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Q12149 (RRP6_YEAST) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 130. 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 exonuclease RRP6

EC=3.1.13.-
Alternative name(s):
Ribosomal RNA-processing protein 6
Gene names
Name:RRP6
Synonyms:UNC733
Ordered Locus Names:YOR001W
OrganismSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) [Reference proteome]
Taxonomic identifier559292 [NCBI]
Taxonomic lineageEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces

Protein attributes

Sequence length733 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Nuclear-specific 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. 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. RRP6 has 3'-5' exonuclease activity which is not modulated upon association with Exo-9 suggesting that the complex inner RNA-binding path is not used to access its active site. Ref.5 Ref.6 Ref.7 Ref.11

Subunit structure

Component of the RNA exosome complex. The catalytically inactive RNA exosome core (Exo-9) complex associates 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. RRP6 specifically is part of the nuclear form of the RNA exosome complex; the association appears to be mediated by Exo-9 and not by DIS3. Interacts with LRP1. Interacts with NPL3, NOP53 and PAP1. Ref.6 Ref.7 Ref.8 Ref.11 Ref.15 Ref.16

Subcellular location

Nucleusnucleolus Ref.6 Ref.7 Ref.9 Ref.11.

Disruption phenotype

Deletion mutant is impaired in growth at all temperatures and is nonviable at 37 degrees Celsius. It is defective in the 3' processing of the 5.8S rRNA and accumulates a discrete species, 5.8S + 30, that is 3' extended by about 30 nucleotides. Deletion also causes an accumulation of 7S RNA and 5' ETS and increases the level of poly(A)+ mRNA. Ref.6 Ref.7 Ref.15

Miscellaneous

Present with 2160 molecules/cell in log phase SD medium.

Sequence similarities

Belongs to the exosome component 10/RRP6 family.

Contains 1 HRDC domain.

Ontologies

Keywords
   Biological processrRNA processing
   Cellular componentExosome
Nucleus
   LigandRNA-binding
   Molecular functionExonuclease
Hydrolase
Nuclease
   PTMPhosphoprotein
   Technical term3D-structure
Complete proteome
Reference proteome
Gene Ontology (GO)
   Biological_processU1 snRNA 3'-end processing

Inferred from mutant phenotype PubMed 10508172. Source: SGD

U4 snRNA 3'-end processing

Inferred from mutant phenotype PubMed 10508172PubMed 10611222PubMed 16373491. Source: SGD

U5 snRNA 3'-end processing

Inferred from mutant phenotype PubMed 10508172. Source: SGD

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 Ref.6PubMed 10508172PubMed 18940861Ref.5. Source: SGD

histone mRNA catabolic process

Inferred from mutant phenotype PubMed 17179095. Source: SGD

nuclear polyadenylation-dependent CUT catabolic process

Inferred from mutant phenotype PubMed 15935759PubMed 16973436PubMed 18007593. Source: SGD

nuclear polyadenylation-dependent antisense transcript catabolic process

Inferred from mutant phenotype PubMed 18022365. Source: SGD

nuclear polyadenylation-dependent mRNA catabolic process

Inferred from mutant phenotype PubMed 16373491PubMed 19369424. Source: SGD

nuclear polyadenylation-dependent rRNA catabolic process

Inferred from mutant phenotype Ref.6PubMed 15173578PubMed 15572680PubMed 16431988PubMed 18007593PubMed 18940861. Source: SGD

nuclear polyadenylation-dependent snRNA catabolic process

Inferred from mutant phenotype PubMed 16431988. Source: SGD

nuclear polyadenylation-dependent snoRNA catabolic process

Inferred from mutant phenotype PubMed 16373491. Source: SGD

nuclear polyadenylation-dependent tRNA catabolic process

Inferred from direct assay PubMed 15828860. Source: SGD

nuclear retention of pre-mRNA at the site of transcription

Inferred from genetic interaction PubMed 17410208. Source: SGD

nuclear retention of pre-mRNA with aberrant 3'-ends at the site of transcription

Inferred from genetic interaction PubMed 11586364PubMed 12417728. Source: SGD

polyadenylation-dependent snoRNA 3'-end processing

Inferred from mutant phenotype PubMed 10611222PubMed 16373491PubMed 18951092. Source: SGD

posttranscriptional tethering of RNA polymerase II gene DNA at nuclear periphery

Inferred from mutant phenotype PubMed 18614049. Source: SGD

   Cellular_componentnuclear exosome (RNase complex)

Inferred from direct assay Ref.6PubMed 19046973. Source: SGD

nucleolus

Inferred from direct assay PubMed 16541108. Source: SGD

nucleus

Inferred from direct assay Ref.7PubMed 23580640. Source: SGD

   Molecular_function3'-5'-exoribonuclease activity

Inferred from direct assay Ref.7. Source: SGD

RNA binding

Inferred from electronic annotation. Source: UniProtKB-KW

nucleotide binding

Inferred from electronic annotation. Source: InterPro

Complete GO annotation...

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 733733Exosome complex exonuclease RRP6
PRO_0000097456

Regions

Domain435 – 51581HRDC

Amino acid modifications

Modified residue1381Phosphoserine Ref.14
Modified residue5201Phosphothreonine Ref.17
Modified residue6401Phosphoserine Ref.18
Modified residue6451Phosphoserine Ref.14 Ref.17 Ref.18

Experimental info

Sequence conflict4021E → G in AAT92869. Ref.4

Secondary structure

................................................................................ 733
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
Q12149 [UniParc].

Last modified November 1, 1996. Version 1.
Checksum: B19A0B2ED74C6DA7

FASTA73384,039
        10         20         30         40         50         60 
MTSENPDVLL SRVINVVRAA SSLASQDVDF YKNLDRGFSK DLKSKADKLA DMANEIILSI 

        70         80         90        100        110        120 
DEHHESFELK EEDISDLWNN FGNIMDNLLE MSDHSLDKLN CAINSKSRGS DLQYLGEFSG 

       130        140        150        160        170        180 
KNFSPTKRVE KPQLKFKSPI DNSESHPFIP LLKEKPNALK PLSESLRLVD DDENNPSHYP 

       190        200        210        220        230        240 
HPYEYEIDHQ EYSPEILQIR EEIPSKSWDD SVPIWVDTST ELESMLEDLK NTKEIAVDLE 

       250        260        270        280        290        300 
HHDYRSYYGI VCLMQISTRE RDYLVDTLKL RENLHILNEV FTNPSIVKVF HGAFMDIIWL 

       310        320        330        340        350        360 
QRDLGLYVVG LFDTYHASKA IGLPRHSLAY LLENFANFKT SKKYQLADWR IRPLSKPMTA 

       370        380        390        400        410        420 
YARADTHFLL NIYDQLRNKL IESNKLAGVL YESRNVAKRR FEYSKYRPLT PSSEVYSPIE 

       430        440        450        460        470        480 
KESPWKILMY QYNIPPEREV LVRELYQWRD LIARRDDESP RFVMPNQLLA ALVAYTPTDV 

       490        500        510        520        530        540 
IGVVSLTNGV TEHVRQNAKL LANLIRDALR NIKNTNEEAT PIPSSETKAD GILLETISVP 

       550        560        570        580        590        600 
QIRDVMERFS VLCNSNISKS RAKPVTNSSI LLGKILPREE HDIAYSKDGL PNKVKTEDIR 

       610        620        630        640        650        660 
IRAQNFKSAL ANLEDIIFEI EKPLVVPVKL EEIKTVDPAS APNHSPEIDN LDDLVVLKKK 

       670        680        690        700        710        720 
NIQKKQPAKE KGVTEKDAVD YSKIPNILSN KPGQNNRQQK KRRFDPSSSD SNGPRAAKKR 

       730 
RPAAKGKNLS FKR 

« Hide

References

« Hide 'large scale' references
[1]"The sequence of a 30 kb fragment on the left arm of chromosome XV from Saccharomyces cerevisiae reveals 15 open reading frames, five of which correspond to previously identified genes."
Sterky F., Holmberg A., Pettersson B., Uhlen M.
Yeast 12:1091-1095(1996) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[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]"The reference genome sequence of Saccharomyces cerevisiae: Then and now."
Engel S.R., Dietrich F.S., Fisk D.G., Binkley G., Balakrishnan R., Costanzo M.C., Dwight S.S., Hitz B.C., Karra K., Nash R.S., Weng S., Wong E.D., Lloyd P., Skrzypek M.S., Miyasato S.R., Simison M., Cherry J.M.
G3 (Bethesda) 4:389-398(2014) [PubMed] [Europe PMC] [Abstract]
Cited for: GENOME REANNOTATION.
Strain: ATCC 204508 / S288c.
[4]"Approaching a complete repository of sequence-verified protein-encoding clones for Saccharomyces cerevisiae."
Hu Y., Rolfs A., Bhullar B., Murthy T.V.S., Zhu C., Berger M.F., Camargo A.A., Kelley F., McCarron S., Jepson D., Richardson A., Raphael J., Moreira D., Taycher E., Zuo D., Mohr S., Kane M.F., Williamson J. expand/collapse author list , Simpson A.J.G., Bulyk M.L., Harlow E., Marsischky G., Kolodner R.D., LaBaer J.
Genome Res. 17:536-543(2007) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
Strain: ATCC 204508 / S288c.
[5]"Rrp6p, the yeast homologue of the human PM-Scl 100-kDa autoantigen, is essential for efficient 5.8 S rRNA 3' end formation."
Briggs M.W., Burkard K.T.D., Butler J.S.
J. Biol. Chem. 273:13255-13263(1998) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION.
[6]"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: FUNCTION, IDENTIFICATION IN THE RNA EXOSOME COMPLEX BY MASS SPECTROMETRY, SUBCELLULAR LOCATION, DISRUPTION PHENOTYPE.
[7]"A nuclear 3'-5' exonuclease involved in mRNA degradation interacts with Poly(A) polymerase and the hnRNA protein Npl3p."
Burkard K.T.D., Butler J.S.
Mol. Cell. Biol. 20:604-616(2000) [PubMed] [Europe PMC] [Abstract]
Cited for: CATALYTIC ACTIVITY, FUNCTION, INTERACTION WITH NPL3 AND PAP1, SUBCELLULAR LOCATION, DISRUPTION PHENOTYPE.
[8]"Rrp47p is an exosome-associated protein required for the 3' processing of stable RNAs."
Mitchell P., Petfalski E., Houalla R., Podtelejnikov A., Mann M., Tollervey D.
Mol. Cell. Biol. 23:6982-6992(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: INTERACTION WITH LRP1.
[9]"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].
[10]"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].
[11]"Genome-wide mRNA surveillance is coupled to mRNA export."
Hieronymus H., Yu M.C., Silver P.A.
Genes Dev. 18:2652-2662(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION, INTERACTION WITH LRP1, SUBCELLULAR LOCATION.
[12]"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: RECONSTITUTION OF THE RNA EXOSOME COMPLEX, EXONUCLEASE ACTIVITY.
[13]Erratum
Liu Q., Greimann J.C., Lima C.D.
Cell 131:188-189(2007)
[14]"Large-scale phosphorylation analysis of alpha-factor-arrested Saccharomyces cerevisiae."
Li X., Gerber S.A., Rudner A.D., Beausoleil S.A., Haas W., Villen J., Elias J.E., Gygi S.P.
J. Proteome Res. 6:1190-1197(2007) [PubMed] [Europe PMC] [Abstract]
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-138 AND SER-645, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
Strain: ADR376.
[15]"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, INTERACTION WITH THE RNA EXOSOME, SUBUNIT, DISRUPTION PHENOTYPE.
[16]"Nop53p interacts with 5.8S rRNA co-transcriptionally, and regulates processing of pre-rRNA by the exosome."
Granato D.C., Machado-Santelli G.M., Oliveira C.C.
FEBS J. 275:4164-4178(2008) [PubMed] [Europe PMC] [Abstract]
Cited for: INTERACTION WITH NOP53.
[17]"A multidimensional chromatography technology for in-depth phosphoproteome analysis."
Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H.
Mol. Cell. Proteomics 7:1389-1396(2008) [PubMed] [Europe PMC] [Abstract]
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-520 AND SER-645, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[18]"Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution."
Holt L.J., Tuch B.B., Villen J., Johnson A.D., Gygi S.P., Morgan D.O.
Science 325:1682-1686(2009) [PubMed] [Europe PMC] [Abstract]
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-640 AND SER-645, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[19]"N-terminal acetylome analyses and functional insights of the N-terminal acetyltransferase NatB."
Van Damme P., Lasa M., Polevoda B., Gazquez C., Elosegui-Artola A., Kim D.S., De Juan-Pardo E., Demeyer K., Hole K., Larrea E., Timmerman E., Prieto J., Arnesen T., Sherman F., Gevaert K., Aldabe R.
Proc. Natl. Acad. Sci. U.S.A. 109:12449-12454(2012) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
Z74909 Genomic DNA. Translation: CAA99189.1.
U43491 Genomic DNA. Translation: AAC49480.1.
AY692850 Genomic DNA. Translation: AAT92869.1.
BK006948 Genomic DNA. Translation: DAA10783.1.
PIRS61984.
RefSeqNP_014643.1. NM_001183420.1.

3D structure databases

PDBe
RCSB-PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1M0Ymodel-A207-382[»]
2HBJX-ray2.10A129-536[»]
2HBKX-ray2.25A129-536[»]
2HBLX-ray2.30A129-536[»]
2HBMX-ray2.70A129-536[»]
4IFDX-ray2.80K518-693[»]
ProteinModelPortalQ12149.
SMRQ12149. Positions 129-516, 532-619.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid34404. 301 interactions.
DIPDIP-4560N.
IntActQ12149. 27 interactions.
MINTMINT-534618.
STRING4932.YOR001W.

Proteomic databases

MaxQBQ12149.
PaxDbQ12149.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblFungiYOR001W; YOR001W; YOR001W.
GeneID854162.
KEGGsce:YOR001W.

Organism-specific databases

CYGDYOR001w.
SGDS000005527. RRP6.

Phylogenomic databases

eggNOGCOG0349.
GeneTreeENSGT00390000015408.
HOGENOMHOG000196525.
KOK12591.
OMAEYKFLHA.
OrthoDBEOG7WT49D.

Enzyme and pathway databases

BioCycYEAST:G3O-33552-MONOMER.

Gene expression databases

GenevestigatorQ12149.

Family and domain databases

Gene3D3.30.420.10. 1 hit.
InterProIPR002562. 3'-5'_exonuclease_dom.
IPR012588. Exosome-assoc_fac_Rrp6_N.
IPR010997. HRDC-like.
IPR002121. HRDC_dom.
IPR012337. RNaseH-like_dom.
[Graphical view]
PfamPF01612. DNA_pol_A_exo1. 1 hit.
PF00570. HRDC. 1 hit.
PF08066. PMC2NT. 1 hit.
[Graphical view]
SMARTSM00474. 35EXOc. 1 hit.
SM00341. HRDC. 1 hit.
[Graphical view]
SUPFAMSSF47819. SSF47819. 1 hit.
SSF53098. SSF53098. 1 hit.
PROSITEPS50967. HRDC. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceQ12149.
NextBio975938.
PROQ12149.

Entry information

Entry nameRRP6_YEAST
AccessionPrimary (citable) accession number: Q12149
Secondary accession number(s): D6W267, Q6B280
Entry history
Integrated into UniProtKB/Swiss-Prot: June 1, 2001
Last sequence update: November 1, 1996
Last modified: July 9, 2014
This is version 130 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