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P47017

- LSM1_YEAST

UniProt

P47017 - LSM1_YEAST

Protein

Sm-like protein LSm1

Gene

LSM1

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 128 (01 Oct 2014)
      Sequence version 1 (01 Feb 1996)
      Previous versions | rss
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    Functioni

    Component of the cytoplasmic LSM1-LSM7 complex which is involved in mRNA degradation by activating the decapping step. The LSM1-LSM7 complex binds RNA with a preference for poly-U ends.4 Publications

    GO - Molecular functioni

    1. chromatin binding Source: SGD
    2. mRNA binding Source: SGD
    3. protein binding Source: IntAct
    4. RNA cap binding Source: SGD

    GO - Biological processi

    1. deadenylation-dependent decapping of nuclear-transcribed mRNA Source: SGD
    2. mRNA processing Source: UniProtKB-KW
    3. nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay Source: SGD

    Keywords - Molecular functioni

    Ribonucleoprotein

    Keywords - Biological processi

    mRNA processing

    Keywords - Ligandi

    RNA-binding

    Enzyme and pathway databases

    BioCyciYEAST:G3O-31575-MONOMER.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Sm-like protein LSm1
    Alternative name(s):
    SPB8 protein
    Gene namesi
    Name:LSM1
    Synonyms:SPB8
    Ordered Locus Names:YJL124C
    ORF Names:J0714
    OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
    Taxonomic identifieri559292 [NCBI]
    Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
    ProteomesiUP000002311: Chromosome X

    Organism-specific databases

    CYGDiYJL124c.
    SGDiS000003660. LSM1.

    Subcellular locationi

    GO - Cellular componenti

    1. cytoplasm Source: SGD
    2. cytoplasmic mRNA processing body Source: SGD
    3. mRNA cap binding complex Source: SGD
    4. nucleus Source: SGD

    Keywords - Cellular componenti

    Cytoplasm, Nucleus

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi105 – 1051R → A: Slightly reduces affinity for poly-U RNA ends. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 172172Sm-like protein LSm1PRO_0000125553Add
    BLAST

    Proteomic databases

    MaxQBiP47017.
    PaxDbiP47017.
    PeptideAtlasiP47017.

    Expressioni

    Gene expression databases

    GenevestigatoriP47017.

    Interactioni

    Subunit structurei

    Component of the heptameric LSM1-LSM7 complex that forms a seven-membered ring structure with a doughnut shape. The LSm subunits are arranged in the order LSM1, LSM2, LSM3, LSM6, LSM5, LSM7 and LSM4. Except for LSM1, where a C-terminal helix crosses the ring structure to form additional interactions with LSM3 and LSM6, each subunit interacts only with its two neighboring subunits. The LSM1-LSM7 complex interacts with PAT1; within the complex PAT1 has direct interactions with LSM2 and LSM3.5 Publications

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    DHH1P395173EBI-174,EBI-158
    LSM2P382036EBI-174,EBI-180
    LSM3P577435EBI-174,EBI-10227
    LSM4P400705EBI-174,EBI-188
    LSM5P400898EBI-174,EBI-10236
    LSM6Q064064EBI-174,EBI-196
    PAT1P256445EBI-174,EBI-204

    Protein-protein interaction databases

    BioGridi33632. 709 interactions.
    DIPiDIP-1330N.
    IntActiP47017. 42 interactions.
    MINTiMINT-390497.
    STRINGi4932.YJL124C.

    Structurei

    Secondary structure

    1
    172
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi42 – 476
    Beta strandi48 – 5811
    Beta strandi63 – 719
    Beta strandi77 – 8812
    Turni89 – 924
    Beta strandi93 – 10412
    Helixi106 – 1083
    Beta strandi109 – 1146
    Helixi117 – 1259
    Beta strandi127 – 1293
    Helixi132 – 15827
    Turni159 – 1613

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    4C8QX-ray3.70A45-145[»]
    4C92X-ray2.30A27-172[»]
    4M75X-ray2.95A/H30-172[»]
    ProteinModelPortaliP47017.
    SMRiP47017. Positions 38-171.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Sequence similaritiesi

    Belongs to the snRNP Sm proteins family.Curated

    Phylogenomic databases

    eggNOGiCOG1958.
    GeneTreeiENSGT00730000111133.
    HOGENOMiHOG000223544.
    KOiK12620.
    OMAiNTVNENT.
    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.

    P47017-1 [UniParc]FASTAAdd to Basket

    « Hide

    MSANSKDRNQ SNQDAKRQQQ NFPKKISEGE ADLYLDQYNF TTTAAIVSSV    50
    DRKIFVLLRD GRMLFGVLRT FDQYANLILQ DCVERIYFSE ENKYAEEDRG 100
    IFMIRGENVV MLGEVDIDKE DQPLEAMERI PFKEAWLTKQ KNDEKRFKEE 150
    THKGKKMARH GIVYDFHKSD MY 172
    Length:172
    Mass (Da):20,307
    Last modified:February 1, 1996 - v1
    Checksum:i2632FA5288E178A2
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    Z49399 Genomic DNA. Translation: CAA89419.1.
    AY558307 Genomic DNA. Translation: AAS56633.1.
    BK006943 Genomic DNA. Translation: DAA08678.1.
    PIRiS56905.
    RefSeqiNP_012411.1. NM_001181557.1.

    Genome annotation databases

    EnsemblFungiiYJL124C; YJL124C; YJL124C.
    GeneIDi853318.
    KEGGisce:YJL124C.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    Z49399 Genomic DNA. Translation: CAA89419.1 .
    AY558307 Genomic DNA. Translation: AAS56633.1 .
    BK006943 Genomic DNA. Translation: DAA08678.1 .
    PIRi S56905.
    RefSeqi NP_012411.1. NM_001181557.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    4C8Q X-ray 3.70 A 45-145 [» ]
    4C92 X-ray 2.30 A 27-172 [» ]
    4M75 X-ray 2.95 A/H 30-172 [» ]
    ProteinModelPortali P47017.
    SMRi P47017. Positions 38-171.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 33632. 709 interactions.
    DIPi DIP-1330N.
    IntActi P47017. 42 interactions.
    MINTi MINT-390497.
    STRINGi 4932.YJL124C.

    Proteomic databases

    MaxQBi P47017.
    PaxDbi P47017.
    PeptideAtlasi P47017.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblFungii YJL124C ; YJL124C ; YJL124C .
    GeneIDi 853318.
    KEGGi sce:YJL124C.

    Organism-specific databases

    CYGDi YJL124c.
    SGDi S000003660. LSM1.

    Phylogenomic databases

    eggNOGi COG1958.
    GeneTreei ENSGT00730000111133.
    HOGENOMi HOG000223544.
    KOi K12620.
    OMAi NTVNENT.
    OrthoDBi EOG7PZSB0.

    Enzyme and pathway databases

    BioCyci YEAST:G3O-31575-MONOMER.

    Miscellaneous databases

    NextBioi 973666.
    PROi P47017.

    Gene expression databases

    Genevestigatori P47017.

    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. "Sequencing analysis of a 40.2 kb fragment of yeast chromosome X reveals 19 open reading frames including URA2 (5' end), TRK1, PBS2, SPT10, GCD14, RPE1, PHO86, NCA3, ASF1, CCT7, GZF3, two tRNA genes, three remnant delta elements and a Ty4 transposon."
      Cziepluch C., Kordes E., Pujol A., Jauniaux J.-C.
      Yeast 12:1471-1474(1996) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: ATCC 96604 / S288c / FY1679.
    2. "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.
    3. Cited for: GENOME REANNOTATION.
      Strain: ATCC 204508 / S288c.
    4. Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: ATCC 204508 / S288c.
    5. "Capped mRNA degradation intermediates accumulate in the yeast spb8-2 mutant."
      Boeck R., Lapeyre B., Brown C.E., Sachs A.B.
      Mol. Cell. Biol. 18:5062-5072(1998) [PubMed] [Europe PMC] [Abstract]
      Cited for: CHARACTERIZATION.
    6. "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 LSM1-LSM7 COMPLEX, ASSOCIATION OF THE LSM1-LSM7 COMPLEX WITH PAT1 AND XRN1, FUNCTION OF THE LSM1-LSM7 COMPLEX, IDENTIFICATION BY MASS SPECTROMETRY.
    7. "The two proteins Pat1p (Mrt1p) and Spb8p interact in vivo, are required for mRNA decay, and are functionally linked to Pab1p."
      Bonnerot C., Boeck R., Lapeyre B.
      Mol. Cell. Biol. 20:5939-5946(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, INTERACTION WITH PAT1.
    8. "Yeast Sm-like proteins function in mRNA decapping and decay."
      Tharun S., He W., Mayes A.E., Lennertz P., Beggs J.D., Parker R.
      Nature 404:515-518(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION OF THE THE LSM1-LSM7 COMPLEX, SUBCELLULAR LOCATION, INTERACTION WITH PAT1.
    9. Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
    10. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
    11. "Architecture of the Lsm1-7-Pat1 complex: a conserved assembly in eukaryotic mRNA turnover."
      Sharif H., Conti E.
      Cell Rep. 5:283-291(2013) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.30 ANGSTROMS) OF 27-172 OF LSM1-LSM7 COMPLEX, SUBUNIT, INTERACTION WITH PAT1.
    12. "Crystal structure and biochemical analysis of the heptameric Lsm1-7 complex."
      Zhou L., Zhou Y., Hang J., Wan R., Lu G., Yan C., Shi Y.
      Cell Res. 24:497-500(2014) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.95 ANGSTROMS) OF LSM1-LSM7 COMPLEX, SUBUNIT, FUNCTION, RNA-BINDING, MUTAGENESIS OF ARG-105.

    Entry informationi

    Entry nameiLSM1_YEAST
    AccessioniPrimary (citable) accession number: P47017
    Secondary accession number(s): D6VW62
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: February 1, 1996
    Last sequence update: February 1, 1996
    Last modified: October 1, 2014
    This is version 128 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 3490 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