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CSL4_YEAST
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   03-AUG-2022, entry version 184.
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   SMR; P53859; -.
DR   BioGRID; 35606; 492.
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; P53859; -.
DR   PRIDE; P53859; -.
DR   EnsemblFungi; YNL232W_mRNA; YNL232W; YNL232W.
DR   GeneID; 855489; -.
DR   KEGG; sce:YNL232W; -.
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   BioCyc; YEAST:G3O-33232-MON; -.
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   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:0070651; P:nonfunctional rRNA decay; IC:SGD.
DR   GO; GO:0071042; P:nuclear polyadenylation-dependent mRNA catabolic process; IC: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:0070478; P:nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay; IC: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:0071051; P:polyadenylation-dependent snoRNA 3'-end processing; IC:SGD.
DR   GO; GO:0006401; P:RNA catabolic process; IDA:ComplexPortal.
DR   GO; GO:0006396; P:RNA processing; IDA:ComplexPortal.
DR   GO; GO:0043628; P:small regulatory ncRNA 3'-end processing; IC:SGD.
DR   Gene3D; 2.40.50.140; -; 1.
DR   InterPro; IPR039771; Csl4.
DR   InterPro; IPR019495; EXOSC1_C.
DR   InterPro; IPR012340; NA-bd_OB-fold.
DR   PANTHER; PTHR12686; PTHR12686; 1.
DR   Pfam; PF10447; EXOSC1; 1.
DR   SUPFAM; SSF50249; SSF50249; 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
 
 
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