Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.

Q06406

- LSM6_YEAST

UniProt

Q06406 - LSM6_YEAST

(max 400 entries)x

Your basket is currently empty.

Select item(s) and click on "Add to basket" to create your own collection here
(400 entries max)

Protein

U6 snRNA-associated Sm-like protein LSm6

Gene

LSM6

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, facilitating the efficient association of RNA processing factors with their substrates. Component of the cytoplasmic LSM1-LSM7 complex, which is involved in mRNA degradation by activating the decapping step in the 5'-to-3' mRNA decay pathway. In association with PAT1, LSM1-LSM7 binds directly to RNAs near the 3'-end and prefers oligoadenylated RNAs over polyadenylated RNAs. 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 di-snRNP, spliceosomal U4/U6.U5 tri-snRNP, and free U6 snRNP). It binds directly to the 3'-terminal U-tract of U6 snRNA and plays a role in the biogenesis and stability of the U6 snRNP and U4/U6 snRNP complexes. LSM2-LSM8 probably also is involved degradation of nuclear pre-mRNA by targeting them for decapping, and in processing of pre-tRNAs, pre-rRNAs and U3 snoRNA. Component of a nucleolar LSM2-LSM7 complex, which associates with the precursor of the RNA component of RNase P (pre-P RNA) and with the small nucleolar RNA (snoRNA) snR5. It may play a role in the maturation of a subset of nucleolus-associated small RNAs.6 Publications

GO - Molecular functioni

  1. RNA binding Source: UniProtKB-KW

GO - Biological processi

  1. maturation of SSU-rRNA Source: SGD
  2. mRNA splicing, via spliceosome Source: SGD
  3. 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-29927-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
U6 snRNA-associated Sm-like protein LSm6
Gene namesi
Name:LSM6
Ordered Locus Names:YDR378C
ORF Names:D9481.18
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
ProteomesiUP000002311: Chromosome IV

Organism-specific databases

SGDiS000002786. LSM6.

Subcellular locationi

Cytoplasm. Nucleusnucleolus
Note: LSM1 and LSM8 act competitively with respect to the localization of LSM1-LSM7 to the cytoplasm and LSM2-LSM8 to the nucleus. LSm proteins shift to the cytoplasm under conditions of stress.

GO - Cellular componenti

  1. cytoplasmic mRNA processing body 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
Mutagenesisi74 – 741R → A: Reduces affinity for poly-U RNA ends. 2 Publications

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 8686U6 snRNA-associated Sm-like protein LSm6PRO_0000125578Add
BLAST

Proteomic databases

MaxQBiQ06406.
PaxDbiQ06406.
PeptideAtlasiQ06406.

Expressioni

Gene expression databases

GenevestigatoriQ06406.

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. LSM1-LSM7 associates also with PAT1 and XRN1. 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. Component of a LSM2-LSM7 complex, which consists of at least LSM2, LSM3, LSM4, LSM5, LSM6 and LSM7. It is not known whether another protein replaces the missing LSm to form a novel heptameric complex. 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 DIB1.7 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
LSM1P470174EBI-196,EBI-174
LSM2P382034EBI-196,EBI-180
LSM4P400705EBI-196,EBI-188
LSM5P400893EBI-196,EBI-10236
LSM8P470934EBI-196,EBI-313

Protein-protein interaction databases

BioGridi32437. 359 interactions.
DIPiDIP-1418N.
IntActiQ06406. 34 interactions.
MINTiMINT-403097.
STRINGi4932.YDR378C.

Structurei

Secondary structure

1
86
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi11 – 177Combined sources
Turni18 – 214Combined sources
Beta strandi22 – 287Combined sources
Beta strandi31 – 4111Combined sources
Beta strandi47 – 5711Combined sources
Turni59 – 613Combined sources
Beta strandi65 – 695Combined sources
Beta strandi71 – 733Combined sources
Helixi75 – 773Combined sources
Beta strandi78 – 836Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
4C8QX-ray3.70F1-86[»]
4C92X-ray2.30F1-86[»]
4M75X-ray2.95D/K1-86[»]
4M77X-ray3.11D/K1-86[»]
4M78X-ray2.79D/K1-86[»]
4M7AX-ray2.78D/K1-86[»]
4M7DX-ray2.60D/K1-86[»]
ProteinModelPortaliQ06406.
SMRiQ06406. Positions 10-86.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Phylogenomic databases

eggNOGiCOG1958.
HOGENOMiHOG000223542.
InParanoidiQ06406.
KOiK12625.
OMAiATEHYES.
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.

Q06406-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MSGKASTEGS VTTEFLSDII GKTVNVKLAS GLLYSGRLES IDGFMNVALS
60 70 80
SATEHYESNN NKLLNKFNSD VFLRGTQVMY ISEQKI
Length:86
Mass (Da):9,398
Last modified:May 20, 2008 - v2
Checksum:i74FE40A4509CEF33
GO

Sequence cautioni

The sequence AAB64814.1 differs from that shown. Reason: Erroneous initiation. Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U28373 Genomic DNA. Translation: AAB64814.1. Different initiation.
BK006938 Genomic DNA. Translation: DAA12220.1.
PIRiS61173.
RefSeqiNP_010666.2. NM_001180686.1.

Genome annotation databases

EnsemblFungiiYDR378C; YDR378C; YDR378C.
GeneIDi851984.
KEGGisce:YDR378C.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U28373 Genomic DNA. Translation: AAB64814.1 . Different initiation.
BK006938 Genomic DNA. Translation: DAA12220.1 .
PIRi S61173.
RefSeqi NP_010666.2. NM_001180686.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
4C8Q X-ray 3.70 F 1-86 [» ]
4C92 X-ray 2.30 F 1-86 [» ]
4M75 X-ray 2.95 D/K 1-86 [» ]
4M77 X-ray 3.11 D/K 1-86 [» ]
4M78 X-ray 2.79 D/K 1-86 [» ]
4M7A X-ray 2.78 D/K 1-86 [» ]
4M7D X-ray 2.60 D/K 1-86 [» ]
ProteinModelPortali Q06406.
SMRi Q06406. Positions 10-86.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

BioGridi 32437. 359 interactions.
DIPi DIP-1418N.
IntActi Q06406. 34 interactions.
MINTi MINT-403097.
STRINGi 4932.YDR378C.

Proteomic databases

MaxQBi Q06406.
PaxDbi Q06406.
PeptideAtlasi Q06406.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblFungii YDR378C ; YDR378C ; YDR378C .
GeneIDi 851984.
KEGGi sce:YDR378C.

Organism-specific databases

SGDi S000002786. LSM6.

Phylogenomic databases

eggNOGi COG1958.
HOGENOMi HOG000223542.
InParanoidi Q06406.
KOi K12625.
OMAi ATEHYES.
OrthoDBi EOG7PZSB0.

Enzyme and pathway databases

BioCyci YEAST:G3O-29927-MONOMER.

Miscellaneous databases

NextBioi 970136.
PROi Q06406.

Gene expression databases

Genevestigatori Q06406.

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. "The nucleotide sequence of Saccharomyces cerevisiae chromosome IV."
    Jacq C., Alt-Moerbe J., Andre B., Arnold W., Bahr A., Ballesta J.P.G., Bargues M., Baron L., Becker A., Biteau N., Bloecker H., Blugeon C., Boskovic J., Brandt P., Brueckner M., Buitrago M.J., Coster F., Delaveau T.
    , del Rey F., Dujon B., Eide L.G., Garcia-Cantalejo J.M., Goffeau A., Gomez-Peris A., Granotier C., Hanemann V., Hankeln T., Hoheisel J.D., Jaeger W., Jimenez A., Jonniaux J.-L., Kraemer C., Kuester H., Laamanen P., Legros Y., Louis E.J., Moeller-Rieker S., Monnet A., Moro M., Mueller-Auer S., Nussbaumer B., Paricio N., Paulin L., Perea J., Perez-Alonso M., Perez-Ortin J.E., Pohl T.M., Prydz H., Purnelle B., Rasmussen S.W., Remacha M.A., Revuelta J.L., Rieger M., Salom D., Saluz H.P., Saiz J.E., Saren A.-M., Schaefer M., Scharfe M., Schmidt E.R., Schneider C., Scholler P., Schwarz S., Soler-Mira A., Urrestarazu L.A., Verhasselt P., Vissers S., Voet M., Volckaert G., Wagner G., Wambutt R., Wedler E., Wedler H., Woelfl S., Harris D.E., Bowman S., Brown D., Churcher C.M., Connor R., Dedman K., Gentles S., Hamlin N., Hunt S., Jones L., McDonald S., Murphy L.D., Niblett D., Odell C., Oliver K., Rajandream M.A., Richards C., Shore L., Walsh S.V., Barrell B.G., Dietrich F.S., Mulligan J.T., Allen E., Araujo R., Aviles E., Berno A., Carpenter J., Chen E., Cherry J.M., Chung E., Duncan M., Hunicke-Smith S., Hyman R.W., Komp C., Lashkari D., Lew H., Lin D., Mosedale D., Nakahara K., Namath A., Oefner P., Oh C., Petel F.X., Roberts D., Schramm S., Schroeder M., Shogren T., Shroff N., Winant A., Yelton M.A., Botstein D., Davis R.W., Johnston M., Andrews S., Brinkman R., Cooper J., Ding H., Du Z., Favello A., Fulton L., Gattung S., Greco T., Hallsworth K., Hawkins J., Hillier L.W., Jier M., Johnson D., Johnston L., Kirsten J., Kucaba T., Langston Y., Latreille P., Le T., Mardis E., Menezes S., Miller N., Nhan M., Pauley A., Peluso D., Rifkin L., Riles L., Taich A., Trevaskis E., Vignati D., Wilcox L., Wohldman P., Vaudin M., Wilson R., Waterston R., Albermann K., Hani J., Heumann K., Kleine K., Mewes H.-W., Zollner A., Zaccaria P.
    Nature 387:75-78(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 204508 / S288c.
  2. Cited for: GENOME REANNOTATION.
    Strain: ATCC 204508 / S288c.
  3. "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.
  4. "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.
  5. "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.
  6. "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, IDENTIFICATION OF PROBABLE INTITIATION SITE.
  7. "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 LSM1-LSM7 COMPLEX.
  8. "An Lsm2-Lsm7 complex in Saccharomyces cerevisiae associates with the small nucleolar RNA snR5."
    Fernandez C.F., Pannone B.K., Chen X., Fuchs G., Wolin S.L.
    Mol. Biol. Cell 15:2842-2852(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION IN THE LSM2-LSM7 COMPLEX, SUBCELLULAR LOCATION.
  9. "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.
  10. "Mapping of transcription start sites in Saccharomyces cerevisiae using 5' SAGE."
    Zhang Z., Dietrich F.S.
    Nucleic Acids Res. 33:2838-2851(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION OF PROBABLE INITIATION SITE.
  11. "Requirements for nuclear localization of the Lsm2-8p complex and competition between nuclear and cytoplasmic Lsm complexes."
    Spiller M.P., Reijns M.A.M., Beggs J.D.
    J. Cell Sci. 120:4310-4320(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: SUBCELLULAR LOCATION.
  12. "The decapping activator Lsm1p-7p-Pat1p complex has the intrinsic ability to distinguish between oligoadenylated and polyadenylated RNAs."
    Chowdhury A., Mukhopadhyay J., Tharun S.
    RNA 13:998-1016(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION OF THE LSM1-LSM7-PAT1 COMPLEX.
  13. "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.
  14. "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-74.
  15. "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-74.

Entry informationi

Entry nameiLSM6_YEAST
AccessioniPrimary (citable) accession number: Q06406
Secondary accession number(s): D6VT10
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 11, 2001
Last sequence update: May 20, 2008
Last modified: November 26, 2014
This is version 128 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

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

External Data

Dasty 3