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P62312

- LSM6_HUMAN

UniProt

P62312 - LSM6_HUMAN

Protein

U6 snRNA-associated Sm-like protein LSm6

Gene

LSM6

Organism
Homo sapiens (Human)
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 thought to be involved in mRNA degradation by activating the decapping step in the 5'-to-3' mRNA decay pathway. 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 By similarity.By similarity

    GO - Molecular functioni

    1. poly(A) RNA binding Source: UniProtKB
    2. protein binding Source: IntAct

    GO - Biological processi

    1. exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay Source: Reactome
    2. gene expression Source: Reactome
    3. mRNA metabolic process Source: Reactome
    4. mRNA processing Source: UniProtKB-KW
    5. nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay Source: Reactome
    6. RNA metabolic process Source: Reactome
    7. RNA splicing Source: UniProtKB
    8. rRNA processing Source: UniProtKB-KW
    9. 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

    ReactomeiREACT_20518. mRNA decay by 5' to 3' exoribonuclease.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    U6 snRNA-associated Sm-like protein LSm6
    Gene namesi
    Name:LSM6
    OrganismiHomo sapiens (Human)
    Taxonomic identifieri9606 [NCBI]
    Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
    ProteomesiUP000005640: Chromosome 4

    Organism-specific databases

    HGNCiHGNC:17017. LSM6.

    Subcellular locationi

    Cytoplasm 1 Publication. Nucleus By similarity

    GO - Cellular componenti

    1. cytosol Source: Reactome
    2. extracellular vesicular exosome Source: UniProt
    3. small nuclear ribonucleoprotein complex Source: UniProtKB
    4. spliceosomal complex Source: UniProtKB-KW

    Keywords - Cellular componenti

    Cytoplasm, Nucleus, Spliceosome

    Pathology & Biotechi

    Organism-specific databases

    PharmGKBiPA128394584.

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 8080U6 snRNA-associated Sm-like protein LSm6PRO_0000125575Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei59 – 591N6-acetyllysine1 Publication

    Keywords - PTMi

    Acetylation

    Proteomic databases

    MaxQBiP62312.
    PaxDbiP62312.
    PeptideAtlasiP62312.
    PRIDEiP62312.

    PTM databases

    PhosphoSiteiP62312.

    Expressioni

    Gene expression databases

    BgeeiP62312.
    CleanExiHS_LSM6.
    GenevestigatoriP62312.

    Organism-specific databases

    HPAiHPA045079.

    Interactioni

    Subunit structurei

    Component of the heptameric LSM1-LSM7 complex, which consists of LSM1, LSM2, LSM3, LSM4, LSM5, LSM6 and LSM7. Component of the heptameric LSM2-LSM8 complex, which consists of LSM2, LSM3, LSM4, LSM5, LSM6, LSM7 and LSM8. The LSm subunits form a seven-membered ring structure with a doughnut shape.2 Publications

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    LSM3P623103EBI-373310,EBI-348239
    LSM5Q9Y4Y94EBI-373310,EBI-373007
    LSM7Q9UK454EBI-373310,EBI-348372

    Protein-protein interaction databases

    BioGridi116328. 23 interactions.
    DIPiDIP-31128N.
    IntActiP62312. 15 interactions.
    MINTiMINT-4100591.
    STRINGi9606.ENSP00000296581.

    Structurei

    3D structure databases

    ProteinModelPortaliP62312.
    SMRiP62312. Positions 7-74.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Sequence similaritiesi

    Phylogenomic databases

    eggNOGiCOG1958.
    HOVERGENiHBG052369.
    InParanoidiP62312.
    KOiK12625.
    OMAiEMETENM.
    OrthoDBiEOG7HXCTK.
    PhylomeDBiP62312.
    TreeFamiTF313751.

    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.

    P62312-1 [UniParc]FASTAAdd to Basket

    « Hide

    MSLRKQTPSD FLKQIIGRPV VVKLNSGVDY RGVLACLDGY MNIALEQTEE   50
    YVNGQLKNKY GDAFIRGNNV LYISTQKRRM 80
    Length:80
    Mass (Da):9,128
    Last modified:July 5, 2004 - v1
    Checksum:i21167891FDE804F1
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AJ238098 mRNA. Translation: CAB45869.1.
    AF182292 mRNA. Translation: AAD56230.1.
    AK312126 mRNA. Translation: BAG35062.1.
    AC097372 Genomic DNA. Translation: AAY41032.1.
    CH471056 Genomic DNA. Translation: EAX05029.1.
    CH471056 Genomic DNA. Translation: EAX05030.1.
    CH471056 Genomic DNA. Translation: EAX05031.1.
    BC016026 mRNA. Translation: AAH16026.1.
    CCDSiCCDS3767.1.
    RefSeqiNP_009011.1. NM_007080.2.
    UniGeneiHs.190520.

    Genome annotation databases

    GeneIDi11157.
    KEGGihsa:11157.
    UCSCiuc003ikq.4. human.

    Polymorphism databases

    DMDMi61227727.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AJ238098 mRNA. Translation: CAB45869.1 .
    AF182292 mRNA. Translation: AAD56230.1 .
    AK312126 mRNA. Translation: BAG35062.1 .
    AC097372 Genomic DNA. Translation: AAY41032.1 .
    CH471056 Genomic DNA. Translation: EAX05029.1 .
    CH471056 Genomic DNA. Translation: EAX05030.1 .
    CH471056 Genomic DNA. Translation: EAX05031.1 .
    BC016026 mRNA. Translation: AAH16026.1 .
    CCDSi CCDS3767.1.
    RefSeqi NP_009011.1. NM_007080.2.
    UniGenei Hs.190520.

    3D structure databases

    ProteinModelPortali P62312.
    SMRi P62312. Positions 7-74.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 116328. 23 interactions.
    DIPi DIP-31128N.
    IntActi P62312. 15 interactions.
    MINTi MINT-4100591.
    STRINGi 9606.ENSP00000296581.

    PTM databases

    PhosphoSitei P62312.

    Polymorphism databases

    DMDMi 61227727.

    Proteomic databases

    MaxQBi P62312.
    PaxDbi P62312.
    PeptideAtlasi P62312.
    PRIDEi P62312.

    Protocols and materials databases

    DNASUi 11157.
    Structural Biology Knowledgebase Search...

    Genome annotation databases

    GeneIDi 11157.
    KEGGi hsa:11157.
    UCSCi uc003ikq.4. human.

    Organism-specific databases

    CTDi 11157.
    GeneCardsi GC04P147097.
    HGNCi HGNC:17017. LSM6.
    HPAi HPA045079.
    MIMi 607286. gene.
    neXtProti NX_P62312.
    PharmGKBi PA128394584.
    GenAtlasi Search...

    Phylogenomic databases

    eggNOGi COG1958.
    HOVERGENi HBG052369.
    InParanoidi P62312.
    KOi K12625.
    OMAi EMETENM.
    OrthoDBi EOG7HXCTK.
    PhylomeDBi P62312.
    TreeFami TF313751.

    Enzyme and pathway databases

    Reactomei REACT_20518. mRNA decay by 5' to 3' exoribonuclease.

    Miscellaneous databases

    GeneWikii LSM6.
    GenomeRNAii 11157.
    NextBioi 42433.
    PROi P62312.
    SOURCEi Search...

    Gene expression databases

    Bgeei P62312.
    CleanExi HS_LSM6.
    Genevestigatori P62312.

    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. "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: NUCLEOTIDE SEQUENCE [MRNA].
    2. "A doughnut-shaped heteromer of human Sm-like proteins binds to the 3'-end of U6 snRNA, thereby facilitating U4/U6 duplex formation in vitro."
      Achsel T., Brahms H., Kastner B., Bachi A., Wilm M., Luehrmann R.
      EMBO J. 18:5789-5802(1999) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [MRNA], PARTIAL PROTEIN SEQUENCE, IDENTIFICATION IN THE LSM2-LSM8 COMPLEX.
    3. "Complete sequencing and characterization of 21,243 full-length human cDNAs."
      Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R., Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H., Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S.
      , Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K., Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S., Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O., Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H., Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B., Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O., Isogai T., Sugano S.
      Nat. Genet. 36:40-45(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    4. "Generation and annotation of the DNA sequences of human chromosomes 2 and 4."
      Hillier L.W., Graves T.A., Fulton R.S., Fulton L.A., Pepin K.H., Minx P., Wagner-McPherson C., Layman D., Wylie K., Sekhon M., Becker M.C., Fewell G.A., Delehaunty K.D., Miner T.L., Nash W.E., Kremitzki C., Oddy L., Du H.
      , Sun H., Bradshaw-Cordum H., Ali J., Carter J., Cordes M., Harris A., Isak A., van Brunt A., Nguyen C., Du F., Courtney L., Kalicki J., Ozersky P., Abbott S., Armstrong J., Belter E.A., Caruso L., Cedroni M., Cotton M., Davidson T., Desai A., Elliott G., Erb T., Fronick C., Gaige T., Haakenson W., Haglund K., Holmes A., Harkins R., Kim K., Kruchowski S.S., Strong C.M., Grewal N., Goyea E., Hou S., Levy A., Martinka S., Mead K., McLellan M.D., Meyer R., Randall-Maher J., Tomlinson C., Dauphin-Kohlberg S., Kozlowicz-Reilly A., Shah N., Swearengen-Shahid S., Snider J., Strong J.T., Thompson J., Yoakum M., Leonard S., Pearman C., Trani L., Radionenko M., Waligorski J.E., Wang C., Rock S.M., Tin-Wollam A.-M., Maupin R., Latreille P., Wendl M.C., Yang S.-P., Pohl C., Wallis J.W., Spieth J., Bieri T.A., Berkowicz N., Nelson J.O., Osborne J., Ding L., Meyer R., Sabo A., Shotland Y., Sinha P., Wohldmann P.E., Cook L.L., Hickenbotham M.T., Eldred J., Williams D., Jones T.A., She X., Ciccarelli F.D., Izaurralde E., Taylor J., Schmutz J., Myers R.M., Cox D.R., Huang X., McPherson J.D., Mardis E.R., Clifton S.W., Warren W.C., Chinwalla A.T., Eddy S.R., Marra M.A., Ovcharenko I., Furey T.S., Miller W., Eichler E.E., Bork P., Suyama M., Torrents D., Waterston R.H., Wilson R.K.
      Nature 434:724-731(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    5. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    6. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
      The MGC Project Team
      Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
      Tissue: Uterus.
    7. "The human LSm1-7 proteins colocalize with the mRNA-degrading enzymes Dcp1/2 and Xrnl in distinct cytoplasmic foci."
      Ingelfinger D., Arndt-Jovin D.J., Luehrmann R., Achsel T.
      RNA 8:1489-1501(2002) [PubMed] [Europe PMC] [Abstract]
      Cited for: SUBCELLULAR LOCATION, IDENTIFICATION IN THE LSM1-LSM7 COMPLEX.
    8. "Lysine acetylation targets protein complexes and co-regulates major cellular functions."
      Choudhary C., Kumar C., Gnad F., Nielsen M.L., Rehman M., Walther T.C., Olsen J.V., Mann M.
      Science 325:834-840(2009) [PubMed] [Europe PMC] [Abstract]
      Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT LYS-59, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    9. Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].

    Entry informationi

    Entry nameiLSM6_HUMAN
    AccessioniPrimary (citable) accession number: P62312
    Secondary accession number(s): Q4W5J5, Q9Y4Y8
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: July 5, 2004
    Last sequence update: July 5, 2004
    Last modified: October 1, 2014
    This is version 98 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programChordata Protein Annotation Program
    DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

    Miscellaneousi

    Keywords - Technical termi

    Complete proteome, Direct protein sequencing, Reference proteome

    Documents

    1. Human chromosome 4
      Human chromosome 4: entries, gene names and cross-references to MIM
    2. MIM cross-references
      Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
    3. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3