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Protein

U6 snRNA-associated Sm-like protein LSm3

Gene

LSM3

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 LSm protein complexes, which are involved in RNA processing and may function in a chaperone-like manner. Component of the cytoplasmic LSM1-LSM7 complex which is involved in mRNA degradation by activating the decapping step. 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, 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 in degradation of nuclear pre-mRNA by targeting them for decapping. LSM3 binds specifically to the 3'-terminal U-tract of U6 snRNA. LSM2-LSM8 probably is involved in processing of pre-tRNAs, pre-rRNAs and U3 snoRNA. LSM3, probably in a complex that contains LSM2-LSM7 but not LSM1 or LSM8, associates with the precursor of the RNA component of RNase P (pre-P RNA) and may be involved in maturing pre-P RNA. LSM3 is required for processing of pre-tRNAs, pre-rRNAs and U3 snoRNA.9 Publications

GO - Molecular functioni

GO - Biological processi

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-32519-MONOMER.
ReactomeiR-SCE-430039. mRNA decay by 5' to 3' exoribonuclease.

Names & Taxonomyi

Protein namesi
Recommended name:
U6 snRNA-associated Sm-like protein LSm3
Alternative name(s):
SmX4 protein
Gene namesi
Name:LSM3
Synonyms:SMX4, USS2
Ordered Locus Names:YLR438C-A
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
Proteomesi
  • UP000002311 Componenti: Chromosome XII

Organism-specific databases

EuPathDBiFungiDB:YLR438C-A.
SGDiS000006434. LSM3.

Subcellular locationi

GO - Cellular componenti

  • catalytic step 2 spliceosome Source: GO_Central
  • cytoplasmic mRNA processing body Source: GO_Central
  • Lsm1-7-Pat1 complex Source: SGD
  • nucleolus Source: SGD
  • precatalytic spliceosome Source: GO_Central
  • small nucleolar ribonucleoprotein complex Source: SGD
  • U4/U6 x U5 tri-snRNP complex Source: SGD
  • U6 snRNP Source: SGD
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Nucleus, Spliceosome

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi36H → A: Strongly reduces affinity for poly-U RNA ends. 1 Publication1
Mutagenesisi38N → A: Strongly reduces affinity for poly-U RNA ends. 1 Publication1
Mutagenesisi69R → A: Strongly reduces affinity for poly-U RNA ends. 2 Publications1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001255631 – 89U6 snRNA-associated Sm-like protein LSm3Add BLAST89

Proteomic databases

MaxQBiP57743.
PRIDEiP57743.

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. 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. A complex comprising LSM2-LSM7 without LSM1 or LSM8 may exist. Likewise, LSM2 and LSM3 can assemble into a doughnut structure that binds PAT1 (in vitro). Besides, LSM3 can form a homooctameric ring (in vitro). 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 DIB1.8 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
LSM1P470175EBI-10227,EBI-174
LSM2P382034EBI-10227,EBI-180
LSM4P400703EBI-10227,EBI-188

Protein-protein interaction databases

BioGridi31697. 210 interactors.
DIPiDIP-2587N.
IntActiP57743. 59 interactors.
MINTiMINT-422505.

Structurei

Secondary structure

189
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi4 – 9Combined sources6
Turni10 – 13Combined sources4
Beta strandi14 – 20Combined sources7
Turni21 – 23Combined sources3
Beta strandi24 – 33Combined sources10
Beta strandi39 – 52Combined sources14
Beta strandi55 – 68Combined sources14
Helixi70 – 72Combined sources3
Beta strandi73 – 77Combined sources5

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3BW1X-ray2.50A/B1-89[»]
3JCMelectron microscopy3.80d1-89[»]
4C8QX-ray3.70C1-89[»]
4C92X-ray2.30C1-89[»]
4M75X-ray2.95C/J1-89[»]
4M77X-ray3.11C/J1-89[»]
4M78X-ray2.79C/J1-89[»]
4M7AX-ray2.78C/J1-89[»]
4M7DX-ray2.60C/J1-89[»]
4N0AX-ray3.15A/B/E/F1-89[»]
5GANelectron microscopy3.6031-89[»]
ProteinModelPortaliP57743.
SMRiP57743.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP57743.

Family & Domainsi

Sequence similaritiesi

Belongs to the snRNP Sm proteins family.Curated

Phylogenomic databases

GeneTreeiENSGT00390000013951.
HOGENOMiHOG000223550.
InParanoidiP57743.
KOiK12622.
OMAiHLNMILS.
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.

P57743-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
METPLDLLKL NLDERVYIKL RGARTLVGTL QAFDSHCNIV LSDAVETIYQ
60 70 80
LNNEELSESE RRCEMVFIRG DTVTLISTPS EDDDGAVEI
Length:89
Mass (Da):10,030
Last modified:January 11, 2001 - v1
Checksum:i787084EF6A5945B7
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z30582 Genomic DNA. Translation: CAA83056.1.
X06790 Genomic DNA. Translation: CAA29948.1.
U21094 Genomic DNA. No translation available.
BK006945 Genomic DNA. Translation: DAA09739.1.
PIRiS78568.
RefSeqiNP_013543.3. NM_001184308.3.

Genome annotation databases

EnsemblFungiiYLR438C-A; YLR438C-A; YLR438C-A.
GeneIDi851159.
KEGGisce:YLR438C-A.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z30582 Genomic DNA. Translation: CAA83056.1.
X06790 Genomic DNA. Translation: CAA29948.1.
U21094 Genomic DNA. No translation available.
BK006945 Genomic DNA. Translation: DAA09739.1.
PIRiS78568.
RefSeqiNP_013543.3. NM_001184308.3.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3BW1X-ray2.50A/B1-89[»]
3JCMelectron microscopy3.80d1-89[»]
4C8QX-ray3.70C1-89[»]
4C92X-ray2.30C1-89[»]
4M75X-ray2.95C/J1-89[»]
4M77X-ray3.11C/J1-89[»]
4M78X-ray2.79C/J1-89[»]
4M7AX-ray2.78C/J1-89[»]
4M7DX-ray2.60C/J1-89[»]
4N0AX-ray3.15A/B/E/F1-89[»]
5GANelectron microscopy3.6031-89[»]
ProteinModelPortaliP57743.
SMRiP57743.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi31697. 210 interactors.
DIPiDIP-2587N.
IntActiP57743. 59 interactors.
MINTiMINT-422505.

Proteomic databases

MaxQBiP57743.
PRIDEiP57743.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYLR438C-A; YLR438C-A; YLR438C-A.
GeneIDi851159.
KEGGisce:YLR438C-A.

Organism-specific databases

EuPathDBiFungiDB:YLR438C-A.
SGDiS000006434. LSM3.

Phylogenomic databases

GeneTreeiENSGT00390000013951.
HOGENOMiHOG000223550.
InParanoidiP57743.
KOiK12622.
OMAiHLNMILS.
OrthoDBiEOG092C5VL3.

Enzyme and pathway databases

BioCyciYEAST:G3O-32519-MONOMER.
ReactomeiR-SCE-430039. mRNA decay by 5' to 3' exoribonuclease.

Miscellaneous databases

EvolutionaryTraceiP57743.
PROiP57743.

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 nameiLSM3_YEAST
AccessioniPrimary (citable) accession number: P57743
Secondary accession number(s): D6VZ73, Q05176, Q06759
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 11, 2001
Last sequence update: January 11, 2001
Last modified: November 2, 2016
This is version 140 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 7060 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 XII
    Yeast (Saccharomyces cerevisiae) chromosome XII: 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.