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P57743

- LSM3_YEAST

UniProt

P57743 - LSM3_YEAST

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Protein

U6 snRNA-associated Sm-like protein LSm3

Gene

LSM3

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 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.9 Publications

GO - Molecular functioni

  1. RNA binding Source: SGD

GO - Biological processi

  1. mRNA splicing, via spliceosome Source: SGD
  2. nuclear-transcribed mRNA catabolic process Source: SGD
  3. rRNA processing Source: UniProtKB-KW
  4. 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-32519-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
U6 snRNA-associated Sm-like protein LSm3
Alternative name(s):
SmX4 protein
Gene namesi
Name:LSM3
Synonyms:SMX4, USS2
Ordered Locus Names:YLR438C-A
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
ProteomesiUP000002311: Chromosome XII

Organism-specific databases

CYGDiYLR438c-a.
SGDiS000006434. LSM3.

Subcellular locationi

Nucleus 1 Publication. Cytoplasm 1 Publication

GO - Cellular componenti

  1. cytoplasm Source: UniProtKB-KW
  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
Mutagenesisi36 – 361H → A: Strongly reduces affinity for poly-U RNA ends. 1 Publication
Mutagenesisi38 – 381N → A: Strongly reduces affinity for poly-U RNA ends. 1 Publication
Mutagenesisi69 – 691R → A: Strongly reduces affinity for poly-U RNA ends. 2 Publications

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 8989U6 snRNA-associated Sm-like protein LSm3PRO_0000125563Add
BLAST

Proteomic databases

MaxQBiP57743.
PaxDbiP57743.
PeptideAtlasiP57743.

Expressioni

Gene expression databases

GenevestigatoriP57743.

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. 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 DIB1.8 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
LSM1P470175EBI-10227,EBI-174
LSM2P382034EBI-10227,EBI-180
LSM4P400703EBI-10227,EBI-188

Protein-protein interaction databases

BioGridi31697. 212 interactions.
DIPiDIP-2587N.
IntActiP57743. 59 interactions.
MINTiMINT-422505.

Structurei

Secondary structure

1
89
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi4 – 96Combined sources
Turni10 – 134Combined sources
Beta strandi14 – 207Combined sources
Turni21 – 233Combined sources
Beta strandi24 – 3310Combined sources
Beta strandi39 – 5214Combined sources
Beta strandi55 – 6814Combined sources
Helixi70 – 723Combined sources
Beta strandi73 – 775Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
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[»]
ProteinModelPortaliP57743.
SMRiP57743. Positions 1-79.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP57743.

Family & Domainsi

Sequence similaritiesi

Belongs to the snRNP Sm proteins family.Curated

Phylogenomic databases

eggNOGiNOG236203.
GeneTreeiENSGT00390000013951.
HOGENOMiHOG000223550.
InParanoidiP57743.
KOiK12622.
OMAiERRCEMV.
OrthoDBiEOG7PZSB0.

Family and domain databases

InterProiIPR010920. LSM_dom.
IPR001163. Ribonucl_LSM.
IPR006649. Ribonucl_LSM_euk/arc.
[Graphical view]
PfamiPF01423. LSM. 1 hit.
[Graphical view]
SMARTiSM00651. Sm. 1 hit.
[Graphical view]
SUPFAMiSSF50182. SSF50182. 1 hit.

Sequencei

Sequence statusi: Complete.

P57743-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
METPLDLLKL NLDERVYIKL RGARTLVGTL QAFDSHCNIV LSDAVETIYQ
60 70 80
LNNEELSESE RRCEMVFIRG DTVTLISTPS EDDDGAVEI
Length:89
Mass (Da):10,030
Last modified:January 11, 2001 - v1
Checksum:i787084EF6A5945B7
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z30582 Genomic DNA. Translation: CAA83056.1.
X06790 Genomic DNA. Translation: CAA29948.1.
U21094 Genomic DNA. No translation available.
BK006945 Genomic DNA. Translation: DAA09739.1.
PIRiS78568.
RefSeqiNP_013543.3. NM_001184308.3.

Genome annotation databases

EnsemblFungiiYLR438C-A; YLR438C-A; YLR438C-A.
GeneIDi851159.
KEGGisce:YLR438C-A.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z30582 Genomic DNA. Translation: CAA83056.1 .
X06790 Genomic DNA. Translation: CAA29948.1 .
U21094 Genomic DNA. No translation available.
BK006945 Genomic DNA. Translation: DAA09739.1 .
PIRi S78568.
RefSeqi NP_013543.3. NM_001184308.3.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
3BW1 X-ray 2.50 A/B 1-89 [» ]
4C8Q X-ray 3.70 C 1-89 [» ]
4C92 X-ray 2.30 C 1-89 [» ]
4M75 X-ray 2.95 C/J 1-89 [» ]
4M77 X-ray 3.11 C/J 1-89 [» ]
4M78 X-ray 2.79 C/J 1-89 [» ]
4M7A X-ray 2.78 C/J 1-89 [» ]
4M7D X-ray 2.60 C/J 1-89 [» ]
4N0A X-ray 3.15 A/B/E/F 1-89 [» ]
ProteinModelPortali P57743.
SMRi P57743. Positions 1-79.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

BioGridi 31697. 212 interactions.
DIPi DIP-2587N.
IntActi P57743. 59 interactions.
MINTi MINT-422505.

Proteomic databases

MaxQBi P57743.
PaxDbi P57743.
PeptideAtlasi P57743.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblFungii YLR438C-A ; YLR438C-A ; YLR438C-A .
GeneIDi 851159.
KEGGi sce:YLR438C-A.

Organism-specific databases

CYGDi YLR438c-a.
SGDi S000006434. LSM3.

Phylogenomic databases

eggNOGi NOG236203.
GeneTreei ENSGT00390000013951.
HOGENOMi HOG000223550.
InParanoidi P57743.
KOi K12622.
OMAi ERRCEMV.
OrthoDBi EOG7PZSB0.

Enzyme and pathway databases

BioCyci YEAST:G3O-32519-MONOMER.

Miscellaneous databases

EvolutionaryTracei P57743.
NextBioi 967948.
PROi P57743.

Gene expression databases

Genevestigatori P57743.

Family and domain databases

InterProi IPR010920. LSM_dom.
IPR001163. Ribonucl_LSM.
IPR006649. Ribonucl_LSM_euk/arc.
[Graphical view ]
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. "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.
    , 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. 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. Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
  14. 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. 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.

Entry informationi

Entry nameiLSM3_YEAST
AccessioniPrimary (citable) accession number: P57743
Secondary accession number(s): D6VZ73, Q05176, Q06759
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 11, 2001
Last sequence update: January 11, 2001
Last modified: October 29, 2014
This is version 121 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 7060 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 XII
    Yeast (Saccharomyces cerevisiae) chromosome XII: entries and gene names

External Data

Dasty 3