Exosome complex component CSL4 - Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)

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P53859 (CSL4_YEAST) Reviewed, UniProtKB/Swiss-Prot

Last modified May 29, 2013. Version 116. History...

Clusters with 100%, 90%, 50% identity |

Documents (4) |

Third-party data

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Names·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents Customize order

Names and origin

Protein names

Recommended name:
Exosome complex component CSL4

Alternative name(s):
CEP1 synthetic lethal protein 4

Gene names

Name:	CSL4
Synonyms:	SKI4
Ordered Locus Names:	YNL232W
ORF Names:	N1154

Organism

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) [Reference proteome]

Taxonomic identifier

559292 [NCBI]

Taxonomic lineage

Eukaryota › Fungi › Dikarya › Ascomycota › Saccharomycotina › Saccharomycetes › Saccharomycetales › Saccharomycetaceae › Saccharomyces ›

Protein attributes

Sequence length	292 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

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. Ref.5 Ref.10 Ref.13
Subunit structure	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. Ref.5 Ref.10
Subcellular location	Cytoplasm. Nucleus › nucleolus Ref.6.
Miscellaneous	Present with 5550 molecules/cell in log phase SD medium.
Sequence similarities	Belongs to the exosome component 1/CSL4 family.
Caution	According to Ref.10 and Ref.8, only DIS3/RRP44 subunit of the exosome core has exonuclease activity.

Ontologies

Keywords
Biological process	rRNA processing
Cellular component	Cytoplasm Exosome Nucleus
Ligand	RNA-binding
PTM	Phosphoprotein
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) Inferred from mutant phenotype Ref.5 PubMed 10508172. Source: SGD nonfunctional rRNA decay Inferred by curator Ref.5. Source: SGD nuclear polyadenylation-dependent mRNA catabolic process Inferred by curator Ref.5. Source: SGD nuclear polyadenylation-dependent rRNA catabolic process Inferred from mutant phenotype Ref.5. Source: SGD nuclear polyadenylation-dependent tRNA catabolic process Inferred from direct assay PubMed 15828860 PubMed 15935758 PubMed 17643380. Source: SGD nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay Inferred by curator Ref.5. Source: SGD nuclear-transcribed mRNA catabolic process, non-stop decay Inferred from mutant phenotype PubMed 11910110. Source: SGD polyadenylation-dependent snoRNA 3'-end processing Inferred by curator Ref.5. Source: SGD
Cellular_component	cytoplasmic exosome (RNase complex) Inferred from direct assay Ref.5 PubMed 19046973. Source: SGD nuclear exosome (RNase complex) Inferred from direct assay Ref.5 PubMed 19046973. Source: SGD nucleolus Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular_function	RNA binding Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
SKI7	Q08491	5	EBI-1731,EBI-1389

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 292

292

Exosome complex component CSL4

PRO_0000079403

Amino acid modifications

Modified residue

Phosphoserine Ref.11 Ref.12

Modified residue

277

Phosphoserine Ref.12

Secondary structure

292

Helix Strand Turn

Details...

Sequences

Sequence

Length

Mass (Da)

Tools

P53859 [UniParc].

Last modified October 1, 1996. Version 1.
Checksum: 52D3416EA183583B
Show »

FASTA

292

31,583

        10         20         30         40         50         60 
MACNFQFPEI AYPGKLICPQ YGTENKDGED IIFNYVPGPG TKLIQYEHNG RTLEAITATL 

        70         80         90        100        110        120 
VGTVRCEEEK KTDQEEEREG TDQSTEEEKS VDASPNDVTR RTVKNILVSV LPGTEKGRKT 

       130        140        150        160        170        180 
NKYANNDFAN NLPKEGDIVL TRVTRLSLQR ANVEILAVED KPSPIDSGIG SNGSGIVAAG 

       190        200        210        220        230        240 
GGSGAATFSV SQASSDLGET FRGIIRSQDV RSTDRDRVKV IECFKPGDIV RAQVLSLGDG 

       250        260        270        280        290 
TNYYLTTARN DLGVVFARAA NGAGGLMYAT DWQMMTSPVT GATEKRKCAK PF

« Hide

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"The DNA sequence of cosmid 14-5 from chromosome XIV reveals 21 open reading frames including a novel gene encoding a globin-like domain." Pandolfo D., de Antoni A., Lanfranchi G., Valle G. Yeast 12:1071-1076(1996) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]	"The nucleotide sequence of Saccharomyces cerevisiae chromosome XIV and its evolutionary implications." 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. Hani J. Nature 387:93-98(1997) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 204508 / S288c.
[3]	Saccharomyces Genome Database Submitted (DEC-2009) to the EMBL/GenBank/DDBJ databases Cited for: GENOME REANNOTATION. Strain: ATCC 204508 / S288c.
[4]	"Mutations synthetically lethal with cep1 target S. cerevisiae kinetochore components." Baker R.E., Harris K., Zhang K. Genetics 149:73-85(1998) [PubMed] [Europe PMC] [Abstract] Cited for: GENE NAME.
[5]	"The yeast exosome and human PM-Scl are related complexes of 3'-->5' exonucleases." Allmang C., Petfalski E., Podtelejnikov A., Mann M., Tollervey D., Mitchell P. Genes Dev. 13:2148-2158(1999) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, IDENTIFICATION IN THE RNA EXOSOME COMPLEX BY MASS SPECTROMETRY.
[6]	"Global analysis of protein localization in budding yeast." Huh W.-K., Falvo J.V., Gerke L.C., Carroll A.S., Howson R.W., Weissman J.S., O'Shea E.K. Nature 425:686-691(2003) [PubMed] [Europe PMC] [Abstract] Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
[7]	"Global analysis of protein expression in yeast." Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N., O'Shea E.K., Weissman J.S. Nature 425:737-741(2003) [PubMed] [Europe PMC] [Abstract] Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
[8]	"Reconstitution, activities, and structure of the eukaryotic RNA exosome." Liu Q., Greimann J.C., Lima C.D. Cell 127:1223-1237(2006) [PubMed] [Europe PMC] [Abstract] Cited for: RECONSTITUTION OF THE RNA EXOSOME COMPLEX, LACK OF EXONUCLEASE ACTIVITY.
[9]	Erratum Liu Q., Greimann J.C., Lima C.D. Cell 131:188-189(2007)
[10]	"A single subunit, Dis3, is essentially responsible for yeast exosome core activity." Dziembowski A., Lorentzen E., Conti E., Seraphin B. Nat. Struct. Mol. Biol. 14:15-22(2007) [PubMed] [Europe PMC] [Abstract] Cited for: IDENTIFICATION BY MASS SPECTROMETRY, FUNCTION OF THE RNA EXOSOME COMPLEX, SUBUNIT.
[11]	"Analysis of phosphorylation sites on proteins from Saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry." 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. Proc. Natl. Acad. Sci. U.S.A. 104:2193-2198(2007) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-94, MASS SPECTROMETRY.
[12]	"A multidimensional chromatography technology for in-depth phosphoproteome analysis." Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H. Mol. Cell. Proteomics 7:1389-1396(2008) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-94 AND SER-277, MASS SPECTROMETRY.
[13]	"The exosome contains domains with specific endoribonuclease, exoribonuclease and cytoplasmic mRNA decay activities." Schaeffer D., Tsanova B., Barbas A., Reis F.P., Dastidar E.G., Sanchez-Rotunno M., Arraiano C.M., van Hoof A. Nat. Struct. Mol. Biol. 16:56-62(2009) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION IN MRNA DEGRADATION.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

Z69381 Genomic DNA. Translation: CAA93366.1.
Z71508 Genomic DNA. Translation: CAA96137.1.
BK006947 Genomic DNA. Translation: DAA10326.1.

PIR

S63198.

RefSeq

NP_014167.1. NM_001183070.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
4IFD	X-ray	2.80	I	1-292	[»]

ProteinModelPortal

P53859.

SMR

P53859. Positions 193-287.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-6785N.

IntAct

P53859. 17 interactions.

MINT

MINT-614245.

STRING

4932.YNL232W.

Proteomic databases

PaxDb

P53859.

PeptideAtlas

P53859.

PRIDE

P53859.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblFungi

YNL232W; YNL232W; YNL232W.

GeneID

855489.

KEGG

sce:YNL232W.

Organism-specific databases

CYGD

YNL232w.

SGD

S000005176. CSL4.

Phylogenomic databases

eggNOG

COG1096.

GeneTree

ENSGT00390000015287.

HOGENOM

HOG000177330.

K07573.

OMA

QRANVEI.

OrthoDB

EOG4CZFRH.

Enzyme and pathway databases

BioCyc

YEAST:G3O-33232-MONOMER.

Gene expression databases

Genevestigator

P53859.

GermOnline

YNL232W. Saccharomyces cerevisiae.

Family and domain databases

InterPro

IPR019495. EXOSC1.
[Graphical view]

Pfam

PF10447. EXOSC1. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

NextBio

979469.

Entry information

Entry name

CSL4_YEAST

Accession

Primary (citable) accession number: P53859
Secondary accession number(s): D6W0W0

Entry history

Integrated into UniProtKB/Swiss-Prot:	October 1, 1996
Last sequence update:	October 1, 1996
Last modified:	May 29, 2013
This is version 116 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Fungal Protein Annotation Program

Relevant documents

Yeast

Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD

Yeast chromosome XIV

Yeast (Saccharomyces cerevisiae) chromosome XIV: entries and gene names

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families

Names·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents

Preferred order of sections

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Binary interactions

With

Entry

#Exp.

IntAct

Notes

Sequence annotation (Features)

Molecule processing

Amino acid modifications

Secondary structure

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

Proteomic databases

Protocols and materials databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Enzyme and pathway databases

Gene expression databases

Family and domain databases

Other

Entry information

Relevant documents