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P40070 (LSM4_YEAST) Reviewed, UniProtKB/Swiss-Prot

Last modified June 11, 2014. Version 129. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (4) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
U6 snRNA-associated Sm-like protein LSm4
Gene names
Name:LSM4
Synonyms:SDB23, USS1
Ordered Locus Names:YER112W
OrganismSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) [Reference proteome]
Taxonomic identifier559292 [NCBI]
Taxonomic lineageEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces

Protein attributes

Sequence length187 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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. Ref.8 Ref.9 Ref.10 Ref.13 Ref.14 Ref.16 Ref.17

Subunit structure

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. Ref.5 Ref.7 Ref.8 Ref.15 Ref.16 Ref.17

Subcellular location

Nucleus. Cytoplasm Ref.11.

Miscellaneous

Present with 3440 molecules/cell in log phase SD medium.

Sequence similarities

Belongs to the snRNP Sm proteins family.

Ontologies

Keywords
   Biological processmRNA processing
mRNA splicing
rRNA processing
tRNA processing
   Cellular componentCytoplasm
Nucleus
Spliceosome
   LigandRNA-binding
   Molecular functionRibonucleoprotein
   Technical term3D-structure
Complete proteome
Reference proteome
Gene Ontology (GO)
   Biological_processcytoplasmic mRNA processing body assembly

Inferred from mutant phenotype PubMed 17984320PubMed 18981231. Source: SGD

mRNA splicing, via spliceosome

Inferred from physical interaction PubMed 10377396. Source: SGD

nuclear-transcribed mRNA catabolic process

Traceable author statement PubMed 15075370. Source: SGD

rRNA processing

Inferred from electronic annotation. Source: UniProtKB-KW

tRNA processing

Inferred from electronic annotation. Source: UniProtKB-KW

   Cellular_componentU4/U6 x U5 tri-snRNP complex

Inferred from direct assay PubMed 10377396Ref.7. Source: SGD

U6 snRNP

Inferred from direct assay Ref.5PubMed 11720284. Source: SGD

cytoplasmic mRNA processing body

Inferred from direct assay PubMed 18611963. Source: SGD

nucleolus

Inferred from direct assay PubMed 15075370. Source: SGD

small nucleolar ribonucleoprotein complex

Inferred from physical interaction PubMed 15075370. Source: SGD

spliceosomal complex

Inferred from electronic annotation. Source: UniProtKB-KW

   Molecular_functionU6 snRNA binding

Inferred from direct assay Ref.5. Source: SGD

protein binding

Inferred from physical interaction PubMed 10688190PubMed 10900456PubMed 11805826PubMed 16429126PubMed 18467557PubMed 18719252PubMed 23267104PubMed 23560879. Source: IntAct

Complete GO annotation...

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 187187U6 snRNA-associated Sm-like protein LSm4
PRO_0000125571

Experimental info

Mutagenesis721R → A: Slightly reduces affinity for poly-U RNA ends. Ref.16 Ref.17
Sequence conflict1551I → N in AAA58257. Ref.2

Secondary structure

.................. 187
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P40070 [UniParc].

Last modified February 1, 1995. Version 1.
Checksum: 69CAC1F01D5BFA98

FASTA18721,276
        10         20         30         40         50         60 
MLPLYLLTNA KGQQMQIELK NGEIIQGILT NVDNWMNLTL SNVTEYSEES AINSEDNAES 

        70         80         90        100        110        120 
SKAVKLNEIY IRGTFIKFIK LQDNIIDKVK QQINSNNNSN SNGPGHKRYY NNRDSNNNRG 

       130        140        150        160        170        180 
NYNRRNNNNG NSNRRPYSQN RQYNNSNSSN INNSINSINS NNQNMNNGLG GSVQHHFNSS 


SPQKVEF 

« Hide

References

« Hide 'large scale' references
[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]"The nucleotide sequence of Saccharomyces cerevisiae chromosome V."
Dietrich F.S., Mulligan J.T., Hennessy K.M., Yelton M.A., Allen E., Araujo R., Aviles E., Berno A., Brennan T., Carpenter J., Chen E., Cherry J.M., Chung E., Duncan M., Guzman E., Hartzell G., Hunicke-Smith S., Hyman R.W. expand/collapse author list , Kayser A., Komp C., Lashkari D., Lew H., Lin D., Mosedale D., Nakahara K., Namath A., Norgren R., Oefner P., Oh C., Petel F.X., Roberts D., Sehl P., Schramm S., Shogren T., Smith V., Taylor P., Wei Y., Botstein D., Davis R.W.
Nature 387:78-81(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: ATCC 204508 / S288c.
[4]"The reference genome sequence of Saccharomyces cerevisiae: Then and now."
Engel S.R., Dietrich F.S., Fisk D.G., Binkley G., Balakrishnan R., Costanzo M.C., Dwight S.S., Hitz B.C., Karra K., Nash R.S., Weng S., Wong E.D., Lloyd P., Skrzypek M.S., Miyasato S.R., Simison M., Cherry J.M.
G3 (Bethesda) 4:389-398(2014) [PubMed] [Europe PMC] [Abstract]
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]"Global analysis of protein localization in budding yeast."
Huh W.-K., Falvo J.V., Gerke L.C., Carroll A.S., Howson R.W., Weissman J.S., O'Shea E.K.
Nature 425:686-691(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
[12]"Global analysis of protein expression in yeast."
Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N., O'Shea E.K., Weissman J.S.
Nature 425:737-741(2003) [PubMed] [Europe PMC] [Abstract]
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.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
X82649 Genomic DNA. Translation: CAA57975.1.
M97918 Genomic DNA. Translation: AAA58257.1.
U18916 Genomic DNA. Translation: AAC03210.1.
BK006939 Genomic DNA. Translation: DAA07772.1.
PIRS50615.
RefSeqNP_011037.3. NM_001179002.3.

3D structure databases

PDBe
RCSB-PDB
PDBj
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[»]
ProteinModelPortalP40070.
SMRP40070. Positions 1-84.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid36857. 183 interactions.
DIPDIP-848N.
IntActP40070. 82 interactions.
MINTMINT-390432.
STRING4932.YER112W.

Proteomic databases

MaxQBP40070.
PaxDbP40070.
PeptideAtlasP40070.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblFungiYER112W; YER112W; YER112W.
GeneID856848.
KEGGsce:YER112W.

Organism-specific databases

CYGDYER112w.
SGDS000000914. LSM4.

Phylogenomic databases

eggNOGCOG1958.
GeneTreeENSGT00610000086173.
KOK12623.
OMAYSEESAI.
OrthoDBEOG7HTHWG.

Enzyme and pathway databases

BioCycYEAST:G3O-30276-MONOMER.

Gene expression databases

GenevestigatorP40070.

Family and domain databases

InterProIPR027141. LSm4/Sm_D1/D3.
IPR010920. LSM_dom.
IPR001163. Ribonucl_LSM.
IPR006649. Ribonucl_LSM_euk/arc.
[Graphical view]
PANTHERPTHR23338. PTHR23338. 1 hit.
PfamPF01423. LSM. 1 hit.
[Graphical view]
SMARTSM00651. Sm. 1 hit.
[Graphical view]
SUPFAMSSF50182. SSF50182. 1 hit.
ProtoNetSearch...

Other

NextBio983177.
PROP40070.

Entry information

Entry nameLSM4_YEAST
AccessionPrimary (citable) accession number: P40070
Secondary accession number(s): D3DM18, Q07091
Entry history
Integrated into UniProtKB/Swiss-Prot: February 1, 1995
Last sequence update: February 1, 1995
Last modified: June 11, 2014
This is version 129 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Relevant documents

Yeast chromosome V

Yeast (Saccharomyces cerevisiae) chromosome V: entries and gene names

Yeast

Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references