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Q06406

- LSM6_YEAST

UniProt

Q06406 - LSM6_YEAST

Protein

U6 snRNA-associated Sm-like protein LSm6

Gene

LSM6

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 LSm protein complexes, which are involved in RNA processing and may function in a chaperone-like manner, facilitating the efficient association of RNA processing factors with their substrates. Component of the cytoplasmic LSM1-LSM7 complex, which is involved in mRNA degradation by activating the decapping step in the 5'-to-3' mRNA decay pathway. In association with PAT1, LSM1-LSM7 binds directly to RNAs near the 3'-end and prefers oligoadenylated RNAs over polyadenylated RNAs. 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 di-snRNP, spliceosomal U4/U6.U5 tri-snRNP, and free U6 snRNP). It binds directly to the 3'-terminal U-tract of U6 snRNA and plays a role in the biogenesis and stability of the U6 snRNP and U4/U6 snRNP complexes. LSM2-LSM8 probably also is involved degradation of nuclear pre-mRNA by targeting them for decapping, and in processing of pre-tRNAs, pre-rRNAs and U3 snoRNA. Component of a nucleolar LSM2-LSM7 complex, which associates with the precursor of the RNA component of RNase P (pre-P RNA) and with the small nucleolar RNA (snoRNA) snR5. It may play a role in the maturation of a subset of nucleolus-associated small RNAs.6 Publications

    GO - Molecular functioni

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

    GO - Biological processi

    1. maturation of SSU-rRNA Source: SGD
    2. mRNA splicing, via spliceosome Source: SGD
    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-29927-MONOMER.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    U6 snRNA-associated Sm-like protein LSm6
    Gene namesi
    Name:LSM6
    Ordered Locus Names:YDR378C
    ORF Names:D9481.18
    OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
    Taxonomic identifieri559292 [NCBI]
    Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
    ProteomesiUP000002311: Chromosome IV

    Organism-specific databases

    SGDiS000002786. LSM6.

    Subcellular locationi

    Cytoplasm. Nucleusnucleolus
    Note: LSM1 and LSM8 act competitively with respect to the localization of LSM1-LSM7 to the cytoplasm and LSM2-LSM8 to the nucleus. LSm proteins shift to the cytoplasm under conditions of stress.

    GO - Cellular componenti

    1. cytoplasmic mRNA processing body Source: SGD
    2. nucleolus Source: SGD
    3. small nucleolar ribonucleoprotein complex 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
    Mutagenesisi74 – 741R → A: Reduces affinity for poly-U RNA ends. 2 Publications

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 8686U6 snRNA-associated Sm-like protein LSm6PRO_0000125578Add
    BLAST

    Proteomic databases

    MaxQBiQ06406.
    PaxDbiQ06406.
    PeptideAtlasiQ06406.

    Expressioni

    Gene expression databases

    GenevestigatoriQ06406.

    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. LSM1-LSM7 associates also with PAT1 and XRN1. 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 a LSM2-LSM7 complex, which consists of at least LSM2, LSM3, LSM4, LSM5, LSM6 and LSM7. It is not known whether another protein replaces the missing LSm to form a novel heptameric complex. Component of the spliceosome 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 DIB1.7 Publications

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    LSM1P470174EBI-196,EBI-174
    LSM2P382034EBI-196,EBI-180
    LSM4P400705EBI-196,EBI-188
    LSM5P400893EBI-196,EBI-10236
    LSM8P470934EBI-196,EBI-313

    Protein-protein interaction databases

    BioGridi32437. 359 interactions.
    DIPiDIP-1418N.
    IntActiQ06406. 34 interactions.
    MINTiMINT-403097.
    STRINGi4932.YDR378C.

    Structurei

    Secondary structure

    1
    86
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi11 – 177
    Turni18 – 214
    Beta strandi22 – 287
    Beta strandi31 – 4111
    Beta strandi47 – 5711
    Turni59 – 613
    Beta strandi65 – 695
    Beta strandi71 – 733
    Helixi75 – 773
    Beta strandi78 – 836

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    4C8QX-ray3.70F1-86[»]
    4C92X-ray2.30F1-86[»]
    4M75X-ray2.95D/K1-86[»]
    4M77X-ray3.11D/K1-86[»]
    4M78X-ray2.79D/K1-86[»]
    4M7AX-ray2.78D/K1-86[»]
    4M7DX-ray2.60D/K1-86[»]
    ProteinModelPortaliQ06406.
    SMRiQ06406. Positions 10-86.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Sequence similaritiesi

    Phylogenomic databases

    eggNOGiCOG1958.
    HOGENOMiHOG000223542.
    KOiK12625.
    OMAiATEHYES.
    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.

    Q06406-1 [UniParc]FASTAAdd to Basket

    « Hide

    MSGKASTEGS VTTEFLSDII GKTVNVKLAS GLLYSGRLES IDGFMNVALS   50
    SATEHYESNN NKLLNKFNSD VFLRGTQVMY ISEQKI 86
    Length:86
    Mass (Da):9,398
    Last modified:May 20, 2008 - v2
    Checksum:i74FE40A4509CEF33
    GO

    Sequence cautioni

    The sequence AAB64814.1 differs from that shown. Reason: Erroneous initiation.

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    U28373 Genomic DNA. Translation: AAB64814.1. Different initiation.
    BK006938 Genomic DNA. Translation: DAA12220.1.
    PIRiS61173.
    RefSeqiNP_010666.2. NM_001180686.1.

    Genome annotation databases

    EnsemblFungiiYDR378C; YDR378C; YDR378C.
    GeneIDi851984.
    KEGGisce:YDR378C.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    U28373 Genomic DNA. Translation: AAB64814.1 . Different initiation.
    BK006938 Genomic DNA. Translation: DAA12220.1 .
    PIRi S61173.
    RefSeqi NP_010666.2. NM_001180686.1.

    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 F 1-86 [» ]
    4C92 X-ray 2.30 F 1-86 [» ]
    4M75 X-ray 2.95 D/K 1-86 [» ]
    4M77 X-ray 3.11 D/K 1-86 [» ]
    4M78 X-ray 2.79 D/K 1-86 [» ]
    4M7A X-ray 2.78 D/K 1-86 [» ]
    4M7D X-ray 2.60 D/K 1-86 [» ]
    ProteinModelPortali Q06406.
    SMRi Q06406. Positions 10-86.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 32437. 359 interactions.
    DIPi DIP-1418N.
    IntActi Q06406. 34 interactions.
    MINTi MINT-403097.
    STRINGi 4932.YDR378C.

    Proteomic databases

    MaxQBi Q06406.
    PaxDbi Q06406.
    PeptideAtlasi Q06406.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblFungii YDR378C ; YDR378C ; YDR378C .
    GeneIDi 851984.
    KEGGi sce:YDR378C.

    Organism-specific databases

    SGDi S000002786. LSM6.

    Phylogenomic databases

    eggNOGi COG1958.
    HOGENOMi HOG000223542.
    KOi K12625.
    OMAi ATEHYES.
    OrthoDBi EOG7PZSB0.

    Enzyme and pathway databases

    BioCyci YEAST:G3O-29927-MONOMER.

    Miscellaneous databases

    NextBioi 970136.
    PROi Q06406.

    Gene expression databases

    Genevestigatori Q06406.

    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. "The nucleotide sequence of Saccharomyces cerevisiae chromosome IV."
      Jacq C., Alt-Moerbe J., Andre B., Arnold W., Bahr A., Ballesta J.P.G., Bargues M., Baron L., Becker A., Biteau N., Bloecker H., Blugeon C., Boskovic J., Brandt P., Brueckner M., Buitrago M.J., Coster F., Delaveau T.
      , del Rey F., Dujon B., Eide L.G., Garcia-Cantalejo J.M., Goffeau A., Gomez-Peris A., Granotier C., Hanemann V., Hankeln T., Hoheisel J.D., Jaeger W., Jimenez A., Jonniaux J.-L., Kraemer C., Kuester H., Laamanen P., Legros Y., Louis E.J., Moeller-Rieker S., Monnet A., Moro M., Mueller-Auer S., Nussbaumer B., Paricio N., Paulin L., Perea J., Perez-Alonso M., Perez-Ortin J.E., Pohl T.M., Prydz H., Purnelle B., Rasmussen S.W., Remacha M.A., Revuelta J.L., Rieger M., Salom D., Saluz H.P., Saiz J.E., Saren A.-M., Schaefer M., Scharfe M., Schmidt E.R., Schneider C., Scholler P., Schwarz S., Soler-Mira A., Urrestarazu L.A., Verhasselt P., Vissers S., Voet M., Volckaert G., Wagner G., Wambutt R., Wedler E., Wedler H., Woelfl S., Harris D.E., Bowman S., Brown D., Churcher C.M., Connor R., Dedman K., Gentles S., Hamlin N., Hunt S., Jones L., McDonald S., Murphy L.D., Niblett D., Odell C., Oliver K., Rajandream M.A., Richards C., Shore L., Walsh S.V., Barrell B.G., Dietrich F.S., Mulligan J.T., Allen E., Araujo R., Aviles E., Berno A., Carpenter J., Chen E., Cherry J.M., Chung E., Duncan M., Hunicke-Smith S., Hyman R.W., Komp C., Lashkari D., Lew H., Lin D., Mosedale D., Nakahara K., Namath A., Oefner P., Oh C., Petel F.X., Roberts D., Schramm S., Schroeder M., Shogren T., Shroff N., Winant A., Yelton M.A., Botstein D., Davis R.W., Johnston M., Andrews S., Brinkman R., Cooper J., Ding H., Du Z., Favello A., Fulton L., Gattung S., Greco T., Hallsworth K., Hawkins J., Hillier L.W., Jier M., Johnson D., Johnston L., Kirsten J., Kucaba T., Langston Y., Latreille P., Le T., Mardis E., Menezes S., Miller N., Nhan M., Pauley A., Peluso D., Rifkin L., Riles L., Taich A., Trevaskis E., Vignati D., Wilcox L., Wohldman P., Vaudin M., Wilson R., Waterston R., Albermann K., Hani J., Heumann K., Kleine K., Mewes H.-W., Zollner A., Zaccaria P.
      Nature 387:75-78(1997) [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. "Sm and Sm-like proteins assemble in two related complexes of deep evolutionary origin."
      Salgado-Garrido J., Bragado-Nilsson E., Kandels-Lewis S., Seraphin B.
      EMBO J. 18:3451-3462(1999) [PubMed] [Europe PMC] [Abstract]
      Cited for: IDENTIFICATION IN THE LSM2-LSM8 COMPLEX, ASSOCIATION WITH PRE-P RNA.
    4. "Characterization of Sm-like proteins in yeast and their association with U6 snRNA."
      Mayes A.E., Verdone L., Legrain P., Beggs J.D.
      EMBO J. 18:4321-4331(1999) [PubMed] [Europe PMC] [Abstract]
      Cited for: CHARACTERIZATION.
    5. "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.
    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 IN THE LSM2-LSM8 COMPLEX, ASSOCIATION OF THE LSM2-LSM8 COMPLEX WITH U6 SNRNA, IDENTIFICATION BY MASS SPECTROMETRY, IDENTIFICATION OF PROBABLE INTITIATION SITE.
    7. "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 LSM1-LSM7 COMPLEX.
    8. "An Lsm2-Lsm7 complex in Saccharomyces cerevisiae associates with the small nucleolar RNA snR5."
      Fernandez C.F., Pannone B.K., Chen X., Fuchs G., Wolin S.L.
      Mol. Biol. Cell 15:2842-2852(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: IDENTIFICATION IN THE LSM2-LSM7 COMPLEX, SUBCELLULAR LOCATION.
    9. "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.
    10. "Mapping of transcription start sites in Saccharomyces cerevisiae using 5' SAGE."
      Zhang Z., Dietrich F.S.
      Nucleic Acids Res. 33:2838-2851(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: IDENTIFICATION OF PROBABLE INITIATION SITE.
    11. "Requirements for nuclear localization of the Lsm2-8p complex and competition between nuclear and cytoplasmic Lsm complexes."
      Spiller M.P., Reijns M.A.M., Beggs J.D.
      J. Cell Sci. 120:4310-4320(2007) [PubMed] [Europe PMC] [Abstract]
      Cited for: SUBCELLULAR LOCATION.
    12. "The decapping activator Lsm1p-7p-Pat1p complex has the intrinsic ability to distinguish between oligoadenylated and polyadenylated RNAs."
      Chowdhury A., Mukhopadhyay J., Tharun S.
      RNA 13:998-1016(2007) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION OF THE LSM1-LSM7-PAT1 COMPLEX.
    13. "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 LSM1-LSM7 COMPLEX, SUBUNIT, INTERACTION WITH PAT1.
    14. "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-74.
    15. "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 LSM2-LSM8 COMPLEX, SUBUNIT, FUNCTION, RNA-BINDING, MUTAGENESIS OF ARG-74.

    Entry informationi

    Entry nameiLSM6_YEAST
    AccessioniPrimary (citable) accession number: Q06406
    Secondary accession number(s): D6VT10
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: January 11, 2001
    Last sequence update: May 20, 2008
    Last modified: October 1, 2014
    This is version 126 of the entry and version 2 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programFungal Protein Annotation Program

    Miscellaneousi

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

    External Data

    Dasty 3