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P48240

- MTR3_YEAST

UniProt

P48240 - MTR3_YEAST

Protein

Exosome complex component MTR3

Gene

MTR3

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 113 (01 Oct 2014)
      Sequence version 1 (01 Feb 1996)
      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. MTR3 is part of the hexameric ring of RNase PH domain-containing subunits proposed to form a central channel which threads RNA substrates for degradation.3 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 mRNA surveillance Source: SGD
    4. nuclear polyadenylation-dependent CUT catabolic process Source: SGD
    5. nuclear polyadenylation-dependent mRNA catabolic process Source: SGD
    6. nuclear polyadenylation-dependent rRNA catabolic process Source: SGD
    7. nuclear polyadenylation-dependent tRNA catabolic process Source: SGD
    8. nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay Source: SGD
    9. nuclear-transcribed mRNA catabolic process, exonucleolytic, 3'-5' Source: SGD
    10. nuclear-transcribed mRNA catabolic process, non-stop decay Source: SGD
    11. polyadenylation-dependent snoRNA 3'-end processing Source: SGD
    12. U4 snRNA 3'-end processing Source: SGD

    Keywords - Biological processi

    rRNA processing

    Keywords - Ligandi

    RNA-binding

    Enzyme and pathway databases

    BioCyciYEAST:G3O-30858-MONOMER.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Exosome complex component MTR3
    Alternative name(s):
    mRNA transport regulator 3
    Gene namesi
    Name:MTR3
    Ordered Locus Names:YGR158C
    ORF Names:G6676
    OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
    Taxonomic identifieri559292 [NCBI]
    Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
    ProteomesiUP000002311: Chromosome VII

    Organism-specific databases

    CYGDiYGR158c.
    SGDiS000003390. MTR3.

    Subcellular locationi

    GO - Cellular componenti

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

    Keywords - Cellular componenti

    Cytoplasm, Exosome, Nucleus

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 250250Exosome complex component MTR3PRO_0000139979Add
    BLAST

    Proteomic databases

    MaxQBiP48240.
    PaxDbiP48240.
    PeptideAtlasiP48240.

    Expressioni

    Gene expression databases

    GenevestigatoriP48240.

    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.2 Publications

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    CSL4P538598EBI-1749,EBI-1731
    RRP42Q122773EBI-1749,EBI-1765
    SKI6P469484EBI-1749,EBI-1788
    YLR345WQ061373EBI-1749,EBI-33827

    Protein-protein interaction databases

    BioGridi33406. 28 interactions.
    DIPiDIP-931N.
    IntActiP48240. 25 interactions.
    MINTiMINT-409300.
    STRINGi4932.YGR158C.

    Structurei

    Secondary structure

    1
    250
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi6 – 83
    Beta strandi45 – 506
    Beta strandi56 – 6611
    Beta strandi69 – 8214
    Beta strandi92 – 998
    Helixi107 – 12115
    Turni122 – 1243
    Helixi127 – 1293
    Beta strandi133 – 14614
    Helixi164 – 1674
    Helixi169 – 18315
    Beta strandi187 – 1893
    Beta strandi192 – 1965
    Beta strandi199 – 2046
    Helixi205 – 2073
    Beta strandi209 – 2157
    Helixi223 – 24725

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    4IFDX-ray2.80F1-250[»]
    ProteinModelPortaliP48240.
    SMRiP48240. Positions 4-248.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Compositional bias

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Compositional biasi216 – 2227Asp/Glu-rich (acidic)

    Sequence similaritiesi

    Belongs to the RNase PH family.Curated

    Phylogenomic databases

    eggNOGiCOG0689.
    HOGENOMiHOG000113690.
    KOiK12587.
    OMAiMNVQDRR.
    OrthoDBiEOG776T1F.

    Family and domain databases

    InterProiIPR001247. ExoRNase_PH_dom1.
    IPR020568. Ribosomal_S5_D2-typ_fold.
    [Graphical view]
    PfamiPF01138. RNase_PH. 1 hit.
    [Graphical view]
    SUPFAMiSSF54211. SSF54211. 1 hit.

    Sequencei

    Sequence statusi: Complete.

    P48240-1 [UniParc]FASTAAdd to Basket

    « Hide

    MNVQDRRRLL GPAAAKPMAF SNTTTHVPEK KSTDLTPKGN ESEQELSLHT    50
    GFIENCNGSA LVEARSLGHQ TSLITAVYGP RSIRGSFTSQ GTISIQLKNG 100
    LLEKYNTNEL KEVSSFLMGI FNSVVNLSRY PKSGIDIFVY LTYDKDLTNN 150
    PQDDDSQSKM MSSQISSLIP HCITSITLAL ADAGIELVDM AGAGEANGTV 200
    VSFIKNGEEI VGFWKDDGDD EDLLECLDRC KEQYNRYRDL MISCLMNQET 250
    Length:250
    Mass (Da):27,577
    Last modified:February 1, 1996 - v1
    Checksum:i2FA07ABB4A1115E0
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    X85807 Genomic DNA. Translation: CAA59815.1.
    S80548 Genomic DNA. Translation: AAB35850.1.
    Z72943 Genomic DNA. Translation: CAA97172.1.
    BK006941 Genomic DNA. Translation: DAA08249.1.
    PIRiS58362.
    RefSeqiNP_011674.3. NM_001181287.3.

    Genome annotation databases

    EnsemblFungiiYGR158C; YGR158C; YGR158C.
    GeneIDi853062.
    KEGGisce:YGR158C.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    X85807 Genomic DNA. Translation: CAA59815.1 .
    S80548 Genomic DNA. Translation: AAB35850.1 .
    Z72943 Genomic DNA. Translation: CAA97172.1 .
    BK006941 Genomic DNA. Translation: DAA08249.1 .
    PIRi S58362.
    RefSeqi NP_011674.3. NM_001181287.3.

    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 F 1-250 [» ]
    ProteinModelPortali P48240.
    SMRi P48240. Positions 4-248.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 33406. 28 interactions.
    DIPi DIP-931N.
    IntActi P48240. 25 interactions.
    MINTi MINT-409300.
    STRINGi 4932.YGR158C.

    Proteomic databases

    MaxQBi P48240.
    PaxDbi P48240.
    PeptideAtlasi P48240.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblFungii YGR158C ; YGR158C ; YGR158C .
    GeneIDi 853062.
    KEGGi sce:YGR158C.

    Organism-specific databases

    CYGDi YGR158c.
    SGDi S000003390. MTR3.

    Phylogenomic databases

    eggNOGi COG0689.
    HOGENOMi HOG000113690.
    KOi K12587.
    OMAi MNVQDRR.
    OrthoDBi EOG776T1F.

    Enzyme and pathway databases

    BioCyci YEAST:G3O-30858-MONOMER.

    Miscellaneous databases

    NextBioi 973001.

    Gene expression databases

    Genevestigatori P48240.

    Family and domain databases

    InterProi IPR001247. ExoRNase_PH_dom1.
    IPR020568. Ribosomal_S5_D2-typ_fold.
    [Graphical view ]
    Pfami PF01138. RNase_PH. 1 hit.
    [Graphical view ]
    SUPFAMi SSF54211. SSF54211. 1 hit.
    ProtoNeti Search...

    Publicationsi

    1. "The sequence of a 27 kb segment on the right arm of chromosome VII from Saccharomyces cerevisiae reveals MOL1, NAT2, RPL30B, RSR1, CYS4, PEM1/CHO2, NSR1 genes and ten new open reading frames."
      Skala J., Nawrocki A., Goffeau A.
      Yeast 11:1421-1427(1995) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: ATCC 204508 / S288c.
    2. "The nucleotide sequence of Saccharomyces cerevisiae chromosome VII."
      Tettelin H., Agostoni-Carbone M.L., Albermann K., Albers M., Arroyo J., Backes U., Barreiros T., Bertani I., Bjourson A.J., Brueckner M., Bruschi C.V., Carignani G., Castagnoli L., Cerdan E., Clemente M.L., Coblenz A., Coglievina M., Coissac E.
      , Defoor E., Del Bino S., Delius H., Delneri D., de Wergifosse P., Dujon B., Durand P., Entian K.-D., Eraso P., Escribano V., Fabiani L., Fartmann B., Feroli F., Feuermann M., Frontali L., Garcia-Gonzalez M., Garcia-Saez M.I., Goffeau A., Guerreiro P., Hani J., Hansen M., Hebling U., Hernandez K., Heumann K., Hilger F., Hofmann B., Indge K.J., James C.M., Klima R., Koetter P., Kramer B., Kramer W., Lauquin G., Leuther H., Louis E.J., Maillier E., Marconi A., Martegani E., Mazon M.J., Mazzoni C., McReynolds A.D.K., Melchioretto P., Mewes H.-W., Minenkova O., Mueller-Auer S., Nawrocki A., Netter P., Neu R., Nombela C., Oliver S.G., Panzeri L., Paoluzi S., Plevani P., Portetelle D., Portillo F., Potier S., Purnelle B., Rieger M., Riles L., Rinaldi T., Robben J., Rodrigues-Pousada C., Rodriguez-Belmonte E., Rodriguez-Torres A.M., Rose M., Ruzzi M., Saliola M., Sanchez-Perez M., Schaefer B., Schaefer M., Scharfe M., Schmidheini T., Schreer A., Skala J., Souciet J.-L., Steensma H.Y., Talla E., Thierry A., Vandenbol M., van der Aart Q.J.M., Van Dyck L., Vanoni M., Verhasselt P., Voet M., Volckaert G., Wambutt R., Watson M.D., Weber N., Wedler E., Wedler H., Wipfli P., Wolf K., Wright L.F., Zaccaria P., Zimmermann M., Zollner A., Kleine K.
      Nature 387:81-84(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: ATCC 204508 / S288c.
    3. Cited for: GENOME REANNOTATION.
      Strain: ATCC 204508 / S288c.
    4. "Mutations in nucleolar proteins lead to nucleolar accumulation of polyA+ RNA in Saccharomyces cerevisiae."
      Kadowaki T., Schneiter R., Hitomi M., Tartakoff A.M.
      Mol. Biol. Cell 6:1103-1110(1995) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, SUBCELLULAR LOCATION.
    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. Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
    7. 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.

    Entry informationi

    Entry nameiMTR3_YEAST
    AccessioniPrimary (citable) accession number: P48240
    Secondary accession number(s): D6VUT8
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: February 1, 1996
    Last sequence update: February 1, 1996
    Last modified: October 1, 2014
    This is version 113 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 7380 molecules/cell in log phase SD medium.1 Publication

    Caution

    According to PubMed:17173052 and PubMed:17174896, only DIS3/RRP44 subunit of the exosome core has exonuclease activity.Curated

    Keywords - Technical termi

    3D-structure, Complete proteome, 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 VII
      Yeast (Saccharomyces cerevisiae) chromosome VII: entries and gene names

    External Data

    Dasty 3