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P53905 (LSM7_YEAST) Reviewed, UniProtKB/Swiss-Prot

Last modified June 11, 2014. Version 120. 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 LSm7
Gene names
Name:LSM7
Ordered Locus Names:YNL147W
ORF Names:N1202, N1780
OrganismSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) [Reference proteome]
Taxonomic identifier559292 [NCBI]
Taxonomic lineageEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces

Protein attributes

Sequence length115 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, spliceosomal 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. LSM7 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. LSM7, 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. Ref.8 Ref.9 Ref.12 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 spliceosome 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.10.

Miscellaneous

Present with 3070 molecules/cell in log phase SD medium.

Sequence similarities

Belongs to the snRNP Sm proteins family.

Sequence caution

The sequence CAA86879.1 differs from that shown. Reason: Erroneous gene model prediction.

The sequence CAA96030.1 differs from that shown. Reason: Erroneous gene model prediction.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 115115U6 snRNA-associated Sm-like protein LSm7
PRO_0000125581

Experimental info

Mutagenesis951R → A: Slightly reduces affinity for poly-U RNA ends. Ref.16 Ref.17

Secondary structure

............... 115
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P53905 [UniParc].

Last modified June 26, 2007. Version 2.
Checksum: EA1D019FC5D1B5C5

FASTA11513,006
        10         20         30         40         50         60 
MHQQHSKSEN KPQQQRKKFE GPKREAILDL AKYKDSKIRV KLMGGKLVIG VLKGYDQLMN 

        70         80         90        100        110 
LVLDDTVEYM SNPDDENNTE LISKNARKLG LTVIRGTILV SLSSAEGSDV LYMQK 

« Hide

References

« Hide 'large scale' references
[1]"A 43.5 kb segment of yeast chromosome XIV, which contains MFA2, MEP2, CAP/SRV2, NAM9, FKB1/FPR1/RBP1, MOM22 and CPT1, predicts an adenosine deaminase gene and 14 new open reading frames."
Mallet L., Bussereau F., Jacquet M.
Yeast 11:1195-1209(1995) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
Strain: ATCC 204508 / S288c.
[2]"The sequence of 36.8 kb from the left arm of chromosome XIV reveals 24 complete open reading frames: 18 correspond to new genes, one of which encodes a protein similar to the human myotonic dystrophy kinase."
Nasr F., Becam A.-M., Herbert C.J.
Yeast 12:169-175(1996) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
Strain: ATCC 96604 / S288c / FY1679.
[3]"The nucleotide sequence of Saccharomyces cerevisiae chromosome XIV and its evolutionary implications."
Philippsen P., Kleine K., Poehlmann R., Duesterhoeft A., Hamberg K., Hegemann J.H., Obermaier B., Urrestarazu L.A., Aert R., Albermann K., Altmann R., Andre B., Baladron V., Ballesta J.P.G., Becam A.-M., Beinhauer J.D., Boskovic J., Buitrago M.J. expand/collapse author list , Bussereau F., Coster F., Crouzet M., D'Angelo M., Dal Pero F., De Antoni A., del Rey F., Doignon F., Domdey H., Dubois E., Fiedler T.A., Fleig U., Floeth M., Fritz C., Gaillardin C., Garcia-Cantalejo J.M., Glansdorff N., Goffeau A., Gueldener U., Herbert C.J., Heumann K., Heuss-Neitzel D., Hilbert H., Hinni K., Iraqui Houssaini I., Jacquet M., Jimenez A., Jonniaux J.-L., Karpfinger-Hartl L., Lanfranchi G., Lepingle A., Levesque H., Lyck R., Maftahi M., Mallet L., Maurer C.T.C., Messenguy F., Mewes H.-W., Moestl D., Nasr F., Nicaud J.-M., Niedenthal R.K., Pandolfo D., Pierard A., Piravandi E., Planta R.J., Pohl T.M., Purnelle B., Rebischung C., Remacha M.A., Revuelta J.L., Rinke M., Saiz J.E., Sartorello F., Scherens B., Sen-Gupta M., Soler-Mira A., Urbanus J.H.M., Valle G., Van Dyck L., Verhasselt P., Vierendeels F., Vissers S., Voet M., Volckaert G., Wach A., Wambutt R., Wedler H., Zollner A., Hani J.
Nature 387:93-98(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]"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].
[11]"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].
[12]"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.
[13]"A large-scale full-length cDNA analysis to explore the budding yeast transcriptome."
Miura F., Kawaguchi N., Sese J., Toyoda A., Hattori M., Morishita S., Ito T.
Proc. Natl. Acad. Sci. U.S.A. 103:17846-17851(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION OF INTRON.
[14]"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].
[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 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-95.
[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 LSM2-LSM8 COMPLEX, SUBUNIT, FUNCTION, RNA-BINDING, MUTAGENESIS OF ARG-95.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
Z46843 Genomic DNA. Translation: CAA86879.1. Sequence problems.
Z71423 Genomic DNA. Translation: CAA96030.1. Sequence problems.
BK006947 Genomic DNA. Translation: DAA10401.1.
PIRS55137.
RefSeqNP_014252.2. NM_001182985.1.

3D structure databases

PDBe
RCSB-PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
4C8QX-ray3.70G1-115[»]
4C92X-ray2.30G1-115[»]
4M75X-ray2.95F/M1-115[»]
4M77X-ray3.11F/M1-115[»]
4M78X-ray2.79F/M1-115[»]
4M7AX-ray2.78F/M1-115[»]
4M7DX-ray2.60F/M1-115[»]
ProteinModelPortalP53905.
SMRP53905. Positions 26-110.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid35681. 363 interactions.
DIPDIP-1419N.
IntActP53905. 26 interactions.
MINTMINT-398907.
STRING4932.YNL147W.

Proteomic databases

MaxQBP53905.
PaxDbP53905.
PeptideAtlasP53905.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblFungiYNL147W; YNL147W; YNL147W.
GeneID855575.
KEGGsce:YNL147W.

Organism-specific databases

CYGDYNL147w.
SGDS000005091. LSM7.

Phylogenomic databases

eggNOGNOG276686.
GeneTreeENSGT00510000047872.
HOGENOMHOG000223548.
KOK12626.
OMAKKFEGPK.
OrthoDBEOG7PZSB0.

Enzyme and pathway databases

BioCycYEAST:G3O-33165-MONOMER.

Gene expression databases

GenevestigatorP53905.

Family and domain databases

InterProIPR010920. LSM_dom.
IPR001163. Ribonucl_LSM.
IPR006649. Ribonucl_LSM_euk/arc.
IPR017132. U6_snRNA_Lsm7.
[Graphical view]
PfamPF01423. LSM. 1 hit.
[Graphical view]
PIRSFPIRSF037188. U6_snRNA_Lsm7. 1 hit.
SMARTSM00651. Sm. 1 hit.
[Graphical view]
SUPFAMSSF50182. SSF50182. 1 hit.
ProtoNetSearch...

Other

NextBio979694.
PROP53905.

Entry information

Entry nameLSM7_YEAST
AccessionPrimary (citable) accession number: P53905
Secondary accession number(s): D6W135
Entry history
Integrated into UniProtKB/Swiss-Prot: October 1, 1996
Last sequence update: June 26, 2007
Last modified: June 11, 2014
This is version 120 of the entry and version 2 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Relevant documents

Yeast chromosome XIV

Yeast (Saccharomyces cerevisiae) chromosome XIV: 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