LSM6_YEAST
ID LSM6_YEAST Reviewed; 86 AA.
AC Q06406; D6VT10;
DT 11-JAN-2001, integrated into UniProtKB/Swiss-Prot.
DT 20-MAY-2008, sequence version 2.
DT 03-AUG-2022, entry version 183.
DE RecName: Full=U6 snRNA-associated Sm-like protein LSm6;
GN Name=LSM6; OrderedLocusNames=YDR378C; ORFNames=D9481.18;
OS Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
OC Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes;
OC Saccharomycetales; Saccharomycetaceae; Saccharomyces.
OX NCBI_TaxID=559292;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=9169867;
RA Jacq C., Alt-Moerbe J., Andre B., Arnold W., Bahr A., Ballesta J.P.G.,
RA Bargues M., Baron L., Becker A., Biteau N., Bloecker H., Blugeon C.,
RA Boskovic J., Brandt P., Brueckner M., Buitrago M.J., Coster F.,
RA Delaveau T., del Rey F., Dujon B., Eide L.G., Garcia-Cantalejo J.M.,
RA Goffeau A., Gomez-Peris A., Granotier C., Hanemann V., Hankeln T.,
RA Hoheisel J.D., Jaeger W., Jimenez A., Jonniaux J.-L., Kraemer C.,
RA Kuester H., Laamanen P., Legros Y., Louis E.J., Moeller-Rieker S.,
RA Monnet A., Moro M., Mueller-Auer S., Nussbaumer B., Paricio N., Paulin L.,
RA Perea J., Perez-Alonso M., Perez-Ortin J.E., Pohl T.M., Prydz H.,
RA Purnelle B., Rasmussen S.W., Remacha M.A., Revuelta J.L., Rieger M.,
RA Salom D., Saluz H.P., Saiz J.E., Saren A.-M., Schaefer M., Scharfe M.,
RA Schmidt E.R., Schneider C., Scholler P., Schwarz S., Soler-Mira A.,
RA Urrestarazu L.A., Verhasselt P., Vissers S., Voet M., Volckaert G.,
RA Wagner G., Wambutt R., Wedler E., Wedler H., Woelfl S., Harris D.E.,
RA Bowman S., Brown D., Churcher C.M., Connor R., Dedman K., Gentles S.,
RA Hamlin N., Hunt S., Jones L., McDonald S., Murphy L.D., Niblett D.,
RA Odell C., Oliver K., Rajandream M.A., Richards C., Shore L., Walsh S.V.,
RA Barrell B.G., Dietrich F.S., Mulligan J.T., Allen E., Araujo R., Aviles E.,
RA Berno A., Carpenter J., Chen E., Cherry J.M., Chung E., Duncan M.,
RA Hunicke-Smith S., Hyman R.W., Komp C., Lashkari D., Lew H., Lin D.,
RA Mosedale D., Nakahara K., Namath A., Oefner P., Oh C., Petel F.X.,
RA Roberts D., Schramm S., Schroeder M., Shogren T., Shroff N., Winant A.,
RA Yelton M.A., Botstein D., Davis R.W., Johnston M., Andrews S., Brinkman R.,
RA Cooper J., Ding H., Du Z., Favello A., Fulton L., Gattung S., Greco T.,
RA Hallsworth K., Hawkins J., Hillier L.W., Jier M., Johnson D., Johnston L.,
RA Kirsten J., Kucaba T., Langston Y., Latreille P., Le T., Mardis E.,
RA Menezes S., Miller N., Nhan M., Pauley A., Peluso D., Rifkin L., Riles L.,
RA Taich A., Trevaskis E., Vignati D., Wilcox L., Wohldman P., Vaudin M.,
RA Wilson R., Waterston R., Albermann K., Hani J., Heumann K., Kleine K.,
RA Mewes H.-W., Zollner A., Zaccaria P.;
RT "The nucleotide sequence of Saccharomyces cerevisiae chromosome IV.";
RL Nature 387:75-78(1997).
RN [2]
RP GENOME REANNOTATION.
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=24374639; DOI=10.1534/g3.113.008995;
RA Engel S.R., Dietrich F.S., Fisk D.G., Binkley G., Balakrishnan R.,
RA Costanzo M.C., Dwight S.S., Hitz B.C., Karra K., Nash R.S., Weng S.,
RA Wong E.D., Lloyd P., Skrzypek M.S., Miyasato S.R., Simison M., Cherry J.M.;
RT "The reference genome sequence of Saccharomyces cerevisiae: Then and now.";
RL G3 (Bethesda) 4:389-398(2014).
RN [3]
RP IDENTIFICATION IN THE LSM2-LSM8 COMPLEX, AND ASSOCIATION WITH PRE-P RNA.
RX PubMed=10369684; DOI=10.1093/emboj/18.12.3451;
RA Salgado-Garrido J., Bragado-Nilsson E., Kandels-Lewis S., Seraphin B.;
RT "Sm and Sm-like proteins assemble in two related complexes of deep
RT evolutionary origin.";
RL EMBO J. 18:3451-3462(1999).
RN [4]
RP CHARACTERIZATION.
RX PubMed=10428970; DOI=10.1093/emboj/18.15.4321;
RA Mayes A.E., Verdone L., Legrain P., Beggs J.D.;
RT "Characterization of Sm-like proteins in yeast and their association with
RT U6 snRNA.";
RL EMBO J. 18:4321-4331(1999).
RN [5]
RP SUBUNIT, IDENTIFICATION IN THE U4/U5/U6 TRI-SNRNP COMPLEX, AND
RP IDENTIFICATION BY MASS SPECTROMETRY.
RX PubMed=10449419; DOI=10.1093/emboj/18.16.4535;
RA Gottschalk A., Neubauer G., Banroques J., Mann M., Luehrmann R.,
RA Fabrizio P.;
RT "Identification by mass spectrometry and functional analysis of novel
RT proteins of the yeast [U4/U6.U5] tri-snRNP.";
RL EMBO J. 18:4535-4548(1999).
RN [6]
RP IDENTIFICATION IN THE LSM1-LSM7 COMPLEX, ASSOCIATION OF THE LSM1-LSM7
RP COMPLEX WITH PAT1 AND XRN1, FUNCTION OF THE LSM1-LSM7 COMPLEX,
RP IDENTIFICATION IN THE LSM2-LSM8 COMPLEX, ASSOCIATION OF THE LSM2-LSM8
RP COMPLEX WITH U6 SNRNA, IDENTIFICATION BY MASS SPECTROMETRY, AND
RP IDENTIFICATION OF PROBABLE INTITIATION SITE.
RX PubMed=10747033; DOI=10.1093/emboj/19.7.1661;
RA Bouveret E., Rigaut G., Shevchenko A., Wilm M., Seraphin B.;
RT "A Sm-like protein complex that participates in mRNA degradation.";
RL EMBO J. 19:1661-1671(2000).
RN [7]
RP FUNCTION OF THE LSM1-LSM7 COMPLEX.
RX PubMed=10761922; DOI=10.1038/35006676;
RA Tharun S., He W., Mayes A.E., Lennertz P., Beggs J.D., Parker R.;
RT "Yeast Sm-like proteins function in mRNA decapping and decay.";
RL Nature 404:515-518(2000).
RN [8]
RP IDENTIFICATION IN THE LSM2-LSM7 COMPLEX, AND SUBCELLULAR LOCATION.
RX PubMed=15075370; DOI=10.1091/mbc.e04-02-0116;
RA Fernandez C.F., Pannone B.K., Chen X., Fuchs G., Wolin S.L.;
RT "An Lsm2-Lsm7 complex in Saccharomyces cerevisiae associates with the small
RT nucleolar RNA snR5.";
RL Mol. Biol. Cell 15:2842-2852(2004).
RN [9]
RP FUNCTION OF THE LSM2-LSM8 COMPLEX IN NUCLEAR MRNA DEGRADATION.
RX PubMed=15485930; DOI=10.1128/mcb.24.21.9646-9657.2004;
RA Kufel J., Bousquet-Antonelli C., Beggs J.D., Tollervey D.;
RT "Nuclear pre-mRNA decapping and 5' degradation in yeast require the Lsm2-8p
RT complex.";
RL Mol. Cell. Biol. 24:9646-9657(2004).
RN [10]
RP IDENTIFICATION OF PROBABLE INITIATION SITE.
RX PubMed=15905473; DOI=10.1093/nar/gki583;
RA Zhang Z., Dietrich F.S.;
RT "Mapping of transcription start sites in Saccharomyces cerevisiae using 5'
RT SAGE.";
RL Nucleic Acids Res. 33:2838-2851(2005).
RN [11]
RP SUBCELLULAR LOCATION.
RX PubMed=18029398; DOI=10.1242/jcs.019943;
RA Spiller M.P., Reijns M.A.M., Beggs J.D.;
RT "Requirements for nuclear localization of the Lsm2-8p complex and
RT competition between nuclear and cytoplasmic Lsm complexes.";
RL J. Cell Sci. 120:4310-4320(2007).
RN [12]
RP FUNCTION OF THE LSM1-LSM7-PAT1 COMPLEX.
RX PubMed=17513695; DOI=10.1261/rna.502507;
RA Chowdhury A., Mukhopadhyay J., Tharun S.;
RT "The decapping activator Lsm1p-7p-Pat1p complex has the intrinsic ability
RT to distinguish between oligoadenylated and polyadenylated RNAs.";
RL RNA 13:998-1016(2007).
RN [13]
RP X-RAY CRYSTALLOGRAPHY (2.30 ANGSTROMS) OF LSM1-LSM7 COMPLEX, SUBUNIT, AND
RP INTERACTION WITH PAT1.
RX PubMed=24139796; DOI=10.1016/j.celrep.2013.10.004;
RA Sharif H., Conti E.;
RT "Architecture of the Lsm1-7-Pat1 complex: a conserved assembly in
RT eukaryotic mRNA turnover.";
RL Cell Rep. 5:283-291(2013).
RN [14]
RP X-RAY CRYSTALLOGRAPHY (2.95 ANGSTROMS) OF LSM1-LSM7 COMPLEX, SUBUNIT,
RP FUNCTION, RNA-BINDING, AND MUTAGENESIS OF ARG-74.
RX PubMed=24513854; DOI=10.1038/cr.2014.18;
RA Zhou L., Zhou Y., Hang J., Wan R., Lu G., Yan C., Shi Y.;
RT "Crystal structure and biochemical analysis of the heptameric Lsm1-7
RT complex.";
RL Cell Res. 24:497-500(2014).
RN [15]
RP X-RAY CRYSTALLOGRAPHY (2.60 ANGSTROMS) OF LSM2-LSM8 COMPLEX, SUBUNIT,
RP FUNCTION, RNA-BINDING, AND MUTAGENESIS OF ARG-74.
RX PubMed=24240276; DOI=10.1038/nature12803;
RA Zhou L., Hang J., Zhou Y., Wan R., Lu G., Yin P., Yan C., Shi Y.;
RT "Crystal structures of the Lsm complex bound to the 3' end sequence of U6
RT small nuclear RNA.";
RL Nature 506:116-120(2014).
CC -!- FUNCTION: Component of LSm protein complexes, which are involved in RNA
CC processing and may function in a chaperone-like manner, facilitating
CC the efficient association of RNA processing factors with their
CC substrates. Component of the cytoplasmic LSM1-LSM7 complex, which is
CC involved in mRNA degradation by activating the decapping step in the
CC 5'-to-3' mRNA decay pathway. In association with PAT1, LSM1-LSM7 binds
CC directly to RNAs near the 3'-end and prefers oligoadenylated RNAs over
CC polyadenylated RNAs. Component of the nuclear LSM2-LSM8 complex, which
CC is involved in splicing of nuclear mRNAs. LSM2-LSM8 associates with
CC multiple snRNP complexes containing the U6 snRNA (U4/U6 di-snRNP,
CC spliceosomal U4/U6.U5 tri-snRNP, and free U6 snRNP). It binds directly
CC to the 3'-terminal U-tract of U6 snRNA and plays a role in the
CC biogenesis and stability of the U6 snRNP and U4/U6 snRNP complexes.
CC LSM2-LSM8 probably also is involved degradation of nuclear pre-mRNA by
CC targeting them for decapping, and in processing of pre-tRNAs, pre-rRNAs
CC and U3 snoRNA. Component of a nucleolar LSM2-LSM7 complex, which
CC associates with the precursor of the RNA component of RNase P (pre-P
CC RNA) and with the small nucleolar RNA (snoRNA) snR5. It may play a role
CC in the maturation of a subset of nucleolus-associated small RNAs.
CC {ECO:0000269|PubMed:10747033, ECO:0000269|PubMed:10761922,
CC ECO:0000269|PubMed:15485930, ECO:0000269|PubMed:17513695,
CC ECO:0000269|PubMed:24240276, ECO:0000269|PubMed:24513854}.
CC -!- SUBUNIT: Component of the heptameric LSM1-LSM7 complex that forms a
CC seven-membered ring structure with a doughnut shape. The LSm subunits
CC are arranged in the order LSM1, LSM2, LSM3, LSM6, LSM5, LSM7 and LSM4.
CC Except for LSM1, where a C-terminal helix crosses the ring structure to
CC form additional interactions with LSM3 and LSM6, each subunit interacts
CC only with its two neighboring subunits. The LSM1-LSM7 complex interacts
CC with PAT1; within the complex PAT1 has direct interactions with LSM2
CC and LSM3. LSM1-LSM7 associates also with PAT1 and XRN1. Component of
CC the heptameric LSM2-LSM8 complex that forms a seven-membered ring
CC structure with a doughnut shape; an RNA strand can pass through the
CC hole in the center of the ring structure. The LSm subunits are arranged
CC in the order LSM8, LSM2, LSM3, LSM6, LSM5, LSM7 and LSM4. LSM2-LSM8
CC associates with PAT1 and XRN1. Component of a LSM2-LSM7 complex, which
CC consists of at least LSM2, LSM3, LSM4, LSM5, LSM6 and LSM7. It is not
CC known whether another protein replaces the missing LSm to form a novel
CC heptameric complex. Component of the spliceosome U4/U6-U5 tri-snRNP
CC complex composed of the U4, U6 and U5 snRNAs and at least PRP3, PRP4,
CC PRP6, PRP8, PRP18, PRP31, PRP38, SNU13, SNU23, SNU66, SNU114, SPP381,
CC SMB1, SMD1, SMD2, SMD3, SMX2, SMX3, LSM2, LSM3, LSM4, LSM5, LSM6, LSM7,
CC LSM8, BRR2 and DIB1. {ECO:0000269|PubMed:10369684,
CC ECO:0000269|PubMed:10449419, ECO:0000269|PubMed:10747033,
CC ECO:0000269|PubMed:15075370, ECO:0000269|PubMed:24139796,
CC ECO:0000269|PubMed:24240276, ECO:0000269|PubMed:24513854}.
CC -!- INTERACTION:
CC Q06406; P47017: LSM1; NbExp=3; IntAct=EBI-196, EBI-174;
CC Q06406; P38203: LSM2; NbExp=7; IntAct=EBI-196, EBI-180;
CC Q06406; P40070: LSM4; NbExp=5; IntAct=EBI-196, EBI-188;
CC Q06406; P40089: LSM5; NbExp=4; IntAct=EBI-196, EBI-10236;
CC Q06406; P47093: LSM8; NbExp=4; IntAct=EBI-196, EBI-313;
CC -!- SUBCELLULAR LOCATION: Cytoplasm. Nucleus, nucleolus. Note=LSM1 and LSM8
CC act competitively with respect to the localization of LSM1-LSM7 to the
CC cytoplasm and LSM2-LSM8 to the nucleus. LSm proteins shift to the
CC cytoplasm under conditions of stress.
CC -!- SIMILARITY: Belongs to the snRNP Sm proteins family. SmF/LSm6
CC subfamily. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAB64814.1; Type=Erroneous initiation; Evidence={ECO:0000305};
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DR EMBL; U28373; AAB64814.1; ALT_INIT; Genomic_DNA.
DR EMBL; BK006938; DAA12220.1; -; Genomic_DNA.
DR PIR; S61173; S61173.
DR RefSeq; NP_010666.2; NM_001180686.1.
DR PDB; 3JCM; EM; 3.80 A; e=1-86.
DR PDB; 4C8Q; X-ray; 3.70 A; F=1-86.
DR PDB; 4C92; X-ray; 2.30 A; F=1-86.
DR PDB; 4M75; X-ray; 2.95 A; D/K=1-86.
DR PDB; 4M77; X-ray; 3.11 A; D/K=1-86.
DR PDB; 4M78; X-ray; 2.79 A; D/K=1-86.
DR PDB; 4M7A; X-ray; 2.78 A; D/K=1-86.
DR PDB; 4M7D; X-ray; 2.60 A; D/K=1-86.
DR PDB; 5GAN; EM; 3.60 A; 6=1-86.
DR PDB; 5NRL; EM; 7.20 A; z=1-86.
DR PDB; 5VSU; X-ray; 3.10 A; F=1-86.
DR PDB; 5ZWM; EM; 3.40 A; x=1-86.
DR PDB; 5ZWO; EM; 3.90 A; x=1-86.
DR PDB; 6ASO; X-ray; 2.71 A; F=1-86.
DR PDBsum; 3JCM; -.
DR PDBsum; 4C8Q; -.
DR PDBsum; 4C92; -.
DR PDBsum; 4M75; -.
DR PDBsum; 4M77; -.
DR PDBsum; 4M78; -.
DR PDBsum; 4M7A; -.
DR PDBsum; 4M7D; -.
DR PDBsum; 5GAN; -.
DR PDBsum; 5NRL; -.
DR PDBsum; 5VSU; -.
DR PDBsum; 5ZWM; -.
DR PDBsum; 5ZWO; -.
DR PDBsum; 6ASO; -.
DR AlphaFoldDB; Q06406; -.
DR SMR; Q06406; -.
DR BioGRID; 32437; 872.
DR ComplexPortal; CPX-112; LSM1-7-PAT1 complex.
DR ComplexPortal; CPX-24; U6 small nuclear ribonucleoprotein complex.
DR ComplexPortal; CPX-25; U4/U6.U5 tri-small nuclear ribonucleoprotein complex.
DR ComplexPortal; CPX-32; U4/U6 small nuclear ribonucleoprotein complex.
DR ComplexPortal; CPX-44; LSM2-8 complex.
DR ComplexPortal; CPX-45; LSM1-7 complex.
DR ComplexPortal; CPX-46; LSM2-7 complex.
DR DIP; DIP-1418N; -.
DR IntAct; Q06406; 35.
DR MINT; Q06406; -.
DR STRING; 4932.YDR378C; -.
DR MoonDB; Q06406; Predicted.
DR MaxQB; Q06406; -.
DR PaxDb; Q06406; -.
DR PRIDE; Q06406; -.
DR EnsemblFungi; YDR378C_mRNA; YDR378C; YDR378C.
DR GeneID; 851984; -.
DR KEGG; sce:YDR378C; -.
DR SGD; S000002786; LSM6.
DR VEuPathDB; FungiDB:YDR378C; -.
DR eggNOG; KOG1783; Eukaryota.
DR GeneTree; ENSGT00940000154978; -.
DR HOGENOM; CLU_076902_7_1_1; -.
DR InParanoid; Q06406; -.
DR OMA; MYISEQK; -.
DR BioCyc; YEAST:G3O-29927-MON; -.
DR Reactome; R-SCE-430039; mRNA decay by 5' to 3' exoribonuclease.
DR PRO; PR:Q06406; -.
DR Proteomes; UP000002311; Chromosome IV.
DR RNAct; Q06406; protein.
DR GO; GO:1990726; C:Lsm1-7-Pat1 complex; IDA:SGD.
DR GO; GO:0005730; C:nucleolus; IDA:SGD.
DR GO; GO:0005634; C:nucleus; IDA:ComplexPortal.
DR GO; GO:0000932; C:P-body; IDA:SGD.
DR GO; GO:0005732; C:sno(s)RNA-containing ribonucleoprotein complex; IPI:SGD.
DR GO; GO:0005681; C:spliceosomal complex; IC:ComplexPortal.
DR GO; GO:0071001; C:U4/U6 snRNP; IC:ComplexPortal.
DR GO; GO:0046540; C:U4/U6 x U5 tri-snRNP complex; IDA:SGD.
DR GO; GO:0005688; C:U6 snRNP; IDA:SGD.
DR GO; GO:0003723; F:RNA binding; IEA:UniProtKB-KW.
DR GO; GO:0000290; P:deadenylation-dependent decapping of nuclear-transcribed mRNA; IMP:ComplexPortal.
DR GO; GO:0030490; P:maturation of SSU-rRNA; IMP:SGD.
DR GO; GO:0000398; P:mRNA splicing, via spliceosome; IMP:SGD.
DR GO; GO:0006364; P:rRNA processing; IMP:ComplexPortal.
DR GO; GO:0008033; P:tRNA processing; IMP:ComplexPortal.
DR DisProt; DP01402; -.
DR InterPro; IPR016487; Lsm6/sSmF.
DR InterPro; IPR001163; LSM_dom_euk/arc.
DR InterPro; IPR010920; LSM_dom_sf.
DR PANTHER; PTHR11021; PTHR11021; 1.
DR Pfam; PF01423; LSM; 1.
DR SMART; SM00651; Sm; 1.
DR SUPFAM; SSF50182; SSF50182; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Cytoplasm; mRNA processing; mRNA splicing; Nucleus;
KW Reference proteome; Ribonucleoprotein; RNA-binding; rRNA processing;
KW Spliceosome; tRNA processing.
FT CHAIN 1..86
FT /note="U6 snRNA-associated Sm-like protein LSm6"
FT /id="PRO_0000125578"
FT MUTAGEN 74
FT /note="R->A: Reduces affinity for poly-U RNA ends."
FT /evidence="ECO:0000269|PubMed:24240276,
FT ECO:0000269|PubMed:24513854"
FT HELIX 11..17
FT /evidence="ECO:0007829|PDB:4C92"
FT TURN 18..21
FT /evidence="ECO:0007829|PDB:4C92"
FT STRAND 22..28
FT /evidence="ECO:0007829|PDB:4C92"
FT STRAND 31..41
FT /evidence="ECO:0007829|PDB:4C92"
FT STRAND 47..57
FT /evidence="ECO:0007829|PDB:4C92"
FT TURN 59..61
FT /evidence="ECO:0007829|PDB:4M75"
FT STRAND 65..69
FT /evidence="ECO:0007829|PDB:4M7A"
FT STRAND 71..73
FT /evidence="ECO:0007829|PDB:4C92"
FT HELIX 75..77
FT /evidence="ECO:0007829|PDB:4C92"
FT STRAND 78..83
FT /evidence="ECO:0007829|PDB:4C92"
SQ SEQUENCE 86 AA; 9398 MW; 74FE40A4509CEF33 CRC64;
MSGKASTEGS VTTEFLSDII GKTVNVKLAS GLLYSGRLES IDGFMNVALS SATEHYESNN
NKLLNKFNSD VFLRGTQVMY ISEQKI
