UniProtKB - P57743 (LSM3_YEAST)
U6 snRNA-associated Sm-like protein LSm3
LSM3
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 PublicationsMiscellaneous
GO - Molecular functioni
- RNA binding Source: UniProtKB-KW
GO - Biological processi
- deadenylation-dependent decapping of nuclear-transcribed mRNA Source: ComplexPortal
- mRNA splicing, via spliceosome Source: SGD
- P-body assembly Source: GO_Central
- rRNA processing Source: ComplexPortal
- tRNA processing Source: ComplexPortal
Keywordsi
Molecular function | Ribonucleoprotein, RNA-binding |
Biological process | mRNA processing, mRNA splicing, rRNA processing, tRNA processing |
Enzyme and pathway databases
Reactomei | R-SCE-430039, mRNA decay by 5' to 3' exoribonuclease |
Names & Taxonomyi
Protein namesi | Recommended name: U6 snRNA-associated Sm-like protein LSm3Alternative name(s): SmX4 protein |
Gene namesi | Name:LSM3 Synonyms:SMX4, USS2 Ordered Locus Names:YLR438C-A |
Organismi | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) |
Taxonomic identifieri | 559292 [NCBI] |
Taxonomic lineagei | Eukaryota › Fungi › Dikarya › Ascomycota › Saccharomycotina › Saccharomycetes › Saccharomycetales › Saccharomycetaceae › Saccharomyces › |
Proteomesi |
|
Organism-specific databases
SGDi | S000006434, LSM3 |
VEuPathDBi | FungiDB:YLR438C-A |
Subcellular locationi
Nucleus
- catalytic step 2 spliceosome Source: GO_Central
- nucleolus Source: SGD
- nucleus Source: ComplexPortal
- precatalytic spliceosome Source: GO_Central
- U4/U6 x U5 tri-snRNP complex Source: SGD
- U6 snRNP Source: SGD
Other locations
- cytoplasm Source: SGD
- Lsm1-7-Pat1 complex Source: SGD
- P-body Source: ComplexPortal
- sno(s)RNA-containing ribonucleoprotein complex Source: SGD
Keywords - Cellular componenti
Cytoplasm, Nucleus, SpliceosomePathology & Biotechi
Mutagenesis
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Mutagenesisi | 36 | H → A: Strongly reduces affinity for poly-U RNA ends. 1 Publication | 1 | |
Mutagenesisi | 38 | N → A: Strongly reduces affinity for poly-U RNA ends. 1 Publication | 1 | |
Mutagenesisi | 69 | R → A: Strongly reduces affinity for poly-U RNA ends. 2 Publications | 1 |
PTM / Processingi
Molecule processing
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
ChainiPRO_0000125563 | 1 – 89 | U6 snRNA-associated Sm-like protein LSm3Add BLAST | 89 |
Proteomic databases
MaxQBi | P57743 |
PaxDbi | P57743 |
PRIDEi | P57743 |
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 PublicationsBinary interactionsi
P57743
With | #Exp. | IntAct |
---|---|---|
LSM1 [P47017] | 4 | EBI-10227,EBI-174 |
LSM2 [P38203] | 7 | EBI-10227,EBI-180 |
LSM4 [P40070] | 3 | EBI-10227,EBI-188 |
Protein-protein interaction databases
BioGRIDi | 31697, 360 interactors |
ComplexPortali | CPX-112, LSM1-7-PAT1 complex CPX-24, U6 small nuclear ribonucleoprotein complex CPX-25, U4/U6.U5 tri-small nuclear ribonucleoprotein complex CPX-32, U4/U6 small nuclear ribonucleoprotein complex CPX-44, LSM2-8 complex CPX-45, LSM1-7 complex CPX-46, LSM2-7 complex |
DIPi | DIP-2587N |
IntActi | P57743, 59 interactors |
MINTi | P57743 |
STRINGi | 4932.YLR438C-A |
Miscellaneous databases
RNActi | P57743, protein |
Structurei
Secondary structure
3D structure databases
SMRi | P57743 |
ModBasei | Search... |
PDBe-KBi | Search... |
Miscellaneous databases
EvolutionaryTracei | P57743 |
Family & Domainsi
Sequence similaritiesi
Phylogenomic databases
eggNOGi | KOG3460, Eukaryota |
GeneTreei | ENSGT00940000175170 |
HOGENOMi | CLU_076902_5_1_1 |
InParanoidi | P57743 |
OMAi | KCKGDRE |
Family and domain databases
CDDi | cd01730, LSm3, 1 hit |
InterProi | View protein in InterPro IPR034105, Lsm3 IPR001163, LSM_dom_euk/arc IPR010920, LSM_dom_sf IPR040002, Sm-like_LSM3 |
PANTHERi | PTHR13110, PTHR13110, 1 hit |
Pfami | View protein in Pfam PF01423, LSM, 1 hit |
SMARTi | View protein in SMART SM00651, Sm, 1 hit |
SUPFAMi | SSF50182, SSF50182, 1 hit |
i Sequence
Sequence statusi: Complete.
10 20 30 40 50
METPLDLLKL NLDERVYIKL RGARTLVGTL QAFDSHCNIV LSDAVETIYQ
60 70 80
LNNEELSESE RRCEMVFIRG DTVTLISTPS EDDDGAVEI
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 |
PIRi | S78568 |
RefSeqi | NP_013543.3, NM_001184308.3 |
Genome annotation databases
EnsemblFungii | YLR438C-A_mRNA; YLR438C-A; YLR438C-A |
GeneIDi | 851159 |
KEGGi | sce:YLR438C-A |
Similar proteinsi
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 |
PIRi | S78568 |
RefSeqi | NP_013543.3, NM_001184308.3 |
3D structure databases
Select the link destinations: PDBei RCSB PDBi PDBji Links Updated | PDB entry | Method | Resolution (Å) | Chain | Positions | PDBsum |
3BW1 | X-ray | 2.50 | A/B | 1-89 | [»] | |
3JCM | electron microscopy | 3.80 | d | 1-89 | [»] | |
4C8Q | X-ray | 3.70 | C | 1-89 | [»] | |
4C92 | X-ray | 2.30 | C | 1-89 | [»] | |
4M75 | X-ray | 2.95 | C/J | 1-89 | [»] | |
4M77 | X-ray | 3.11 | C/J | 1-89 | [»] | |
4M78 | X-ray | 2.79 | C/J | 1-89 | [»] | |
4M7A | X-ray | 2.78 | C/J | 1-89 | [»] | |
4M7D | X-ray | 2.60 | C/J | 1-89 | [»] | |
4N0A | X-ray | 3.15 | A/B/E/F | 1-89 | [»] | |
5GAN | electron microscopy | 3.60 | 3 | 1-89 | [»] | |
5NRL | electron microscopy | 7.20 | 3 | 1-89 | [»] | |
5VSU | X-ray | 3.10 | C | 1-89 | [»] | |
5ZWM | electron microscopy | 3.40 | r | 1-89 | [»] | |
5ZWO | electron microscopy | 3.90 | r | 1-89 | [»] | |
6ASO | X-ray | 2.71 | C | 1-89 | [»] | |
SMRi | P57743 | |||||
ModBasei | Search... | |||||
PDBe-KBi | Search... |
Protein-protein interaction databases
BioGRIDi | 31697, 360 interactors |
ComplexPortali | CPX-112, LSM1-7-PAT1 complex CPX-24, U6 small nuclear ribonucleoprotein complex CPX-25, U4/U6.U5 tri-small nuclear ribonucleoprotein complex CPX-32, U4/U6 small nuclear ribonucleoprotein complex CPX-44, LSM2-8 complex CPX-45, LSM1-7 complex CPX-46, LSM2-7 complex |
DIPi | DIP-2587N |
IntActi | P57743, 59 interactors |
MINTi | P57743 |
STRINGi | 4932.YLR438C-A |
Proteomic databases
MaxQBi | P57743 |
PaxDbi | P57743 |
PRIDEi | P57743 |
Genome annotation databases
EnsemblFungii | YLR438C-A_mRNA; YLR438C-A; YLR438C-A |
GeneIDi | 851159 |
KEGGi | sce:YLR438C-A |
Organism-specific databases
SGDi | S000006434, LSM3 |
VEuPathDBi | FungiDB:YLR438C-A |
Phylogenomic databases
eggNOGi | KOG3460, Eukaryota |
GeneTreei | ENSGT00940000175170 |
HOGENOMi | CLU_076902_5_1_1 |
InParanoidi | P57743 |
OMAi | KCKGDRE |
Enzyme and pathway databases
Reactomei | R-SCE-430039, mRNA decay by 5' to 3' exoribonuclease |
Miscellaneous databases
EvolutionaryTracei | P57743 |
PROi | PR:P57743 |
RNActi | P57743, protein |
Family and domain databases
CDDi | cd01730, LSm3, 1 hit |
InterProi | View protein in InterPro IPR034105, Lsm3 IPR001163, LSM_dom_euk/arc IPR010920, LSM_dom_sf IPR040002, Sm-like_LSM3 |
PANTHERi | PTHR13110, PTHR13110, 1 hit |
Pfami | View protein in Pfam PF01423, LSM, 1 hit |
SMARTi | View protein in SMART SM00651, Sm, 1 hit |
SUPFAMi | SSF50182, SSF50182, 1 hit |
MobiDBi | Search... |
Entry informationi
Entry namei | LSM3_YEAST | |
Accessioni | P57743Primary (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: | February 23, 2022 | |
This is version 176 of the entry and version 1 of the sequence. See complete history. | ||
Entry statusi | Reviewed (UniProtKB/Swiss-Prot) | |
Annotation program | Fungal Protein Annotation Program |
Miscellaneousi
Keywords - Technical termi
3D-structure, Reference proteomeDocuments
- Yeast
Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD - Yeast chromosome XII
Yeast (Saccharomyces cerevisiae) chromosome XII: entries and gene names - PDB cross-references
Index of Protein Data Bank (PDB) cross-references - SIMILARITY comments
Index of protein domains and families