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P40070

- LSM4_YEAST

UniProt

P40070 - LSM4_YEAST

Protein

U6 snRNA-associated Sm-like protein LSm4

Gene

LSM4

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 130 (01 Oct 2014)
      Sequence version 1 (01 Feb 1995)
      Previous versions | rss
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    Functioni

    Component of LSm protein complexes, which are involved in RNA processing and may function in a chaperone-like manner. Component of the cytoplasmic LSM1-LSM7 complex which is involved in mRNA degradation by activating the decapping step. Component of the nuclear LSM2-LSM8 complex, which is involved in splicing of nuclear mRNAs. LSM2-LSM8 associates with multiple spliceosome snRNP complexes containing the U6 snRNA (U4/U6 snRNP, 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. LSM4 binds specifically to the 3'-terminal U-tract of U6 snRNA. LSM2-LSM8 probably is involved in processing of pre-tRNAs, pre-rRNAs and U3 snoRNA. LSM4, probably in a complex that contains LSM2-LSM7 but not LSM1 or LSM8, associates with the precursor of the RNA component of RNase P (pre-P RNA) and may be involved in maturing pre-P RNA. LSM4 is required for processing of pre-tRNAs, pre-rRNAs and U3 snoRNA.7 Publications

    GO - Molecular functioni

    1. protein binding Source: IntAct
    2. U6 snRNA binding Source: SGD

    GO - Biological processi

    1. cytoplasmic mRNA processing body assembly Source: SGD
    2. mRNA splicing, via spliceosome Source: SGD
    3. nuclear-transcribed mRNA catabolic process Source: SGD
    4. rRNA processing Source: UniProtKB-KW
    5. 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-30276-MONOMER.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    U6 snRNA-associated Sm-like protein LSm4
    Gene namesi
    Name:LSM4
    Synonyms:SDB23, USS1
    Ordered Locus Names:YER112W
    OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
    Taxonomic identifieri559292 [NCBI]
    Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
    ProteomesiUP000002311: Chromosome V

    Organism-specific databases

    CYGDiYER112w.
    SGDiS000000914. LSM4.

    Subcellular locationi

    Nucleus 1 Publication. Cytoplasm 1 Publication

    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
    Mutagenesisi72 – 721R → A: Slightly reduces affinity for poly-U RNA ends. 2 Publications

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 187187U6 snRNA-associated Sm-like protein LSm4PRO_0000125571Add
    BLAST

    Proteomic databases

    MaxQBiP40070.
    PaxDbiP40070.
    PeptideAtlasiP40070.

    Expressioni

    Gene expression databases

    GenevestigatoriP40070.

    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. 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. A complex comprising LSM2-LSM7 without LSM1 or LSM8 may exist. 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 DIB1.6 Publications

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    DHH1P395173EBI-188,EBI-158
    LSM1P470175EBI-188,EBI-174
    LSM3P577433EBI-188,EBI-10227
    LSM6Q064065EBI-188,EBI-196
    LSM7P539053EBI-188,EBI-141
    LSM8P470933EBI-188,EBI-313
    PAT1P256444EBI-188,EBI-204
    SMD2Q062173EBI-188,EBI-235
    XRN1P221473EBI-188,EBI-9642

    Protein-protein interaction databases

    BioGridi36857. 183 interactions.
    DIPiDIP-848N.
    IntActiP40070. 82 interactions.
    MINTiMINT-390432.
    STRINGi4932.YER112W.

    Structurei

    Secondary structure

    1
    187
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi2 – 87
    Turni9 – 124
    Beta strandi14 – 196
    Beta strandi22 – 3211
    Beta strandi38 – 4710
    Helixi48 – 536
    Beta strandi64 – 718
    Helixi73 – 753
    Beta strandi76 – 816
    Helixi83 – 864

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    4C8QX-ray3.70D1-114[»]
    4C92X-ray2.30D1-114[»]
    4M75X-ray2.95G/N1-93[»]
    4M77X-ray3.11G/N1-93[»]
    4M78X-ray2.79G/N1-93[»]
    4M7AX-ray2.78G/N1-93[»]
    4M7DX-ray2.60G/N1-93[»]
    ProteinModelPortaliP40070.
    SMRiP40070. Positions 1-84.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Sequence similaritiesi

    Belongs to the snRNP Sm proteins family.Curated

    Phylogenomic databases

    eggNOGiCOG1958.
    GeneTreeiENSGT00610000086173.
    KOiK12623.
    OMAiYSEESAI.
    OrthoDBiEOG7HTHWG.

    Family and domain databases

    InterProiIPR027141. LSm4/Sm_D1/D3.
    IPR010920. LSM_dom.
    IPR001163. Ribonucl_LSM.
    IPR006649. Ribonucl_LSM_euk/arc.
    [Graphical view]
    PANTHERiPTHR23338. PTHR23338. 1 hit.
    PfamiPF01423. LSM. 1 hit.
    [Graphical view]
    SMARTiSM00651. Sm. 1 hit.
    [Graphical view]
    SUPFAMiSSF50182. SSF50182. 1 hit.

    Sequencei

    Sequence statusi: Complete.

    P40070-1 [UniParc]FASTAAdd to Basket

    « Hide

    MLPLYLLTNA KGQQMQIELK NGEIIQGILT NVDNWMNLTL SNVTEYSEES    50
    AINSEDNAES SKAVKLNEIY IRGTFIKFIK LQDNIIDKVK QQINSNNNSN 100
    SNGPGHKRYY NNRDSNNNRG NYNRRNNNNG NSNRRPYSQN RQYNNSNSSN 150
    INNSINSINS NNQNMNNGLG GSVQHHFNSS SPQKVEF 187
    Length:187
    Mass (Da):21,276
    Last modified:February 1, 1995 - v1
    Checksum:i69CAC1F01D5BFA98
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti155 – 1551I → N in AAA58257. (PubMed:8497280)Curated

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    X82649 Genomic DNA. Translation: CAA57975.1.
    M97918 Genomic DNA. Translation: AAA58257.1.
    U18916 Genomic DNA. Translation: AAC03210.1.
    BK006939 Genomic DNA. Translation: DAA07772.1.
    PIRiS50615.
    RefSeqiNP_011037.3. NM_001179002.3.

    Genome annotation databases

    EnsemblFungiiYER112W; YER112W; YER112W.
    GeneIDi856848.
    KEGGisce:YER112W.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    X82649 Genomic DNA. Translation: CAA57975.1 .
    M97918 Genomic DNA. Translation: AAA58257.1 .
    U18916 Genomic DNA. Translation: AAC03210.1 .
    BK006939 Genomic DNA. Translation: DAA07772.1 .
    PIRi S50615.
    RefSeqi NP_011037.3. NM_001179002.3.

    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 D 1-114 [» ]
    4C92 X-ray 2.30 D 1-114 [» ]
    4M75 X-ray 2.95 G/N 1-93 [» ]
    4M77 X-ray 3.11 G/N 1-93 [» ]
    4M78 X-ray 2.79 G/N 1-93 [» ]
    4M7A X-ray 2.78 G/N 1-93 [» ]
    4M7D X-ray 2.60 G/N 1-93 [» ]
    ProteinModelPortali P40070.
    SMRi P40070. Positions 1-84.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 36857. 183 interactions.
    DIPi DIP-848N.
    IntActi P40070. 82 interactions.
    MINTi MINT-390432.
    STRINGi 4932.YER112W.

    Proteomic databases

    MaxQBi P40070.
    PaxDbi P40070.
    PeptideAtlasi P40070.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblFungii YER112W ; YER112W ; YER112W .
    GeneIDi 856848.
    KEGGi sce:YER112W.

    Organism-specific databases

    CYGDi YER112w.
    SGDi S000000914. LSM4.

    Phylogenomic databases

    eggNOGi COG1958.
    GeneTreei ENSGT00610000086173.
    KOi K12623.
    OMAi YSEESAI.
    OrthoDBi EOG7HTHWG.

    Enzyme and pathway databases

    BioCyci YEAST:G3O-30276-MONOMER.

    Miscellaneous databases

    NextBioi 983177.
    PROi P40070.

    Gene expression databases

    Genevestigatori P40070.

    Family and domain databases

    InterProi IPR027141. LSm4/Sm_D1/D3.
    IPR010920. LSM_dom.
    IPR001163. Ribonucl_LSM.
    IPR006649. Ribonucl_LSM_euk/arc.
    [Graphical view ]
    PANTHERi PTHR23338. PTHR23338. 1 hit.
    Pfami PF01423. LSM. 1 hit.
    [Graphical view ]
    SMARTi SM00651. Sm. 1 hit.
    [Graphical view ]
    SUPFAMi SSF50182. SSF50182. 1 hit.
    ProtoNeti Search...

    Publicationsi

    1. "Identification and characterization of Uss1p (Sdb23p): a novel U6 snRNA-associated protein with significant similarity to core proteins of small nuclear ribonucleoproteins."
      Cooper M., Johnston L.H., Beggs J.D.
      EMBO J. 14:2066-2075(1995) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], CHARACTERIZATION.
    2. "Multiple SWI6-dependent cis-acting elements control SWI4 transcription through the cell cycle."
      Foster R., Mikesell G.E., Breeden L.
      Mol. Biol. Cell 13:3792-3801(1993) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: ATCC 204508 / S288c.
    4. Cited for: GENOME REANNOTATION.
      Strain: ATCC 204508 / S288c.
    5. "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.
    6. "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.
    7. "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.
    8. "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.
    9. "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.
    10. "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.
    11. Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
    12. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
    13. "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.
    14. "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.
    15. "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 1-114 OF LSM1-LSM7 COMPLEX, SUBUNIT, INTERACTION WITH PAT1.
    16. "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-72.
    17. "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 1-93 OF LSM2-LSM8 COMPLEX, SUBUNIT, FUNCTION, RNA-BINDING, MUTAGENESIS OF ARG-72.

    Entry informationi

    Entry nameiLSM4_YEAST
    AccessioniPrimary (citable) accession number: P40070
    Secondary accession number(s): D3DM18, Q07091
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: February 1, 1995
    Last sequence update: February 1, 1995
    Last modified: October 1, 2014
    This is version 130 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 3440 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 V
      Yeast (Saccharomyces cerevisiae) chromosome V: entries and gene names

    External Data

    Dasty 3