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P47093 (LSM8_YEAST) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 109. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (4) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
U6 snRNA-associated Sm-like protein LSm8
Gene names
Name:LSM8
Ordered Locus Names:YJR022W
ORF Names:J1464, YJR83.16
OrganismSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) [Reference proteome]
Taxonomic identifier559292 [NCBI]
Taxonomic lineageEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces

Protein attributes

Sequence length109 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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. Ref.6 Ref.7 Ref.11 Ref.14

Subunit structure

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. Ref.4 Ref.5 Ref.12 Ref.14

Subcellular location

Nucleus. Cytoplasm Ref.10.

Miscellaneous

Present with 1440 molecules/cell in log phase SD medium.

Sequence similarities

Belongs to the snRNP Sm proteins family.

Sequence caution

The sequence CAA60945.1 differs from that shown. Reason: Erroneous initiation.

The sequence CAA89547.1 differs from that shown. Reason: Erroneous initiation.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 109109U6 snRNA-associated Sm-like protein LSm8
PRO_0000203088

Experimental info

Mutagenesis571R → A: Reduces affinity for poly-U RNA ends. Ref.14

Secondary structure

................ 109
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P47093 [UniParc].

Last modified October 3, 2006. Version 2.
Checksum: B6E37F585B6292EA

FASTA10912,385
        10         20         30         40         50         60 
MSATLKDYLN KRVVIIKVDG ECLIASLNGF DKNTNLFITN VFNRISKEFI CKAQLLRGSE 

        70         80         90        100 
IALVGLIDAE NDDSLAPIDE KKVPMLKDTK NKIENEHVIW EKVYESKTK 

« Hide

References

« Hide 'large scale' references
[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. expand/collapse author list , 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]Saccharomyces Genome Database
Submitted (DEC-2009) to the EMBL/GenBank/DDBJ databases
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]"Global analysis of protein expression in yeast."
Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N., O'Shea E.K., Weissman J.S.
Nature 425:737-741(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
[10]"Global analysis of protein localization in budding yeast."
Huh W.-K., Falvo J.V., Gerke L.C., Carroll A.S., Howson R.W., Weissman J.S., O'Shea E.K.
Nature 425:686-691(2003) [PubMed] [Europe PMC] [Abstract]
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]"N-terminal acetylome analyses and functional insights of the N-terminal acetyltransferase NatB."
Van Damme P., Lasa M., Polevoda B., Gazquez C., Elosegui-Artola A., Kim D.S., De Juan-Pardo E., Demeyer K., Hole K., Larrea E., Timmerman E., Prieto J., Arnesen T., Sherman F., Gevaert K., Aldabe R.
Proc. Natl. Acad. Sci. U.S.A. 109:12449-12454(2012) [PubMed] [Europe PMC] [Abstract]
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.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
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.
PIRS55211.
RefSeqNP_012556.2. NM_001181680.1.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
4M77X-ray3.11A/H1-109[»]
4M78X-ray2.79A/H1-96[»]
4M7AX-ray2.78A/H1-96[»]
4M7DX-ray2.60A/H1-96[»]
ProteinModelPortalP47093.
SMRP47093. Positions 3-104.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid33776. 87 interactions.
DIPDIP-903N.
IntActP47093. 64 interactions.
MINTMINT-383498.
STRING4932.YJR022W.

Proteomic databases

PaxDbP47093.
PeptideAtlasP47093.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblFungiYJR022W; YJR022W; YJR022W.
GeneID853479.
KEGGsce:YJR022W.

Organism-specific databases

CYGDYJR022w.
SGDS000003783. LSM8.

Phylogenomic databases

eggNOGNOG258647.
HOGENOMHOG000000816.
KOK12627.
OrthoDBEOG7PZSB0.

Enzyme and pathway databases

BioCycYEAST:G3O-31662-MONOMER.

Gene expression databases

GenevestigatorP47093.

Family and domain databases

InterProIPR010920. LSM_dom.
IPR001163. Ribonucl_LSM.
IPR006649. Ribonucl_LSM_euk/arc.
[Graphical view]
PfamPF01423. LSM. 1 hit.
[Graphical view]
SMARTSM00651. Sm. 1 hit.
[Graphical view]
SUPFAMSSF50182. SSF50182. 1 hit.
ProtoNetSearch...

Other

NextBio974089.
PROP47093.

Entry information

Entry nameLSM8_YEAST
AccessionPrimary (citable) accession number: P47093
Secondary accession number(s): D6VWJ6
Entry history
Integrated into UniProtKB/Swiss-Prot: February 1, 1996
Last sequence update: October 3, 2006
Last modified: April 16, 2014
This is version 109 of the entry and version 2 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Relevant documents

Yeast chromosome X

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

Yeast

Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references