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P47017

- LSM1_YEAST

UniProt

P47017 - LSM1_YEAST

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Protein

Sm-like protein LSm1

Gene
LSM1, SPB8, YJL124C, J0714
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 cytoplasmic LSM1-LSM7 complex which is involved in mRNA degradation by activating the decapping step. The LSM1-LSM7 complex binds RNA with a preference for poly-U ends.4 Publications

GO - Molecular functioni

  1. chromatin binding Source: SGD
  2. mRNA binding Source: SGD
  3. protein binding Source: IntAct
  4. RNA cap binding Source: SGD

GO - Biological processi

  1. deadenylation-dependent decapping of nuclear-transcribed mRNA Source: SGD
  2. mRNA processing Source: UniProtKB-KW
  3. nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay Source: SGD
Complete GO annotation...

Keywords - Molecular functioni

Ribonucleoprotein

Keywords - Biological processi

mRNA processing

Keywords - Ligandi

RNA-binding

Enzyme and pathway databases

BioCyciYEAST:G3O-31575-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Sm-like protein LSm1
Alternative name(s):
SPB8 protein
Gene namesi
Name:LSM1
Synonyms:SPB8
Ordered Locus Names:YJL124C
ORF Names:J0714
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
ProteomesiUP000002311: Chromosome X

Organism-specific databases

CYGDiYJL124c.
SGDiS000003660. LSM1.

Subcellular locationi

Nucleus. Cytoplasm. CytoplasmP-body 2 Publications

GO - Cellular componenti

  1. cytoplasm Source: SGD
  2. cytoplasmic mRNA processing body Source: SGD
  3. mRNA cap binding complex Source: SGD
  4. nucleus Source: SGD
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Nucleus

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi105 – 1051R → A: Slightly reduces affinity for poly-U RNA ends. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 172172Sm-like protein LSm1PRO_0000125553Add
BLAST

Proteomic databases

MaxQBiP47017.
PaxDbiP47017.
PeptideAtlasiP47017.

Expressioni

Gene expression databases

GenevestigatoriP47017.

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 LSM3.5 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
DHH1P395173EBI-174,EBI-158
LSM2P382036EBI-174,EBI-180
LSM3P577435EBI-174,EBI-10227
LSM4P400705EBI-174,EBI-188
LSM5P400898EBI-174,EBI-10236
LSM6Q064064EBI-174,EBI-196
PAT1P256445EBI-174,EBI-204

Protein-protein interaction databases

BioGridi33632. 708 interactions.
DIPiDIP-1330N.
IntActiP47017. 42 interactions.
MINTiMINT-390497.
STRINGi4932.YJL124C.

Structurei

Secondary structure

1
172
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi42 – 476
Beta strandi48 – 5811
Beta strandi63 – 719
Beta strandi77 – 8812
Turni89 – 924
Beta strandi93 – 10412
Helixi106 – 1083
Beta strandi109 – 1146
Helixi117 – 1259
Beta strandi127 – 1293
Helixi132 – 15827
Turni159 – 1613

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
4C8QX-ray3.70A45-145[»]
4C92X-ray2.30A27-172[»]
4M75X-ray2.95A/H30-172[»]
ProteinModelPortaliP47017.
SMRiP47017. Positions 38-171.

Family & Domainsi

Sequence similaritiesi

Belongs to the snRNP Sm proteins family.

Phylogenomic databases

eggNOGiCOG1958.
GeneTreeiENSGT00730000111133.
HOGENOMiHOG000223544.
KOiK12620.
OMAiNTVNENT.
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.

P47017-1 [UniParc]FASTAAdd to Basket

« Hide

MSANSKDRNQ SNQDAKRQQQ NFPKKISEGE ADLYLDQYNF TTTAAIVSSV    50
DRKIFVLLRD GRMLFGVLRT FDQYANLILQ DCVERIYFSE ENKYAEEDRG 100
IFMIRGENVV MLGEVDIDKE DQPLEAMERI PFKEAWLTKQ KNDEKRFKEE 150
THKGKKMARH GIVYDFHKSD MY 172
Length:172
Mass (Da):20,307
Last modified:February 1, 1996 - v1
Checksum:i2632FA5288E178A2
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
Z49399 Genomic DNA. Translation: CAA89419.1.
AY558307 Genomic DNA. Translation: AAS56633.1.
BK006943 Genomic DNA. Translation: DAA08678.1.
PIRiS56905.
RefSeqiNP_012411.1. NM_001181557.1.

Genome annotation databases

EnsemblFungiiYJL124C; YJL124C; YJL124C.
GeneIDi853318.
KEGGisce:YJL124C.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
Z49399 Genomic DNA. Translation: CAA89419.1 .
AY558307 Genomic DNA. Translation: AAS56633.1 .
BK006943 Genomic DNA. Translation: DAA08678.1 .
PIRi S56905.
RefSeqi NP_012411.1. NM_001181557.1.

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 A 45-145 [» ]
4C92 X-ray 2.30 A 27-172 [» ]
4M75 X-ray 2.95 A/H 30-172 [» ]
ProteinModelPortali P47017.
SMRi P47017. Positions 38-171.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

BioGridi 33632. 708 interactions.
DIPi DIP-1330N.
IntActi P47017. 42 interactions.
MINTi MINT-390497.
STRINGi 4932.YJL124C.

Proteomic databases

MaxQBi P47017.
PaxDbi P47017.
PeptideAtlasi P47017.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblFungii YJL124C ; YJL124C ; YJL124C .
GeneIDi 853318.
KEGGi sce:YJL124C.

Organism-specific databases

CYGDi YJL124c.
SGDi S000003660. LSM1.

Phylogenomic databases

eggNOGi COG1958.
GeneTreei ENSGT00730000111133.
HOGENOMi HOG000223544.
KOi K12620.
OMAi NTVNENT.
OrthoDBi EOG7PZSB0.

Enzyme and pathway databases

BioCyci YEAST:G3O-31575-MONOMER.

Miscellaneous databases

NextBioi 973666.
PROi P47017.

Gene expression databases

Genevestigatori P47017.

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. "Sequencing analysis of a 40.2 kb fragment of yeast chromosome X reveals 19 open reading frames including URA2 (5' end), TRK1, PBS2, SPT10, GCD14, RPE1, PHO86, NCA3, ASF1, CCT7, GZF3, two tRNA genes, three remnant delta elements and a Ty4 transposon."
    Cziepluch C., Kordes E., Pujol A., Jauniaux J.-C.
    Yeast 12:1471-1474(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: ATCC 96604 / S288c / FY1679.
  2. "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.
  3. Cited for: GENOME REANNOTATION.
    Strain: ATCC 204508 / S288c.
  4. Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: ATCC 204508 / S288c.
  5. "Capped mRNA degradation intermediates accumulate in the yeast spb8-2 mutant."
    Boeck R., Lapeyre B., Brown C.E., Sachs A.B.
    Mol. Cell. Biol. 18:5062-5072(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: CHARACTERIZATION.
  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 BY MASS SPECTROMETRY.
  7. "The two proteins Pat1p (Mrt1p) and Spb8p interact in vivo, are required for mRNA decay, and are functionally linked to Pab1p."
    Bonnerot C., Boeck R., Lapeyre B.
    Mol. Cell. Biol. 20:5939-5946(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, INTERACTION WITH PAT1.
  8. "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, SUBCELLULAR LOCATION, INTERACTION WITH PAT1.
  9. Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
  10. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
  11. "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 27-172 OF LSM1-LSM7 COMPLEX, SUBUNIT, INTERACTION WITH PAT1.
  12. "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-105.

Entry informationi

Entry nameiLSM1_YEAST
AccessioniPrimary (citable) accession number: P47017
Secondary accession number(s): D6VW62
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 1, 1996
Last sequence update: February 1, 1996
Last modified: July 9, 2014
This is version 127 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 3490 molecules/cell in log phase SD medium.

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

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