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P57743 (LSM3_YEAST) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 119. 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 LSm3
Alternative name(s):
SmX4 protein
Gene names
Name:LSM3
Synonyms:SMX4, USS2
Ordered Locus Names:YLR438C-A
OrganismSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) [Reference proteome]
Taxonomic identifier559292 [NCBI]
Taxonomic lineageEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces

Protein attributes

Sequence length89 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 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. 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. Ref.1 Ref.9 Ref.10 Ref.11 Ref.12 Ref.15 Ref.19 Ref.20 Ref.21

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. 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. Ref.6 Ref.8 Ref.9 Ref.17 Ref.18 Ref.19 Ref.20 Ref.21

Subcellular location

Nucleus. Cytoplasm Ref.13.

Miscellaneous

Present with 7060 molecules/cell in log phase SD medium.

Sequence similarities

Belongs to the snRNP Sm proteins family.

Binary interactions

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 8989U6 snRNA-associated Sm-like protein LSm3
PRO_0000125563

Experimental info

Mutagenesis361H → A: Strongly reduces affinity for poly-U RNA ends. Ref.21
Mutagenesis381N → A: Strongly reduces affinity for poly-U RNA ends. Ref.21
Mutagenesis691R → A: Strongly reduces affinity for poly-U RNA ends. Ref.19 Ref.21

Secondary structure

.............. 89
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P57743 [UniParc].

Last modified January 11, 2001. Version 1.
Checksum: 787084EF6A5945B7

FASTA8910,030
        10         20         30         40         50         60 
METPLDLLKL NLDERVYIKL RGARTLVGTL QAFDSHCNIV LSDAVETIYQ LNNEELSESE 

        70         80 
RRCEMVFIRG DTVTLISTPS EDDDGAVEI 

« Hide

References

« Hide 'large scale' references
[1]"Sm and Sm-like proteins belong to a large family: identification of proteins of the U6 as well as the U1, U2, U4 and U5 snRNPs."
Seraphin B.
EMBO J. 14:2089-2099(1995) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], IDENTIFICATION, FUNCTION.
[2]"The nucleotide sequence of Saccharomyces cerevisiae chromosome XII."
Johnston M., Hillier L.W., Riles L., Albermann K., Andre B., Ansorge W., Benes V., Brueckner M., Delius H., Dubois E., Duesterhoeft A., Entian K.-D., Floeth M., Goffeau A., Hebling U., Heumann K., Heuss-Neitzel D., Hilbert H. expand/collapse author list , Hilger F., Kleine K., Koetter P., Louis E.J., Messenguy F., Mewes H.-W., Miosga T., Moestl D., Mueller-Auer S., Nentwich U., Obermaier B., Piravandi E., Pohl T.M., Portetelle D., Purnelle B., Rechmann S., Rieger M., Rinke M., Rose M., Scharfe M., Scherens B., Scholler P., Schwager C., Schwarz S., Underwood A.P., Urrestarazu L.A., Vandenbol M., Verhasselt P., Vierendeels F., Voet M., Volckaert G., Voss H., Wambutt R., Wedler E., Wedler H., Zimmermann F.K., Zollner A., Hani J., Hoheisel J.D.
Nature 387:87-90(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: ATCC 204508 / S288c.
[3]"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.
[4]"Gene MRP-L4, encoding mitochondrial ribosomal protein YmL4, is indispensable for proper non-respiratory cell functions in yeast."
Graack H.-R., Grohmann L., Kitakawa M., Goldschmidt-Reisin S.
Gene 152:107-112(1995) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-33.
Strain: 07173.
[5]"Functional analysis of the regulatory region adjacent to the cargB gene of Saccharomyces cerevisiae. Nucleotide sequence, gene fusion experiments and cis-dominant regulatory mutation analysis."
Degols G.
Eur. J. Biochem. 169:193-200(1987) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 34-89.
[6]"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.
[7]"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: IDENTIFICATION, CHARACTERIZATION.
[8]"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.
[9]"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.
[10]"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.
[11]"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.
[12]"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.
[13]"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].
[14]"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].
[15]"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.
[16]"N-terminal acetylome analyses and functional insights of the N-terminal acetyltransferase NatB."
Van Damme P., Lasa M., Polevoda B., Gazquez C., Elosegui-Artola A., Kim D.S., De Juan-Pardo E., Demeyer K., Hole K., Larrea E., Timmerman E., Prieto J., Arnesen T., Sherman F., Gevaert K., Aldabe R.
Proc. Natl. Acad. Sci. U.S.A. 109:12449-12454(2012) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[17]"Crystal structure of Lsm3 octamer from Saccharomyces cerevisiae: implications for Lsm ring organisation and recruitment."
Naidoo N., Harrop S.J., Sobti M., Haynes P.A., Szymczyna B.R., Williamson J.R., Curmi P.M., Mabbutt B.C.
J. Mol. Biol. 377:1357-1371(2008) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.50 ANGSTROMS), SUBUNIT.
[18]"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 LSM1-LSM7 COMPLEX, SUBUNIT, INTERACTION WITH PAT1.
[19]"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-69.
[20]"Lsm2 and Lsm3 bridge the interaction of the Lsm1-7 complex with Pat1 for decapping activation."
Wu D., Muhlrad D., Bowler M.W., Jiang S., Liu Z., Parker R., Song H.
Cell Res. 24:233-246(2014) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (3.15 ANGSTROMS), SUBUNIT, INTERACTION WITH PAT1, FUNCTION, RNA-BINDING.
[21]"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 LSM2-LSM8 COMPLEX, SUBUNIT, FUNCTION, RNA-BINDING, MUTAGENESIS OF HIS-36; ASN-38 AND ARG-69.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
Z30582 Genomic DNA. Translation: CAA83056.1.
X06790 Genomic DNA. Translation: CAA29948.1.
U21094 Genomic DNA. No translation available.
BK006945 Genomic DNA. Translation: DAA09739.1.
PIRS78568.
RefSeqNP_013543.3. NM_001184308.3.

3D structure databases

PDBe
RCSB-PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
3BW1X-ray2.50A/B1-89[»]
4C8QX-ray3.70C1-89[»]
4C92X-ray2.30C1-89[»]
4M75X-ray2.95C/J1-89[»]
4M77X-ray3.11C/J1-89[»]
4M78X-ray2.79C/J1-89[»]
4M7AX-ray2.78C/J1-89[»]
4M7DX-ray2.60C/J1-89[»]
4N0AX-ray3.15A/B/E/F1-89[»]
ProteinModelPortalP57743.
SMRP57743. Positions 1-79.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid31697. 212 interactions.
DIPDIP-2587N.
IntActP57743. 59 interactions.
MINTMINT-422505.

Proteomic databases

MaxQBP57743.
PaxDbP57743.
PeptideAtlasP57743.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblFungiYLR438C-A; YLR438C-A; YLR438C-A.
GeneID851159.
KEGGsce:YLR438C-A.

Organism-specific databases

CYGDYLR438c-a.
SGDS000006434. LSM3.

Phylogenomic databases

eggNOGNOG236203.
GeneTreeENSGT00390000013951.
HOGENOMHOG000223550.
KOK12622.
OMAERRCEMV.
OrthoDBEOG7PZSB0.

Enzyme and pathway databases

BioCycYEAST:G3O-32519-MONOMER.

Gene expression databases

GenevestigatorP57743.

Family and domain databases

InterProIPR010920. LSM_dom.
IPR001163. Ribonucl_LSM.
IPR006649. Ribonucl_LSM_euk/arc.
[Graphical view]
PfamPF01423. LSM. 1 hit.
[Graphical view]
SMARTSM00651. Sm. 1 hit.
[Graphical view]
SUPFAMSSF50182. SSF50182. 1 hit.
ProtoNetSearch...

Other

EvolutionaryTraceP57743.
NextBio967948.
PROP57743.

Entry information

Entry nameLSM3_YEAST
AccessionPrimary (citable) accession number: P57743
Secondary accession number(s): D6VZ73, Q05176, Q06759
Entry history
Integrated into UniProtKB/Swiss-Prot: January 11, 2001
Last sequence update: January 11, 2001
Last modified: July 9, 2014
This is version 119 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 XII

Yeast (Saccharomyces cerevisiae) chromosome XII: 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