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Protein

U6 snRNA-associated Sm-like protein LSm4

Gene

LSM4

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 spliceosome 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 degradation of nuclear pre-mRNA by targeting them for decapping. LSM4 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. LSM4, 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. LSM4 is required for processing of pre-tRNAs, pre-rRNAs and U3 snoRNA.7 Publications

GO - Molecular functioni

  • U6 snRNA binding Source: SGD

GO - Biological processi

  • cytoplasmic mRNA processing body assembly Source: SGD
  • mRNA splicing, via spliceosome Source: SGD
  • nuclear-transcribed mRNA catabolic process Source: SGD
  • rRNA processing Source: UniProtKB-KW
  • spliceosomal complex assembly Source: GO_Central
  • spliceosomal snRNP assembly Source: GO_Central
  • tRNA processing Source: UniProtKB-KW
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-30276-MONOMER.
ReactomeiR-SCE-430039. mRNA decay by 5' to 3' exoribonuclease.

Names & Taxonomyi

Protein namesi
Recommended name:
U6 snRNA-associated Sm-like protein LSm4
Gene namesi
Name:LSM4
Synonyms:SDB23, USS1
Ordered Locus Names:YER112W
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
Proteomesi
  • UP000002311 Componenti: Chromosome V

Organism-specific databases

EuPathDBiFungiDB:YER112W.
SGDiS000000914. LSM4.

Subcellular locationi

GO - Cellular componenti

  • cytoplasmic mRNA processing body Source: SGD
  • Lsm1-7-Pat1 complex Source: SGD
  • nucleolus Source: SGD
  • small nucleolar ribonucleoprotein complex Source: SGD
  • spliceosomal complex Source: UniProtKB-KW
  • 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)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi72 – 721R → A: Slightly reduces affinity for poly-U RNA ends. 2 Publications

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 187187U6 snRNA-associated Sm-like protein LSm4PRO_0000125571Add
BLAST

Proteomic databases

MaxQBiP40070.

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. 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 DIB1.6 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
DHH1P395173EBI-188,EBI-158
LSM1P470175EBI-188,EBI-174
LSM3P577433EBI-188,EBI-10227
LSM6Q064065EBI-188,EBI-196
LSM7P539053EBI-188,EBI-141
LSM8P470933EBI-188,EBI-313
PAT1P256444EBI-188,EBI-204
SMD2Q062173EBI-188,EBI-235
XRN1P221473EBI-188,EBI-9642

Protein-protein interaction databases

BioGridi36857. 186 interactions.
DIPiDIP-848N.
IntActiP40070. 83 interactions.
MINTiMINT-390432.

Structurei

Secondary structure

1
187
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi2 – 87Combined sources
Turni9 – 124Combined sources
Beta strandi14 – 196Combined sources
Beta strandi22 – 3211Combined sources
Beta strandi38 – 4710Combined sources
Helixi48 – 536Combined sources
Beta strandi64 – 718Combined sources
Helixi73 – 753Combined sources
Beta strandi76 – 816Combined sources
Helixi83 – 864Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3JCMelectron microscopy3.80h1-187[»]
4C8QX-ray3.70D1-114[»]
4C92X-ray2.30D1-114[»]
4M75X-ray2.95G/N1-93[»]
4M77X-ray3.11G/N1-93[»]
4M78X-ray2.79G/N1-93[»]
4M7AX-ray2.78G/N1-93[»]
4M7DX-ray2.60G/N1-93[»]
5GANelectron microscopy3.6041-187[»]
ProteinModelPortaliP40070.
SMRiP40070. Positions 1-84.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the snRNP Sm proteins family.Curated

Phylogenomic databases

GeneTreeiENSGT00610000086173.
InParanoidiP40070.
KOiK12623.
OMAiNHIKYLR.
OrthoDBiEOG092C5VL3.

Family and domain databases

InterProiIPR027141. LSm4/Sm_D1/D3.
IPR010920. LSM_dom.
IPR001163. LSM_dom_euk/arc.
[Graphical view]
PANTHERiPTHR23338. PTHR23338. 1 hit.
PfamiPF01423. LSM. 1 hit.
[Graphical view]
SMARTiSM00651. Sm. 1 hit.
[Graphical view]
SUPFAMiSSF50182. SSF50182. 1 hit.

Sequencei

Sequence statusi: Complete.

P40070-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MLPLYLLTNA KGQQMQIELK NGEIIQGILT NVDNWMNLTL SNVTEYSEES
60 70 80 90 100
AINSEDNAES SKAVKLNEIY IRGTFIKFIK LQDNIIDKVK QQINSNNNSN
110 120 130 140 150
SNGPGHKRYY NNRDSNNNRG NYNRRNNNNG NSNRRPYSQN RQYNNSNSSN
160 170 180
INNSINSINS NNQNMNNGLG GSVQHHFNSS SPQKVEF
Length:187
Mass (Da):21,276
Last modified:February 1, 1995 - v1
Checksum:i69CAC1F01D5BFA98
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti155 – 1551I → N in AAA58257 (PubMed:8497280).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X82649 Genomic DNA. Translation: CAA57975.1.
M97918 Genomic DNA. Translation: AAA58257.1.
U18916 Genomic DNA. Translation: AAC03210.1.
BK006939 Genomic DNA. Translation: DAA07772.1.
PIRiS50615.
RefSeqiNP_011037.3. NM_001179002.3.

Genome annotation databases

EnsemblFungiiYER112W; YER112W; YER112W.
GeneIDi856848.
KEGGisce:YER112W.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X82649 Genomic DNA. Translation: CAA57975.1.
M97918 Genomic DNA. Translation: AAA58257.1.
U18916 Genomic DNA. Translation: AAC03210.1.
BK006939 Genomic DNA. Translation: DAA07772.1.
PIRiS50615.
RefSeqiNP_011037.3. NM_001179002.3.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3JCMelectron microscopy3.80h1-187[»]
4C8QX-ray3.70D1-114[»]
4C92X-ray2.30D1-114[»]
4M75X-ray2.95G/N1-93[»]
4M77X-ray3.11G/N1-93[»]
4M78X-ray2.79G/N1-93[»]
4M7AX-ray2.78G/N1-93[»]
4M7DX-ray2.60G/N1-93[»]
5GANelectron microscopy3.6041-187[»]
ProteinModelPortaliP40070.
SMRiP40070. Positions 1-84.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi36857. 186 interactions.
DIPiDIP-848N.
IntActiP40070. 83 interactions.
MINTiMINT-390432.

Proteomic databases

MaxQBiP40070.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYER112W; YER112W; YER112W.
GeneIDi856848.
KEGGisce:YER112W.

Organism-specific databases

EuPathDBiFungiDB:YER112W.
SGDiS000000914. LSM4.

Phylogenomic databases

GeneTreeiENSGT00610000086173.
InParanoidiP40070.
KOiK12623.
OMAiNHIKYLR.
OrthoDBiEOG092C5VL3.

Enzyme and pathway databases

BioCyciYEAST:G3O-30276-MONOMER.
ReactomeiR-SCE-430039. mRNA decay by 5' to 3' exoribonuclease.

Miscellaneous databases

PROiP40070.

Family and domain databases

InterProiIPR027141. LSm4/Sm_D1/D3.
IPR010920. LSM_dom.
IPR001163. LSM_dom_euk/arc.
[Graphical view]
PANTHERiPTHR23338. PTHR23338. 1 hit.
PfamiPF01423. LSM. 1 hit.
[Graphical view]
SMARTiSM00651. Sm. 1 hit.
[Graphical view]
SUPFAMiSSF50182. SSF50182. 1 hit.
ProtoNetiSearch...

Entry informationi

Entry nameiLSM4_YEAST
AccessioniPrimary (citable) accession number: P40070
Secondary accession number(s): D3DM18, Q07091
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 1, 1995
Last sequence update: February 1, 1995
Last modified: September 7, 2016
This is version 147 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 3440 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 V
    Yeast (Saccharomyces cerevisiae) chromosome V: 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.