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Exosome complex component MTR3 (mRNA transport regulator 3)

 MTR3_YEAST              Reviewed;         250 AA.
P48240; D6VUT8;
01-FEB-1996, integrated into UniProtKB/Swiss-Prot.
01-FEB-1996, sequence version 1.
22-NOV-2017, entry version 138.
RecName: Full=Exosome complex component MTR3;
AltName: Full=mRNA transport regulator 3;
Name=MTR3; OrderedLocusNames=YGR158C; ORFNames=G6676;
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina;
Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces.
NCBI_TaxID=559292;
[1]
NUCLEOTIDE SEQUENCE [GENOMIC DNA].
STRAIN=ATCC 204508 / S288c;
PubMed=8585325; DOI=10.1002/yea.320111410;
Skala J., Nawrocki A., Goffeau A.;
"The sequence of a 27 kb segment on the right arm of chromosome VII
from Saccharomyces cerevisiae reveals MOL1, NAT2, RPL30B, RSR1, CYS4,
PEM1/CHO2, NSR1 genes and ten new open reading frames.";
Yeast 11:1421-1427(1995).
[2]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=ATCC 204508 / S288c;
PubMed=9169869;
Tettelin H., Agostoni-Carbone M.L., Albermann K., Albers M.,
Arroyo J., Backes U., Barreiros T., Bertani I., Bjourson A.J.,
Brueckner M., Bruschi C.V., Carignani G., Castagnoli L., Cerdan E.,
Clemente M.L., Coblenz A., Coglievina M., Coissac E., Defoor E.,
Del Bino S., Delius H., Delneri D., de Wergifosse P., Dujon B.,
Durand P., Entian K.-D., Eraso P., Escribano V., Fabiani L.,
Fartmann B., Feroli F., Feuermann M., Frontali L., Garcia-Gonzalez M.,
Garcia-Saez M.I., Goffeau A., Guerreiro P., Hani J., Hansen M.,
Hebling U., Hernandez K., Heumann K., Hilger F., Hofmann B.,
Indge K.J., James C.M., Klima R., Koetter P., Kramer B., Kramer W.,
Lauquin G., Leuther H., Louis E.J., Maillier E., Marconi A.,
Martegani E., Mazon M.J., Mazzoni C., McReynolds A.D.K.,
Melchioretto P., Mewes H.-W., Minenkova O., Mueller-Auer S.,
Nawrocki A., Netter P., Neu R., Nombela C., Oliver S.G., Panzeri L.,
Paoluzi S., Plevani P., Portetelle D., Portillo F., Potier S.,
Purnelle B., Rieger M., Riles L., Rinaldi T., Robben J.,
Rodrigues-Pousada C., Rodriguez-Belmonte E., Rodriguez-Torres A.M.,
Rose M., Ruzzi M., Saliola M., Sanchez-Perez M., Schaefer B.,
Schaefer M., Scharfe M., Schmidheini T., Schreer A., Skala J.,
Souciet J.-L., Steensma H.Y., Talla E., Thierry A., Vandenbol M.,
van der Aart Q.J.M., Van Dyck L., Vanoni M., Verhasselt P., Voet M.,
Volckaert G., Wambutt R., Watson M.D., Weber N., Wedler E., Wedler H.,
Wipfli P., Wolf K., Wright L.F., Zaccaria P., Zimmermann M.,
Zollner A., Kleine K.;
"The nucleotide sequence of Saccharomyces cerevisiae chromosome VII.";
Nature 387:81-84(1997).
[3]
GENOME REANNOTATION.
STRAIN=ATCC 204508 / S288c;
PubMed=24374639; DOI=10.1534/g3.113.008995;
Engel S.R., Dietrich F.S., Fisk D.G., Binkley G., Balakrishnan R.,
Costanzo M.C., Dwight S.S., Hitz B.C., Karra K., Nash R.S., Weng S.,
Wong E.D., Lloyd P., Skrzypek M.S., Miyasato S.R., Simison M.,
Cherry J.M.;
"The reference genome sequence of Saccharomyces cerevisiae: Then and
now.";
G3 (Bethesda) 4:389-398(2014).
[4]
FUNCTION, AND SUBCELLULAR LOCATION.
PubMed=8534909; DOI=10.1091/mbc.6.9.1103;
Kadowaki T., Schneiter R., Hitomi M., Tartakoff A.M.;
"Mutations in nucleolar proteins lead to nucleolar accumulation of
polyA+ RNA in Saccharomyces cerevisiae.";
Mol. Biol. Cell 6:1103-1110(1995).
[5]
FUNCTION, AND IDENTIFICATION IN THE RNA EXOSOME COMPLEX BY MASS
SPECTROMETRY.
PubMed=10465791; DOI=10.1101/gad.13.16.2148;
Allmang C., Petfalski E., Podtelejnikov A., Mann M., Tollervey D.,
Mitchell P.;
"The yeast exosome and human PM-Scl are related complexes of 3'-->5'
exonucleases.";
Genes Dev. 13:2148-2158(1999).
[6]
SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
PubMed=14562095; DOI=10.1038/nature02026;
Huh W.-K., Falvo J.V., Gerke L.C., Carroll A.S., Howson R.W.,
Weissman J.S., O'Shea E.K.;
"Global analysis of protein localization in budding yeast.";
Nature 425:686-691(2003).
[7]
LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
PubMed=14562106; DOI=10.1038/nature02046;
Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A.,
Dephoure N., O'Shea E.K., Weissman J.S.;
"Global analysis of protein expression in yeast.";
Nature 425:737-741(2003).
[8]
RECONSTITUTION OF THE RNA EXOSOME COMPLEX, AND LACK OF EXONUCLEASE
ACTIVITY.
PubMed=17174896; DOI=10.1016/j.cell.2006.10.037;
Liu Q., Greimann J.C., Lima C.D.;
"Reconstitution, activities, and structure of the eukaryotic RNA
exosome.";
Cell 127:1223-1237(2006).
[9]
ERRATUM.
Liu Q., Greimann J.C., Lima C.D.;
Cell 131:188-189(2007).
[10]
IDENTIFICATION BY MASS SPECTROMETRY, FUNCTION OF THE RNA EXOSOME
COMPLEX, AND SUBUNIT.
PubMed=17173052; DOI=10.1038/nsmb1184;
Dziembowski A., Lorentzen E., Conti E., Seraphin B.;
"A single subunit, Dis3, is essentially responsible for yeast exosome
core activity.";
Nat. Struct. Mol. Biol. 14:15-22(2007).
-!- FUNCTION: Non-catalytic component of the RNA exosome complex which
has 3'->5' exoribonuclease activity and participates in a
multitude of cellular RNA processing and degradation events. In
the nucleus, the RNA exosome complex is involved in proper
maturation of stable RNA species such as rRNA, snRNA and snoRNA,
in the elimination of RNA processing by-products and non-coding
'pervasive' transcripts, such as antisense RNA species and cryptic
unstable transcripts (CUTs), and of mRNAs with processing defects,
thereby limiting or excluding their export to the cytoplasm. In
the cytoplasm, the RNA exosome complex is involved in general mRNA
turnover and in RNA surveillance pathways, preventing translation
of aberrant mRNAs. The catalytic inactive RNA exosome core complex
of 9 subunits (Exo-9) is proposed to play a pivotal role in the
binding and presentation of RNA for ribonucleolysis, and to serve
as a scaffold for the association with catalytic subunits and
accessory proteins or complexes. MTR3 is part of the hexameric
ring of RNase PH domain-containing subunits proposed to form a
central channel which threads RNA substrates for degradation.
{ECO:0000269|PubMed:10465791, ECO:0000269|PubMed:17173052,
ECO:0000269|PubMed:8534909}.
-!- SUBUNIT: Component of the RNA exosome complex. Specifically part
of the catalytically inactive RNA exosome core (Exo-9) complex
which associates with catalytic subunits DIS3 and RRP6 in
cytoplasmic- and nuclear-specific RNA exosome complex forms. Exo-9
is formed by a hexameric ring of RNase PH domain-containing
subunits and peripheral S1 domain-containing components CSL4, RRP4
and RRP40 located on the top of the ring structure.
{ECO:0000269|PubMed:10465791, ECO:0000269|PubMed:17173052}.
-!- INTERACTION:
P53859:CSL4; NbExp=16; IntAct=EBI-1749, EBI-1731;
Q12277:RRP42; NbExp=11; IntAct=EBI-1749, EBI-1765;
P46948:SKI6; NbExp=8; IntAct=EBI-1749, EBI-1788;
-!- SUBCELLULAR LOCATION: Cytoplasm. Nucleus, nucleolus.
-!- MISCELLANEOUS: Present with 7380 molecules/cell in log phase SD
medium. {ECO:0000269|PubMed:14562106}.
-!- SIMILARITY: Belongs to the RNase PH family. {ECO:0000305}.
-!- CAUTION: According to PubMed:17173052 and PubMed:17174896, only
DIS3/RRP44 subunit of the exosome core has exonuclease activity.
{ECO:0000305}.
-----------------------------------------------------------------------
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EMBL; X85807; CAA59815.1; -; Genomic_DNA.
EMBL; S80548; AAB35850.1; -; Genomic_DNA.
EMBL; Z72943; CAA97172.1; -; Genomic_DNA.
EMBL; BK006941; DAA08249.1; -; Genomic_DNA.
PIR; S58362; S58362.
RefSeq; NP_011674.3; NM_001181287.3.
PDB; 4IFD; X-ray; 2.80 A; F=1-250.
PDB; 4OO1; X-ray; 3.30 A; F=1-250.
PDB; 5C0W; X-ray; 4.60 A; F=1-250.
PDB; 5C0X; X-ray; 3.81 A; F=1-250.
PDB; 5G06; EM; 4.20 A; F=1-250.
PDB; 5JEA; X-ray; 2.65 A; F=1-250.
PDB; 5K36; X-ray; 3.10 A; F=1-250.
PDB; 5OKZ; X-ray; 3.20 A; F/P/Z/j=1-250.
PDB; 5VZJ; X-ray; 3.30 A; F=1-250.
PDBsum; 4IFD; -.
PDBsum; 4OO1; -.
PDBsum; 5C0W; -.
PDBsum; 5C0X; -.
PDBsum; 5G06; -.
PDBsum; 5JEA; -.
PDBsum; 5K36; -.
PDBsum; 5OKZ; -.
PDBsum; 5VZJ; -.
ProteinModelPortal; P48240; -.
SMR; P48240; -.
BioGrid; 33406; 100.
DIP; DIP-931N; -.
IntAct; P48240; 25.
MINT; MINT-409300; -.
STRING; 4932.YGR158C; -.
iPTMnet; P48240; -.
MaxQB; P48240; -.
PRIDE; P48240; -.
EnsemblFungi; YGR158C; YGR158C; YGR158C.
GeneID; 853062; -.
KEGG; sce:YGR158C; -.
EuPathDB; FungiDB:YGR158C; -.
SGD; S000003390; MTR3.
HOGENOM; HOG000113690; -.
InParanoid; P48240; -.
KO; K12587; -.
OMA; MNVQDRR; -.
OrthoDB; EOG092C4NRQ; -.
BioCyc; YEAST:G3O-30858-MONOMER; -.
PRO; PR:P48240; -.
Proteomes; UP000002311; Chromosome VII.
GO; GO:0000177; C:cytoplasmic exosome (RNase complex); IDA:SGD.
GO; GO:0000176; C:nuclear exosome (RNase complex); IDA:SGD.
GO; GO:0005730; C:nucleolus; IDA:SGD.
GO; GO:0003723; F:RNA binding; IEA:UniProtKB-KW.
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.
GO; GO:0070651; P:nonfunctional rRNA decay; IC:SGD.
GO; GO:0071028; P:nuclear mRNA surveillance; IMP:SGD.
GO; GO:0071039; P:nuclear polyadenylation-dependent CUT catabolic process; IMP:SGD.
GO; GO:0071042; P:nuclear polyadenylation-dependent mRNA catabolic process; IC:SGD.
GO; GO:0071035; P:nuclear polyadenylation-dependent rRNA catabolic process; IMP:SGD.
GO; GO:0071038; P:nuclear polyadenylation-dependent tRNA catabolic process; IDA:SGD.
GO; GO:0070478; P:nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay; IC:SGD.
GO; GO:0034427; P:nuclear-transcribed mRNA catabolic process, exonucleolytic, 3'-5'; IBA:GO_Central.
GO; GO:0070481; P:nuclear-transcribed mRNA catabolic process, non-stop decay; IC:SGD.
GO; GO:0071051; P:polyadenylation-dependent snoRNA 3'-end processing; IMP:SGD.
GO; GO:0034475; P:U4 snRNA 3'-end processing; IMP:SGD.
Gene3D; 3.30.230.70; -; 1.
InterPro; IPR001247; ExoRNase_PH_dom1.
InterPro; IPR027408; PNPase/RNase_PH_dom_sf.
InterPro; IPR020568; Ribosomal_S5_D2-typ_fold.
Pfam; PF01138; RNase_PH; 1.
SUPFAM; SSF54211; SSF54211; 1.
1: Evidence at protein level;
3D-structure; Complete proteome; Cytoplasm; Exosome; Nucleus;
Reference proteome; RNA-binding; rRNA processing.
CHAIN 1 250 Exosome complex component MTR3.
/FTId=PRO_0000139979.
COMPBIAS 216 222 Asp/Glu-rich (acidic).
STRAND 6 8 {ECO:0000244|PDB:4IFD}.
STRAND 15 17 {ECO:0000244|PDB:5OKZ}.
STRAND 22 24 {ECO:0000244|PDB:5K36}.
STRAND 45 50 {ECO:0000244|PDB:5JEA}.
STRAND 56 66 {ECO:0000244|PDB:5JEA}.
STRAND 69 81 {ECO:0000244|PDB:5JEA}.
STRAND 84 86 {ECO:0000244|PDB:5JEA}.
STRAND 89 99 {ECO:0000244|PDB:5JEA}.
STRAND 101 103 {ECO:0000244|PDB:5K36}.
HELIX 107 124 {ECO:0000244|PDB:5JEA}.
HELIX 127 129 {ECO:0000244|PDB:5JEA}.
STRAND 133 146 {ECO:0000244|PDB:5JEA}.
HELIX 165 182 {ECO:0000244|PDB:5JEA}.
STRAND 187 189 {ECO:0000244|PDB:5JEA}.
STRAND 192 196 {ECO:0000244|PDB:5JEA}.
STRAND 199 204 {ECO:0000244|PDB:5JEA}.
HELIX 205 207 {ECO:0000244|PDB:5JEA}.
STRAND 209 215 {ECO:0000244|PDB:5JEA}.
HELIX 223 247 {ECO:0000244|PDB:5JEA}.
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


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