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Protein

Exosome complex component RRP46

Gene

EXOSC5

Organism
Homo sapiens (Human)
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 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.2 Publications

GO - Molecular functioni

  • 3'-5'-exoribonuclease activity Source: UniProtKB
  • RNA binding Source: UniProtKB-KW

GO - Biological processi

  • defense response to virus Source: MGI
  • DNA deamination Source: UniProtKB
  • exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay Source: UniProtKB
  • nuclear mRNA surveillance Source: GO_Central
  • nuclear-transcribed mRNA catabolic process, exonucleolytic, 3'-5' Source: GO_Central
  • polyadenylation-dependent snoRNA 3'-end processing Source: GO_Central
  • regulation of mRNA stability Source: Reactome
  • rRNA 3'-end processing Source: GO_Central
  • rRNA catabolic process Source: GO_Central
  • rRNA processing Source: UniProtKB
  • U4 snRNA 3'-end processing Source: GO_Central
Complete GO annotation...

Keywords - Biological processi

rRNA processing

Keywords - Ligandi

RNA-binding

Enzyme and pathway databases

BioCyciZFISH:ENSG00000077348-MONOMER.
ReactomeiR-HSA-380994. ATF4 activates genes.
R-HSA-429958. mRNA decay by 3' to 5' exoribonuclease.
R-HSA-450385. Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA.
R-HSA-450513. Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA.
R-HSA-450604. KSRP (KHSRP) binds and destabilizes mRNA.
R-HSA-6791226. Major pathway of rRNA processing in the nucleolus and cytosol.

Names & Taxonomyi

Protein namesi
Recommended name:
Exosome complex component RRP46
Alternative name(s):
Chronic myelogenous leukemia tumor antigen 28
Exosome component 5
Ribosomal RNA-processing protein 46
p12B
Gene namesi
Name:EXOSC5
Synonyms:CML28, RRP46
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 19

Organism-specific databases

HGNCiHGNC:24662. EXOSC5.

Subcellular locationi

GO - Cellular componenti

  • cytoplasm Source: UniProtKB
  • cytoplasmic exosome (RNase complex) Source: GO_Central
  • cytosol Source: Reactome
  • exosome (RNase complex) Source: UniProtKB
  • nuclear exosome (RNase complex) Source: GO_Central
  • nucleolus Source: UniProtKB
  • nucleoplasm Source: Reactome
  • nucleus Source: HPA
  • transcriptionally active chromatin Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Exosome, Nucleus

Pathology & Biotechi

Organism-specific databases

DisGeNETi56915.
OpenTargetsiENSG00000077348.
PharmGKBiPA134890468.

Polymorphism and mutation databases

BioMutaiEXOSC5.
DMDMi14285757.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001399751 – 235Exosome complex component RRP46Add BLAST235

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei20PhosphoserineCombined sources1

Keywords - PTMi

Phosphoprotein

Proteomic databases

EPDiQ9NQT4.
MaxQBiQ9NQT4.
PaxDbiQ9NQT4.
PeptideAtlasiQ9NQT4.
PRIDEiQ9NQT4.

PTM databases

iPTMnetiQ9NQT4.
PhosphoSitePlusiQ9NQT4.

Expressioni

Tissue specificityi

Highly expressed in a variety of hematopoietic and epithelial tumor cell lines, but not in normal hematopoietic tissues or other normal tissue, with the exception of testis.

Gene expression databases

BgeeiENSG00000077348.
CleanExiHS_EXOSC5.
ExpressionAtlasiQ9NQT4. baseline and differential.
GenevisibleiQ9NQT4. HS.

Organism-specific databases

HPAiHPA053150.
HPA055677.

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 with EXOSC1. Interacts with GTPBP1. Interacts with ZC3HAV1. Interacts with DDX17 only in the presence of ZC3HAV1 in an RNA-independent manner.6 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
BIRC2Q134905EBI-371876,EBI-514538
CALCOCO2Q131373EBI-371876,EBI-739580
DOCK8Q8NF50-23EBI-371876,EBI-10174653
EXOSC1Q9Y3B224EBI-371876,EBI-371892
EXOSC10Q017803EBI-371876,EBI-358236
EXOSC3Q9NQT58EBI-371876,EBI-371866
EXOSC8Q96B2614EBI-371876,EBI-371922
FCHO1O145263EBI-371876,EBI-719823
GOLGA2Q083793EBI-371876,EBI-618309
IKZF3Q9UKT95EBI-371876,EBI-747204
KRT13A1A4E93EBI-371876,EBI-10171552
RELQ048643EBI-371876,EBI-307352
TNFAIP1Q138295EBI-371876,EBI-2505861
TRIM54Q9BYV25EBI-371876,EBI-2130429

Protein-protein interaction databases

BioGridi121243. 67 interactors.
DIPiDIP-29846N.
IntActiQ9NQT4. 70 interactors.
MINTiMINT-1479651.
STRINGi9606.ENSP00000221233.

Structurei

Secondary structure

1235
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi31 – 36Combined sources6
Beta strandi39 – 49Combined sources11
Beta strandi52 – 63Combined sources12
Beta strandi74 – 81Combined sources8
Beta strandi83 – 85Combined sources3
Helixi89 – 105Combined sources17
Helixi107 – 109Combined sources3
Beta strandi111 – 124Combined sources14
Helixi129 – 143Combined sources15
Beta strandi152 – 159Combined sources8
Beta strandi165 – 168Combined sources4
Helixi171 – 176Combined sources6
Beta strandi178 – 186Combined sources9
Turni187 – 189Combined sources3
Beta strandi194 – 200Combined sources7
Helixi203 – 231Combined sources29

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2NN6X-ray3.35D1-235[»]
ProteinModelPortaliQ9NQT4.
SMRiQ9NQT4.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ9NQT4.

Family & Domainsi

Sequence similaritiesi

Belongs to the RNase PH family.Curated

Phylogenomic databases

eggNOGiKOG1069. Eukaryota.
COG0689. LUCA.
GeneTreeiENSGT00550000075002.
HOGENOMiHOG000229515.
HOVERGENiHBG051520.
InParanoidiQ9NQT4.
KOiK12590.
OMAiTCEASLL.
OrthoDBiEOG091G0N6V.
PhylomeDBiQ9NQT4.
TreeFamiTF315920.

Family and domain databases

Gene3Di3.30.230.70. 1 hit.
InterProiIPR001247. ExoRNase_PH_dom1.
IPR015847. ExoRNase_PH_dom2.
IPR027408. PNPase/RNase_PH_dom.
IPR020568. Ribosomal_S5_D2-typ_fold.
[Graphical view]
PfamiPF01138. RNase_PH. 1 hit.
PF03725. RNase_PH_C. 1 hit.
[Graphical view]
SUPFAMiSSF54211. SSF54211. 1 hit.
SSF55666. SSF55666. 1 hit.

Sequencei

Sequence statusi: Complete.

Q9NQT4-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MEEETHTDAK IRAENGTGSS PRGPGCSLRH FACEQNLLSR PDGSASFLQG
60 70 80 90 100
DTSVLAGVYG PAEVKVSKEI FNKATLEVIL RPKIGLPGVA EKSRERLIRN
110 120 130 140 150
TCEAVVLGTL HPRTSITVVL QVVSDAGSLL ACCLNAACMA LVDAGVPMRA
160 170 180 190 200
LFCGVACALD SDGTLVLDPT SKQEKEARAV LTFALDSVER KLLMSSTKGL
210 220 230
YSDTELQQCL AAAQAASQHV FRFYRESLQR RYSKS
Length:235
Mass (Da):25,249
Last modified:October 1, 2000 - v1
Checksum:iC3C1FCB39D85B1EE
GO

Sequence cautioni

The sequence AAM75154 differs from that shown. Reason: Erroneous initiation.Curated

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_0307885T → M.1 PublicationCorresponds to variant rs10853751dbSNPEnsembl.1
Natural variantiVAR_05186833C → W.Corresponds to variant rs34500671dbSNPEnsembl.1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF281134 mRNA. Translation: AAF82135.1.
AF285785 mRNA. Translation: AAM75154.1. Different initiation.
AC011462 Genomic DNA. No translation available.
BC007742 mRNA. Translation: AAH07742.1.
BC107696 mRNA. Translation: AAI07697.1.
CCDSiCCDS12580.1.
RefSeqiNP_064543.3. NM_020158.3.
UniGeneiHs.283741.

Genome annotation databases

EnsembliENST00000221233; ENSP00000221233; ENSG00000077348.
GeneIDi56915.
KEGGihsa:56915.
UCSCiuc002oqo.4. human.

Keywords - Coding sequence diversityi

Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF281134 mRNA. Translation: AAF82135.1.
AF285785 mRNA. Translation: AAM75154.1. Different initiation.
AC011462 Genomic DNA. No translation available.
BC007742 mRNA. Translation: AAH07742.1.
BC107696 mRNA. Translation: AAI07697.1.
CCDSiCCDS12580.1.
RefSeqiNP_064543.3. NM_020158.3.
UniGeneiHs.283741.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2NN6X-ray3.35D1-235[»]
ProteinModelPortaliQ9NQT4.
SMRiQ9NQT4.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi121243. 67 interactors.
DIPiDIP-29846N.
IntActiQ9NQT4. 70 interactors.
MINTiMINT-1479651.
STRINGi9606.ENSP00000221233.

PTM databases

iPTMnetiQ9NQT4.
PhosphoSitePlusiQ9NQT4.

Polymorphism and mutation databases

BioMutaiEXOSC5.
DMDMi14285757.

Proteomic databases

EPDiQ9NQT4.
MaxQBiQ9NQT4.
PaxDbiQ9NQT4.
PeptideAtlasiQ9NQT4.
PRIDEiQ9NQT4.

Protocols and materials databases

DNASUi56915.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000221233; ENSP00000221233; ENSG00000077348.
GeneIDi56915.
KEGGihsa:56915.
UCSCiuc002oqo.4. human.

Organism-specific databases

CTDi56915.
DisGeNETi56915.
GeneCardsiEXOSC5.
HGNCiHGNC:24662. EXOSC5.
HPAiHPA053150.
HPA055677.
MIMi606492. gene.
neXtProtiNX_Q9NQT4.
OpenTargetsiENSG00000077348.
PharmGKBiPA134890468.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG1069. Eukaryota.
COG0689. LUCA.
GeneTreeiENSGT00550000075002.
HOGENOMiHOG000229515.
HOVERGENiHBG051520.
InParanoidiQ9NQT4.
KOiK12590.
OMAiTCEASLL.
OrthoDBiEOG091G0N6V.
PhylomeDBiQ9NQT4.
TreeFamiTF315920.

Enzyme and pathway databases

BioCyciZFISH:ENSG00000077348-MONOMER.
ReactomeiR-HSA-380994. ATF4 activates genes.
R-HSA-429958. mRNA decay by 3' to 5' exoribonuclease.
R-HSA-450385. Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA.
R-HSA-450513. Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA.
R-HSA-450604. KSRP (KHSRP) binds and destabilizes mRNA.
R-HSA-6791226. Major pathway of rRNA processing in the nucleolus and cytosol.

Miscellaneous databases

EvolutionaryTraceiQ9NQT4.
GeneWikiiExosome_component_5.
GenomeRNAii56915.
PROiQ9NQT4.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000077348.
CleanExiHS_EXOSC5.
ExpressionAtlasiQ9NQT4. baseline and differential.
GenevisibleiQ9NQT4. HS.

Family and domain databases

Gene3Di3.30.230.70. 1 hit.
InterProiIPR001247. ExoRNase_PH_dom1.
IPR015847. ExoRNase_PH_dom2.
IPR027408. PNPase/RNase_PH_dom.
IPR020568. Ribosomal_S5_D2-typ_fold.
[Graphical view]
PfamiPF01138. RNase_PH. 1 hit.
PF03725. RNase_PH_C. 1 hit.
[Graphical view]
SUPFAMiSSF54211. SSF54211. 1 hit.
SSF55666. SSF55666. 1 hit.
ProtoNetiSearch...

Entry informationi

Entry nameiEXOS5_HUMAN
AccessioniPrimary (citable) accession number: Q9NQT4
Secondary accession number(s): Q32Q81, Q8NG16, Q96I89
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 1, 2001
Last sequence update: October 1, 2000
Last modified: November 30, 2016
This is version 152 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Miscellaneousi

Caution

The six exosome core subunits containing a RNase PH-domain are not phosphorolytically active.Curated

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Human chromosome 19
    Human chromosome 19: entries, gene names and cross-references to MIM
  2. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  3. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  4. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  5. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  6. 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.