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Protein

U6 snRNA-associated Sm-like protein LSm7

Gene

LSM7

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed-Annotation score: 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, 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.5 Publications

GO - Molecular functioni

  1. RNA binding Source: SGD

GO - Biological processi

  1. maturation of SSU-rRNA Source: SGD
  2. mRNA splicing, via spliceosome Source: SGD
  3. nuclear-transcribed mRNA catabolic process Source: SGD
  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-33165-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
U6 snRNA-associated Sm-like protein LSm7
Gene namesi
Name:LSM7
Ordered Locus Names:YNL147W
ORF Names:N1202, N1780
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
ProteomesiUP000002311 Componenti: Chromosome XIV

Organism-specific databases

CYGDiYNL147w.
EuPathDBiFungiDB:YNL147W.
SGDiS000005091. LSM7.

Subcellular locationi

  1. Nucleus 1 Publication
  2. Cytoplasm 1 Publication

GO - Cellular componenti

  1. cytoplasm Source: SGD
  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
Mutagenesisi95 – 951R → A: Slightly reduces affinity for poly-U RNA ends. 2 Publications

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 115115U6 snRNA-associated Sm-like protein LSm7PRO_0000125581Add
BLAST

Proteomic databases

MaxQBiP53905.
PaxDbiP53905.
PeptideAtlasiP53905.

Expressioni

Gene expression databases

GenevestigatoriP53905.

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. 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 DIB1.6 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
DHH1P395173EBI-141,EBI-158
LSM2P382033EBI-141,EBI-180
LSM4P400703EBI-141,EBI-188
PAT1P256443EBI-141,EBI-204
PRP24P499603EBI-141,EBI-212
PRP4P200533EBI-141,EBI-219

Protein-protein interaction databases

BioGridi35681. 364 interactions.
DIPiDIP-1419N.
IntActiP53905. 26 interactions.
MINTiMINT-398907.
STRINGi4932.YNL147W.

Structurei

Secondary structure

1
115
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi30 – 334Combined sources
Beta strandi36 – 427Combined sources
Turni43 – 453Combined sources
Beta strandi47 – 559Combined sources
Beta strandi61 – 699Combined sources
Beta strandi86 – 949Combined sources
Helixi96 – 983Combined sources
Beta strandi99 – 1057Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
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[»]
ProteinModelPortaliP53905.
SMRiP53905. Positions 26-110.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the snRNP Sm proteins family.Curated

Phylogenomic databases

eggNOGiNOG276686.
GeneTreeiENSGT00510000047872.
HOGENOMiHOG000223548.
InParanoidiP53905.
KOiK12626.
OMAiKKFEGPK.
OrthoDBiEOG7PZSB0.

Family and domain databases

InterProiIPR017132. Lsm7/snRNP-G.
IPR010920. LSM_dom.
IPR001163. Ribonucl_LSM.
IPR006649. Ribonucl_LSM_euk/arc.
[Graphical view]
PfamiPF01423. LSM. 1 hit.
[Graphical view]
PIRSFiPIRSF037188. U6_snRNA_Lsm7. 1 hit.
SMARTiSM00651. Sm. 1 hit.
[Graphical view]
SUPFAMiSSF50182. SSF50182. 1 hit.

Sequencei

Sequence statusi: Complete.

P53905-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MHQQHSKSEN KPQQQRKKFE GPKREAILDL AKYKDSKIRV KLMGGKLVIG
60 70 80 90 100
VLKGYDQLMN LVLDDTVEYM SNPDDENNTE LISKNARKLG LTVIRGTILV
110
SLSSAEGSDV LYMQK
Length:115
Mass (Da):13,006
Last modified:June 26, 2007 - v2
Checksum:iEA1D019FC5D1B5C5
GO

Sequence cautioni

The sequence CAA86879.1 differs from that shown. Reason: Erroneous gene model prediction. Curated
The sequence CAA96030.1 differs from that shown. Reason: Erroneous gene model prediction. Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z46843 Genomic DNA. Translation: CAA86879.1. Sequence problems.
Z71423 Genomic DNA. Translation: CAA96030.1. Sequence problems.
BK006947 Genomic DNA. Translation: DAA10401.1.
PIRiS55137.
RefSeqiNP_014252.2. NM_001182985.1.

Genome annotation databases

EnsemblFungiiYNL147W; YNL147W; YNL147W.
GeneIDi855575.
KEGGisce:YNL147W.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z46843 Genomic DNA. Translation: CAA86879.1. Sequence problems.
Z71423 Genomic DNA. Translation: CAA96030.1. Sequence problems.
BK006947 Genomic DNA. Translation: DAA10401.1.
PIRiS55137.
RefSeqiNP_014252.2. NM_001182985.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
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[»]
ProteinModelPortaliP53905.
SMRiP53905. Positions 26-110.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi35681. 364 interactions.
DIPiDIP-1419N.
IntActiP53905. 26 interactions.
MINTiMINT-398907.
STRINGi4932.YNL147W.

Proteomic databases

MaxQBiP53905.
PaxDbiP53905.
PeptideAtlasiP53905.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYNL147W; YNL147W; YNL147W.
GeneIDi855575.
KEGGisce:YNL147W.

Organism-specific databases

CYGDiYNL147w.
EuPathDBiFungiDB:YNL147W.
SGDiS000005091. LSM7.

Phylogenomic databases

eggNOGiNOG276686.
GeneTreeiENSGT00510000047872.
HOGENOMiHOG000223548.
InParanoidiP53905.
KOiK12626.
OMAiKKFEGPK.
OrthoDBiEOG7PZSB0.

Enzyme and pathway databases

BioCyciYEAST:G3O-33165-MONOMER.

Miscellaneous databases

NextBioi979694.
PROiP53905.

Gene expression databases

GenevestigatoriP53905.

Family and domain databases

InterProiIPR017132. Lsm7/snRNP-G.
IPR010920. LSM_dom.
IPR001163. Ribonucl_LSM.
IPR006649. Ribonucl_LSM_euk/arc.
[Graphical view]
PfamiPF01423. LSM. 1 hit.
[Graphical view]
PIRSFiPIRSF037188. U6_snRNA_Lsm7. 1 hit.
SMARTiSM00651. Sm. 1 hit.
[Graphical view]
SUPFAMiSSF50182. SSF50182. 1 hit.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  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.
    , 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. 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. Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
  11. 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. 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.

Entry informationi

Entry nameiLSM7_YEAST
AccessioniPrimary (citable) accession number: P53905
Secondary accession number(s): D6W135
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 1, 1996
Last sequence update: June 26, 2007
Last modified: April 29, 2015
This is version 127 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Miscellaneous

Present with 3070 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 XIV
    Yeast (Saccharomyces cerevisiae) chromosome XIV: entries and gene names

External Data

Dasty 3

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.