LSM4_YEAST
ID LSM4_YEAST Reviewed; 187 AA.
AC P40070; D3DM18; Q07091;
DT 01-FEB-1995, integrated into UniProtKB/Swiss-Prot.
DT 01-FEB-1995, sequence version 1.
DT 03-AUG-2022, entry version 187.
DE RecName: Full=U6 snRNA-associated Sm-like protein LSm4 {ECO:0000305};
DE AltName: Full=Like-SM protein 4 {ECO:0000303|PubMed:10428970};
GN Name=LSM4 {ECO:0000303|PubMed:10428970};
GN Synonyms=SDB23, USS1 {ECO:0000303|PubMed:7744012};
GN OrderedLocusNames=YER112W;
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], AND CHARACTERIZATION.
RX PubMed=7744012; DOI=10.1002/j.1460-2075.1995.tb07198.x;
RA Cooper M., Johnston L.H., Beggs J.D.;
RT "Identification and characterization of Uss1p (Sdb23p): a novel U6 snRNA-
RT associated protein with significant similarity to core proteins of small
RT nuclear ribonucleoproteins.";
RL EMBO J. 14:2066-2075(1995).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=8497280; DOI=10.1128/mcb.13.6.3792-3801.1993;
RA Foster R., Mikesell G.E., Breeden L.;
RT "Multiple SWI6-dependent cis-acting elements control SWI4 transcription
RT through the cell cycle.";
RL Mol. Biol. Cell 13:3792-3801(1993).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=9169868;
RA Dietrich F.S., Mulligan J.T., Hennessy K.M., Yelton M.A., Allen E.,
RA Araujo R., Aviles E., Berno A., Brennan T., Carpenter J., Chen E.,
RA Cherry J.M., Chung E., Duncan M., Guzman E., Hartzell G., Hunicke-Smith S.,
RA Hyman R.W., Kayser A., Komp C., Lashkari D., Lew H., Lin D., Mosedale D.,
RA Nakahara K., Namath A., Norgren R., Oefner P., Oh C., Petel F.X.,
RA Roberts D., Sehl P., Schramm S., Shogren T., Smith V., Taylor P., Wei Y.,
RA Botstein D., Davis R.W.;
RT "The nucleotide sequence of Saccharomyces cerevisiae chromosome V.";
RL Nature 387:78-81(1997).
RN [4]
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 [5]
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 [6]
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 [7]
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 [8]
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 [9]
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 [10]
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 [11]
RP SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
RX PubMed=14562095; DOI=10.1038/nature02026;
RA Huh W.-K., Falvo J.V., Gerke L.C., Carroll A.S., Howson R.W.,
RA Weissman J.S., O'Shea E.K.;
RT "Global analysis of protein localization in budding yeast.";
RL Nature 425:686-691(2003).
RN [12]
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 [13]
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 [14]
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 [15]
RP METHYLATION AT ARG-119.
RX PubMed=26046779; DOI=10.1002/pmic.201500032;
RA Plank M., Fischer R., Geoghegan V., Charles P.D., Konietzny R., Acuto O.,
RA Pears C., Schofield C.J., Kessler B.M.;
RT "Expanding the yeast protein arginine methylome.";
RL Proteomics 15:3232-3243(2015).
RN [16]
RP PHOSPHORYLATION AT SER-181.
RX PubMed=33856219; DOI=10.1021/acs.jproteome.0c00927;
RA Hamey J.J., Nguyen A., Wilkins M.R.;
RT "Discovery of arginine methylation, phosphorylation, and their co-
RT occurrence in condensate-associated proteins in Saccharomyces cerevisiae.";
RL J. Proteome Res. 20:2420-2434(2021).
RN [17]
RP X-RAY CRYSTALLOGRAPHY (2.30 ANGSTROMS) OF 1-114 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 [18]
RP X-RAY CRYSTALLOGRAPHY (2.95 ANGSTROMS) OF LSM1-LSM7 COMPLEX, SUBUNIT,
RP FUNCTION, RNA-BINDING, AND MUTAGENESIS OF ARG-72.
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 [19]
RP X-RAY CRYSTALLOGRAPHY (2.60 ANGSTROMS) OF 1-93 OF LSM2-LSM8 COMPLEX,
RP SUBUNIT, FUNCTION, RNA-BINDING, AND MUTAGENESIS OF ARG-72.
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 spliceosome snRNP complexes containing the U6
CC snRNA (U4/U6 snRNP, U4/U6.U5 snRNP, and free U6 snRNP). It binds
CC directly to the U6 snRNA and plays a role in the biogenesis and
CC stability of the U6 snRNP and U4/U6 snRNP complexes. It probably also
CC is involved in degradation of nuclear pre-mRNA by targeting them for
CC decapping. LSM4 binds specifically to the 3'-terminal U-tract of U6
CC snRNA. LSM2-LSM8 probably is involved in processing of pre-tRNAs, pre-
CC rRNAs and U3 snoRNA. LSM4, probably in a complex that contains LSM2-
CC LSM7 but not LSM1 or LSM8, associates with the precursor of the RNA
CC component of RNase P (pre-P RNA) and may be involved in maturing pre-P
CC RNA. LSM4 is required for processing of pre-tRNAs, pre-rRNAs and U3
CC snoRNA. {ECO:0000269|PubMed:10747033, ECO:0000269|PubMed:10761922,
CC ECO:0000269|PubMed:12077351, ECO:0000269|PubMed:12438310,
CC ECO:0000269|PubMed:15485930, ECO:0000269|PubMed:24240276,
CC 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. Component of the U4/U6-U5
CC tri-snRNP complex composed of the U4, U6 and U5 snRNAs and at least
CC PRP3, PRP4, PRP6, PRP8, PRP18, PRP31, PRP38, SNU13, SNU23, SNU66,
CC SNU114, SPP381, SMB1, SMD1, SMD2, SMD3, SMX2, SMX3, LSM2, LSM3, LSM4,
CC LSM5, LSM6, LSM7, LSM8, BRR2 and DIB1. {ECO:0000269|PubMed:10369684,
CC ECO:0000269|PubMed:10449419, ECO:0000269|PubMed:10747033,
CC ECO:0000269|PubMed:24139796, ECO:0000269|PubMed:24240276,
CC ECO:0000269|PubMed:24513854}.
CC -!- INTERACTION:
CC P40070; P39517: DHH1; NbExp=3; IntAct=EBI-188, EBI-158;
CC P40070; P47017: LSM1; NbExp=4; IntAct=EBI-188, EBI-174;
CC P40070; P38203: LSM2; NbExp=6; IntAct=EBI-188, EBI-180;
CC P40070; P57743: LSM3; NbExp=3; IntAct=EBI-188, EBI-10227;
CC P40070; Q06406: LSM6; NbExp=5; IntAct=EBI-188, EBI-196;
CC P40070; P47093: LSM8; NbExp=3; IntAct=EBI-188, EBI-313;
CC P40070; P25644: PAT1; NbExp=7; IntAct=EBI-188, EBI-204;
CC P40070; Q06217: SMD2; NbExp=3; IntAct=EBI-188, EBI-235;
CC P40070; P22147: XRN1; NbExp=3; IntAct=EBI-188, EBI-9642;
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:14562095}. Cytoplasm
CC {ECO:0000269|PubMed:14562095}.
CC -!- MISCELLANEOUS: Present with 3440 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; X82649; CAA57975.1; -; Genomic_DNA.
DR EMBL; M97918; AAA58257.1; -; Genomic_DNA.
DR EMBL; U18916; AAC03210.1; -; Genomic_DNA.
DR EMBL; BK006939; DAA07772.1; -; Genomic_DNA.
DR PIR; S50615; S50615.
DR RefSeq; NP_011037.3; NM_001179002.3.
DR PDB; 3JCM; EM; 3.80 A; h=1-187.
DR PDB; 4C8Q; X-ray; 3.70 A; D=1-114.
DR PDB; 4C92; X-ray; 2.30 A; D=1-114.
DR PDB; 4M75; X-ray; 2.95 A; G/N=1-93.
DR PDB; 4M77; X-ray; 3.11 A; G/N=1-93.
DR PDB; 4M78; X-ray; 2.79 A; G/N=1-93.
DR PDB; 4M7A; X-ray; 2.78 A; G/N=1-93.
DR PDB; 4M7D; X-ray; 2.60 A; G/N=1-93.
DR PDB; 5GAN; EM; 3.60 A; 4=1-187.
DR PDB; 5NRL; EM; 7.20 A; j=1-187.
DR PDB; 5VSU; X-ray; 3.10 A; D=1-93.
DR PDB; 5ZWM; EM; 3.40 A; s=1-187.
DR PDB; 5ZWO; EM; 3.90 A; s=1-187.
DR PDB; 6ASO; X-ray; 2.71 A; D=1-93.
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; P40070; -.
DR SMR; P40070; -.
DR BioGRID; 36857; 198.
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-848N; -.
DR IntAct; P40070; 87.
DR MINT; P40070; -.
DR STRING; 4932.YER112W; -.
DR iPTMnet; P40070; -.
DR MaxQB; P40070; -.
DR PaxDb; P40070; -.
DR PRIDE; P40070; -.
DR EnsemblFungi; YER112W_mRNA; YER112W; YER112W.
DR GeneID; 856848; -.
DR KEGG; sce:YER112W; -.
DR SGD; S000000914; LSM4.
DR VEuPathDB; FungiDB:YER112W; -.
DR eggNOG; KOG3293; Eukaryota.
DR GeneTree; ENSGT00610000086173; -.
DR HOGENOM; CLU_099537_0_0_1; -.
DR InParanoid; P40070; -.
DR OMA; RAEMNKN; -.
DR BioCyc; YEAST:G3O-30276-MON; -.
DR Reactome; R-SCE-430039; mRNA decay by 5' to 3' exoribonuclease.
DR PRO; PR:P40070; -.
DR Proteomes; UP000002311; Chromosome V.
DR RNAct; P40070; protein.
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:0005732; C:sno(s)RNA-containing ribonucleoprotein complex; IPI:SGD.
DR GO; GO:0005681; C:spliceosomal complex; IC:ComplexPortal.
DR GO; GO:0097526; C:spliceosomal tri-snRNP complex; IBA:GO_Central.
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; IBA:GO_Central.
DR GO; GO:0017070; F:U6 snRNA binding; IDA:SGD.
DR GO; GO:0000290; P:deadenylation-dependent decapping of nuclear-transcribed mRNA; IMP:ComplexPortal.
DR GO; GO:0000398; P:mRNA splicing, via spliceosome; IMP:SGD.
DR GO; GO:0033962; P:P-body assembly; IMP:SGD.
DR GO; GO:0006364; P:rRNA processing; IMP:ComplexPortal.
DR GO; GO:0000387; P:spliceosomal snRNP assembly; IBA:GO_Central.
DR GO; GO:0008033; P:tRNA processing; IMP:ComplexPortal.
DR CDD; cd01723; LSm4; 1.
DR InterPro; IPR034101; Lsm4.
DR InterPro; IPR027141; LSm4/Sm_D1/D3.
DR InterPro; IPR001163; LSM_dom_euk/arc.
DR InterPro; IPR010920; LSM_dom_sf.
DR PANTHER; PTHR23338; PTHR23338; 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; Methylation; mRNA processing; mRNA splicing;
KW Nucleus; Phosphoprotein; Reference proteome; Ribonucleoprotein;
KW RNA-binding; rRNA processing; Spliceosome; tRNA processing.
FT CHAIN 1..187
FT /note="U6 snRNA-associated Sm-like protein LSm4"
FT /id="PRO_0000125571"
FT REGION 93..187
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOD_RES 119
FT /note="Omega-N-methylarginine"
FT /evidence="ECO:0000269|PubMed:26046779"
FT MOD_RES 181
FT /note="Phosphoserine"
FT /evidence="ECO:0000269|PubMed:33856219"
FT MUTAGEN 72
FT /note="R->A: Slightly reduces affinity for poly-U RNA
FT ends."
FT /evidence="ECO:0000269|PubMed:24240276,
FT ECO:0000269|PubMed:24513854"
FT CONFLICT 155
FT /note="I -> N (in Ref. 2; AAA58257)"
FT /evidence="ECO:0000305"
FT HELIX 2..8
FT /evidence="ECO:0007829|PDB:4C92"
FT TURN 9..12
FT /evidence="ECO:0007829|PDB:6ASO"
FT STRAND 14..19
FT /evidence="ECO:0007829|PDB:4C92"
FT STRAND 22..32
FT /evidence="ECO:0007829|PDB:4C92"
FT STRAND 38..47
FT /evidence="ECO:0007829|PDB:4C92"
FT HELIX 48..53
FT /evidence="ECO:0007829|PDB:4C92"
FT STRAND 64..71
FT /evidence="ECO:0007829|PDB:4C92"
FT HELIX 73..75
FT /evidence="ECO:0007829|PDB:4C92"
FT STRAND 76..81
FT /evidence="ECO:0007829|PDB:4C92"
FT HELIX 83..86
FT /evidence="ECO:0007829|PDB:4M7D"
SQ SEQUENCE 187 AA; 21276 MW; 69CAC1F01D5BFA98 CRC64;
MLPLYLLTNA KGQQMQIELK NGEIIQGILT NVDNWMNLTL SNVTEYSEES AINSEDNAES
SKAVKLNEIY IRGTFIKFIK LQDNIIDKVK QQINSNNNSN SNGPGHKRYY NNRDSNNNRG
NYNRRNNNNG NSNRRPYSQN RQYNNSNSSN INNSINSINS NNQNMNNGLG GSVQHHFNSS
SPQKVEF
