with 5550 molecules/cell in log phase SD
medium. {ECO:0000269|PubMed:14562106}.
-!- SIMILARITY: Belongs to the CSL4 family. {ECO:0000305}.
-!- CAUTION: According to PubMed:17173052 and PubMed:17174896, only
DIS3/RRP44 subunit of the exosome core has exonuclease activity.
{ECO:0000305}.
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EMBL; Z69381; CAA93366.1; -; Genomic_DNA.
EMBL; Z71508; CAA96137.1; -; Genomic_DNA.
EMBL; BK006947; DAA10326.1; -; Genomic_DNA.
PIR; S63198; S63198.
RefSeq; NP_014167.1; NM_001183070.1.
PDB; 4IFD; X-ray; 2.80 A; I=1-292.
PDB; 4OO1; X-ray; 3.30 A; I=1-292.
PDB; 5C0W; X-ray; 4.60 A; I=1-292.
PDB; 5C0X; X-ray; 3.81 A; I=1-292.
PDB; 5G06; EM; 4.20 A; I=1-292.
PDB; 5JEA; X-ray; 2.65 A; I=1-292.
PDB; 5K36; X-ray; 3.10 A; I=1-292.
PDBsum; 4IFD; -.
PDBsum; 4OO1; -.
PDBsum; 5C0W; -.
PDBsum; 5C0X; -.
PDBsum; 5G06; -.
PDBsum; 5JEA; -.
PDBsum; 5K36; -.
ProteinModelPortal; P53859; -.
SMR; P53859; -.
BioGrid; 35606; 431.
DIP; DIP-6785N; -.
IntAct; P53859; 26.
MINT; MINT-614245; -.
STRING; 4932.YNL232W; -.
iPTMnet; P53859; -.
MaxQB; P53859; -.
PRIDE; P53859; -.
EnsemblFungi; YNL232W; YNL232W; YNL232W.
GeneID; 855489; -.
KEGG; sce:YNL232W; -.
EuPathDB; FungiDB:YNL232W; -.
SGD; S000005176; CSL4.
GeneTree; ENSGT00390000015287; -.
HOGENOM; HOG000177330; -.
InParanoid; P53859; -.
KO; K07573; -.
OMA; MYAIDWQ; -.
OrthoDB; EOG092C53BP; -.
BioCyc; YEAST:G3O-33232-MONOMER; -.
Reactome; R-SCE-429958; mRNA decay by 3' to 5' exoribonuclease.
Reactome; R-SCE-6791226; Major pathway of rRNA processing in the nucleolus and cytosol.
PRO; PR:P53859; -.
Proteomes; UP000002311; Chromosome XIV.
GO; GO:0005737; C:cytoplasm; IDA:SGD.
GO; GO:0000177; C:cytoplasmic exosome (RNase complex); IDA:SGD.
GO; GO:0000176; C:nuclear exosome (RNase complex); IDA:SGD.
GO; GO:0005730; C:nucleolus; IEA:UniProtKB-SubCell.
GO; GO:0005634; C:nucleus; IDA:SGD.
GO; GO:0003723; F:RNA binding; IEA:UniProtKB-KW.
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.
GO; GO:0043628; P:ncRNA 3'-end processing; IC:SGD.
GO; GO:0070651; P:nonfunctional rRNA decay; IC:SGD.
GO; GO:0071042; P:nuclear polyadenylation-dependent mRNA catabolic process; IC:SGD.
GO; GO:0071035; P:nuclear polyadenylation-dependent rRNA catabolic process; IMP:SGD.
GO; GO:0071038; P:nuclear polyadenylation-dependent tRNA catabolic process; IDA:SGD.
GO; GO:0070478; P:nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay; IC:SGD.
GO; GO:0034427; P:nuclear-transcribed mRNA catabolic process, exonucleolytic, 3'-5'; IMP:SGD.
GO; GO:0070481; P:nuclear-transcribed mRNA catabolic process, non-stop decay; IMP:SGD.
GO; GO:0016973; P:poly(A)+ mRNA export from nucleus; IMP:SGD.
GO; GO:0071051; P:polyadenylation-dependent snoRNA 3'-end processing; IC:SGD.
InterPro; IPR019495; EXOSC1.
InterPro; IPR012340; NA-bd_OB-fold.
Pfam; PF10447; EXOSC1; 1.
SUPFAM; SSF50249; SSF50249; 2.
1: Evidence at protein level;
3D-structure; Complete proteome; Cytoplasm; Exosome; Nucleus;
Phosphoprotein; Reference proteome; RNA-binding; rRNA processing.
CHAIN 1 292 Exosome complex component CSL4.
/FTId=PRO_0000079403.
MOD_RES 94 94 Phosphoserine.
{ECO:0000244|PubMed:17287358,
ECO:0000244|PubMed:18407956}.
STRAND 9 11 {ECO:0000244|PDB:5JEA}.
STRAND 15 23 {ECO:0000244|PDB:5JEA}.
STRAND 32 37 {ECO:0000244|PDB:5JEA}.
STRAND 41 48 {ECO:0000244|PDB:5JEA}.
STRAND 51 58 {ECO:0000244|PDB:5JEA}.
STRAND 60 67 {ECO:0000244|PDB:5JEA}.
STRAND 106 112 {ECO:0000244|PDB:5JEA}.
HELIX 115 120 {ECO:0000244|PDB:5K36}.
TURN 121 123 {ECO:0000244|PDB:5K36}.
HELIX 124 130 {ECO:0000244|PDB:5K36}.
STRAND 138 146 {ECO:0000244|PDB:5JEA}.
STRAND 148 160 {ECO:0000244|PDB:5JEA}.
STRAND 162 165 {ECO:0000244|PDB:5JEA}.
HELIX 183 186 {ECO:0000244|PDB:5JEA}.
TURN 190 192 {ECO:0000244|PDB:5JEA}.
TURN 195 198 {ECO:0000244|PDB:4IFD}.
STRAND 202 206 {ECO:0000244|PDB:5JEA}.
HELIX 207 209 {ECO:0000244|PDB:5JEA}.
STRAND 212 214 {ECO:0000244|PDB:5JEA}.
HELIX 215 217 {ECO:0000244|PDB:5JEA}.
HELIX 220 222 {ECO:0000244|PDB:5JEA}.
STRAND 229 236 {ECO:0000244|PDB:5JEA}.
STRAND 240 246 {ECO:0000244|PDB:5JEA}.
STRAND 253 256 {ECO:0000244|PDB:5JEA}.
TURN 259 263 {ECO:0000244|PDB:5JEA}.
STRAND 268 271 {ECO:0000244|PDB:5JEA}.
STRAND 274 276 {ECO:0000244|PDB:5JEA}.
TURN 278 280 {ECO:0000244|PDB:5JEA}.
STRAND 283 285 {ECO:0000244|PDB:4IFD}.
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


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