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P47093

- LSM8_YEAST

UniProt

P47093 - LSM8_YEAST

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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

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. 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
Complete GO annotation...

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-KW
  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
Complete GO annotation...

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 – 83Combined sources
Beta strandi11 – 177Combined sources
Beta strandi22 – 309Combined sources
Beta strandi36 – 438Combined sources
Turni44 – 474Combined sources
Beta strandi48 – 569Combined sources
Helixi58 – 603Combined sources
Beta strandi61 – 666Combined sources
Helixi96 – 1027Combined sources

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.
InParanoidiP47093.
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

        10         20         30         40         50
MSATLKDYLN KRVVIIKVDG ECLIASLNGF DKNTNLFITN VFNRISKEFI
60 70 80 90 100
CKAQLLRGSE IALVGLIDAE NDDSLAPIDE KKVPMLKDTK NKIENEHVIW

EKVYESKTK
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.
InParanoidi P47093.
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

« Hide 'large scale' publications
  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 29, 2014
This is version 113 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