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P47093

- LSM8_YEAST

UniProt

P47093 - LSM8_YEAST

Protein

U6 snRNA-associated Sm-like protein LSm8

Gene

LSM8

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
  1. Functioni

    Component of the nuclear LSM2-LSM8 complex, which is involved in splicing of nuclear mRNAs. LSM2-LSM8 associates with multiple snRNP complexes containing the U6 snRNA (U4/U6 snRNP, spliceosomal U4/U6.U5 snRNP, and free U6 snRNP). It binds directly to the U6 snRNA and plays a role in the biogenesis and stability of the U6 snRNP and U4/U6 snRNP complexes. It probably also is involved degradation of nuclear pre-mRNA by targeting them for decapping. LSM2-LSM8 probably is involved in processing of pre-tRNAs, pre-rRNAs and U3 snoRNA. LSM2 is required for processing of pre-tRNAs, pre-rRNAs and U3 snoRNA.4 Publications

    GO - Molecular functioni

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

    GO - Biological processi

    1. mRNA splicing, via spliceosome Source: SGD
    2. rRNA processing Source: UniProtKB-KW
    3. tRNA processing Source: UniProtKB-KW

    Keywords - Molecular functioni

    Ribonucleoprotein

    Keywords - Biological processi

    mRNA processing, mRNA splicing, rRNA processing, tRNA processing

    Keywords - Ligandi

    RNA-binding

    Enzyme and pathway databases

    BioCyciYEAST:G3O-31662-MONOMER.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    U6 snRNA-associated Sm-like protein LSm8
    Gene namesi
    Name:LSM8
    Ordered Locus Names:YJR022W
    ORF Names:J1464, YJR83.16
    OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
    Taxonomic identifieri559292 [NCBI]
    Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
    ProteomesiUP000002311: Chromosome X

    Organism-specific databases

    CYGDiYJR022w.
    SGDiS000003783. LSM8.

    Subcellular locationi

    Nucleus 1 Publication. Cytoplasm 1 Publication

    GO - Cellular componenti

    1. cytoplasm Source: UniProtKB-SubCell
    2. nucleolus Source: SGD
    3. nucleus Source: SGD
    4. spliceosomal complex Source: UniProtKB-KW
    5. U4/U6 x U5 tri-snRNP complex Source: SGD
    6. U6 snRNP Source: SGD

    Keywords - Cellular componenti

    Cytoplasm, Nucleus, Spliceosome

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi57 – 571R → A: Reduces affinity for poly-U RNA ends. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 109109U6 snRNA-associated Sm-like protein LSm8PRO_0000203088Add
    BLAST

    Proteomic databases

    MaxQBiP47093.
    PaxDbiP47093.
    PeptideAtlasiP47093.

    Expressioni

    Gene expression databases

    GenevestigatoriP47093.

    Interactioni

    Subunit structurei

    Component of the heptameric LSM2-LSM8 complex that forms a seven-membered ring structure with a doughnut shape; an RNA strand can pass through the hole in the center of the ring structure. The LSm subunits are arranged in the order LSM8, LSM2, LSM3, LSM6, LSM5, LSM7 and LSM4. LSM2-LSM8 associates with PAT1 and XRN1. Component of the U4/U6-U5 tri-snRNP complex composed of the U4, U6 and U5 snRNAs and at least PRP3, PRP4, PRP6, PRP8, PRP18, PRP31, PRP38, SNU13, SNU23, SNU66, SNU114, SPP381, SMB1, SMD1, SMD2, SMD3, SMX2, SMX3, LSM2, LSM3, LSM4, LSM5, LSM6, LSM7, LSM8, BRR2 and DIB1.4 Publications

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    HSH49Q991813EBI-313,EBI-8579
    LSM2P382035EBI-313,EBI-180
    LSM4P400703EBI-313,EBI-188
    LSM6Q064064EBI-313,EBI-196
    PRP24P499603EBI-313,EBI-212
    PRP4P200533EBI-313,EBI-219

    Protein-protein interaction databases

    BioGridi33776. 87 interactions.
    DIPiDIP-903N.
    IntActiP47093. 64 interactions.
    MINTiMINT-383498.
    STRINGi4932.YJR022W.

    Structurei

    Secondary structure

    1
    109
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi6 – 83
    Beta strandi11 – 177
    Beta strandi22 – 309
    Beta strandi36 – 438
    Turni44 – 474
    Beta strandi48 – 569
    Helixi58 – 603
    Beta strandi61 – 666
    Helixi96 – 1027

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    4M77X-ray3.11A/H1-109[»]
    4M78X-ray2.79A/H1-96[»]
    4M7AX-ray2.78A/H1-96[»]
    4M7DX-ray2.60A/H1-96[»]
    ProteinModelPortaliP47093.
    SMRiP47093. Positions 3-104.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Sequence similaritiesi

    Belongs to the snRNP Sm proteins family.Curated

    Phylogenomic databases

    eggNOGiNOG258647.
    HOGENOMiHOG000000816.
    KOiK12627.
    OrthoDBiEOG7PZSB0.

    Family and domain databases

    InterProiIPR010920. LSM_dom.
    IPR001163. Ribonucl_LSM.
    IPR006649. Ribonucl_LSM_euk/arc.
    [Graphical view]
    PfamiPF01423. LSM. 1 hit.
    [Graphical view]
    SMARTiSM00651. Sm. 1 hit.
    [Graphical view]
    SUPFAMiSSF50182. SSF50182. 1 hit.

    Sequencei

    Sequence statusi: Complete.

    P47093-1 [UniParc]FASTAAdd to Basket

    « Hide

    MSATLKDYLN KRVVIIKVDG ECLIASLNGF DKNTNLFITN VFNRISKEFI    50
    CKAQLLRGSE IALVGLIDAE NDDSLAPIDE KKVPMLKDTK NKIENEHVIW 100
    EKVYESKTK 109
    Length:109
    Mass (Da):12,385
    Last modified:October 3, 2006 - v2
    Checksum:iB6E37F585B6292EA
    GO

    Sequence cautioni

    The sequence CAA60945.1 differs from that shown. Reason: Erroneous initiation.
    The sequence CAA89547.1 differs from that shown. Reason: Erroneous initiation.

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    X87611 Genomic DNA. Translation: CAA60945.1. Different initiation.
    Z49522 Genomic DNA. Translation: CAA89547.1. Different initiation.
    X87297 Genomic DNA. No translation available.
    BK006943 Genomic DNA. Translation: DAA08812.1.
    PIRiS55211.
    RefSeqiNP_012556.2. NM_001181680.1.

    Genome annotation databases

    EnsemblFungiiYJR022W; YJR022W; YJR022W.
    GeneIDi853479.
    KEGGisce:YJR022W.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    X87611 Genomic DNA. Translation: CAA60945.1 . Different initiation.
    Z49522 Genomic DNA. Translation: CAA89547.1 . Different initiation.
    X87297 Genomic DNA. No translation available.
    BK006943 Genomic DNA. Translation: DAA08812.1 .
    PIRi S55211.
    RefSeqi NP_012556.2. NM_001181680.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    4M77 X-ray 3.11 A/H 1-109 [» ]
    4M78 X-ray 2.79 A/H 1-96 [» ]
    4M7A X-ray 2.78 A/H 1-96 [» ]
    4M7D X-ray 2.60 A/H 1-96 [» ]
    ProteinModelPortali P47093.
    SMRi P47093. Positions 3-104.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 33776. 87 interactions.
    DIPi DIP-903N.
    IntActi P47093. 64 interactions.
    MINTi MINT-383498.
    STRINGi 4932.YJR022W.

    Proteomic databases

    MaxQBi P47093.
    PaxDbi P47093.
    PeptideAtlasi P47093.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblFungii YJR022W ; YJR022W ; YJR022W .
    GeneIDi 853479.
    KEGGi sce:YJR022W.

    Organism-specific databases

    CYGDi YJR022w.
    SGDi S000003783. LSM8.

    Phylogenomic databases

    eggNOGi NOG258647.
    HOGENOMi HOG000000816.
    KOi K12627.
    OrthoDBi EOG7PZSB0.

    Enzyme and pathway databases

    BioCyci YEAST:G3O-31662-MONOMER.

    Miscellaneous databases

    NextBioi 974089.
    PROi P47093.

    Gene expression databases

    Genevestigatori P47093.

    Family and domain databases

    InterProi IPR010920. LSM_dom.
    IPR001163. Ribonucl_LSM.
    IPR006649. Ribonucl_LSM_euk/arc.
    [Graphical view ]
    Pfami PF01423. LSM. 1 hit.
    [Graphical view ]
    SMARTi SM00651. Sm. 1 hit.
    [Graphical view ]
    SUPFAMi SSF50182. SSF50182. 1 hit.
    ProtoNeti Search...

    Publicationsi

    1. "Complete nucleotide sequence of Saccharomyces cerevisiae chromosome X."
      Galibert F., Alexandraki D., Baur A., Boles E., Chalwatzis N., Chuat J.-C., Coster F., Cziepluch C., de Haan M., Domdey H., Durand P., Entian K.-D., Gatius M., Goffeau A., Grivell L.A., Hennemann A., Herbert C.J., Heumann K.
      , Hilger F., Hollenberg C.P., Huang M.-E., Jacq C., Jauniaux J.-C., Katsoulou C., Kirchrath L., Kleine K., Kordes E., Koetter P., Liebl S., Louis E.J., Manus V., Mewes H.-W., Miosga T., Obermaier B., Perea J., Pohl T.M., Portetelle D., Pujol A., Purnelle B., Ramezani Rad M., Rasmussen S.W., Rose M., Rossau R., Schaaff-Gerstenschlaeger I., Smits P.H.M., Scarcez T., Soriano N., To Van D., Tzermia M., Van Broekhoven A., Vandenbol M., Wedler H., von Wettstein D., Wambutt R., Zagulski M., Zollner A., Karpfinger-Hartl L.
      EMBO J. 15:2031-2049(1996) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: ATCC 204508 / S288c.
    2. Cited for: GENOME REANNOTATION.
      Strain: ATCC 204508 / S288c.
    3. "The sequence of 24.3 kb from chromosome X reveals five complete open reading frames, all of which correspond to new genes, and a tandem insertion of a Ty1 transposon."
      Zagulski M., Babinska B., Gromadka R., Migdalski A., Rytka J., Sulicka J., Herbert C.J.
      Yeast 11:1179-1186(1995) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 48-109.
    4. "Identification by mass spectrometry and functional analysis of novel proteins of the yeast [U4/U6.U5] tri-snRNP."
      Gottschalk A., Neubauer G., Banroques J., Mann M., Luehrmann R., Fabrizio P.
      EMBO J. 18:4535-4548(1999) [PubMed] [Europe PMC] [Abstract]
      Cited for: SUBUNIT, IDENTIFICATION IN THE U4/U5/U6 TRI-SNRNP COMPLEX, IDENTIFICATION BY MASS SPECTROMETRY.
    5. "A Sm-like protein complex that participates in mRNA degradation."
      Bouveret E., Rigaut G., Shevchenko A., Wilm M., Seraphin B.
      EMBO J. 19:1661-1671(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: IDENTIFICATION IN THE LSM2-LSM8 COMPLEX, ASSOCIATION OF THE LSM2-LSM8 COMPLEX WITH U6 SNRNA, IDENTIFICATION BY MASS SPECTROMETRY.
    6. "Lsm proteins are required for normal processing of pre-tRNAs and their efficient association with La-homologous protein Lhp1p."
      Kufel J., Allmang C., Verdone L., Beggs J.D., Tollervey D.
      Mol. Cell. Biol. 22:5248-5256(2002) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION IN PROCESSING OF PRE-TRNAS.
    7. "Lsm Proteins are required for normal processing and stability of ribosomal RNAs."
      Kufel J., Allmang C., Petfalski E., Beggs J.D., Tollervey D.
      J. Biol. Chem. 278:2147-2156(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION IN PROCESSING OF PRE-RRNAS.
    8. "Sequencing and comparison of yeast species to identify genes and regulatory elements."
      Kellis M., Patterson N., Endrizzi M., Birren B.W., Lander E.S.
      Nature 423:241-254(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: IDENTIFICATION OF PROBABLE INITIATION SITE.
    9. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
    10. Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
    11. "Nuclear pre-mRNA decapping and 5' degradation in yeast require the Lsm2-8p complex."
      Kufel J., Bousquet-Antonelli C., Beggs J.D., Tollervey D.
      Mol. Cell. Biol. 24:9646-9657(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION OF THE LSM2-LSM8 COMPLEX IN NUCLEAR MRNA DEGRADATION.
    12. "Localization of Prp8, Brr2, Snu114 and U4/U6 proteins in the yeast tri-snRNP by electron microscopy."
      Hacker I., Sander B., Golas M.M., Wolf E., Karagoz E., Kastner B., Stark H., Fabrizio P., Luhrmann R.
      Nat. Struct. Mol. Biol. 15:1206-1212(2008) [PubMed] [Europe PMC] [Abstract]
      Cited for: SUBUNIT, IDENTIFICATION IN THE U4/U5/U6 TRI-SNRNP COMPLEX, ELECTRON MICROSCOPY.
    13. Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    14. "Crystal structures of the Lsm complex bound to the 3' end sequence of U6 small nuclear RNA."
      Zhou L., Hang J., Zhou Y., Wan R., Lu G., Yin P., Yan C., Shi Y.
      Nature 506:116-120(2014) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.60 ANGSTROMS) OF 1-96 OF LSM2-LSM8 COMPLEX, SUBUNIT, FUNCTION, RNA-BINDING, MUTAGENESIS OF ARG-57.

    Entry informationi

    Entry nameiLSM8_YEAST
    AccessioniPrimary (citable) accession number: P47093
    Secondary accession number(s): D6VWJ6
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: February 1, 1996
    Last sequence update: October 3, 2006
    Last modified: October 1, 2014
    This is version 112 of the entry and version 2 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programFungal Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    Present with 1440 molecules/cell in log phase SD medium.1 Publication

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

    External Data

    Dasty 3