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Q08162 (RRP44_YEAST) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 119. 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·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Exosome complex exonuclease DIS3

EC=3.1.13.-
EC=3.1.26.-
Alternative name(s):
Chromosome disjunction protein 3
Ribosomal RNA-processing protein 44
Gene names
Name:DIS3
Synonyms:RRP44
Ordered Locus Names:YOL021C
ORF Names:O2197
OrganismSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) [Reference proteome]
Taxonomic identifier559292 [NCBI]
Taxonomic lineageEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces

Protein attributes

Sequence length1001 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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. DIS3 has both 3'-5' exonuclease and endonuclease activities. The exonuclease activity of DIS3 is down-regulated upon association with Exo-9 possibly involving a conformational change in the catalytic domain and threading of the RNA substrate through the complex central channel. Structured substrates can be degraded if they have a 3' single-stranded extension sufficiently long (such as 35 nt poly(A)) to span the proposed complex inner RNA-binding path and to reach the exonuclease site provided by DIS3. Plays a role in mitotic control. Ref.1 Ref.4 Ref.11

Cofactor

Mg2+. Ref.11

Subunit structure

Component of the RNA exosome complex. The catalytically inactive RNA exosome core (Exo-9) complex which is believed to associate 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. DIS3 associates at the respective bottom side with Exo-9. Interacts with GSP1. Ref.1 Ref.4 Ref.5 Ref.9 Ref.11

Subcellular location

Cytoplasm. Mitochondrion. Nucleusnucleolus Ref.6 Ref.8 Ref.10.

Miscellaneous

Present with 606 molecules/cell in log phase SD medium.

Mn2+ doesn't support the hydrolytic activity. Activity is KCl or NaCl dependent and activity is slightly increased in the presence of reducing agents such as DTT or beta-mercaptoethanol and doesn't vary notably between pH 6.8 and 8.8.

Sequence similarities

Belongs to the RNR ribonuclease family.

Contains 1 S1 motif domain.

Caution

It was originally thought (Ref.4) that there are multiple subunits in the exosome that have exonuclease activity but it was later shown (Ref.11 and Ref.9) that only this DIS3/RRP44 subunit of the exosome core has this activity.

Ontologies

Keywords
   Biological processrRNA processing
   Cellular componentCytoplasm
Exosome
Mitochondrion
Nucleus
   LigandRNA-binding
   Molecular functionEndonuclease
Exonuclease
Hydrolase
Nuclease
   Technical term3D-structure
Complete proteome
Reference proteome
Gene Ontology (GO)
   Biological_processRNA phosphodiester bond hydrolysis, endonucleolytic

Inferred from direct assay PubMed 19060886Ref.12PubMed 19129231. Source: GOC

exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)

Inferred from mutant phenotype PubMed 10508172Ref.4. Source: SGD

ncRNA 3'-end processing

Inferred from mutant phenotype PubMed 11352936. Source: SGD

nonfunctional rRNA decay

Inferred from mutant phenotype PubMed 19481524. Source: SGD

nuclear mRNA surveillance

Inferred from mutant phenotype PubMed 11030620. Source: SGD

nuclear polyadenylation-dependent CUT catabolic process

Inferred from mutant phenotype PubMed 15935759. Source: SGD

nuclear polyadenylation-dependent mRNA catabolic process

Inferred by curator Ref.5. Source: SGD

nuclear polyadenylation-dependent rRNA catabolic process

Inferred from mutant phenotype PubMed 16431988PubMed 18940861. Source: SGD

nuclear polyadenylation-dependent tRNA catabolic process

Inferred from direct assay PubMed 15828860PubMed 15935758PubMed 17643380. Source: SGD

nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay

Inferred by curator Ref.5. Source: SGD

nuclear-transcribed mRNA catabolic process, non-stop decay

Inferred by curator Ref.5. Source: SGD

polyadenylation-dependent snoRNA 3'-end processing

Inferred by curator Ref.5. Source: SGD

rRNA catabolic process

Inferred from mutant phenotype PubMed 10508172. Source: SGD

   Cellular_componentcytoplasmic exosome (RNase complex)

Inferred from direct assay Ref.5PubMed 19046973. Source: SGD

mitochondrion

Inferred from electronic annotation. Source: UniProtKB-SubCell

nuclear exosome (RNase complex)

Inferred from direct assay Ref.5PubMed 19046973. Source: SGD

nucleolus

Inferred from direct assay PubMed 9562621. Source: SGD

   Molecular_function3'-5'-exoribonuclease activity

Inferred from direct assay Ref.11PubMed 17643380. Source: SGD

endoribonuclease activity

Inferred from direct assay PubMed 19060886Ref.12PubMed 19129231. Source: SGD

tRNA binding

Inferred from direct assay PubMed 17643380. Source: SGD

Complete GO annotation...

Binary interactions

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 10011001Exosome complex exonuclease DIS3
PRO_0000166423

Regions

Domain904 – 100198S1 motif
Region1 – 235235Endoribonuclease

Experimental info

Mutagenesis471C → S: Slow growth; when associated with S-52 and S-55. Ref.12
Mutagenesis521C → S: Slow growth; when associated with S-47 and S-55. Ref.12
Mutagenesis551C → S: Slow growth; when associated with S-47 and S-52. Ref.12
Mutagenesis1711D → A: Abolishes endoribonucleolytic activity; no effect on growth. No growth; when associated with N-551. Ref.12
Mutagenesis1981D → A: Abolishes endoribonucleolytic activity; no effect on growth. No growth; when associated with N-551. Ref.12
Mutagenesis5511D → N: Exoribonucleolytic activity abolished. Accumulation of partially processed 5.8S rRNA and partially degraded 5' ETS. No growth; when associated with A-171. No growth; when associated with A-198. Ref.11 Ref.12 Ref.13

Secondary structure

..................................................................................................................................................................................... 1001
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
Q08162 [UniParc].

Last modified November 1, 1997. Version 1.
Checksum: 00DD31BD2D6904F4

FASTA1,001113,707
        10         20         30         40         50         60 
MSVPAIAPRR KRLADGLSVT QKVFVRSRNG GATKIVREHY LRSDIPCLSR SCTKCPQIVV 

        70         80         90        100        110        120 
PDAQNELPKF ILSDSPLELS APIGKHYVVL DTNVVLQAID LLENPNCFFD VIVPQIVLDE 

       130        140        150        160        170        180 
VRNKSYPVYT RLRTLCRDSD DHKRFIVFHN EFSEHTFVER LPNETINDRN DRAIRKTCQW 

       190        200        210        220        230        240 
YSEHLKPYDI NVVLVTNDRL NREAATKEVE SNIITKSLVQ YIELLPNADD IRDSIPQMDS 

       250        260        270        280        290        300 
FDKDLERDTF SDFTFPEYYS TARVMGGLKN GVLYQGNIQI SEYNFLEGSV SLPRFSKPVL 

       310        320        330        340        350        360 
IVGQKNLNRA FNGDQVIVEL LPQSEWKAPS SIVLDSEHFD VNDNPDIEAG DDDDNNESSS 

       370        380        390        400        410        420 
NTTVISDKQR RLLAKDAMIA QRSKKIQPTA KVVYIQRRSW RQYVGQLAPS SVDPQSSSTQ 

       430        440        450        460        470        480 
NVFVILMDKC LPKVRIRTRR AAELLDKRIV ISIDSWPTTH KYPLGHFVRD LGTIESAQAE 

       490        500        510        520        530        540 
TEALLLEHDV EYRPFSKKVL ECLPAEGHDW KAPTKLDDPE AVSKDPLLTK RKDLRDKLIC 

       550        560        570        580        590        600 
SIDPPGCVDI DDALHAKKLP NGNWEVGVHI ADVTHFVKPG TALDAEGAAR GTSVYLVDKR 

       610        620        630        640        650        660 
IDMLPMLLGT DLCSLKPYVD RFAFSVIWEL DDSANIVNVN FMKSVIRSRE AFSYEQAQLR 

       670        680        690        700        710        720 
IDDKTQNDEL TMGMRALLKL SVKLKQKRLE AGALNLASPE VKVHMDSETS DPNEVEIKKL 

       730        740        750        760        770        780 
LATNSLVEEF MLLANISVAR KIYDAFPQTA MLRRHAAPPS TNFEILNEML NTRKNMSISL 

       790        800        810        820        830        840 
ESSKALADSL DRCVDPEDPY FNTLVRIMST RCMMAAQYFY SGAYSYPDFR HYGLAVDIYT 

       850        860        870        880        890        900 
HFTSPIRRYC DVVAHRQLAG AIGYEPLSLT HRDKNKMDMI CRNINRKHRN AQFAGRASIE 

       910        920        930        940        950        960 
YYVGQVMRNN ESTETGYVIK VFNNGIVVLV PKFGVEGLIR LDNLTEDPNS AAFDEVEYKL 

       970        980        990       1000 
TFVPTNSDKP RDVYVFDKVE VQVRSVMDPI TSKRKAELLL K 

« Hide

References

« Hide 'large scale' references
[1]"Dis3, implicated in mitotic control, binds directly to Ran and enhances the GEF activity of RCC1."
Noguchi E., Hayashi N., Azuma Y., Seki T., Nakamura M., Nakashima N., Yanagida M., He X., Mueller U., Sazer S., Nishimoto T.
EMBO J. 15:5595-5605(1996) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION, INTERACTION WITH GSP1.
[2]"The nucleotide sequence of Saccharomyces cerevisiae chromosome XV."
Dujon B., Albermann K., Aldea M., Alexandraki D., Ansorge W., Arino J., Benes V., Bohn C., Bolotin-Fukuhara M., Bordonne R., Boyer J., Camasses A., Casamayor A., Casas C., Cheret G., Cziepluch C., Daignan-Fornier B., Dang V.-D. expand/collapse author list , de Haan M., Delius H., Durand P., Fairhead C., Feldmann H., Gaillon L., Galisson F., Gamo F.-J., Gancedo C., Goffeau A., Goulding S.E., Grivell L.A., Habbig B., Hand N.J., Hani J., Hattenhorst U., Hebling U., Hernando Y., Herrero E., Heumann K., Hiesel R., Hilger F., Hofmann B., Hollenberg C.P., Hughes B., Jauniaux J.-C., Kalogeropoulos A., Katsoulou C., Kordes E., Lafuente M.J., Landt O., Louis E.J., Maarse A.C., Madania A., Mannhaupt G., Marck C., Martin R.P., Mewes H.-W., Michaux G., Paces V., Parle-McDermott A.G., Pearson B.M., Perrin A., Pettersson B., Poch O., Pohl T.M., Poirey R., Portetelle D., Pujol A., Purnelle B., Ramezani Rad M., Rechmann S., Schwager C., Schweizer M., Sor F., Sterky F., Tarassov I.A., Teodoru C., Tettelin H., Thierry A., Tobiasch E., Tzermia M., Uhlen M., Unseld M., Valens M., Vandenbol M., Vetter I., Vlcek C., Voet M., Volckaert G., Voss H., Wambutt R., Wedler H., Wiemann S., Winsor B., Wolfe K.H., Zollner A., Zumstein E., Kleine K.
Nature 387:98-102(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: ATCC 204508 / S288c.
[3]Saccharomyces Genome Database
Submitted (DEC-2009) to the EMBL/GenBank/DDBJ databases
Cited for: GENOME REANNOTATION.
Strain: ATCC 204508 / S288c.
[4]"The exosome: a conserved eukaryotic RNA processing complex containing multiple 3'-->5' exoribonucleases."
Mitchell P., Petfalski E., Shevchenko A., Mann M., Tollervey D.
Cell 91:457-466(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION BY MASS SPECTROMETRY, CATALYTIC ACTIVITY, FUNCTION, SUBUNIT.
[5]"The yeast exosome and human PM-Scl are related complexes of 3'-->5' exonucleases."
Allmang C., Petfalski E., Podtelejnikov A., Mann M., Tollervey D., Mitchell P.
Genes Dev. 13:2148-2158(1999) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION IN THE EXOSOME COMPLEX BY MASS SPECTROMETRY.
[6]"Global analysis of protein localization in budding yeast."
Huh W.-K., Falvo J.V., Gerke L.C., Carroll A.S., Howson R.W., Weissman J.S., O'Shea E.K.
Nature 425:686-691(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
[7]"Global analysis of protein expression in yeast."
Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N., O'Shea E.K., Weissman J.S.
Nature 425:737-741(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
[8]"The proteome of Saccharomyces cerevisiae mitochondria."
Sickmann A., Reinders J., Wagner Y., Joppich C., Zahedi R.P., Meyer H.E., Schoenfisch B., Perschil I., Chacinska A., Guiard B., Rehling P., Pfanner N., Meisinger C.
Proc. Natl. Acad. Sci. U.S.A. 100:13207-13212(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
Strain: ATCC 76625 / YPH499.
[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: EXOSOME EXONUCLEASE ACTIVITY, SUBUNIT.
[10]"Toward the complete yeast mitochondrial proteome: multidimensional separation techniques for mitochondrial proteomics."
Reinders J., Zahedi R.P., Pfanner N., Meisinger C., Sickmann A.
J. Proteome Res. 5:1543-1554(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
[11]"A single subunit, Dis3, is essentially responsible for yeast exosome core activity."
Dziembowski A., Lorentzen E., Conti E., Seraphin B.
Nat. Struct. Mol. Biol. 14:15-22(2007) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION BY MASS SPECTROMETRY, CATALYTIC ACTIVITY, FUNCTION, COFACTOR, INTERACTION OF THE EXOSOME WITH RRP6 AND SKI7, SUBUNIT, MUTAGENESIS OF ASP-551.
[12]"The exosome contains domains with specific endoribonuclease, exoribonuclease and cytoplasmic mRNA decay activities."
Schaeffer D., Tsanova B., Barbas A., Reis F.P., Dastidar E.G., Sanchez-Rotunno M., Arraiano C.M., van Hoof A.
Nat. Struct. Mol. Biol. 16:56-62(2009) [PubMed] [Europe PMC] [Abstract]
Cited for: CATALYTIC ACTIVITY AS ENDONUCLEASE, MUTAGENESIS OF CYS-47; CYS-52; CYS-55; ASP-171; ASP-198 AND ASP-551.
[13]"Structure of the active subunit of the yeast exosome core, Rrp44: diverse modes of substrate recruitment in the RNase II nuclease family."
Lorentzen E., Basquin J., Tomecki R., Dziembowski A., Conti E.
Mol. Cell 29:717-728(2008) [PubMed] [Europe PMC] [Abstract]
Cited for: CATALYTIC ACTIVITY, X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) OF 242-1001 IN COMPLEX WITH SINGLE-STRANDED RNA AND MAGNESIUM ION, MUTAGENESIS OF ASP-551.
[14]"The yeast exosome functions as a macromolecular cage to channel RNA substrates for degradation."
Bonneau F., Basquin J., Ebert J., Lorentzen E., Conti E.
Cell 139:547-559(2009) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (3.0 ANGSTROMS) IN COMPLEX WITH SKI6 AND RRP45.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
D76430 Genomic DNA. Translation: BAA11176.1.
Z74763 Genomic DNA. Translation: CAA99021.1.
BK006948 Genomic DNA. Translation: DAA10760.1.
PIRS66704.
RefSeqNP_014621.1. NM_001183275.1.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
2VNUX-ray2.30D242-1001[»]
2WP8X-ray3.00J25-1001[»]
4IFDX-ray2.80J1-1001[»]
ProteinModelPortalQ08162.
SMRQ08162. Positions 9-1001.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid34381. 61 interactions.
DIPDIP-2355N.
IntActQ08162. 21 interactions.
MINTMINT-614156.
STRING4932.YOL021C.

Proteomic databases

PaxDbQ08162.
PeptideAtlasQ08162.
PRIDEQ08162.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblFungiYOL021C; YOL021C; YOL021C.
GeneID854138.
KEGGsce:YOL021C.

Organism-specific databases

CYGDYOL021c.
SGDS000005381. DIS3.

Phylogenomic databases

eggNOGCOG0557.
GeneTreeENSGT00530000063106.
HOGENOMHOG000191945.
KOK12585.
OMALLGTDLC.
OrthoDBEOG7FR7R3.

Enzyme and pathway databases

BioCycYEAST:G3O-33437-MONOMER.

Gene expression databases

GenevestigatorQ08162.

Family and domain databases

InterProIPR012340. NA-bd_OB-fold.
IPR002716. PIN_dom.
IPR003029. Rbsml_prot_S1_RNA-bd_dom.
IPR022967. RNA-binding_domain_S1.
IPR022966. RNase_II/R_CS.
[Graphical view]
PfamPF13638. PIN_4. 1 hit.
[Graphical view]
SMARTSM00670. PINc. 1 hit.
SM00316. S1. 1 hit.
[Graphical view]
SUPFAMSSF50249. SSF50249. 4 hits.
PROSITEPS01175. RIBONUCLEASE_II. 1 hit.
PS50126. S1. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceQ08162.
NextBio975871.
PROQ08162.

Entry information

Entry nameRRP44_YEAST
AccessionPrimary (citable) accession number: Q08162
Secondary accession number(s): D6W244
Entry history
Integrated into UniProtKB/Swiss-Prot: November 1, 1997
Last sequence update: November 1, 1997
Last modified: April 16, 2014
This is version 119 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Relevant documents

Yeast chromosome XV

Yeast (Saccharomyces cerevisiae) chromosome XV: entries and gene names

Yeast

Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references