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Q5RKV6 (EXOS6_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 90. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (4) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Exosome complex component MTR3
Alternative name(s):
Exosome component 6
mRNA transport regulator 3 homolog
Short name=hMtr3
p11
Gene names
Name:EXOSC6
Synonyms:MTR3
OrganismHomo sapiens (Human) [Reference proteome]
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo

Protein attributes

Sequence length272 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

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 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. Ref.8

Subunit structure

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. Ref.3 Ref.6

Subcellular location

Cytoplasm Probable. Nucleusnucleolus Probable. Nucleus Probable.

Sequence similarities

Belongs to the RNase PH family.

Caution

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

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 272272Exosome complex component MTR3
PRO_0000287478

Secondary structure

................................ 272
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
Q5RKV6 [UniParc].

Last modified December 21, 2004. Version 1.
Checksum: F31729E0D1545F94

FASTA27228,235
        10         20         30         40         50         60 
MPGDHRRIRG PEESQPPQLY AADEEEAPGT RDPTRLRPVY ARAGLLSQAK GSAYLEAGGT 

        70         80         90        100        110        120 
KVLCAVSGPR QAEGGERGGG PAGAGGEAPA ALRGRLLCDF RRAPFAGRRR RAPPGGCEER 

       130        140        150        160        170        180 
ELALALQEAL EPAVRLGRYP RAQLEVSALL LEDGGSALAA ALTAAALALA DAGVEMYDLV 

       190        200        210        220        230        240 
VGCGLSLAPG PAPTWLLDPT RLEEERAAAG LTVALMPVLN QVAGLLGSGE GGLTESWAEA 

       250        260        270 
VRLGLEGCQR LYPVLQQSLV RAARRRGAAA QP 

« Hide

References

« Hide 'large scale' references
[1]"The sequence and analysis of duplication-rich human chromosome 16."
Martin J., Han C., Gordon L.A., Terry A., Prabhakar S., She X., Xie G., Hellsten U., Chan Y.M., Altherr M., Couronne O., Aerts A., Bajorek E., Black S., Blumer H., Branscomb E., Brown N.C., Bruno W.J. expand/collapse author list , Buckingham J.M., Callen D.F., Campbell C.S., Campbell M.L., Campbell E.W., Caoile C., Challacombe J.F., Chasteen L.A., Chertkov O., Chi H.C., Christensen M., Clark L.M., Cohn J.D., Denys M., Detter J.C., Dickson M., Dimitrijevic-Bussod M., Escobar J., Fawcett J.J., Flowers D., Fotopulos D., Glavina T., Gomez M., Gonzales E., Goodstein D., Goodwin L.A., Grady D.L., Grigoriev I., Groza M., Hammon N., Hawkins T., Haydu L., Hildebrand C.E., Huang W., Israni S., Jett J., Jewett P.B., Kadner K., Kimball H., Kobayashi A., Krawczyk M.-C., Leyba T., Longmire J.L., Lopez F., Lou Y., Lowry S., Ludeman T., Manohar C.F., Mark G.A., McMurray K.L., Meincke L.J., Morgan J., Moyzis R.K., Mundt M.O., Munk A.C., Nandkeshwar R.D., Pitluck S., Pollard M., Predki P., Parson-Quintana B., Ramirez L., Rash S., Retterer J., Ricke D.O., Robinson D.L., Rodriguez A., Salamov A., Saunders E.H., Scott D., Shough T., Stallings R.L., Stalvey M., Sutherland R.D., Tapia R., Tesmer J.G., Thayer N., Thompson L.S., Tice H., Torney D.C., Tran-Gyamfi M., Tsai M., Ulanovsky L.E., Ustaszewska A., Vo N., White P.S., Williams A.L., Wills P.L., Wu J.-R., Wu K., Yang J., DeJong P., Bruce D., Doggett N.A., Deaven L., Schmutz J., Grimwood J., Richardson P., Rokhsar D.S., Eichler E.E., Gilna P., Lucas S.M., Myers R.M., Rubin E.M., Pennacchio L.A.
Nature 432:988-994(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Tissue: Salivary gland.
[2]"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: Salivary gland.
[3]"AU binding proteins recruit the exosome to degrade ARE-containing mRNAs."
Chen C.-Y., Gherzi R., Ong S.-E., Chan E.L., Raijmakers R., Pruijn G.J.M., Stoecklin G., Moroni C., Mann M., Karin M.
Cell 107:451-464(2001) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION BY MASS SPECTROMETRY, IDENTIFICATION IN THE RNA EXOSOME CORE COMPLEX.
[4]"Protein-protein interactions between human exosome components support the assembly of RNase PH-type subunits into a six-membered PNPase-like ring."
Raijmakers R., Vree Egberts W., van Venrooij W.J., Pruijn G.J.M.
J. Mol. Biol. 323:653-663(2002) [PubMed] [Europe PMC] [Abstract]
Cited for: PROTEIN INTERACTION.
[5]"A protein interaction framework for human mRNA degradation."
Lehner B., Sanderson C.M.
Genome Res. 14:1315-1323(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: PROTEIN INTERACTION.
[6]"Dis3-like 1: a novel exoribonuclease associated with the human exosome."
Staals R.H., Bronkhorst A.W., Schilders G., Slomovic S., Schuster G., Heck A.J., Raijmakers R., Pruijn G.J.
EMBO J. 29:2358-2367(2010) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION IN THE RNA EXOSOME COMPLEX, IDENTIFICATION BY MASS SPECTROMETRY.
[7]"Initial characterization of the human central proteome."
Burkard T.R., Planyavsky M., Kaupe I., Breitwieser F.P., Buerckstuemmer T., Bennett K.L., Superti-Furga G., Colinge J.
BMC Syst. Biol. 5:17-17(2011) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[8]"The RNA exosome targets the AID cytidine deaminase to both strands of transcribed duplex DNA substrates."
Basu U., Meng F.L., Keim C., Grinstein V., Pefanis E., Eccleston J., Zhang T., Myers D., Wasserman C.R., Wesemann D.R., Januszyk K., Gregory R.I., Deng H., Lima C.D., Alt F.W.
Cell 144:353-363(2011) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION IN DEAMINATION OF TRANSCRIBED DNA SUBSTRATE.
[9]"Reconstitution, activities, and structure of the eukaryotic RNA exosome."
Liu Q., Greimann J.C., Lima C.D.
Cell 127:1223-1237(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (3.35 ANGSTROMS), LACK OF CATALYTIC ACTIVITY, RECONSTITUTION OF THE RNA EXOSOME CORE COMPLEX.
[10]Erratum
Liu Q., Greimann J.C., Lima C.D.
Cell 131:188-189(2007)
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
AC009060 Genomic DNA. No translation available.
BC052252 mRNA. Translation: AAH52252.1.
RefSeqNP_478126.1. NM_058219.2.
UniGeneHs.660633.
Hs.744085.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
2NN6X-ray3.35F1-272[»]
ProteinModelPortalQ5RKV6.
SMRQ5RKV6. Positions 29-260.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid125608. 39 interactions.
IntActQ5RKV6. 10 interactions.
MINTMINT-4887413.
STRING9606.ENSP00000398597.

PTM databases

PhosphoSiteQ5RKV6.

Polymorphism databases

DMDM74736141.

Proteomic databases

PaxDbQ5RKV6.
PeptideAtlasQ5RKV6.
PRIDEQ5RKV6.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENST00000435634; ENSP00000398597; ENSG00000223496.
GeneID118460.
KEGGhsa:118460.
UCSCuc002eym.1. human.

Organism-specific databases

CTD118460.
GeneCardsGC16M070284.
HGNCHGNC:19055. EXOSC6.
MIM606490. gene.
neXtProtNX_Q5RKV6.
PharmGKBPA134932096.
GenAtlasSearch...

Phylogenomic databases

eggNOGNOG303282.
HOGENOMHOG000229515.
HOVERGENHBG057826.
InParanoidQ5RKV6.
KOK12587.
OMAFDRRRIN.
OrthoDBEOG7JX35Q.
PhylomeDBQ5RKV6.
TreeFamTF323886.

Enzyme and pathway databases

ReactomeREACT_21257. Metabolism of RNA.
REACT_71. Gene Expression.

Gene expression databases

BgeeQ5RKV6.
CleanExHS_EXOSC6.
GenevestigatorQ5RKV6.

Family and domain databases

Gene3D3.30.230.70. 1 hit.
InterProIPR001247. ExoRNase_PH_dom1.
IPR015847. ExoRNase_PH_dom2.
IPR027408. PNPase/RNase_PH_dom.
IPR020568. Ribosomal_S5_D2-typ_fold.
[Graphical view]
PfamPF01138. RNase_PH. 1 hit.
[Graphical view]
SUPFAMSSF54211. SSF54211. 1 hit.
SSF55666. SSF55666. 1 hit.
ProtoNetSearch...

Other

ChiTaRSEXOSC6. human.
EvolutionaryTraceQ5RKV6.
GenomeRNAi118460.
NextBio80292.
PROQ5RKV6.
SOURCESearch...

Entry information

Entry nameEXOS6_HUMAN
AccessionPrimary (citable) accession number: Q5RKV6
Entry history
Integrated into UniProtKB/Swiss-Prot: May 15, 2007
Last sequence update: December 21, 2004
Last modified: April 16, 2014
This is version 90 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (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.

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

MIM cross-references

Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot

Human chromosome 16

Human chromosome 16: entries, gene names and cross-references to MIM