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P40070

- LSM4_YEAST

UniProt

P40070 - LSM4_YEAST

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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: 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

  1. U6 snRNA binding Source: SGD

GO - Biological processi

  1. cytoplasmic mRNA processing body assembly Source: SGD
  2. mRNA splicing, via spliceosome Source: SGD
  3. nuclear-transcribed mRNA catabolic process Source: SGD
  4. rRNA processing Source: UniProtKB-KW
  5. 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.

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
ProteomesiUP000002311: Chromosome V

Organism-specific databases

CYGDiYER112w.
SGDiS000000914. LSM4.

Subcellular locationi

Nucleus 1 Publication. Cytoplasm 1 Publication

GO - Cellular componenti

  1. cytoplasmic mRNA processing body Source: SGD
  2. nucleolus Source: SGD
  3. small nucleolar ribonucleoprotein complex Source: SGD
  4. spliceosomal complex Source: UniProtKB-KW
  5. U4/U6 x U5 tri-snRNP complex Source: SGD
  6. 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.
PaxDbiP40070.
PeptideAtlasiP40070.

Expressioni

Gene expression databases

GenevestigatoriP40070.

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. 182 interactions.
DIPiDIP-848N.
IntActiP40070. 82 interactions.
MINTiMINT-390432.
STRINGi4932.YER112W.

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
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[»]
ProteinModelPortaliP40070.
SMRiP40070. Positions 1-84.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the snRNP Sm proteins family.Curated

Phylogenomic databases

eggNOGiCOG1958.
GeneTreeiENSGT00610000086173.
InParanoidiP40070.
KOiK12623.
OMAiYSEESAI.
OrthoDBiEOG7HTHWG.

Family and domain databases

InterProiIPR027141. LSm4/Sm_D1/D3.
IPR010920. LSM_dom.
IPR001163. Ribonucl_LSM.
IPR006649. Ribonucl_LSM_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 .
PIRi S50615.
RefSeqi NP_011037.3. NM_001179002.3.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
4C8Q X-ray 3.70 D 1-114 [» ]
4C92 X-ray 2.30 D 1-114 [» ]
4M75 X-ray 2.95 G/N 1-93 [» ]
4M77 X-ray 3.11 G/N 1-93 [» ]
4M78 X-ray 2.79 G/N 1-93 [» ]
4M7A X-ray 2.78 G/N 1-93 [» ]
4M7D X-ray 2.60 G/N 1-93 [» ]
ProteinModelPortali P40070.
SMRi P40070. Positions 1-84.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

BioGridi 36857. 182 interactions.
DIPi DIP-848N.
IntActi P40070. 82 interactions.
MINTi MINT-390432.
STRINGi 4932.YER112W.

Proteomic databases

MaxQBi P40070.
PaxDbi P40070.
PeptideAtlasi P40070.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblFungii YER112W ; YER112W ; YER112W .
GeneIDi 856848.
KEGGi sce:YER112W.

Organism-specific databases

CYGDi YER112w.
SGDi S000000914. LSM4.

Phylogenomic databases

eggNOGi COG1958.
GeneTreei ENSGT00610000086173.
InParanoidi P40070.
KOi K12623.
OMAi YSEESAI.
OrthoDBi EOG7HTHWG.

Enzyme and pathway databases

BioCyci YEAST:G3O-30276-MONOMER.

Miscellaneous databases

NextBioi 983177.
PROi P40070.

Gene expression databases

Genevestigatori P40070.

Family and domain databases

InterProi IPR027141. LSm4/Sm_D1/D3.
IPR010920. LSM_dom.
IPR001163. Ribonucl_LSM.
IPR006649. Ribonucl_LSM_euk/arc.
[Graphical view ]
PANTHERi PTHR23338. PTHR23338. 1 hit.
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. "Identification and characterization of Uss1p (Sdb23p): a novel U6 snRNA-associated protein with significant similarity to core proteins of small nuclear ribonucleoproteins."
    Cooper M., Johnston L.H., Beggs J.D.
    EMBO J. 14:2066-2075(1995) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], CHARACTERIZATION.
  2. "Multiple SWI6-dependent cis-acting elements control SWI4 transcription through the cell cycle."
    Foster R., Mikesell G.E., Breeden L.
    Mol. Biol. Cell 13:3792-3801(1993) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 204508 / S288c.
  4. Cited for: GENOME REANNOTATION.
    Strain: ATCC 204508 / S288c.
  5. "Sm and Sm-like proteins assemble in two related complexes of deep evolutionary origin."
    Salgado-Garrido J., Bragado-Nilsson E., Kandels-Lewis S., Seraphin B.
    EMBO J. 18:3451-3462(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION IN THE LSM2-LSM8 COMPLEX, ASSOCIATION WITH PRE-P RNA.
  6. "Characterization of Sm-like proteins in yeast and their association with U6 snRNA."
    Mayes A.E., Verdone L., Legrain P., Beggs J.D.
    EMBO J. 18:4321-4331(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: CHARACTERIZATION.
  7. "Identification by mass spectrometry and functional analysis of novel proteins of the yeast [U4/U6.U5] tri-snRNP."
    Gottschalk A., Neubauer G., Banroques J., Mann M., Luehrmann R., Fabrizio P.
    EMBO J. 18:4535-4548(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: SUBUNIT, IDENTIFICATION IN THE U4/U5/U6 TRI-SNRNP COMPLEX, IDENTIFICATION BY MASS SPECTROMETRY.
  8. "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 IN THE LSM2-LSM8 COMPLEX, ASSOCIATION OF THE LSM2-LSM8 COMPLEX WITH U6 SNRNA, IDENTIFICATION BY MASS SPECTROMETRY.
  9. "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.
  10. "Lsm proteins are required for normal processing of pre-tRNAs and their efficient association with La-homologous protein Lhp1p."
    Kufel J., Allmang C., Verdone L., Beggs J.D., Tollervey D.
    Mol. Cell. Biol. 22:5248-5256(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION IN PROCESSING OF PRE-TRNAS.
  11. Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
  12. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
  13. "Lsm Proteins are required for normal processing and stability of ribosomal RNAs."
    Kufel J., Allmang C., Petfalski E., Beggs J.D., Tollervey D.
    J. Biol. Chem. 278:2147-2156(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION IN PROCESSING OF PRE-RRNAS.
  14. "Nuclear pre-mRNA decapping and 5' degradation in yeast require the Lsm2-8p complex."
    Kufel J., Bousquet-Antonelli C., Beggs J.D., Tollervey D.
    Mol. Cell. Biol. 24:9646-9657(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION OF THE LSM2-LSM8 COMPLEX IN NUCLEAR MRNA DEGRADATION.
  15. "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 1-114 OF LSM1-LSM7 COMPLEX, SUBUNIT, INTERACTION WITH PAT1.
  16. "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-72.
  17. "Crystal structures of the Lsm complex bound to the 3' end sequence of U6 small nuclear RNA."
    Zhou L., Hang J., Zhou Y., Wan R., Lu G., Yin P., Yan C., Shi Y.
    Nature 506:116-120(2014) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.60 ANGSTROMS) OF 1-93 OF LSM2-LSM8 COMPLEX, SUBUNIT, FUNCTION, RNA-BINDING, MUTAGENESIS OF ARG-72.

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: November 26, 2014
This is version 132 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

External Data

Dasty 3