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Protein

Exosome complex exonuclease DIS3

Gene

DIS3

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

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.3 Publications

Cofactori

Mg2+1 Publication

GO - Molecular functioni

  • 3'-5'-exoribonuclease activity Source: SGD
  • endoribonuclease activity Source: SGD
  • tRNA binding Source: SGD

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
  • ncRNA 3'-end processing 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, non-stop decay Source: SGD
  • polyadenylation-dependent snoRNA 3'-end processing Source: SGD
  • rRNA catabolic process Source: SGD
Complete GO annotation...

Keywords - Molecular functioni

Endonuclease, Exonuclease, Hydrolase, Nuclease

Keywords - Biological processi

rRNA processing

Keywords - Ligandi

RNA-binding

Enzyme and pathway databases

BioCyciYEAST:G3O-33437-MONOMER.
BRENDAi3.1.13.1. 984.
ReactomeiR-SCE-429958. mRNA decay by 3' to 5' exoribonuclease.

Names & Taxonomyi

Protein namesi
Recommended 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 namesi
Name:DIS3
Synonyms:RRP44
Ordered Locus Names:YOL021C
ORF Names:O2197
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
Proteomesi
  • UP000002311 Componenti: Chromosome XV

Organism-specific databases

EuPathDBiFungiDB:YOL021C.
SGDiS000005381. DIS3.

Subcellular locationi

GO - Cellular componenti

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

Keywords - Cellular componenti

Cytoplasm, Exosome, Mitochondrion, Nucleus

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi47C → S: Slow growth; when associated with S-52 and S-55. 1 Publication1
Mutagenesisi52C → S: Slow growth; when associated with S-47 and S-55. 1 Publication1
Mutagenesisi55C → S: Slow growth; when associated with S-47 and S-52. 1 Publication1
Mutagenesisi171D → A: Abolishes endoribonucleolytic activity; no effect on growth. No growth; when associated with N-551. 1 Publication1
Mutagenesisi198D → A: Abolishes endoribonucleolytic activity; no effect on growth. No growth; when associated with N-551. 1 Publication1
Mutagenesisi551D → 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. 3 Publications1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001664231 – 1001Exosome complex exonuclease DIS3Add BLAST1001

Proteomic databases

MaxQBiQ08162.
PRIDEiQ08162.

Interactioni

Subunit structurei

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 GSP1.7 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
RRP4P387926EBI-1740,EBI-1757
RRP40Q082854EBI-1740,EBI-1831
RRP46P532566EBI-1740,EBI-1842
SKI6P4694810EBI-1740,EBI-1788

Protein-protein interaction databases

BioGridi34381. 62 interactors.
DIPiDIP-2355N.
IntActiQ08162. 21 interactors.
MINTiMINT-614156.

Structurei

Secondary structure

11001
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi14 – 16Combined sources3
Beta strandi18 – 26Combined sources9
Beta strandi33 – 43Combined sources11
Beta strandi49 – 51Combined sources3
Helixi55 – 58Combined sources4
Turni80 – 83Combined sources4
Beta strandi85 – 90Combined sources6
Helixi92 – 102Combined sources11
Turni105 – 107Combined sources3
Beta strandi110 – 114Combined sources5
Helixi115 – 124Combined sources10
Helixi126 – 137Combined sources12
Beta strandi144 – 148Combined sources5
Turni150 – 152Combined sources3
Turni154 – 156Combined sources3
Helixi166 – 185Combined sources20
Turni186 – 189Combined sources4
Beta strandi191 – 195Combined sources5
Helixi199 – 206Combined sources8
Beta strandi214 – 216Combined sources3
Helixi218 – 223Combined sources6
Helixi228 – 231Combined sources4
Helixi232 – 234Combined sources3
Helixi261 – 269Combined sources9
Beta strandi272 – 280Combined sources9
Beta strandi282 – 284Combined sources3
Beta strandi287 – 290Combined sources4
Beta strandi293 – 297Combined sources5
Beta strandi299 – 303Combined sources5
Helixi304 – 307Combined sources4
Beta strandi315 – 320Combined sources6
Helixi323 – 325Combined sources3
Turni336 – 338Combined sources3
Helixi367 – 383Combined sources17
Beta strandi385 – 387Combined sources3
Beta strandi389 – 397Combined sources9
Beta strandi402 – 407Combined sources6
Helixi409 – 411Combined sources3
Beta strandi420 – 428Combined sources9
Beta strandi434 – 438Combined sources5
Helixi441 – 444Combined sources4
Beta strandi447 – 455Combined sources9
Beta strandi464 – 475Combined sources12
Helixi478 – 487Combined sources10
Helixi497 – 500Combined sources4
Helixi507 – 509Combined sources3
Helixi519 – 524Combined sources6
Helixi526 – 530Combined sources5
Beta strandi531 – 533Combined sources3
Beta strandi540 – 546Combined sources7
Beta strandi552 – 558Combined sources7
Beta strandi564 – 571Combined sources8
Helixi573 – 576Combined sources4
Beta strandi579 – 581Combined sources3
Helixi582 – 590Combined sources9
Beta strandi594 – 596Combined sources3
Beta strandi599 – 601Combined sources3
Helixi606 – 609Combined sources4
Turni610 – 612Combined sources3
Beta strandi619 – 630Combined sources12
Beta strandi636 – 653Combined sources18
Helixi654 – 662Combined sources9
Beta strandi663 – 665Combined sources3
Helixi669 – 690Combined sources22
Beta strandi701 – 705Combined sources5
Beta strandi707 – 710Combined sources4
Beta strandi712 – 717Combined sources6
Helixi722 – 745Combined sources24
Turni747 – 749Combined sources3
Beta strandi751 – 755Combined sources5
Helixi760 – 763Combined sources4
Helixi764 – 774Combined sources11
Helixi783 – 791Combined sources9
Helixi801 – 810Combined sources10
Beta strandi817 – 820Combined sources4
Helixi821 – 823Combined sources3
Helixi826 – 829Combined sources4
Turni832 – 835Combined sources4
Beta strandi836 – 838Combined sources3
Turni845 – 847Combined sources3
Helixi849 – 861Combined sources13
Helixi869 – 872Combined sources4
Helixi874 – 908Combined sources35
Beta strandi912 – 922Combined sources11
Beta strandi925 – 929Combined sources5
Turni931 – 933Combined sources3
Beta strandi936 – 940Combined sources5
Helixi941 – 944Combined sources4
Helixi948 – 950Combined sources3
Beta strandi952 – 954Combined sources3
Turni955 – 958Combined sources4
Beta strandi959 – 962Combined sources4
Beta strandi964 – 967Combined sources4
Beta strandi971 – 974Combined sources4
Beta strandi978 – 983Combined sources6
Beta strandi985 – 987Combined sources3
Turni989 – 991Combined sources3
Beta strandi995 – 997Combined sources3
Beta strandi998 – 1000Combined sources3

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2VNUX-ray2.30D242-1001[»]
2WP8X-ray3.00J25-1001[»]
4IFDX-ray2.80J1-1001[»]
5C0WX-ray4.60J1-1001[»]
5C0XX-ray3.81J1-1001[»]
5G06electron microscopy4.20J1-1001[»]
5JEAX-ray2.65J1-1001[»]
ProteinModelPortaliQ08162.
SMRiQ08162.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ08162.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini904 – 1001S1 motifPROSITE-ProRule annotationAdd BLAST98

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni1 – 235EndoribonucleaseAdd BLAST235

Sequence similaritiesi

Belongs to the RNR ribonuclease family.Curated
Contains 1 S1 motif domain.PROSITE-ProRule annotation

Phylogenomic databases

GeneTreeiENSGT00530000063106.
HOGENOMiHOG000191945.
InParanoidiQ08162.
KOiK12585.
OMAiKKAHGKN.
OrthoDBiEOG092C0VEN.

Family and domain databases

Gene3Di3.40.50.1010. 1 hit.
InterProiIPR012340. NA-bd_OB-fold.
IPR002716. PIN_dom.
IPR029060. PIN_domain-like.
IPR022966. RNase_II/R_CS.
IPR033771. Rrp44_CSD1.
IPR033770. RRP44_S1.
IPR022967. S1_dom.
IPR003029. S1_domain.
[Graphical view]
PfamiPF13638. PIN_4. 1 hit.
PF17216. Rrp44_CSD1. 1 hit.
PF17215. Rrp44_S1. 1 hit.
[Graphical view]
SMARTiSM00670. PINc. 1 hit.
SM00316. S1. 1 hit.
[Graphical view]
SUPFAMiSSF50249. SSF50249. 4 hits.
SSF88723. SSF88723. 1 hit.
PROSITEiPS01175. RIBONUCLEASE_II. 1 hit.
PS50126. S1. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q08162-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSVPAIAPRR KRLADGLSVT QKVFVRSRNG GATKIVREHY LRSDIPCLSR
60 70 80 90 100
SCTKCPQIVV PDAQNELPKF ILSDSPLELS APIGKHYVVL DTNVVLQAID
110 120 130 140 150
LLENPNCFFD VIVPQIVLDE VRNKSYPVYT RLRTLCRDSD DHKRFIVFHN
160 170 180 190 200
EFSEHTFVER LPNETINDRN DRAIRKTCQW YSEHLKPYDI NVVLVTNDRL
210 220 230 240 250
NREAATKEVE SNIITKSLVQ YIELLPNADD IRDSIPQMDS FDKDLERDTF
260 270 280 290 300
SDFTFPEYYS TARVMGGLKN GVLYQGNIQI SEYNFLEGSV SLPRFSKPVL
310 320 330 340 350
IVGQKNLNRA FNGDQVIVEL LPQSEWKAPS SIVLDSEHFD VNDNPDIEAG
360 370 380 390 400
DDDDNNESSS NTTVISDKQR RLLAKDAMIA QRSKKIQPTA KVVYIQRRSW
410 420 430 440 450
RQYVGQLAPS SVDPQSSSTQ NVFVILMDKC LPKVRIRTRR AAELLDKRIV
460 470 480 490 500
ISIDSWPTTH KYPLGHFVRD LGTIESAQAE TEALLLEHDV EYRPFSKKVL
510 520 530 540 550
ECLPAEGHDW KAPTKLDDPE AVSKDPLLTK RKDLRDKLIC SIDPPGCVDI
560 570 580 590 600
DDALHAKKLP NGNWEVGVHI ADVTHFVKPG TALDAEGAAR GTSVYLVDKR
610 620 630 640 650
IDMLPMLLGT DLCSLKPYVD RFAFSVIWEL DDSANIVNVN FMKSVIRSRE
660 670 680 690 700
AFSYEQAQLR IDDKTQNDEL TMGMRALLKL SVKLKQKRLE AGALNLASPE
710 720 730 740 750
VKVHMDSETS DPNEVEIKKL LATNSLVEEF MLLANISVAR KIYDAFPQTA
760 770 780 790 800
MLRRHAAPPS TNFEILNEML NTRKNMSISL ESSKALADSL DRCVDPEDPY
810 820 830 840 850
FNTLVRIMST RCMMAAQYFY SGAYSYPDFR HYGLAVDIYT HFTSPIRRYC
860 870 880 890 900
DVVAHRQLAG AIGYEPLSLT HRDKNKMDMI CRNINRKHRN AQFAGRASIE
910 920 930 940 950
YYVGQVMRNN ESTETGYVIK VFNNGIVVLV PKFGVEGLIR LDNLTEDPNS
960 970 980 990 1000
AAFDEVEYKL TFVPTNSDKP RDVYVFDKVE VQVRSVMDPI TSKRKAELLL

K
Length:1,001
Mass (Da):113,707
Last modified:November 1, 1997 - v1
Checksum:i00DD31BD2D6904F4
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
D76430 Genomic DNA. Translation: BAA11176.1.
Z74763 Genomic DNA. Translation: CAA99021.1.
BK006948 Genomic DNA. Translation: DAA10760.1.
PIRiS66704.
RefSeqiNP_014621.1. NM_001183275.1.

Genome annotation databases

EnsemblFungiiYOL021C; YOL021C; YOL021C.
GeneIDi854138.
KEGGisce:YOL021C.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
D76430 Genomic DNA. Translation: BAA11176.1.
Z74763 Genomic DNA. Translation: CAA99021.1.
BK006948 Genomic DNA. Translation: DAA10760.1.
PIRiS66704.
RefSeqiNP_014621.1. NM_001183275.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2VNUX-ray2.30D242-1001[»]
2WP8X-ray3.00J25-1001[»]
4IFDX-ray2.80J1-1001[»]
5C0WX-ray4.60J1-1001[»]
5C0XX-ray3.81J1-1001[»]
5G06electron microscopy4.20J1-1001[»]
5JEAX-ray2.65J1-1001[»]
ProteinModelPortaliQ08162.
SMRiQ08162.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi34381. 62 interactors.
DIPiDIP-2355N.
IntActiQ08162. 21 interactors.
MINTiMINT-614156.

Proteomic databases

MaxQBiQ08162.
PRIDEiQ08162.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYOL021C; YOL021C; YOL021C.
GeneIDi854138.
KEGGisce:YOL021C.

Organism-specific databases

EuPathDBiFungiDB:YOL021C.
SGDiS000005381. DIS3.

Phylogenomic databases

GeneTreeiENSGT00530000063106.
HOGENOMiHOG000191945.
InParanoidiQ08162.
KOiK12585.
OMAiKKAHGKN.
OrthoDBiEOG092C0VEN.

Enzyme and pathway databases

BioCyciYEAST:G3O-33437-MONOMER.
BRENDAi3.1.13.1. 984.
ReactomeiR-SCE-429958. mRNA decay by 3' to 5' exoribonuclease.

Miscellaneous databases

EvolutionaryTraceiQ08162.
PROiQ08162.

Family and domain databases

Gene3Di3.40.50.1010. 1 hit.
InterProiIPR012340. NA-bd_OB-fold.
IPR002716. PIN_dom.
IPR029060. PIN_domain-like.
IPR022966. RNase_II/R_CS.
IPR033771. Rrp44_CSD1.
IPR033770. RRP44_S1.
IPR022967. S1_dom.
IPR003029. S1_domain.
[Graphical view]
PfamiPF13638. PIN_4. 1 hit.
PF17216. Rrp44_CSD1. 1 hit.
PF17215. Rrp44_S1. 1 hit.
[Graphical view]
SMARTiSM00670. PINc. 1 hit.
SM00316. S1. 1 hit.
[Graphical view]
SUPFAMiSSF50249. SSF50249. 4 hits.
SSF88723. SSF88723. 1 hit.
PROSITEiPS01175. RIBONUCLEASE_II. 1 hit.
PS50126. S1. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiRRP44_YEAST
AccessioniPrimary (citable) accession number: Q08162
Secondary accession number(s): D6W244
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1997
Last sequence update: November 1, 1997
Last modified: November 30, 2016
This is version 144 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 606 molecules/cell in log phase SD medium.1 Publication
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.

Caution

It was originally thought that there are multiple subunits in the exosome that have exonuclease activity but it was later shown (PubMed:17173052 and PubMed:17174896) that only this DIS3/RRP44 subunit of the exosome core has this activity.1 Publication

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 XV
    Yeast (Saccharomyces cerevisiae) chromosome XV: 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.