SMD2_YEAST
ID SMD2_YEAST Reviewed; 110 AA.
AC Q06217; D6VYS2;
DT 01-NOV-1997, integrated into UniProtKB/Swiss-Prot.
DT 30-MAY-2000, sequence version 2.
DT 03-AUG-2022, entry version 177.
DE RecName: Full=Small nuclear ribonucleoprotein Sm D2;
DE Short=Sm-D2;
DE AltName: Full=snRNP core protein D2;
GN Name=SMD2; OrderedLocusNames=YLR275W; ORFNames=L9328.5;
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].
RX PubMed=9528767; DOI=10.1128/mcb.18.4.1956;
RA Camasses A., Bragado-Nilsson E., Martin R., Seraphin B., Bordonne R.;
RT "Interactions within the yeast Sm core complex: from proteins to amino
RT acids.";
RL Mol. Cell. Biol. 18:1956-1966(1998).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND RNA-BINDING.
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 [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=9169871;
RA Johnston M., Hillier L.W., Riles L., Albermann K., Andre B., Ansorge W.,
RA Benes V., Brueckner M., Delius H., Dubois E., Duesterhoeft A.,
RA Entian K.-D., Floeth M., Goffeau A., Hebling U., Heumann K.,
RA Heuss-Neitzel D., Hilbert H., Hilger F., Kleine K., Koetter P., Louis E.J.,
RA Messenguy F., Mewes H.-W., Miosga T., Moestl D., Mueller-Auer S.,
RA Nentwich U., Obermaier B., Piravandi E., Pohl T.M., Portetelle D.,
RA Purnelle B., Rechmann S., Rieger M., Rinke M., Rose M., Scharfe M.,
RA Scherens B., Scholler P., Schwager C., Schwarz S., Underwood A.P.,
RA Urrestarazu L.A., Vandenbol M., Verhasselt P., Vierendeels F., Voet M.,
RA Volckaert G., Voss H., Wambutt R., Wedler E., Wedler H., Zimmermann F.K.,
RA Zollner A., Hani J., Hoheisel J.D.;
RT "The nucleotide sequence of Saccharomyces cerevisiae chromosome XII.";
RL Nature 387:87-90(1997).
RN [4]
RP SEQUENCE REVISION.
RA Cherry J.M.;
RL Submitted (AUG-1997) to the EMBL/GenBank/DDBJ databases.
RN [5]
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 [6]
RP PARTIAL PROTEIN SEQUENCE, AND IDENTIFICATION.
RX PubMed=9012791; DOI=10.1073/pnas.94.2.385;
RA Neubauer G., Gottschalk A., Fabrizio P., Seraphin B., Luehrmann R.,
RA Mann M.;
RT "Identification of the proteins of the yeast U1 small nuclear
RT ribonucleoprotein complex by mass spectrometry.";
RL Proc. Natl. Acad. Sci. U.S.A. 94:385-390(1997).
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 SUBUNIT.
RX PubMed=11302706; DOI=10.1006/jmbi.2001.4549;
RA Walke S., Bragado-Nilsson E., Seraphin B., Nagai K.;
RT "Stoichiometry of the Sm proteins in yeast spliceosomal snRNPs supports the
RT heptamer ring model of the core domain.";
RL J. Mol. Biol. 308:49-58(2001).
RN [9]
RP CHARACTERIZATION OF THE SPLICEOSOME.
RX PubMed=11804584; DOI=10.1016/s1097-2765(02)00436-7;
RA Stevens S.W., Ryan D.E., Ge H.Y., Moore R.E., Young M.K., Lee T.D.,
RA Abelson J.;
RT "Composition and functional characterization of the yeast spliceosomal
RT penta-snRNP.";
RL Mol. Cell 9:31-44(2002).
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 IDENTIFICATION IN THE CWC COMPLEX, AND IDENTIFICATION BY MASS SPECTROMETRY.
RX PubMed=11884590; DOI=10.1128/mcb.22.7.2011-2024.2002;
RA Ohi M.D., Link A.J., Ren L., Jennings J.L., McDonald W.H., Gould K.L.;
RT "Proteomics analysis reveals stable multiprotein complexes in both fission
RT and budding yeasts containing Myb-related Cdc5p/Cef1p, novel pre-mRNA
RT splicing factors, and snRNAs.";
RL Mol. Cell. Biol. 22:2011-2024(2002).
CC -!- FUNCTION: Plays a role in pre-mRNA splicing as a core component of the
CC spliceosomal U1, U2, U4 and U5 small nuclear ribonucleoproteins
CC (snRNPs), the building blocks of the spliceosome.
CC {ECO:0000269|PubMed:11804584}.
CC -!- SUBUNIT: Component of the Sm core complex, present in spliceosomal
CC snRNP U1, U2, U4/U6 and U5. The core complex contains SMB1, SMD1, SMD2,
CC SMD3, SME1, SMX3 and SMX2 (Sm proteins B, D1, D2, D3, E, F and G,
CC respectively), and is probably a heptameric ring structure. Belongs to
CC the CWC complex (or CEF1-associated complex), a spliceosome sub-complex
CC reminiscent of a late-stage spliceosome composed of the U2, U5 and U6
CC snRNAs and at least BUD13, BUD31, BRR2, CDC40, CEF1, CLF1, CUS1, CWC2,
CC CWC15, CWC21, CWC22, CWC23, CWC24, CWC25, CWC27, ECM2, HSH155, IST3,
CC ISY1, LEA1, MSL1, NTC20, PRP8, PRP9, PRP11, PRP19, PRP21, PRP22, PRP45,
CC PRP46, SLU7, SMB1, SMD1, SMD2, SMD3, SMX2, SMX3, SNT309, SNU114, SPP2,
CC SYF1, SYF2, RSE1 and YJU2. Component of the U4/U6-U5 tri-snRNP complex
CC composed of the U4, U6 and U5 snRNAs and at least PRP3, PRP4, PRP6,
CC PRP8, PRP18, PRP31, PRP38, SNU13, SNU23, SNU66, SNU114, SPP381, SMB1,
CC SMD1, SMD2, SMD3, SMX2, SMX3, LSM2, LSM3, LSM4, LSM5, LSM6, LSM7, LSM8,
CC BRR2 and DIB1. {ECO:0000269|PubMed:10449419,
CC ECO:0000269|PubMed:11302706, ECO:0000269|PubMed:11884590}.
CC -!- INTERACTION:
CC Q06217; P38203: LSM2; NbExp=3; IntAct=EBI-235, EBI-180;
CC Q06217; P40070: LSM4; NbExp=3; IntAct=EBI-235, EBI-188;
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000250|UniProtKB:P62316}.
CC Cytoplasm, cytosol {ECO:0000250|UniProtKB:P62316}.
CC -!- MISCELLANEOUS: Present with 799 molecules/cell in log phase SD medium.
CC {ECO:0000269|PubMed:14562106}.
CC -!- SIMILARITY: Belongs to the snRNP core protein family. {ECO:0000305}.
CC ---------------------------------------------------------------------------
CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC ---------------------------------------------------------------------------
DR EMBL; U17245; AAB67368.1; -; Genomic_DNA.
DR EMBL; BK006945; DAA09588.1; -; Genomic_DNA.
DR PIR; S69326; S69326.
DR RefSeq; NP_013377.1; NM_001182162.1.
DR PDB; 3JCM; EM; 3.80 A; Q/U=1-110.
DR PDB; 5GAM; EM; 3.70 A; j=1-110.
DR PDB; 5GAN; EM; 3.60 A; j/m=1-110.
DR PDB; 5GAO; EM; 3.60 A; m=1-110.
DR PDB; 5GM6; EM; 3.50 A; g=15-108.
DR PDB; 5GMK; EM; 3.40 A; e/g=1-110.
DR PDB; 5LJ3; EM; 3.80 A; j/m=1-110.
DR PDB; 5LJ5; EM; 3.80 A; j/m=1-110.
DR PDB; 5LQW; EM; 5.80 A; j=1-110.
DR PDB; 5MPS; EM; 3.85 A; j=1-110.
DR PDB; 5MQ0; EM; 4.17 A; j/m=1-110.
DR PDB; 5NRL; EM; 7.20 A; i/m/u=1-110.
DR PDB; 5WSG; EM; 4.00 A; W/g=1-110.
DR PDB; 5Y88; EM; 3.70 A; g/n=1-110.
DR PDB; 5YLZ; EM; 3.60 A; g/n=1-110.
DR PDB; 5ZWM; EM; 3.40 A; R/c/n=1-110.
DR PDB; 5ZWN; EM; 3.30 A; c=1-110.
DR PDB; 5ZWO; EM; 3.90 A; R/c/n=1-110.
DR PDB; 6BK8; EM; 3.30 A; a/q=1-110.
DR PDB; 6EXN; EM; 3.70 A; j/m=1-110.
DR PDB; 6G90; EM; 4.00 A; i/u=1-110.
DR PDB; 6J6G; EM; 3.20 A; e/g=1-110.
DR PDB; 6J6H; EM; 3.60 A; e/g=1-110.
DR PDB; 6J6N; EM; 3.86 A; e/g=1-110.
DR PDB; 6J6Q; EM; 3.70 A; e/g=1-110.
DR PDB; 6N7P; EM; 3.60 A; M=1-110.
DR PDB; 6N7R; EM; 3.20 A; M=1-110.
DR PDB; 6N7X; EM; 3.60 A; M=1-110.
DR PDB; 7B9V; EM; 2.80 A; j/m=1-110.
DR PDB; 7OQB; EM; 9.00 A; u=1-110.
DR PDB; 7OQC; EM; 4.10 A; i=1-110.
DR PDB; 7OQE; EM; 5.90 A; i/u=1-110.
DR PDBsum; 3JCM; -.
DR PDBsum; 5GAM; -.
DR PDBsum; 5GAN; -.
DR PDBsum; 5GAO; -.
DR PDBsum; 5GM6; -.
DR PDBsum; 5GMK; -.
DR PDBsum; 5LJ3; -.
DR PDBsum; 5LJ5; -.
DR PDBsum; 5LQW; -.
DR PDBsum; 5MPS; -.
DR PDBsum; 5MQ0; -.
DR PDBsum; 5NRL; -.
DR PDBsum; 5WSG; -.
DR PDBsum; 5Y88; -.
DR PDBsum; 5YLZ; -.
DR PDBsum; 5ZWM; -.
DR PDBsum; 5ZWN; -.
DR PDBsum; 5ZWO; -.
DR PDBsum; 6BK8; -.
DR PDBsum; 6EXN; -.
DR PDBsum; 6G90; -.
DR PDBsum; 6J6G; -.
DR PDBsum; 6J6H; -.
DR PDBsum; 6J6N; -.
DR PDBsum; 6J6Q; -.
DR PDBsum; 6N7P; -.
DR PDBsum; 6N7R; -.
DR PDBsum; 6N7X; -.
DR PDBsum; 7B9V; -.
DR PDBsum; 7OQB; -.
DR PDBsum; 7OQC; -.
DR PDBsum; 7OQE; -.
DR AlphaFoldDB; Q06217; -.
DR SMR; Q06217; -.
DR BioGRID; 31543; 729.
DR ComplexPortal; CPX-1651; PRP19-associated complex.
DR ComplexPortal; CPX-23; U1 small nuclear ribonucleoprotein complex.
DR ComplexPortal; CPX-25; U4/U6.U5 tri-small nuclear ribonucleoprotein complex.
DR ComplexPortal; CPX-26; U2 small nuclear ribonucleoprotein complex.
DR ComplexPortal; CPX-29; U5 small nuclear ribonucleoprotein complex.
DR ComplexPortal; CPX-30; U5 small nuclear ribonucleoprotein complex, AAR2 variant.
DR ComplexPortal; CPX-31; U4 small nuclear ribonucleoprotein complex.
DR ComplexPortal; CPX-32; U4/U6 small nuclear ribonucleoprotein complex.
DR ComplexPortal; CPX-43; Sm complex.
DR DIP; DIP-1421N; -.
DR IntAct; Q06217; 36.
DR MINT; Q06217; -.
DR STRING; 4932.YLR275W; -.
DR MaxQB; Q06217; -.
DR PaxDb; Q06217; -.
DR PRIDE; Q06217; -.
DR EnsemblFungi; YLR275W_mRNA; YLR275W; YLR275W.
DR GeneID; 850981; -.
DR KEGG; sce:YLR275W; -.
DR SGD; S000004265; SMD2.
DR VEuPathDB; FungiDB:YLR275W; -.
DR eggNOG; KOG3459; Eukaryota.
DR GeneTree; ENSGT00390000017608; -.
DR HOGENOM; CLU_076902_2_1_1; -.
DR InParanoid; Q06217; -.
DR OMA; GPMSLIN; -.
DR BioCyc; YEAST:G3O-32374-MON; -.
DR PRO; PR:Q06217; -.
DR Proteomes; UP000002311; Chromosome XII.
DR RNAct; Q06217; protein.
DR GO; GO:0071013; C:catalytic step 2 spliceosome; IBA:GO_Central.
DR GO; GO:0000243; C:commitment complex; IC:ComplexPortal.
DR GO; GO:0005737; C:cytoplasm; IC:ComplexPortal.
DR GO; GO:0005829; C:cytosol; IEA:UniProtKB-SubCell.
DR GO; GO:0005634; C:nucleus; IC:ComplexPortal.
DR GO; GO:0071011; C:precatalytic spliceosome; IBA:GO_Central.
DR GO; GO:0005681; C:spliceosomal complex; IC:ComplexPortal.
DR GO; GO:0005685; C:U1 snRNP; IDA:SGD.
DR GO; GO:0005686; C:U2 snRNP; IBA:GO_Central.
DR GO; GO:0071004; C:U2-type prespliceosome; IDA:SGD.
DR GO; GO:0005687; C:U4 snRNP; IPI: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:0005682; C:U5 snRNP; IDA:SGD.
DR GO; GO:0003723; F:RNA binding; IEA:UniProtKB-KW.
DR GO; GO:0036261; P:7-methylguanosine cap hypermethylation; IMP:ComplexPortal.
DR GO; GO:0000395; P:mRNA 5'-splice site recognition; IC:ComplexPortal.
DR GO; GO:0000398; P:mRNA splicing, via spliceosome; IPI:ComplexPortal.
DR GO; GO:0000245; P:spliceosomal complex assembly; IC:ComplexPortal.
DR GO; GO:0000387; P:spliceosomal snRNP assembly; IBA:GO_Central.
DR GO; GO:1903241; P:U2-type prespliceosome assembly; IC:ComplexPortal.
DR CDD; cd01720; Sm_D2; 1.
DR InterPro; IPR001163; LSM_dom_euk/arc.
DR InterPro; IPR010920; LSM_dom_sf.
DR InterPro; IPR027248; Sm_D2.
DR PANTHER; PTHR12777; PTHR12777; 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; Direct protein sequencing; mRNA processing;
KW mRNA splicing; Nucleus; Reference proteome; Ribonucleoprotein; RNA-binding.
FT CHAIN 1..110
FT /note="Small nuclear ribonucleoprotein Sm D2"
FT /id="PRO_0000122213"
FT HELIX 3..7
FT /evidence="ECO:0007829|PDB:6N7R"
FT TURN 10..12
FT /evidence="ECO:0007829|PDB:6N7R"
FT HELIX 15..27
FT /evidence="ECO:0007829|PDB:6J6G"
FT STRAND 28..30
FT /evidence="ECO:0007829|PDB:6N7R"
FT HELIX 32..40
FT /evidence="ECO:0007829|PDB:6J6G"
FT STRAND 44..51
FT /evidence="ECO:0007829|PDB:6J6G"
FT STRAND 53..61
FT /evidence="ECO:0007829|PDB:6J6G"
FT STRAND 67..82
FT /evidence="ECO:0007829|PDB:6J6G"
FT STRAND 84..96
FT /evidence="ECO:0007829|PDB:6J6G"
FT STRAND 100..106
FT /evidence="ECO:0007829|PDB:6J6G"
SQ SEQUENCE 110 AA; 12853 MW; 7287070B10E090C0 CRC64;
MSSQIIDRPK HELSRAELEE LEEFEFKHGP MSLINDAMVT RTPVIISLRN NHKIIARVKA
FDRHCNMVLE NVKELWTEKK GKNVINRERF ISKLFLRGDS VIVVLKTPVE
