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Protein

Exosome complex component MTR3

Gene

MTR3

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

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.3 Publications

GO - Molecular functioni

GO - Biological processi

  • exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) Source: SGD
  • nonfunctional rRNA decay Source: SGD
  • nuclear mRNA surveillance Source: SGD
  • nuclear polyadenylation-dependent CUT catabolic process Source: SGD
  • nuclear polyadenylation-dependent mRNA catabolic process Source: SGD
  • nuclear polyadenylation-dependent rRNA catabolic process Source: SGD
  • nuclear polyadenylation-dependent tRNA catabolic process Source: SGD
  • nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay Source: SGD
  • nuclear-transcribed mRNA catabolic process, exonucleolytic, 3'-5' Source: SGD
  • nuclear-transcribed mRNA catabolic process, non-stop decay Source: SGD
  • polyadenylation-dependent snoRNA 3'-end processing Source: SGD
  • U4 snRNA 3'-end processing Source: SGD
Complete GO annotation...

Keywords - Biological processi

rRNA processing

Keywords - Ligandi

RNA-binding

Enzyme and pathway databases

BioCyciYEAST:G3O-30858-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Exosome complex component MTR3
Alternative name(s):
mRNA transport regulator 3
Gene namesi
Name:MTR3
Ordered Locus Names:YGR158C
ORF Names:G6676
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
Proteomesi
  • UP000002311 Componenti: Chromosome VII

Organism-specific databases

EuPathDBiFungiDB:YGR158C.
SGDiS000003390. MTR3.

Subcellular locationi

GO - Cellular componenti

  • cytoplasmic exosome (RNase complex) Source: SGD
  • nuclear exosome (RNase complex) Source: SGD
  • nucleolus Source: SGD
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Exosome, Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001399791 – 250Exosome complex component MTR3Add BLAST250

Proteomic databases

MaxQBiP48240.
PRIDEiP48240.

PTM databases

iPTMnetiP48240.

Interactioni

Subunit structurei

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.2 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
CSL4P538598EBI-1749,EBI-1731
RRP42Q122773EBI-1749,EBI-1765
SKI6P469484EBI-1749,EBI-1788
YLR345WQ061373EBI-1749,EBI-33827

Protein-protein interaction databases

BioGridi33406. 28 interactors.
DIPiDIP-931N.
IntActiP48240. 25 interactors.
MINTiMINT-409300.

Structurei

Secondary structure

1250
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi6 – 8Combined sources3
Beta strandi45 – 50Combined sources6
Beta strandi56 – 66Combined sources11
Beta strandi69 – 81Combined sources13
Beta strandi84 – 86Combined sources3
Beta strandi89 – 99Combined sources11
Helixi107 – 124Combined sources18
Helixi127 – 129Combined sources3
Beta strandi133 – 146Combined sources14
Helixi165 – 182Combined sources18
Beta strandi187 – 189Combined sources3
Beta strandi192 – 196Combined sources5
Beta strandi199 – 204Combined sources6
Helixi205 – 207Combined sources3
Beta strandi209 – 215Combined sources7
Helixi223 – 247Combined sources25

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
4IFDX-ray2.80F1-250[»]
4OO1X-ray3.30F1-250[»]
5C0WX-ray4.60F1-250[»]
5C0XX-ray3.81F1-250[»]
5G06electron microscopy4.20F1-250[»]
5JEAX-ray2.65F1-250[»]
ProteinModelPortaliP48240.
SMRiP48240.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi216 – 222Asp/Glu-rich (acidic)7

Sequence similaritiesi

Belongs to the RNase PH family.Curated

Phylogenomic databases

HOGENOMiHOG000113690.
InParanoidiP48240.
KOiK12587.
OMAiMNVQDRR.
OrthoDBiEOG092C4NRQ.

Family and domain databases

InterProiIPR001247. ExoRNase_PH_dom1.
IPR020568. Ribosomal_S5_D2-typ_fold.
[Graphical view]
PfamiPF01138. RNase_PH. 1 hit.
[Graphical view]
SUPFAMiSSF54211. SSF54211. 1 hit.

Sequencei

Sequence statusi: Complete.

P48240-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MNVQDRRRLL GPAAAKPMAF SNTTTHVPEK KSTDLTPKGN ESEQELSLHT
60 70 80 90 100
GFIENCNGSA LVEARSLGHQ TSLITAVYGP RSIRGSFTSQ GTISIQLKNG
110 120 130 140 150
LLEKYNTNEL KEVSSFLMGI FNSVVNLSRY PKSGIDIFVY LTYDKDLTNN
160 170 180 190 200
PQDDDSQSKM MSSQISSLIP HCITSITLAL ADAGIELVDM AGAGEANGTV
210 220 230 240 250
VSFIKNGEEI VGFWKDDGDD EDLLECLDRC KEQYNRYRDL MISCLMNQET
Length:250
Mass (Da):27,577
Last modified:February 1, 1996 - v1
Checksum:i2FA07ABB4A1115E0
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X85807 Genomic DNA. Translation: CAA59815.1.
S80548 Genomic DNA. Translation: AAB35850.1.
Z72943 Genomic DNA. Translation: CAA97172.1.
BK006941 Genomic DNA. Translation: DAA08249.1.
PIRiS58362.
RefSeqiNP_011674.3. NM_001181287.3.

Genome annotation databases

EnsemblFungiiYGR158C; YGR158C; YGR158C.
GeneIDi853062.
KEGGisce:YGR158C.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X85807 Genomic DNA. Translation: CAA59815.1.
S80548 Genomic DNA. Translation: AAB35850.1.
Z72943 Genomic DNA. Translation: CAA97172.1.
BK006941 Genomic DNA. Translation: DAA08249.1.
PIRiS58362.
RefSeqiNP_011674.3. NM_001181287.3.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
4IFDX-ray2.80F1-250[»]
4OO1X-ray3.30F1-250[»]
5C0WX-ray4.60F1-250[»]
5C0XX-ray3.81F1-250[»]
5G06electron microscopy4.20F1-250[»]
5JEAX-ray2.65F1-250[»]
ProteinModelPortaliP48240.
SMRiP48240.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi33406. 28 interactors.
DIPiDIP-931N.
IntActiP48240. 25 interactors.
MINTiMINT-409300.

PTM databases

iPTMnetiP48240.

Proteomic databases

MaxQBiP48240.
PRIDEiP48240.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYGR158C; YGR158C; YGR158C.
GeneIDi853062.
KEGGisce:YGR158C.

Organism-specific databases

EuPathDBiFungiDB:YGR158C.
SGDiS000003390. MTR3.

Phylogenomic databases

HOGENOMiHOG000113690.
InParanoidiP48240.
KOiK12587.
OMAiMNVQDRR.
OrthoDBiEOG092C4NRQ.

Enzyme and pathway databases

BioCyciYEAST:G3O-30858-MONOMER.

Miscellaneous databases

PROiP48240.

Family and domain databases

InterProiIPR001247. ExoRNase_PH_dom1.
IPR020568. Ribosomal_S5_D2-typ_fold.
[Graphical view]
PfamiPF01138. RNase_PH. 1 hit.
[Graphical view]
SUPFAMiSSF54211. SSF54211. 1 hit.
ProtoNetiSearch...

Entry informationi

Entry nameiMTR3_YEAST
AccessioniPrimary (citable) accession number: P48240
Secondary accession number(s): D6VUT8
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 1, 1996
Last sequence update: February 1, 1996
Last modified: November 2, 2016
This is version 129 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Miscellaneous

Present with 7380 molecules/cell in log phase SD medium.1 Publication

Caution

According to PubMed:17173052 and PubMed:17174896, only DIS3/RRP44 subunit of the exosome core has exonuclease activity.Curated

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families
  3. Yeast
    Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
  4. Yeast chromosome VII
    Yeast (Saccharomyces cerevisiae) chromosome VII: entries and gene names

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.