LSM5_YEAST
ID LSM5_YEAST Reviewed; 93 AA.
AC P40089; D3DM53;
DT 01-FEB-1995, integrated into UniProtKB/Swiss-Prot.
DT 01-FEB-1995, sequence version 1.
DT 03-AUG-2022, entry version 180.
DE RecName: Full=U6 snRNA-associated Sm-like protein LSm5;
GN Name=LSM5; OrderedLocusNames=YER146W;
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=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 [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 NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=17322287; DOI=10.1101/gr.6037607;
RA Hu Y., Rolfs A., Bhullar B., Murthy T.V.S., Zhu C., Berger M.F.,
RA Camargo A.A., Kelley F., McCarron S., Jepson D., Richardson A., Raphael J.,
RA Moreira D., Taycher E., Zuo D., Mohr S., Kane M.F., Williamson J.,
RA Simpson A.J.G., Bulyk M.L., Harlow E., Marsischky G., Kolodner R.D.,
RA LaBaer J.;
RT "Approaching a complete repository of sequence-verified protein-encoding
RT clones for Saccharomyces cerevisiae.";
RL Genome Res. 17:536-543(2007).
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 OF THE LSM1-LSM7 COMPLEX, AND INTERACTION WITH PAT1.
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 [9]
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 [10]
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 [11]
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 [12]
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 [13]
RP X-RAY CRYSTALLOGRAPHY (2.95 ANGSTROMS) OF LSM1-LSM7 COMPLEX, SUBUNIT,
RP FUNCTION, RNA-BINDING, AND MUTAGENESIS OF SER-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 [14]
RP X-RAY CRYSTALLOGRAPHY (2.60 ANGSTROMS) OF LSM2-LSM8 COMPLEX, SUBUNIT,
RP FUNCTION, RNA-BINDING, AND MUTAGENESIS OF SER-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. 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. LSM5 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. LSM5,
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. LSM5 is required for
CC processing of pre-tRNAs, pre-rRNAs and U3 snoRNA.
CC {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 spliceosome
CC U4/U6-U5 tri-snRNP complex composed of the U4, U6 and U5 snRNAs and at
CC least 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. Interacts with PAT1.
CC {ECO:0000269|PubMed:10369684, ECO:0000269|PubMed:10449419,
CC ECO:0000269|PubMed:10747033, ECO:0000269|PubMed:10761922,
CC ECO:0000269|PubMed:24139796, ECO:0000269|PubMed:24240276,
CC ECO:0000269|PubMed:24513854}.
CC -!- INTERACTION:
CC P40089; P47017: LSM1; NbExp=6; IntAct=EBI-10236, EBI-174;
CC P40089; P38203: LSM2; NbExp=6; IntAct=EBI-10236, EBI-180;
CC P40089; Q06406: LSM6; NbExp=4; IntAct=EBI-10236, EBI-196;
CC -!- SUBCELLULAR LOCATION: Nucleus.
CC -!- SIMILARITY: Belongs to the snRNP Sm proteins family. {ECO:0000305}.
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DR EMBL; U18917; AAB64673.1; -; Genomic_DNA.
DR EMBL; AY557783; AAS56109.1; -; Genomic_DNA.
DR EMBL; BK006939; DAA07807.1; -; Genomic_DNA.
DR PIR; S50649; S50649.
DR RefSeq; NP_011073.1; NM_001179036.1.
DR PDB; 3JCM; EM; 3.80 A; f=1-93.
DR PDB; 4C8Q; X-ray; 3.70 A; E=1-93.
DR PDB; 4C92; X-ray; 2.30 A; E=1-93.
DR PDB; 4M75; X-ray; 2.95 A; E/L=1-93.
DR PDB; 4M77; X-ray; 3.11 A; E/L=1-93.
DR PDB; 4M78; X-ray; 2.79 A; E/L=1-93.
DR PDB; 4M7A; X-ray; 2.78 A; E/L=1-93.
DR PDB; 4M7D; X-ray; 2.60 A; E/L=1-93.
DR PDB; 5GAN; EM; 3.60 A; 5=1-93.
DR PDB; 5NRL; EM; 7.20 A; o=1-93.
DR PDB; 5VSU; X-ray; 3.10 A; E=1-93.
DR PDB; 5ZWM; EM; 3.40 A; t=1-93.
DR PDB; 5ZWO; EM; 3.90 A; t=1-93.
DR PDB; 6ASO; X-ray; 2.71 A; E=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; P40089; -.
DR SMR; P40089; -.
DR BioGRID; 36895; 73.
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-1417N; -.
DR IntAct; P40089; 34.
DR MINT; P40089; -.
DR STRING; 4932.YER146W; -.
DR MaxQB; P40089; -.
DR PaxDb; P40089; -.
DR PRIDE; P40089; -.
DR TopDownProteomics; P40089; -.
DR EnsemblFungi; YER146W_mRNA; YER146W; YER146W.
DR GeneID; 856889; -.
DR KEGG; sce:YER146W; -.
DR SGD; S000000948; LSM5.
DR VEuPathDB; FungiDB:YER146W; -.
DR eggNOG; KOG1775; Eukaryota.
DR GeneTree; ENSGT00390000001455; -.
DR HOGENOM; CLU_076902_6_0_1; -.
DR InParanoid; P40089; -.
DR OMA; MEHHGRM; -.
DR BioCyc; YEAST:G3O-30307-MON; -.
DR Reactome; R-SCE-430039; mRNA decay by 5' to 3' exoribonuclease.
DR PRO; PR:P40089; -.
DR Proteomes; UP000002311; Chromosome V.
DR RNAct; P40089; 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:ComplexPortal.
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; IMP:SGD.
DR GO; GO:0000956; P:nuclear-transcribed mRNA catabolic process; TAS:SGD.
DR GO; GO:0006364; P:rRNA processing; IMP:ComplexPortal.
DR GO; GO:0008033; P:tRNA processing; IMP:ComplexPortal.
DR CDD; cd01732; LSm5; 1.
DR InterPro; IPR033871; LSm5.
DR InterPro; IPR001163; LSM_dom_euk/arc.
DR InterPro; IPR010920; LSM_dom_sf.
DR PANTHER; PTHR20971; PTHR20971; 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; mRNA processing; mRNA splicing; Nucleus; Reference proteome;
KW Ribonucleoprotein; RNA-binding; rRNA processing; Spliceosome;
KW tRNA processing.
FT CHAIN 1..93
FT /note="U6 snRNA-associated Sm-like protein LSm5"
FT /id="PRO_0000125574"
FT MUTAGEN 74
FT /note="S->A: Slightly increases affinity for poly-U RNA
FT ends."
FT /evidence="ECO:0000269|PubMed:24240276,
FT ECO:0000269|PubMed:24513854"
FT HELIX 8..13
FT /evidence="ECO:0007829|PDB:4C92"
FT TURN 15..17
FT /evidence="ECO:0007829|PDB:4M7D"
FT STRAND 18..37
FT /evidence="ECO:0007829|PDB:4C92"
FT STRAND 43..52
FT /evidence="ECO:0007829|PDB:4C92"
FT STRAND 62..66
FT /evidence="ECO:0007829|PDB:4C92"
FT STRAND 69..73
FT /evidence="ECO:0007829|PDB:4C92"
FT STRAND 77..83
FT /evidence="ECO:0007829|PDB:4C92"
SQ SEQUENCE 93 AA; 10423 MW; 84E8A1E8E2F078FE CRC64;
MSLPEILPLE VIDKTINQKV LIVLQSNREF EGTLVGFDDF VNVILEDAVE WLIDPEDESR
NEKVMQHHGR MLLSGNNIAI LVPGGKKTPT EAL
