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Protein

Sm-like protein LSm1

Gene

LSM1

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed-Annotation score: 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

  • chromatin binding Source: SGD
  • mRNA binding Source: SGD
  • RNA cap binding Source: SGD

GO - Biological processi

  • deadenylation-dependent decapping of nuclear-transcribed mRNA Source: SGD
  • mRNA processing Source: UniProtKB-KW
  • 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.
ReactomeiR-SCE-430039. mRNA decay by 5' to 3' exoribonuclease.

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
Proteomesi
  • UP000002311 Componenti: Chromosome X

Organism-specific databases

EuPathDBiFungiDB:YJL124C.
SGDiS000003660. LSM1.

Subcellular locationi

GO - Cellular componenti

  • cytoplasm Source: SGD
  • cytoplasmic mRNA processing body Source: SGD
  • Lsm1-7-Pat1 complex Source: SGD
  • mRNA cap binding complex Source: SGD
  • nucleus Source: SGD
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Nucleus

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi105R → A: Slightly reduces affinity for poly-U RNA ends. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001255531 – 172Sm-like protein LSm1Add BLAST172

Proteomic databases

MaxQBiP47017.
PRIDEiP47017.

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. 706 interactors.
DIPiDIP-1330N.
IntActiP47017. 43 interactors.
MINTiMINT-390497.

Structurei

Secondary structure

1172
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi42 – 47Combined sources6
Beta strandi48 – 58Combined sources11
Beta strandi63 – 71Combined sources9
Beta strandi77 – 88Combined sources12
Turni89 – 92Combined sources4
Beta strandi93 – 104Combined sources12
Helixi106 – 108Combined sources3
Beta strandi109 – 114Combined sources6
Helixi117 – 125Combined sources9
Beta strandi127 – 129Combined sources3
Helixi132 – 158Combined sources27
Turni159 – 161Combined sources3

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
4C8QX-ray3.70A45-145[»]
4C92X-ray2.30A27-172[»]
4M75X-ray2.95A/H30-172[»]
ProteinModelPortaliP47017.
SMRiP47017.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the snRNP Sm proteins family.Curated

Phylogenomic databases

GeneTreeiENSGT00730000111133.
HOGENOMiHOG000223544.
InParanoidiP47017.
KOiK12620.
OMAiFMVRGEN.
OrthoDBiEOG092C5VL3.

Family and domain databases

InterProiIPR010920. LSM_dom.
IPR001163. LSM_dom_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

        10         20         30         40         50
MSANSKDRNQ SNQDAKRQQQ NFPKKISEGE ADLYLDQYNF TTTAAIVSSV
60 70 80 90 100
DRKIFVLLRD GRMLFGVLRT FDQYANLILQ DCVERIYFSE ENKYAEEDRG
110 120 130 140 150
IFMIRGENVV MLGEVDIDKE DQPLEAMERI PFKEAWLTKQ KNDEKRFKEE
160 170
THKGKKMARH GIVYDFHKSD MY
Length:172
Mass (Da):20,307
Last modified:February 1, 1996 - v1
Checksum:i2632FA5288E178A2
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
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:
EMBLi
GenBanki
DDBJi
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.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
4C8QX-ray3.70A45-145[»]
4C92X-ray2.30A27-172[»]
4M75X-ray2.95A/H30-172[»]
ProteinModelPortaliP47017.
SMRiP47017.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi33632. 706 interactors.
DIPiDIP-1330N.
IntActiP47017. 43 interactors.
MINTiMINT-390497.

Proteomic databases

MaxQBiP47017.
PRIDEiP47017.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

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

Organism-specific databases

EuPathDBiFungiDB:YJL124C.
SGDiS000003660. LSM1.

Phylogenomic databases

GeneTreeiENSGT00730000111133.
HOGENOMiHOG000223544.
InParanoidiP47017.
KOiK12620.
OMAiFMVRGEN.
OrthoDBiEOG092C5VL3.

Enzyme and pathway databases

BioCyciYEAST:G3O-31575-MONOMER.
ReactomeiR-SCE-430039. mRNA decay by 5' to 3' exoribonuclease.

Miscellaneous databases

PROiP47017.

Family and domain databases

InterProiIPR010920. LSM_dom.
IPR001163. LSM_dom_euk/arc.
[Graphical view]
PfamiPF01423. LSM. 1 hit.
[Graphical view]
SMARTiSM00651. Sm. 1 hit.
[Graphical view]
SUPFAMiSSF50182. SSF50182. 1 hit.
ProtoNetiSearch...

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: November 2, 2016
This is version 144 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.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

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.