MTR3_YEAST
ID MTR3_YEAST Reviewed; 250 AA.
AC P48240; D6VUT8;
DT 01-FEB-1996, integrated into UniProtKB/Swiss-Prot.
DT 01-FEB-1996, sequence version 1.
DT 03-AUG-2022, entry version 169.
DE RecName: Full=Exosome complex component MTR3;
DE AltName: Full=mRNA transport regulator 3;
GN Name=MTR3; OrderedLocusNames=YGR158C; ORFNames=G6676;
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=8585325; DOI=10.1002/yea.320111410;
RA Skala J., Nawrocki A., Goffeau A.;
RT "The sequence of a 27 kb segment on the right arm of chromosome VII from
RT Saccharomyces cerevisiae reveals MOL1, NAT2, RPL30B, RSR1, CYS4, PEM1/CHO2,
RT NSR1 genes and ten new open reading frames.";
RL Yeast 11:1421-1427(1995).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=9169869;
RA Tettelin H., Agostoni-Carbone M.L., Albermann K., Albers M., Arroyo J.,
RA Backes U., Barreiros T., Bertani I., Bjourson A.J., Brueckner M.,
RA Bruschi C.V., Carignani G., Castagnoli L., Cerdan E., Clemente M.L.,
RA Coblenz A., Coglievina M., Coissac E., Defoor E., Del Bino S., Delius H.,
RA Delneri D., de Wergifosse P., Dujon B., Durand P., Entian K.-D., Eraso P.,
RA Escribano V., Fabiani L., Fartmann B., Feroli F., Feuermann M.,
RA Frontali L., Garcia-Gonzalez M., Garcia-Saez M.I., Goffeau A.,
RA Guerreiro P., Hani J., Hansen M., Hebling U., Hernandez K., Heumann K.,
RA Hilger F., Hofmann B., Indge K.J., James C.M., Klima R., Koetter P.,
RA Kramer B., Kramer W., Lauquin G., Leuther H., Louis E.J., Maillier E.,
RA Marconi A., Martegani E., Mazon M.J., Mazzoni C., McReynolds A.D.K.,
RA Melchioretto P., Mewes H.-W., Minenkova O., Mueller-Auer S., Nawrocki A.,
RA Netter P., Neu R., Nombela C., Oliver S.G., Panzeri L., Paoluzi S.,
RA Plevani P., Portetelle D., Portillo F., Potier S., Purnelle B., Rieger M.,
RA Riles L., Rinaldi T., Robben J., Rodrigues-Pousada C.,
RA Rodriguez-Belmonte E., Rodriguez-Torres A.M., Rose M., Ruzzi M.,
RA Saliola M., Sanchez-Perez M., Schaefer B., Schaefer M., Scharfe M.,
RA Schmidheini T., Schreer A., Skala J., Souciet J.-L., Steensma H.Y.,
RA Talla E., Thierry A., Vandenbol M., van der Aart Q.J.M., Van Dyck L.,
RA Vanoni M., Verhasselt P., Voet M., Volckaert G., Wambutt R., Watson M.D.,
RA Weber N., Wedler E., Wedler H., Wipfli P., Wolf K., Wright L.F.,
RA Zaccaria P., Zimmermann M., Zollner A., Kleine K.;
RT "The nucleotide sequence of Saccharomyces cerevisiae chromosome VII.";
RL Nature 387:81-84(1997).
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 FUNCTION, AND SUBCELLULAR LOCATION.
RX PubMed=8534909; DOI=10.1091/mbc.6.9.1103;
RA Kadowaki T., Schneiter R., Hitomi M., Tartakoff A.M.;
RT "Mutations in nucleolar proteins lead to nucleolar accumulation of polyA+
RT RNA in Saccharomyces cerevisiae.";
RL Mol. Biol. Cell 6:1103-1110(1995).
RN [5]
RP FUNCTION, AND IDENTIFICATION IN THE RNA EXOSOME COMPLEX BY MASS
RP SPECTROMETRY.
RX PubMed=10465791; DOI=10.1101/gad.13.16.2148;
RA Allmang C., Petfalski E., Podtelejnikov A., Mann M., Tollervey D.,
RA Mitchell P.;
RT "The yeast exosome and human PM-Scl are related complexes of 3'-->5'
RT exonucleases.";
RL Genes Dev. 13:2148-2158(1999).
RN [6]
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 [7]
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 [8]
RP RECONSTITUTION OF THE RNA EXOSOME COMPLEX, AND LACK OF EXONUCLEASE
RP ACTIVITY.
RX PubMed=17174896; DOI=10.1016/j.cell.2006.10.037;
RA Liu Q., Greimann J.C., Lima C.D.;
RT "Reconstitution, activities, and structure of the eukaryotic RNA exosome.";
RL Cell 127:1223-1237(2006).
RN [9]
RP ERRATUM OF PUBMED:17174896.
RA Liu Q., Greimann J.C., Lima C.D.;
RL Cell 131:188-189(2007).
RN [10]
RP IDENTIFICATION BY MASS SPECTROMETRY, FUNCTION OF THE RNA EXOSOME COMPLEX,
RP AND SUBUNIT.
RX PubMed=17173052; DOI=10.1038/nsmb1184;
RA Dziembowski A., Lorentzen E., Conti E., Seraphin B.;
RT "A single subunit, Dis3, is essentially responsible for yeast exosome core
RT activity.";
RL Nat. Struct. Mol. Biol. 14:15-22(2007).
CC -!- FUNCTION: Non-catalytic component of the RNA exosome complex which has
CC 3'->5' exoribonuclease activity and participates in a multitude of
CC cellular RNA processing and degradation events. In the nucleus, the RNA
CC exosome complex is involved in proper maturation of stable RNA species
CC such as rRNA, snRNA and snoRNA, in the elimination of RNA processing
CC by-products and non-coding 'pervasive' transcripts, such as antisense
CC RNA species and cryptic unstable transcripts (CUTs), and of mRNAs with
CC processing defects, thereby limiting or excluding their export to the
CC cytoplasm. In the cytoplasm, the RNA exosome complex is involved in
CC general mRNA turnover and in RNA surveillance pathways, preventing
CC translation of aberrant mRNAs. The catalytic inactive RNA exosome core
CC complex of 9 subunits (Exo-9) is proposed to play a pivotal role in the
CC binding and presentation of RNA for ribonucleolysis, and to serve as a
CC scaffold for the association with catalytic subunits and accessory
CC proteins or complexes. MTR3 is part of the hexameric ring of RNase PH
CC domain-containing subunits proposed to form a central channel which
CC threads RNA substrates for degradation. {ECO:0000269|PubMed:10465791,
CC ECO:0000269|PubMed:17173052, ECO:0000269|PubMed:8534909}.
CC -!- SUBUNIT: Component of the RNA exosome complex. Specifically part of the
CC catalytically inactive RNA exosome core (Exo-9) complex which
CC associates with catalytic subunits DIS3 and RRP6 in cytoplasmic- and
CC nuclear-specific RNA exosome complex forms. Exo-9 is formed by a
CC hexameric ring of RNase PH domain-containing subunits and peripheral S1
CC domain-containing components CSL4, RRP4 and RRP40 located on the top of
CC the ring structure. {ECO:0000269|PubMed:10465791,
CC ECO:0000269|PubMed:17173052}.
CC -!- INTERACTION:
CC P48240; P53859: CSL4; NbExp=16; IntAct=EBI-1749, EBI-1731;
CC P48240; Q12277: RRP42; NbExp=11; IntAct=EBI-1749, EBI-1765;
CC P48240; P46948: SKI6; NbExp=8; IntAct=EBI-1749, EBI-1788;
CC -!- SUBCELLULAR LOCATION: Cytoplasm. Nucleus, nucleolus.
CC -!- MISCELLANEOUS: Present with 7380 molecules/cell in log phase SD medium.
CC {ECO:0000269|PubMed:14562106}.
CC -!- SIMILARITY: Belongs to the RNase PH family. {ECO:0000305}.
CC -!- CAUTION: According to PubMed:17173052 and PubMed:17174896, only
CC DIS3/RRP44 subunit of the exosome core has exonuclease activity.
CC {ECO:0000305}.
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DR EMBL; X85807; CAA59815.1; -; Genomic_DNA.
DR EMBL; S80548; AAB35850.1; -; Genomic_DNA.
DR EMBL; Z72943; CAA97172.1; -; Genomic_DNA.
DR EMBL; BK006941; DAA08249.1; -; Genomic_DNA.
DR PIR; S58362; S58362.
DR RefSeq; NP_011674.3; NM_001181287.3.
DR PDB; 4IFD; X-ray; 2.80 A; F=1-250.
DR PDB; 4OO1; X-ray; 3.30 A; F=1-250.
DR PDB; 5C0W; X-ray; 4.60 A; F=1-250.
DR PDB; 5C0X; X-ray; 3.81 A; F=1-250.
DR PDB; 5G06; EM; 4.20 A; F=1-250.
DR PDB; 5JEA; X-ray; 2.65 A; F=1-250.
DR PDB; 5K36; X-ray; 3.10 A; F=1-250.
DR PDB; 5OKZ; X-ray; 3.20 A; F/P/Z/j=1-250.
DR PDB; 5VZJ; X-ray; 3.30 A; F=1-250.
DR PDB; 6FSZ; EM; 4.60 A; FF=1-250.
DR PDB; 6LQS; EM; 3.80 A; M3=1-250.
DR PDB; 7AJT; EM; 4.60 A; EG=1-250.
DR PDB; 7AJU; EM; 3.80 A; EG=1-250.
DR PDB; 7D4I; EM; 4.00 A; M3=1-250.
DR PDBsum; 4IFD; -.
DR PDBsum; 4OO1; -.
DR PDBsum; 5C0W; -.
DR PDBsum; 5C0X; -.
DR PDBsum; 5G06; -.
DR PDBsum; 5JEA; -.
DR PDBsum; 5K36; -.
DR PDBsum; 5OKZ; -.
DR PDBsum; 5VZJ; -.
DR PDBsum; 6FSZ; -.
DR PDBsum; 6LQS; -.
DR PDBsum; 7AJT; -.
DR PDBsum; 7AJU; -.
DR PDBsum; 7D4I; -.
DR AlphaFoldDB; P48240; -.
DR SMR; P48240; -.
DR BioGRID; 33406; 113.
DR ComplexPortal; CPX-599; Nuclear/nucleolar exosome complex, DIS3-RRP6 variant.
DR ComplexPortal; CPX-603; Cytoplasmic exosome complex, DIS3 variant.
DR DIP; DIP-931N; -.
DR IntAct; P48240; 26.
DR MINT; P48240; -.
DR STRING; 4932.YGR158C; -.
DR iPTMnet; P48240; -.
DR MaxQB; P48240; -.
DR PaxDb; P48240; -.
DR PRIDE; P48240; -.
DR EnsemblFungi; YGR158C_mRNA; YGR158C; YGR158C.
DR GeneID; 853062; -.
DR KEGG; sce:YGR158C; -.
DR SGD; S000003390; MTR3.
DR VEuPathDB; FungiDB:YGR158C; -.
DR eggNOG; KOG1068; Eukaryota.
DR GeneTree; ENSGT00940000153348; -.
DR HOGENOM; CLU_078569_0_0_1; -.
DR InParanoid; P48240; -.
DR OMA; ILPTCIN; -.
DR BioCyc; YEAST:G3O-30858-MON; -.
DR Reactome; R-SCE-429958; mRNA decay by 3' to 5' exoribonuclease.
DR Reactome; R-SCE-450385; Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA.
DR Reactome; R-SCE-450513; Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA.
DR Reactome; R-SCE-6791226; Major pathway of rRNA processing in the nucleolus and cytosol.
DR PRO; PR:P48240; -.
DR Proteomes; UP000002311; Chromosome VII.
DR RNAct; P48240; protein.
DR GO; GO:0000177; C:cytoplasmic exosome (RNase complex); IDA:SGD.
DR GO; GO:0000178; C:exosome (RNase complex); IPI:ComplexPortal.
DR GO; GO:0000176; C:nuclear exosome (RNase complex); IDA:SGD.
DR GO; GO:0005730; C:nucleolus; IDA:SGD.
DR GO; GO:0005634; C:nucleus; IDA:ComplexPortal.
DR GO; GO:0003723; F:RNA binding; IEA:UniProtKB-KW.
DR GO; GO:0000467; P:exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA); IMP:SGD.
DR GO; GO:0070651; P:nonfunctional rRNA decay; IC:SGD.
DR GO; GO:0071028; P:nuclear mRNA surveillance; IMP:SGD.
DR GO; GO:0071039; P:nuclear polyadenylation-dependent CUT catabolic process; IMP:SGD.
DR GO; GO:0071042; P:nuclear polyadenylation-dependent mRNA catabolic process; IC:SGD.
DR GO; GO:0071035; P:nuclear polyadenylation-dependent rRNA catabolic process; IMP:SGD.
DR GO; GO:0071038; P:nuclear polyadenylation-dependent tRNA catabolic process; IDA:SGD.
DR GO; GO:0070478; P:nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay; IC:SGD.
DR GO; GO:0034427; P:nuclear-transcribed mRNA catabolic process, exonucleolytic, 3'-5'; IBA:GO_Central.
DR GO; GO:0070481; P:nuclear-transcribed mRNA catabolic process, non-stop decay; IC:SGD.
DR GO; GO:0071051; P:polyadenylation-dependent snoRNA 3'-end processing; IMP:SGD.
DR GO; GO:0006401; P:RNA catabolic process; IDA:ComplexPortal.
DR GO; GO:0006396; P:RNA processing; IDA:ComplexPortal.
DR GO; GO:0016075; P:rRNA catabolic process; IBA:GO_Central.
DR GO; GO:0034475; P:U4 snRNA 3'-end processing; IMP:SGD.
DR Gene3D; 3.30.230.70; -; 1.
DR InterPro; IPR001247; ExoRNase_PH_dom1.
DR InterPro; IPR027408; PNPase/RNase_PH_dom_sf.
DR InterPro; IPR020568; Ribosomal_S5_D2-typ_fold.
DR Pfam; PF01138; RNase_PH; 1.
DR SUPFAM; SSF54211; SSF54211; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Cytoplasm; Exosome; Nucleus; Reference proteome; RNA-binding;
KW rRNA processing.
FT CHAIN 1..250
FT /note="Exosome complex component MTR3"
FT /id="PRO_0000139979"
FT REGION 1..44
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT STRAND 6..8
FT /evidence="ECO:0007829|PDB:4IFD"
FT STRAND 15..17
FT /evidence="ECO:0007829|PDB:5OKZ"
FT STRAND 22..24
FT /evidence="ECO:0007829|PDB:5K36"
FT STRAND 45..50
FT /evidence="ECO:0007829|PDB:5JEA"
FT STRAND 56..66
FT /evidence="ECO:0007829|PDB:5JEA"
FT STRAND 69..81
FT /evidence="ECO:0007829|PDB:5JEA"
FT STRAND 84..86
FT /evidence="ECO:0007829|PDB:5JEA"
FT STRAND 89..99
FT /evidence="ECO:0007829|PDB:5JEA"
FT STRAND 101..103
FT /evidence="ECO:0007829|PDB:5K36"
FT HELIX 107..124
FT /evidence="ECO:0007829|PDB:5JEA"
FT HELIX 127..129
FT /evidence="ECO:0007829|PDB:5JEA"
FT STRAND 133..146
FT /evidence="ECO:0007829|PDB:5JEA"
FT HELIX 165..182
FT /evidence="ECO:0007829|PDB:5JEA"
FT STRAND 187..189
FT /evidence="ECO:0007829|PDB:5JEA"
FT STRAND 192..196
FT /evidence="ECO:0007829|PDB:5JEA"
FT STRAND 199..204
FT /evidence="ECO:0007829|PDB:5JEA"
FT HELIX 205..207
FT /evidence="ECO:0007829|PDB:5JEA"
FT STRAND 209..215
FT /evidence="ECO:0007829|PDB:5JEA"
FT HELIX 223..247
FT /evidence="ECO:0007829|PDB:5JEA"
SQ SEQUENCE 250 AA; 27577 MW; 2FA07ABB4A1115E0 CRC64;
MNVQDRRRLL GPAAAKPMAF SNTTTHVPEK KSTDLTPKGN ESEQELSLHT GFIENCNGSA
LVEARSLGHQ TSLITAVYGP RSIRGSFTSQ GTISIQLKNG LLEKYNTNEL KEVSSFLMGI
FNSVVNLSRY PKSGIDIFVY LTYDKDLTNN PQDDDSQSKM MSSQISSLIP HCITSITLAL
ADAGIELVDM AGAGEANGTV VSFIKNGEEI VGFWKDDGDD EDLLECLDRC KEQYNRYRDL
MISCLMNQET
