U6 snRNA-associated Sm-like protein LSm4 - Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)

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P40070 (LSM4_YEAST) Reviewed, UniProtKB/Swiss-Prot

Last modified May 29, 2013. Version 119. History...

Clusters with 100%, 90%, 50% identity |

Documents (3) |

Third-party data

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Names·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents Customize order

Names and origin

Protein names

Recommended name:
U6 snRNA-associated Sm-like protein LSm4

Gene names

Name:	LSM4
Synonyms:	SDB23, USS1
Ordered Locus Names:	YER112W

Organism

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) [Reference proteome]

Taxonomic identifier

559292 [NCBI]

Taxonomic lineage

Eukaryota › Fungi › Dikarya › Ascomycota › Saccharomycotina › Saccharomycetes › Saccharomycetales › Saccharomycetaceae › Saccharomyces ›

Protein attributes

Sequence length	187 AA.
Sequence status	Complete.
Protein existence	Evidence 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 thought to be 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
Subunit structure	Component of the heptameric LSM1-LSM7 complex, which consists of LSM1, LSM2, LSM3, LSM4, LSM5, LSM6 and LSM7. Component of the heptameric LSM2-LSM8 complex, which consists of LSM2, LSM3, LSM4, LSM5, LSM6, LSM7 and LSM8. LSM2-LSM8 associates with PAT1 and XRN1. The LSm subunits form a seven-membered ring structure with a doughnut shape. 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
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 process	mRNA processing mRNA splicing rRNA processing tRNA processing
Cellular component	Cytoplasm Nucleus Spliceosome
Ligand	RNA-binding
Molecular function	Ribonucleoprotein
PTM	Phosphoprotein
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	cytoplasmic mRNA processing body assembly Inferred from mutant phenotype PubMed 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_component	U4/U6 x U5 tri-snRNP complex Inferred from direct assay PubMed 10377396 Ref.7. Source: SGD U6 snRNP Inferred from direct assay Ref.5 PubMed 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_function	U6 snRNA binding Inferred from direct assay Ref.5. Source: SGD
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct
DHH1	P39517	3	EBI-188,EBI-158
LSM1	P47017	5	EBI-188,EBI-174
LSM2	P38203	3	EBI-188,EBI-180
LSM3	P57743	3	EBI-188,EBI-10227
LSM6	Q06406	4	EBI-188,EBI-196
LSM7	P53905	3	EBI-188,EBI-141
LSM8	P47093	2	EBI-188,EBI-313
PAT1	P25644	6	EBI-188,EBI-204

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 187

187

U6 snRNA-associated Sm-like protein LSm4

PRO_0000125571

Amino acid modifications

Modified residue

181

Phosphoserine Ref.15

Experimental info

Sequence conflict

155

I → N in AAA58257. Ref.2

Sequences

Sequence

Length

Mass (Da)

Tools

P40070 [UniParc].

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

187

21,276

        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' referencesShow '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. Davis R.W. Nature 387:78-81(1997) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 204511 / S288c / AB972.
[4]	Saccharomyces Genome Database Submitted (DEC-2009) to the EMBL/GenBank/DDBJ databases 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, 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, 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]	"A multidimensional chromatography technology for in-depth phosphoproteome analysis." Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H. Mol. Cell. Proteomics 7:1389-1396(2008) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-181, MASS SPECTROMETRY.
+	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.
PIR	S50615.
RefSeq	NP_011037.3. NM_001179002.3.
3D structure databases
ProteinModelPortal	P40070.
SMR	P40070. Positions 1-85.
ModBase	Search...
Protein-protein interaction databases
DIP	DIP-848N.
IntAct	P40070. 65 interactions.
MINT	MINT-390432.
STRING	4932.YER112W.
Proteomic databases
PaxDb	P40070.
PeptideAtlas	P40070.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblFungi	YER112W; YER112W; YER112W.
GeneID	856848.
KEGG	sce:YER112W.
Organism-specific databases
CYGD	YER112w.
SGD	S000000914. LSM4.
Phylogenomic databases
eggNOG	COG1958.
GeneTree	ENSGT00610000086173.
KO	K12623.
OMA	IMDYAKE.
OrthoDB	EOG49S9H0.
Enzyme and pathway databases
BioCyc	YEAST:G3O-30276-MONOMER.
Gene expression databases
Genevestigator	P40070.
GermOnline	YER112W. Saccharomyces cerevisiae.
Family and domain databases
InterPro	IPR027141. LSm4/Sm_D1/D3. IPR010920. LSM_dom. IPR001163. Ribonucl_LSM. IPR006649. Ribonucl_LSM_euk/arc. [Graphical view]
PANTHER	PTHR23338. PTHR23338. 1 hit.
Pfam	PF01423. LSM. 1 hit. [Graphical view]
SMART	SM00651. Sm. 1 hit. [Graphical view]
SUPFAM	SSF50182. Sm_like_riboprot. 1 hit.
ProtoNet	Search...
Other
NextBio	983177.

Entry information

Entry name

LSM4_YEAST

Accession

Primary (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:	May 29, 2013
This is version 119 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Fungal Protein Annotation Program

Relevant documents

Yeast

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

Yeast chromosome V

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

SIMILARITY comments

Index of protein domains and families

Names·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents

Preferred order of sections

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Binary interactions

With

Entry

#Exp.

IntAct

Notes

Sequence annotation (Features)

Molecule processing

Amino acid modifications

Experimental info

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

Proteomic databases

Protocols and materials databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Enzyme and pathway databases

Gene expression databases

Family and domain databases

Other

Entry information

Relevant documents