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P38792

- RRP4_YEAST

UniProt

P38792 - RRP4_YEAST

Protein

Exosome complex component RRP4

Gene

RRP4

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 122 (01 Oct 2014)
      Sequence version 1 (01 Feb 1995)
      Previous versions | rss
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    Functioni

    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. RRP4 as peripheral part of the Exo-9 complex is thought to stabilize the hexameric ring of RNase PH-domain subunits.4 Publications

    GO - Molecular functioni

    1. protein binding Source: IntAct
    2. RNA binding Source: UniProtKB-KW

    GO - Biological processi

    1. exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) Source: SGD
    2. nonfunctional rRNA decay Source: SGD
    3. nuclear polyadenylation-dependent mRNA catabolic process Source: SGD
    4. nuclear polyadenylation-dependent rRNA catabolic process Source: SGD
    5. nuclear polyadenylation-dependent tRNA catabolic process Source: SGD
    6. nuclear retention of pre-mRNA with aberrant 3'-ends at the site of transcription Source: SGD
    7. nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay Source: SGD
    8. nuclear-transcribed mRNA catabolic process, exonucleolytic, 3'-5' Source: SGD
    9. nuclear-transcribed mRNA catabolic process, non-stop decay Source: SGD
    10. polyadenylation-dependent snoRNA 3'-end processing Source: SGD
    11. U4 snRNA 3'-end processing Source: SGD

    Keywords - Biological processi

    rRNA processing

    Keywords - Ligandi

    RNA-binding

    Enzyme and pathway databases

    BioCyciYEAST:G3O-31119-MONOMER.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Exosome complex component RRP4
    Alternative name(s):
    Ribosomal RNA-processing protein 4
    Gene namesi
    Name:RRP4
    Ordered Locus Names:YHR069C
    OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
    Taxonomic identifieri559292 [NCBI]
    Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
    ProteomesiUP000002311: Chromosome VIII

    Organism-specific databases

    CYGDiYHR069c.
    SGDiS000001111. RRP4.

    Subcellular locationi

    GO - Cellular componenti

    1. cytoplasmic exosome (RNase complex) Source: SGD
    2. nuclear exosome (RNase complex) Source: SGD
    3. nucleolus Source: UniProtKB-SubCell

    Keywords - Cellular componenti

    Cytoplasm, Exosome, Nucleus

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Initiator methioninei1 – 11Removed1 Publication
    Chaini2 – 359358Exosome complex component RRP4PRO_0000097455Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei2 – 21N-acetylserine1 Publication
    Modified residuei28 – 281Phosphoserine2 Publications
    Modified residuei268 – 2681Phosphoserine1 Publication

    Keywords - PTMi

    Acetylation, Phosphoprotein

    Proteomic databases

    MaxQBiP38792.
    PaxDbiP38792.

    Expressioni

    Gene expression databases

    GenevestigatoriP38792.

    Interactioni

    Subunit structurei

    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. Interacts with LRP1/RRP47.4 Publications

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    CSL4P538597EBI-1757,EBI-1731
    DIS3Q081626EBI-1757,EBI-1740
    SKI6P469484EBI-1757,EBI-1788

    Protein-protein interaction databases

    BioGridi36501. 45 interactions.
    DIPiDIP-5888N.
    IntActiP38792. 21 interactions.
    MINTiMINT-649511.
    STRINGi4932.YHR069C.

    Structurei

    Secondary structure

    1
    359
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi7 – 126
    Beta strandi60 – 623
    Beta strandi67 – 693
    Beta strandi73 – 764
    Beta strandi79 – 9113
    Beta strandi94 – 1018
    Beta strandi111 – 12010
    Beta strandi123 – 1275
    Beta strandi129 – 1324
    Beta strandi134 – 1374
    Helixi138 – 1403
    Helixi146 – 1483
    Turni153 – 1575
    Helixi159 – 1613
    Beta strandi168 – 1769
    Beta strandi178 – 1803
    Beta strandi182 – 1854
    Beta strandi188 – 1936
    Beta strandi196 – 2016
    Helixi204 – 2063
    Beta strandi214 – 2174
    Turni218 – 2203
    Beta strandi221 – 2255
    Beta strandi229 – 2357
    Helixi238 – 2425
    Helixi276 – 2783
    Beta strandi279 – 2813
    Helixi291 – 30919
    Helixi316 – 32510
    Helixi326 – 3283
    Beta strandi329 – 3313
    Helixi332 – 3365
    Helixi338 – 35619

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    4IFDX-ray2.80H1-359[»]
    ProteinModelPortaliP38792.
    SMRiP38792. Positions 2-357.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini107 – 18781S1 motifAdd
    BLAST

    Sequence similaritiesi

    Belongs to the RRP4 family.Curated
    Contains 1 S1 motif domain.Curated

    Phylogenomic databases

    eggNOGiCOG1097.
    GeneTreeiENSGT00440000033656.
    HOGENOMiHOG000193685.
    KOiK03679.
    OMAiHTHNLPG.
    OrthoDBiEOG7712J5.

    Family and domain databases

    InterProiIPR025721. Exosome_cplx_N_dom.
    IPR026699. Exosome_RNA_bind1/RRP40/RRP4.
    IPR004088. KH_dom_type_1.
    IPR012340. NA-bd_OB-fold.
    IPR022967. RNA-binding_domain_S1.
    [Graphical view]
    PANTHERiPTHR21321. PTHR21321. 1 hit.
    PfamiPF14382. ECR1_N. 1 hit.
    [Graphical view]
    SMARTiSM00316. S1. 1 hit.
    [Graphical view]
    SUPFAMiSSF50249. SSF50249. 1 hit.
    SSF54791. SSF54791. 2 hits.

    Sequencei

    Sequence statusi: Complete.

    Sequence processingi: The displayed sequence is further processed into a mature form.

    P38792-1 [UniParc]FASTAAdd to Basket

    « Hide

    MSEVITITKR NGAFQNSSNL SYNNTGISDD ENDEEDIYMH DVNSASKSES    50
    DSQIVTPGEL VTDDPIWMRG HGTYFLDNMT YSSVAGTVSR VNRLLSVIPL 100
    KGRYAPETGD HVVGRIAEVG NKRWKVDIGG KQHAVLMLGS VNLPGGILRR 150
    KSESDELQMR SFLKEGDLLN AEVQSLFQDG SASLHTRSLK YGKLRNGMFC 200
    QVPSSLIVRA KNHTHNLPGN ITVVLGVNGY IWLRKTSQMD LARDTPSANN 250
    SSSIKSTGPT GAVSLNPSIT RLEEESSWQI YSDENDPSIS NNIRQAICRY 300
    ANVIKALAFC EIGITQQRIV SAYEASMVYS NVGELIEKNV MESIGSDILT 350
    AEKMRGNGN 359
    Length:359
    Mass (Da):39,427
    Last modified:February 1, 1995 - v1
    Checksum:i0718A7ABF42E9B9B
    GO

    Natural variant

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Natural varianti136 – 1361L → P in RRP4-1; temperature-sensitive(ts) lethal mutation.

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    U00061 Genomic DNA. Translation: AAB68393.1.
    BK006934 Genomic DNA. Translation: DAA06762.1.
    PIRiS46714.
    RefSeqiNP_011936.1. NM_001179199.1.

    Genome annotation databases

    EnsemblFungiiYHR069C; YHR069C; YHR069C.
    GeneIDi856466.
    KEGGisce:YHR069C.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    U00061 Genomic DNA. Translation: AAB68393.1 .
    BK006934 Genomic DNA. Translation: DAA06762.1 .
    PIRi S46714.
    RefSeqi NP_011936.1. NM_001179199.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    4IFD X-ray 2.80 H 1-359 [» ]
    ProteinModelPortali P38792.
    SMRi P38792. Positions 2-357.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 36501. 45 interactions.
    DIPi DIP-5888N.
    IntActi P38792. 21 interactions.
    MINTi MINT-649511.
    STRINGi 4932.YHR069C.

    Proteomic databases

    MaxQBi P38792.
    PaxDbi P38792.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblFungii YHR069C ; YHR069C ; YHR069C .
    GeneIDi 856466.
    KEGGi sce:YHR069C.

    Organism-specific databases

    CYGDi YHR069c.
    SGDi S000001111. RRP4.

    Phylogenomic databases

    eggNOGi COG1097.
    GeneTreei ENSGT00440000033656.
    HOGENOMi HOG000193685.
    KOi K03679.
    OMAi HTHNLPG.
    OrthoDBi EOG7712J5.

    Enzyme and pathway databases

    BioCyci YEAST:G3O-31119-MONOMER.

    Miscellaneous databases

    NextBioi 982123.
    PROi P38792.

    Gene expression databases

    Genevestigatori P38792.

    Family and domain databases

    InterProi IPR025721. Exosome_cplx_N_dom.
    IPR026699. Exosome_RNA_bind1/RRP40/RRP4.
    IPR004088. KH_dom_type_1.
    IPR012340. NA-bd_OB-fold.
    IPR022967. RNA-binding_domain_S1.
    [Graphical view ]
    PANTHERi PTHR21321. PTHR21321. 1 hit.
    Pfami PF14382. ECR1_N. 1 hit.
    [Graphical view ]
    SMARTi SM00316. S1. 1 hit.
    [Graphical view ]
    SUPFAMi SSF50249. SSF50249. 1 hit.
    SSF54791. SSF54791. 2 hits.
    ProtoNeti Search...

    Publicationsi

    1. "The exosome: a conserved eukaryotic RNA processing complex containing multiple 3'-->5' exoribonucleases."
      Mitchell P., Petfalski E., Shevchenko A., Mann M., Tollervey D.
      Cell 91:457-466(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 94-101; 256-271 AND 306-318, FUNCTION, SUBUNIT, IDENTIFICATION BY MASS SPECTROMETRY.
    2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: ATCC 204508 / S288c.
    3. Cited for: GENOME REANNOTATION.
      Strain: ATCC 204508 / S288c.
    4. "The 3' end of yeast 5.8S rRNA is generated by an exonuclease processing mechanism."
      Mitchell P., Petfalski E., Tollervey D.
      Genes Dev. 10:502-513(1996) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, VARIANT RRP4-1.
    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: IDENTIFICATION IN THE RNA EXOSOME COMPLEX BY MASS SPECTROMETRY, SUBCELLULAR LOCATION.
    6. "Rrp47p is an exosome-associated protein required for the 3' processing of stable RNAs."
      Mitchell P., Petfalski E., Houalla R., Podtelejnikov A., Mann M., Tollervey D.
      Mol. Cell. Biol. 23:6982-6992(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: INTERACTION WITH LRP1.
    7. Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
    8. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
    9. "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.
    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, INTERACTION OF THE EXOSOME WITH RRP6 AND SKI7, SUBUNIT.
    11. "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-28 AND SER-268, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    12. "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 RNA EXOSOME COMPLEX STABILITY.
    13. "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution."
      Holt L.J., Tuch B.B., Villen J., Johnson A.D., Gygi S.P., Morgan D.O.
      Science 325:1682-1686(2009) [PubMed] [Europe PMC] [Abstract]
      Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-28, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    14. Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT SER-2, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS], CLEAVAGE OF INITIATOR METHIONINE [LARGE SCALE ANALYSIS].

    Entry informationi

    Entry nameiRRP4_YEAST
    AccessioniPrimary (citable) accession number: P38792
    Secondary accession number(s): D3DL18
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: February 1, 1995
    Last sequence update: February 1, 1995
    Last modified: October 1, 2014
    This is version 122 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programFungal Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    Present with 4840 molecules/cell in log phase SD medium.1 Publication

    Caution

    Was originally (PubMed:9390555 and PubMed:8600032) thought to have exonuclease activity but it was later shown (PubMed:17173052 and PubMed:17174896) that only DIS3/RRP44 subunit of the exosome core has this activity.Curated

    Keywords - Technical termi

    3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

    Documents

    1. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    2. SIMILARITY comments
      Index of protein domains and families
    3. Yeast
      Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
    4. Yeast chromosome VIII
      Yeast (Saccharomyces cerevisiae) chromosome VIII: entries and gene names

    External Data

    Dasty 3