LSM2_YEAST
ID LSM2_YEAST Reviewed; 95 AA.
AC P38203; D6VPX4;
DT 01-OCT-1994, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-1994, sequence version 1.
DT 03-AUG-2022, entry version 184.
DE RecName: Full=U6 snRNA-associated Sm-like protein LSm2;
DE AltName: Full=Small nuclear ribonucleoprotein D homolog SNP3;
GN Name=LSM2; Synonyms=SMX5, SNP3; OrderedLocusNames=YBL026W;
GN ORFNames=YBL0425;
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 [GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=7725803; DOI=10.1002/yea.320101217;
RA van Dyck L., Jonniaux J.-L., Barreiros T.D.M., Kleine K., Goffeau A.;
RT "Analysis of a 17.4 kb DNA segment of yeast chromosome II encompassing the
RT ribosomal protein L19 as well as proteins with homologies to components of
RT the hnRNP and snRNP complexes and to the human proliferation-associated
RT p120 antigen.";
RL Yeast 10:1663-1673(1994).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=7813418; DOI=10.1002/j.1460-2075.1994.tb06923.x;
RA Feldmann H., Aigle M., Aljinovic G., Andre B., Baclet M.C., Barthe C.,
RA Baur A., Becam A.-M., Biteau N., Boles E., Brandt T., Brendel M.,
RA Brueckner M., Bussereau F., Christiansen C., Contreras R., Crouzet M.,
RA Cziepluch C., Demolis N., Delaveau T., Doignon F., Domdey H.,
RA Duesterhus S., Dubois E., Dujon B., El Bakkoury M., Entian K.-D.,
RA Feuermann M., Fiers W., Fobo G.M., Fritz C., Gassenhuber J., Glansdorff N.,
RA Goffeau A., Grivell L.A., de Haan M., Hein C., Herbert C.J.,
RA Hollenberg C.P., Holmstroem K., Jacq C., Jacquet M., Jauniaux J.-C.,
RA Jonniaux J.-L., Kallesoee T., Kiesau P., Kirchrath L., Koetter P.,
RA Korol S., Liebl S., Logghe M., Lohan A.J.E., Louis E.J., Li Z.Y.,
RA Maat M.J., Mallet L., Mannhaupt G., Messenguy F., Miosga T., Molemans F.,
RA Mueller S., Nasr F., Obermaier B., Perea J., Pierard A., Piravandi E.,
RA Pohl F.M., Pohl T.M., Potier S., Proft M., Purnelle B., Ramezani Rad M.,
RA Rieger M., Rose M., Schaaff-Gerstenschlaeger I., Scherens B.,
RA Schwarzlose C., Skala J., Slonimski P.P., Smits P.H.M., Souciet J.-L.,
RA Steensma H.Y., Stucka R., Urrestarazu L.A., van der Aart Q.J.M.,
RA Van Dyck L., Vassarotti A., Vetter I., Vierendeels F., Vissers S.,
RA Wagner G., de Wergifosse P., Wolfe K.H., Zagulski M., Zimmermann F.K.,
RA Mewes H.-W., Kleine K.;
RT "Complete DNA sequence of yeast chromosome II.";
RL EMBO J. 13:5795-5809(1994).
RN [3]
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 [4]
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 [5]
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 [6]
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 [7]
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, AND IDENTIFICATION BY MASS SPECTROMETRY.
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 [8]
RP FUNCTION IN PROCESSING OF PRE-TRNAS.
RX PubMed=12077351; DOI=10.1128/mcb.22.14.5248-5256.2002;
RA Kufel J., Allmang C., Verdone L., Beggs J.D., Tollervey D.;
RT "Lsm proteins are required for normal processing of pre-tRNAs and their
RT efficient association with La-homologous protein Lhp1p.";
RL Mol. Cell. Biol. 22:5248-5256(2002).
RN [9]
RP FUNCTION IN PROCESSING OF PRE-RRNAS.
RX PubMed=12438310; DOI=10.1074/jbc.m208856200;
RA Kufel J., Allmang C., Petfalski E., Beggs J.D., Tollervey D.;
RT "Lsm Proteins are required for normal processing and stability of ribosomal
RT RNAs.";
RL J. Biol. Chem. 278:2147-2156(2003).
RN [10]
RP LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
RX PubMed=14562106; DOI=10.1038/nature02046;
RA Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N.,
RA O'Shea E.K., Weissman J.S.;
RT "Global analysis of protein expression in yeast.";
RL Nature 425:737-741(2003).
RN [11]
RP FUNCTION IN PROCESSING OF U3 SNORNA.
RX PubMed=14627812; DOI=10.1093/nar/gkg904;
RA Kufel J., Allmang C., Verdone L., Beggs J., Tollervey D.;
RT "A complex pathway for 3' processing of the yeast U3 snoRNA.";
RL Nucleic Acids Res. 31:6788-6797(2003).
RN [12]
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 [13]
RP X-RAY CRYSTALLOGRAPHY (2.30 ANGSTROMS) OF 27-172 OF LSM1-LSM7 COMPLEX,
RP SUBUNIT, AND 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-63.
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 (3.15 ANGSTROMS), SUBUNIT, INTERACTION WITH PAT1,
RP FUNCTION, AND RNA-BINDING.
RX PubMed=24247251; DOI=10.1038/cr.2013.152;
RA Wu D., Muhlrad D., Bowler M.W., Jiang S., Liu Z., Parker R., Song H.;
RT "Lsm2 and Lsm3 bridge the interaction of the Lsm1-7 complex with Pat1 for
RT decapping activation.";
RL Cell Res. 24:233-246(2014).
RN [16]
RP X-RAY CRYSTALLOGRAPHY (2.60 ANGSTROMS) OF LSM2-LSM8 COMPLEX, SUBUNIT,
RP FUNCTION, RNA-BINDING, AND MUTAGENESIS OF PHE-35; ASN-37 AND ARG-63.
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. Component of
CC the cytoplasmic LSM1-LSM7 complex which is involved in mRNA degradation
CC by activating the decapping step. Component of the nuclear LSM2-LSM8
CC complex, which is involved in splicing of nuclear mRNAs. LSM2-LSM8
CC associates with multiple snRNP complexes containing the U6 snRNA (U4/U6
CC snRNP, U4/U6.U5 snRNP, and free U6 snRNP). It binds directly to the U6
CC snRNA and plays a role in the biogenesis and stability of the U6 snRNP
CC and U4/U6 snRNP complexes. It probably also is involved in degradation
CC of nuclear pre-mRNA by targeting them for decapping. LSM2 binds
CC specifically to the 3'-terminal U-tract of U6 snRNA. LSM2-LSM8 probably
CC is involved in processing of pre-tRNAs, pre-rRNAs and U3 snoRNA. LSM2,
CC probably in a complex that contains LSM2-LSM7 but not LSM1 or LSM8,
CC associates with the precursor of the RNA component of RNase P (pre-P
CC RNA) and may be involved in maturing pre-P RNA. LSM2 is required for
CC processing of pre-tRNAs, pre-rRNAs and U3 snoRNA.
CC {ECO:0000269|PubMed:10747033, ECO:0000269|PubMed:12077351,
CC ECO:0000269|PubMed:12438310, ECO:0000269|PubMed:14627812,
CC ECO:0000269|PubMed:15485930, ECO:0000269|PubMed:24240276,
CC ECO:0000269|PubMed:24247251, 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. Component of the heptameric LSM2-LSM8 complex that forms a
CC seven-membered ring structure with a doughnut shape; an RNA strand can
CC pass through the hole in the center of the ring structure. The LSm
CC subunits are arranged in the order LSM8, LSM2, LSM3, LSM6, LSM5, LSM7
CC and LSM4. LSM2-LSM8 associates with PAT1 and XRN1. A complex comprising
CC LSM2-LSM7 without LSM1 or LSM8 may exist. Likewise, LSM2 and LSM3 can
CC assemble into a doughnut structure that binds PAT1 (in vitro).
CC Component of the U4/U6-U5 tri-snRNP complex composed of the U4, U6 and
CC U5 snRNAs and at least PRP3, PRP4, PRP6, PRP8, PRP18, PRP31, PRP38,
CC SNU13, SNU23, SNU66, SNU114, SPP381, SMB1, SMD1, SMD2, SMD3, SMX2,
CC SMX3, LSM2, LSM3, LSM4, LSM5, LSM6, LSM7, LSM8, BRR2 and DIB1.
CC {ECO:0000269|PubMed:10369684, ECO:0000269|PubMed:10449419,
CC ECO:0000269|PubMed:10747033, ECO:0000269|PubMed:24139796,
CC ECO:0000269|PubMed:24240276, ECO:0000269|PubMed:24247251,
CC ECO:0000269|PubMed:24513854}.
CC -!- INTERACTION:
CC P38203; P39517: DHH1; NbExp=3; IntAct=EBI-180, EBI-158;
CC P38203; P47017: LSM1; NbExp=6; IntAct=EBI-180, EBI-174;
CC P38203; P57743: LSM3; NbExp=7; IntAct=EBI-180, EBI-10227;
CC P38203; P40070: LSM4; NbExp=6; IntAct=EBI-180, EBI-188;
CC P38203; P40089: LSM5; NbExp=6; IntAct=EBI-180, EBI-10236;
CC P38203; Q06406: LSM6; NbExp=7; IntAct=EBI-180, EBI-196;
CC P38203; P53905: LSM7; NbExp=6; IntAct=EBI-180, EBI-141;
CC P38203; P47093: LSM8; NbExp=10; IntAct=EBI-180, EBI-313;
CC P38203; P25644: PAT1; NbExp=5; IntAct=EBI-180, EBI-204;
CC P38203; Q06217: SMD2; NbExp=3; IntAct=EBI-180, EBI-235;
CC -!- SUBCELLULAR LOCATION: Nucleus. Cytoplasm {ECO:0000305}.
CC -!- MISCELLANEOUS: Present with 2210 molecules/cell in log phase SD medium.
CC {ECO:0000269|PubMed:14562106}.
CC -!- SIMILARITY: Belongs to the snRNP Sm proteins family. {ECO:0000305}.
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DR EMBL; X77291; CAA54505.1; -; Genomic_DNA.
DR EMBL; Z35787; CAA84845.1; -; Genomic_DNA.
DR EMBL; BK006936; DAA07094.1; -; Genomic_DNA.
DR PIR; S45760; S45760.
DR RefSeq; NP_009527.1; NM_001178266.1.
DR PDB; 3JCM; EM; 3.80 A; c=1-95.
DR PDB; 4C8Q; X-ray; 3.70 A; B=2-95.
DR PDB; 4C92; X-ray; 2.30 A; B=2-95.
DR PDB; 4M75; X-ray; 2.95 A; B/I=1-95.
DR PDB; 4M77; X-ray; 3.11 A; B/I=1-95.
DR PDB; 4M78; X-ray; 2.79 A; B/I=1-95.
DR PDB; 4M7A; X-ray; 2.78 A; B/I=1-95.
DR PDB; 4M7D; X-ray; 2.60 A; B/I=1-95.
DR PDB; 4N0A; X-ray; 3.15 A; C/D/G=1-95.
DR PDB; 5GAN; EM; 3.60 A; 2=1-95.
DR PDB; 5NRL; EM; 7.20 A; a=1-95.
DR PDB; 5VSU; X-ray; 3.10 A; B=1-95.
DR PDB; 5ZWM; EM; 3.40 A; q=1-95.
DR PDB; 5ZWO; EM; 3.90 A; q=1-95.
DR PDB; 6ASO; X-ray; 2.71 A; B=1-95.
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; 4N0A; -.
DR PDBsum; 5GAN; -.
DR PDBsum; 5NRL; -.
DR PDBsum; 5VSU; -.
DR PDBsum; 5ZWM; -.
DR PDBsum; 5ZWO; -.
DR PDBsum; 6ASO; -.
DR AlphaFoldDB; P38203; -.
DR SMR; P38203; -.
DR BioGRID; 32672; 333.
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-794N; -.
DR IntAct; P38203; 83.
DR MINT; P38203; -.
DR STRING; 4932.YBL026W; -.
DR MaxQB; P38203; -.
DR PaxDb; P38203; -.
DR PRIDE; P38203; -.
DR EnsemblFungi; YBL026W_mRNA; YBL026W; YBL026W.
DR GeneID; 852255; -.
DR KEGG; sce:YBL026W; -.
DR SGD; S000000122; LSM2.
DR VEuPathDB; FungiDB:YBL026W; -.
DR eggNOG; KOG3448; Eukaryota.
DR GeneTree; ENSGT00390000016597; -.
DR HOGENOM; CLU_130474_3_0_1; -.
DR InParanoid; P38203; -.
DR OMA; EERYPHM; -.
DR BioCyc; YEAST:G3O-28929-MON; -.
DR Reactome; R-SCE-430039; mRNA decay by 5' to 3' exoribonuclease.
DR PRO; PR:P38203; -.
DR Proteomes; UP000002311; Chromosome II.
DR RNAct; P38203; protein.
DR GO; GO:0071013; C:catalytic step 2 spliceosome; IBA:GO_Central.
DR GO; GO:0005737; C:cytoplasm; HDA:SGD.
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:0071011; C:precatalytic spliceosome; IBA:GO_Central.
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:0000398; P:mRNA splicing, via spliceosome; IDA:SGD.
DR GO; GO:0006364; P:rRNA processing; IMP:ComplexPortal.
DR GO; GO:0008033; P:tRNA processing; IMP:ComplexPortal.
DR CDD; cd01725; LSm2; 1.
DR InterPro; IPR001163; LSM_dom_euk/arc.
DR InterPro; IPR010920; LSM_dom_sf.
DR InterPro; IPR016654; U6_snRNA_Lsm2.
DR PANTHER; PTHR13829; PTHR13829; 1.
DR Pfam; PF01423; LSM; 1.
DR PIRSF; PIRSF016394; U6_snRNA_Lsm2; 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..95
FT /note="U6 snRNA-associated Sm-like protein LSm2"
FT /id="PRO_0000125559"
FT MUTAGEN 35
FT /note="F->A: Strongly reduces affinity for poly-U RNA
FT ends."
FT /evidence="ECO:0000269|PubMed:24240276"
FT MUTAGEN 37
FT /note="N->A: Strongly reduces affinity for poly-U RNA
FT ends."
FT /evidence="ECO:0000269|PubMed:24240276"
FT MUTAGEN 63
FT /note="R->A: Strongly reduces affinity for poly-U RNA
FT ends."
FT /evidence="ECO:0000269|PubMed:24240276,
FT ECO:0000269|PubMed:24513854"
FT HELIX 2..8
FT /evidence="ECO:0007829|PDB:4C92"
FT TURN 9..12
FT /evidence="ECO:0007829|PDB:4C92"
FT STRAND 13..19
FT /evidence="ECO:0007829|PDB:4C92"
FT TURN 20..22
FT /evidence="ECO:0007829|PDB:4M7D"
FT STRAND 24..32
FT /evidence="ECO:0007829|PDB:4C92"
FT STRAND 38..45
FT /evidence="ECO:0007829|PDB:4C92"
FT STRAND 49..51
FT /evidence="ECO:0007829|PDB:4C92"
FT STRAND 54..56
FT /evidence="ECO:0007829|PDB:6ASO"
FT STRAND 60..62
FT /evidence="ECO:0007829|PDB:4C92"
FT HELIX 64..66
FT /evidence="ECO:0007829|PDB:4C92"
FT STRAND 67..72
FT /evidence="ECO:0007829|PDB:4C92"
FT HELIX 74..76
FT /evidence="ECO:0007829|PDB:4C92"
FT HELIX 79..93
FT /evidence="ECO:0007829|PDB:4C92"
SQ SEQUENCE 95 AA; 11163 MW; C23856268CEE92E2 CRC64;
MLFFSFFKTL VDQEVVVELK NDIEIKGTLQ SVDQFLNLKL DNISCTDEKK YPHLGSVRNI
FIRGSTVRYV YLNKNMVDTN LLQDATRREV MTERK
