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Protein

Exosome complex component RRP45

Gene

Exosc9

Organism
Rattus norvegicus (Rat)
Status
Reviewed-Annotation score: Annotation score: 4 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 promoter-upstream transcripts (PROMPTs), and of mRNAs with processing defects, thereby limiting or excluding their export to the cytoplasm. The RNA exosome may be involved in Ig class switch recombination (CSR) and/or Ig variable region somatic hypermutation (SHM) by targeting AICDA deamination activity to transcribed dsDNA substrates. In the cytoplasm, the RNA exosome complex is involved in general mRNA turnover and specifically degrades inherently unstable mRNAs containing AU-rich elements (AREs) within their 3' untranslated regions, and in RNA surveillance pathways, preventing translation of aberrant mRNAs. It seems to be involved in degradation of histone mRNA. 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. EXOSC9 binds to ARE-containing RNAs (By similarity).By similarity

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Biological processi

rRNA processing

Keywords - Ligandi

RNA-binding

Enzyme and pathway databases

ReactomeiR-RNO-429958. mRNA decay by 3' to 5' exoribonuclease.
R-RNO-450385. Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA.
R-RNO-450604. KSRP (KHSRP) binds and destabilizes mRNA.
R-RNO-6791226. Major pathway of rRNA processing in the nucleolus.

Names & Taxonomyi

Protein namesi
Recommended name:
Exosome complex component RRP45
Alternative name(s):
Exosome component 9
Gene namesi
Name:Exosc9
OrganismiRattus norvegicus (Rat)
Taxonomic identifieri10116 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeRattus
Proteomesi
  • UP000002494 Componenti: Chromosome 2

Organism-specific databases

RGDi1307888. Exosc9.

Subcellular locationi

  • Cytoplasm By similarity
  • Nucleusnucleolus By similarity
  • Nucleus By similarity
  • Nucleusnucleoplasm By similarity

  • Note: Colocalizes with SETX in nuclear foci upon induction of transcription-related DNA damage at the S phase (By similarity).By similarity

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Exosome, Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 437437Exosome complex component RRP45PRO_0000287543Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei297 – 2971N6-acetyllysine; alternateBy similarity
Cross-linki297 – 297Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2); alternateBy similarity
Modified residuei306 – 3061PhosphoserineBy similarity
Modified residuei346 – 3461PhosphoserineBy similarity
Modified residuei392 – 3921PhosphoserineCombined sources
Modified residuei394 – 3941PhosphoserineCombined sources
Modified residuei407 – 4071PhosphoserineCombined sources

Keywords - PTMi

Acetylation, Isopeptide bond, Phosphoprotein, Ubl conjugation

Proteomic databases

PaxDbiQ4QR75.
PRIDEiQ4QR75.

PTM databases

iPTMnetiQ4QR75.

Expressioni

Gene expression databases

ExpressionAtlasiQ4QR75. baseline.
GenevisibleiQ4QR75. RN.

Interactioni

Subunit structurei

Component of the RNA exosome complex. Specifically part of the catalytically inactive RNA exosome core (Exo-9) complex which is believed to associate with catalytic subunits EXOSC10, and DIS3 or DIS3L in cytoplasmic- and nuclear-specific RNA exosome complex forms. Exo-9 is formed by a hexameric ring of RNase PH domain-containing subunits specifically containing the heterodimers EXOSC4-EXOSC9, EXOSC5-EXOSC8 and EXOSC6-EXOSC7, and peripheral S1 domain-containing components EXOSC1, EXOSC2 and EXOSC3 located on the top of the ring structure. Interacts (via C-terminus region) with SETX (via N-terminus domain); the interaction enhances SETX sumoylation (By similarity).By similarity

GO - Molecular functioni

  • RNA polymerase II activating transcription factor binding Source: RGD

Protein-protein interaction databases

BioGridi254846. 1 interaction.
STRINGi10116.ENSRNOP00000020662.

Family & Domainsi

Sequence similaritiesi

Belongs to the RNase PH family.Curated

Phylogenomic databases

eggNOGiKOG1614. Eukaryota.
COG2123. LUCA.
GeneTreeiENSGT00530000063093.
HOGENOMiHOG000229504.
HOVERGENiHBG051523.
InParanoidiQ4QR75.
KOiK03678.
OMAiKMDTGVE.
OrthoDBiEOG7X9G70.
PhylomeDBiQ4QR75.
TreeFamiTF300092.

Family and domain databases

InterProiIPR001247. ExoRNase_PH_dom1.
IPR015847. ExoRNase_PH_dom2.
IPR020568. Ribosomal_S5_D2-typ_fold.
IPR033100. Rrp45.
[Graphical view]
PANTHERiPTHR11097:SF14. PTHR11097:SF14. 1 hit.
PfamiPF01138. RNase_PH. 1 hit.
PF03725. RNase_PH_C. 1 hit.
[Graphical view]
SUPFAMiSSF54211. SSF54211. 2 hits.
SSF55666. SSF55666. 1 hit.

Sequencei

Sequence statusi: Complete.

Q4QR75-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKETPLSNCE RRFLLRAIEE KKRLDGRQTY DYRNIRISFG TDYGCCIVEL
60 70 80 90 100
GKTRVLGQVS CELVSPKLNR ATEGILFFNL ELSQMAAPAF EPGRQSDLLV
110 120 130 140 150
KLNRLLERCL RNSKCIDTES LCVVAGEKVW QIRVDLHLLN HDGNIIDAAS
160 170 180 190 200
IAAIVALCHF RRPDVSVQGE EVTLYTPEER DPVPLSIHHM PICVSFAFFQ
210 220 230 240 250
QGTYLLVDPN EREERVMDGL LVIAMNKHRE ICTIQSSGGI MLLKDQVFRC
260 270 280 290 300
SKIAGVKVAE ITELIQKALE NDQRVRKEGG KFGFAESIAN QRITAFKMEK
310 320 330 340 350
APIDTSNIEE KAEEIIAEAE PPPEVVSKPV LWTPGTAQIG EGIENSWGDL
360 370 380 390 400
EDSEKEEEEE GGIDETVILD DTKMDTGEVS DIGSQGAPIV LSDSEEEEMI
410 420 430
ILEPEKSPKK IRAQTSANQK APSKSQGKRR KKKRTAN
Length:437
Mass (Da):48,882
Last modified:July 19, 2005 - v1
Checksum:i3F3B725EB5C6B3B1
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BC097413 mRNA. Translation: AAH97413.1.
RefSeqiNP_001020577.1. NM_001025406.1.
UniGeneiRn.13826.

Genome annotation databases

EnsembliENSRNOT00000020662; ENSRNOP00000020662; ENSRNOG00000014674.
GeneIDi294975.
KEGGirno:294975.
UCSCiRGD:1307888. rat.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BC097413 mRNA. Translation: AAH97413.1.
RefSeqiNP_001020577.1. NM_001025406.1.
UniGeneiRn.13826.

3D structure databases

ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi254846. 1 interaction.
STRINGi10116.ENSRNOP00000020662.

PTM databases

iPTMnetiQ4QR75.

Proteomic databases

PaxDbiQ4QR75.
PRIDEiQ4QR75.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSRNOT00000020662; ENSRNOP00000020662; ENSRNOG00000014674.
GeneIDi294975.
KEGGirno:294975.
UCSCiRGD:1307888. rat.

Organism-specific databases

CTDi5393.
RGDi1307888. Exosc9.

Phylogenomic databases

eggNOGiKOG1614. Eukaryota.
COG2123. LUCA.
GeneTreeiENSGT00530000063093.
HOGENOMiHOG000229504.
HOVERGENiHBG051523.
InParanoidiQ4QR75.
KOiK03678.
OMAiKMDTGVE.
OrthoDBiEOG7X9G70.
PhylomeDBiQ4QR75.
TreeFamiTF300092.

Enzyme and pathway databases

ReactomeiR-RNO-429958. mRNA decay by 3' to 5' exoribonuclease.
R-RNO-450385. Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA.
R-RNO-450604. KSRP (KHSRP) binds and destabilizes mRNA.
R-RNO-6791226. Major pathway of rRNA processing in the nucleolus.

Miscellaneous databases

PROiQ4QR75.

Gene expression databases

ExpressionAtlasiQ4QR75. baseline.
GenevisibleiQ4QR75. RN.

Family and domain databases

InterProiIPR001247. ExoRNase_PH_dom1.
IPR015847. ExoRNase_PH_dom2.
IPR020568. Ribosomal_S5_D2-typ_fold.
IPR033100. Rrp45.
[Graphical view]
PANTHERiPTHR11097:SF14. PTHR11097:SF14. 1 hit.
PfamiPF01138. RNase_PH. 1 hit.
PF03725. RNase_PH_C. 1 hit.
[Graphical view]
SUPFAMiSSF54211. SSF54211. 2 hits.
SSF55666. SSF55666. 1 hit.
ProtoNetiSearch...

Publicationsi

  1. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
    The MGC Project Team
    Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Tissue: Testis.
  2. "Quantitative maps of protein phosphorylation sites across 14 different rat organs and tissues."
    Lundby A., Secher A., Lage K., Nordsborg N.B., Dmytriyev A., Lundby C., Olsen J.V.
    Nat. Commun. 3:876-876(2012) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-392; SER-394 AND SER-407, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].

Entry informationi

Entry nameiEXOS9_RAT
AccessioniPrimary (citable) accession number: Q4QR75
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 15, 2007
Last sequence update: July 19, 2005
Last modified: June 8, 2016
This is version 81 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families

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.