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Q12277

- RRP42_YEAST

UniProt

Q12277 - RRP42_YEAST

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Protein

Exosome complex component RRP42

Gene

RRP42

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed - 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 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. RRP42 is part of the hexameric ring of RNase PH domain-containing subunits proposed to form a central channel which threads RNA substrates for degradation.2 Publications

GO - Molecular functioni

  1. RNA binding Source: UniProtKB-KW

GO - Biological processi

  1. exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) Source: SGD
  2. ncRNA 3'-end processing Source: SGD
  3. nonfunctional rRNA decay Source: SGD
  4. nuclear polyadenylation-dependent mRNA catabolic process Source: SGD
  5. nuclear polyadenylation-dependent tRNA catabolic process Source: SGD
  6. nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay Source: SGD
  7. nuclear-transcribed mRNA catabolic process, exonucleolytic, 3'-5' Source: SGD
  8. nuclear-transcribed mRNA catabolic process, non-stop decay Source: SGD
  9. polyadenylation-dependent snoRNA 3'-end processing Source: SGD
  10. rRNA catabolic process Source: SGD
Complete GO annotation...

Keywords - Biological processi

rRNA processing

Keywords - Ligandi

RNA-binding

Enzyme and pathway databases

BioCyciYEAST:G3O-29512-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Exosome complex component RRP42
Alternative name(s):
Ribosomal RNA-processing protein 42
Gene namesi
Name:RRP42
Ordered Locus Names:YDL111C
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
ProteomesiUP000002311: Chromosome IV

Organism-specific databases

CYGDiYDL111c.
SGDiS000002269. RRP42.

Subcellular locationi

Cytoplasm 1 Publication. Nucleusnucleolus 1 Publication

GO - Cellular componenti

  1. cytoplasmic exosome (RNase complex) Source: SGD
  2. nuclear exosome (RNase complex) Source: SGD
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Exosome, Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 265265Exosome complex component RRP42PRO_0000139966Add
BLAST

Proteomic databases

MaxQBiQ12277.
PaxDbiQ12277.

Expressioni

Gene expression databases

GenevestigatoriQ12277.

Interactioni

Subunit structurei

Component of the RNA exosome complex. Specifically part of the catalytically inactive RNA exosome core (Exo-9) complex which 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.3 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
CSL4P538598EBI-1765,EBI-1731
MTR3P482403EBI-1765,EBI-1749
SKI6P469484EBI-1765,EBI-1788

Protein-protein interaction databases

BioGridi31951. 50 interactions.
DIPiDIP-1463N.
IntActiQ12277. 25 interactions.
MINTiMINT-410864.
STRINGi4932.YDL111C.

Structurei

Secondary structure

1
265
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi5 – 1612Combined sources
Beta strandi17 – 193Combined sources
Beta strandi34 – 396Combined sources
Beta strandi44 – 518Combined sources
Beta strandi53 – 553Combined sources
Beta strandi57 – 6812Combined sources
Turni69 – 713Combined sources
Beta strandi75 – 828Combined sources
Helixi90 – 10213Combined sources
Turni105 – 1073Combined sources
Helixi111 – 1144Combined sources
Beta strandi117 – 13216Combined sources
Helixi138 – 14912Combined sources
Beta strandi153 – 1575Combined sources
Turni163 – 1664Combined sources
Beta strandi172 – 1798Combined sources
Beta strandi186 – 1938Combined sources
Beta strandi196 – 2005Combined sources
Helixi203 – 2086Combined sources
Beta strandi210 – 2189Combined sources
Beta strandi221 – 2288Combined sources
Beta strandi233 – 2353Combined sources
Helixi241 – 26222Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
4IFDX-ray2.80E1-265[»]
4OO1X-ray3.30E1-265[»]
ProteinModelPortaliQ12277.
SMRiQ12277. Positions 1-265.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the RNase PH family.Curated

Phylogenomic databases

eggNOGiCOG2123.
HOGENOMiHOG000248003.
InParanoidiQ12277.
KOiK12589.
OMAiECIVSVK.
OrthoDBiEOG71GB6Q.

Family and domain databases

InterProiIPR001247. ExoRNase_PH_dom1.
IPR020568. Ribosomal_S5_D2-typ_fold.
[Graphical view]
PfamiPF01138. RNase_PH. 1 hit.
[Graphical view]
SUPFAMiSSF54211. SSF54211. 2 hits.

Sequencei

Sequence statusi: Complete.

Q12277-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MSLSVAEKSY LYDSLASTPS IRPDGRLPHQ FRPIEIFTDF LPSSNGSSRI
60 70 80 90 100
IASDGSECIV SIKSKVVDHH VENELLQVDV DIAGQRDDAL VVETITSLLN
110 120 130 140 150
KVLKSGSGVD SSKLQLTKKY SFKIFVDVLV ISSHSHPVSL ISFAIYSALN
160 170 180 190 200
STYLPKLISA FDDLEVEELP TFHDYDMVKL DINPPLVFIL AVVGNNMLLD
210 220 230 240 250
PAANESEVAN NGLIISWSNG KITSPIRSVA LNDSNVKSFK PHLLKQGLAM
260
VEKYAPDVVR SLENL
Length:265
Mass (Da):29,055
Last modified:November 1, 1996 - v1
Checksum:i806C60979642C67E
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X95644 Genomic DNA. Translation: CAA64901.1.
Z74159 Genomic DNA. Translation: CAA98678.1.
BK006938 Genomic DNA. Translation: DAA11749.1.
PIRiS67653.
RefSeqiNP_010172.1. NM_001180170.1.

Genome annotation databases

EnsemblFungiiYDL111C; YDL111C; YDL111C.
GeneIDi851447.
KEGGisce:YDL111C.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X95644 Genomic DNA. Translation: CAA64901.1 .
Z74159 Genomic DNA. Translation: CAA98678.1 .
BK006938 Genomic DNA. Translation: DAA11749.1 .
PIRi S67653.
RefSeqi NP_010172.1. NM_001180170.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
4IFD X-ray 2.80 E 1-265 [» ]
4OO1 X-ray 3.30 E 1-265 [» ]
ProteinModelPortali Q12277.
SMRi Q12277. Positions 1-265.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

BioGridi 31951. 50 interactions.
DIPi DIP-1463N.
IntActi Q12277. 25 interactions.
MINTi MINT-410864.
STRINGi 4932.YDL111C.

Proteomic databases

MaxQBi Q12277.
PaxDbi Q12277.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblFungii YDL111C ; YDL111C ; YDL111C .
GeneIDi 851447.
KEGGi sce:YDL111C.

Organism-specific databases

CYGDi YDL111c.
SGDi S000002269. RRP42.

Phylogenomic databases

eggNOGi COG2123.
HOGENOMi HOG000248003.
InParanoidi Q12277.
KOi K12589.
OMAi ECIVSVK.
OrthoDBi EOG71GB6Q.

Enzyme and pathway databases

BioCyci YEAST:G3O-29512-MONOMER.

Miscellaneous databases

NextBioi 968699.

Gene expression databases

Genevestigatori Q12277.

Family and domain databases

InterProi IPR001247. ExoRNase_PH_dom1.
IPR020568. Ribosomal_S5_D2-typ_fold.
[Graphical view ]
Pfami PF01138. RNase_PH. 1 hit.
[Graphical view ]
SUPFAMi SSF54211. SSF54211. 2 hits.
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  1. "The sequence of a 16,691 bp segment of Saccharomyces cerevisiae chromosome IV identifies the DUN1, PMT1, PMT5, SRP14 and DPR1 genes, and five new open reading frames."
    Boskovic J., Soler-Mira A., Garcia-Cantalejo J.M., Ballesta J.P.G., Jimenez A., Remacha M.A.
    Yeast 12:1377-1384(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: ATCC 96604 / S288c / FY1679.
  2. "The nucleotide sequence of Saccharomyces cerevisiae chromosome IV."
    Jacq C., Alt-Moerbe J., Andre B., Arnold W., Bahr A., Ballesta J.P.G., Bargues M., Baron L., Becker A., Biteau N., Bloecker H., Blugeon C., Boskovic J., Brandt P., Brueckner M., Buitrago M.J., Coster F., Delaveau T.
    , del Rey F., Dujon B., Eide L.G., Garcia-Cantalejo J.M., Goffeau A., Gomez-Peris A., Granotier C., Hanemann V., Hankeln T., Hoheisel J.D., Jaeger W., Jimenez A., Jonniaux J.-L., Kraemer C., Kuester H., Laamanen P., Legros Y., Louis E.J., Moeller-Rieker S., Monnet A., Moro M., Mueller-Auer S., Nussbaumer B., Paricio N., Paulin L., Perea J., Perez-Alonso M., Perez-Ortin J.E., Pohl T.M., Prydz H., Purnelle B., Rasmussen S.W., Remacha M.A., Revuelta J.L., Rieger M., Salom D., Saluz H.P., Saiz J.E., Saren A.-M., Schaefer M., Scharfe M., Schmidt E.R., Schneider C., Scholler P., Schwarz S., Soler-Mira A., Urrestarazu L.A., Verhasselt P., Vissers S., Voet M., Volckaert G., Wagner G., Wambutt R., Wedler E., Wedler H., Woelfl S., Harris D.E., Bowman S., Brown D., Churcher C.M., Connor R., Dedman K., Gentles S., Hamlin N., Hunt S., Jones L., McDonald S., Murphy L.D., Niblett D., Odell C., Oliver K., Rajandream M.A., Richards C., Shore L., Walsh S.V., Barrell B.G., Dietrich F.S., Mulligan J.T., Allen E., Araujo R., Aviles E., Berno A., Carpenter J., Chen E., Cherry J.M., Chung E., Duncan M., Hunicke-Smith S., Hyman R.W., Komp C., Lashkari D., Lew H., Lin D., Mosedale D., Nakahara K., Namath A., Oefner P., Oh C., Petel F.X., Roberts D., Schramm S., Schroeder M., Shogren T., Shroff N., Winant A., Yelton M.A., Botstein D., Davis R.W., Johnston M., Andrews S., Brinkman R., Cooper J., Ding H., Du Z., Favello A., Fulton L., Gattung S., Greco T., Hallsworth K., Hawkins J., Hillier L.W., Jier M., Johnson D., Johnston L., Kirsten J., Kucaba T., Langston Y., Latreille P., Le T., Mardis E., Menezes S., Miller N., Nhan M., Pauley A., Peluso D., Rifkin L., Riles L., Taich A., Trevaskis E., Vignati D., Wilcox L., Wohldman P., Vaudin M., Wilson R., Waterston R., Albermann K., Hani J., Heumann K., Kleine K., Mewes H.-W., Zollner A., Zaccaria P.
    Nature 387:75-78(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 204508 / S288c.
  3. 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, 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. Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
  7. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
  8. "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, LACK OF EXONUCLEASE ACTIVITY.
  9. Erratum
    Liu Q., Greimann J.C., Lima C.D.
    Cell 131:188-189(2007)
  10. "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, FUNCTION OF THE RNA EXOSOME COMPLEX, SUBUNIT.

Entry informationi

Entry nameiRRP42_YEAST
AccessioniPrimary (citable) accession number: Q12277
Secondary accession number(s): D6VRN9
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1997
Last sequence update: November 1, 1996
Last modified: November 26, 2014
This is version 118 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 7110 molecules/cell in log phase SD medium.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 IV
    Yeast (Saccharomyces cerevisiae) chromosome IV: entries and gene names

External Data

Dasty 3