Q12277 (RRP42_YEAST) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Exosome complex component RRP42

Alternative name(s):
Ribosomal RNA-processing protein 42

Gene names

Name:	RRP42
Ordered Locus Names:	YDL111C

Organism

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) [Reference proteome]

Taxonomic identifier

559292 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Fungi › Dikarya › Ascomycota › saccharomyceta › Saccharomycotina › Saccharomycetes › Saccharomycetales › Saccharomycetaceae › Saccharomyces › Saccharomyces cerevisiae

Protein attributes

Sequence length	265 AA.
Sequence status	Complete.
Protein existence	Evidence 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 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. Ref.4 Ref.10
Subunit structure	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. Ref.4 Ref.5 Ref.10
Subcellular location	Cytoplasm. Nucleus › nucleolus Ref.6.
Miscellaneous	Present with 7110 molecules/cell in log phase SD medium.
Sequence similarities	Belongs to the RNase PH family.

Ontologies

Keywords
Biological process	rRNA processing
Cellular component	Cytoplasm Exosome Nucleus
Ligand	RNA-binding
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	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 nonfunctional rRNA decay Inferred by curator Ref.5. Source: SGD nuclear polyadenylation-dependent mRNA catabolic process Inferred by curator Ref.5. Source: SGD nuclear polyadenylation-dependent tRNA catabolic process Inferred from direct assay PubMed 15828860PubMed 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
Cellular_component	cytoplasmic exosome (RNase complex) Inferred from direct assay Ref.5PubMed 19046973. Source: SGD nuclear exosome (RNase complex) Inferred from direct assay Ref.5PubMed 19046973. Source: SGD nucleolus Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular_function	RNA binding Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
MTR3	P48240	3	EBI-1765,EBI-1749

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 265

265

Exosome complex component RRP42

PRO_0000139966

Secondary structure

1

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

265

Helix Strand Turn

Details...

Helix

5 – 16

12

Beta strand

17 – 19

3

Beta strand

34 – 39

6

Beta strand

44 – 51

8

Beta strand

57 – 68

12

Turn

69 – 71

3

Beta strand

75 – 82

8

Helix

90 – 102

13

Turn

105 – 107

3

Helix

111 – 114

4

Beta strand

117 – 132

16

Helix

138 – 149

12

Beta strand

153 – 157

5

Turn

163 – 166

4

Beta strand

172 – 179

8

Beta strand

186 – 193

8

Beta strand

196 – 200

5

Helix

203 – 208

6

Beta strand

210 – 218

9

Beta strand

221 – 228

8

Beta strand

233 – 235

3

Helix

241 – 262

22

Sequences

	Sequence		Length	Mass (Da)
	Q12277 [UniParc]. Last modified November 1, 1996. Version 1. Checksum: 806C60979642C67E	FASTA	265	29,055
	10 20 30 40 50 60 MSLSVAEKSY LYDSLASTPS IRPDGRLPHQ FRPIEIFTDF LPSSNGSSRI IASDGSECIV 70 80 90 100 110 120 SIKSKVVDHH VENELLQVDV DIAGQRDDAL VVETITSLLN KVLKSGSGVD SSKLQLTKKY 130 140 150 160 170 180 SFKIFVDVLV ISSHSHPVSL ISFAIYSALN STYLPKLISA FDDLEVEELP TFHDYDMVKL 190 200 210 220 230 240 DINPPLVFIL AVVGNNMLLD PAANESEVAN NGLIISWSNG KITSPIRSVA LNDSNVKSFK 250 260 PHLLKQGLAM VEKYAPDVVR SLENL

References

	« Hide 'large scale' referencesShow 'large scale' references »
[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]	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, 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]	"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.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

X95644 Genomic DNA. Translation: CAA64901.1.
Z74159 Genomic DNA. Translation: CAA98678.1.
BK006938 Genomic DNA. Translation: DAA11749.1.

PIR

S67653.

RefSeq

NP_010172.1. NM_001180170.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
4IFD	X-ray	2.80	E	1-265	[»]

ProteinModelPortal

Q12277.

SMR

Q12277. Positions 2-230.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-1463N.

IntAct

Q12277. 26 interactions.

MINT

MINT-410864.

STRING

4932.YDL111C.

Proteomic databases

PaxDb

Q12277.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblFungi

YDL111C; YDL111C; YDL111C.

GeneID

851447.

KEGG

sce:YDL111C.

Organism-specific databases

CYGD

YDL111c.

SGD

S000002269. RRP42.

Phylogenomic databases

eggNOG

COG2123.

HOGENOM

HOG000248003.

KO

K12589.

OMA

SDGSECI.

OrthoDB

EOG4Q5CZP.

Gene expression databases

Genevestigator

Q12277.

GermOnline

YDL111C. Saccharomyces cerevisiae.

Family and domain databases

InterPro

IPR001247. ExoRNase_PH_dom1.
IPR020568. Ribosomal_S5_D2-typ_fold.
[Graphical view]

Pfam

PF01138. RNase_PH. 1 hit.
[Graphical view]

SUPFAM

SSF54211. Ribosomal_S5_D2-typ_fold. 1 hit.

ProtoNet

Search...

Other

NextBio

968699.

Entry information

Entry name

RRP42_YEAST

Accession

Primary (citable) accession number: Q12277
Secondary accession number(s): D6VRN9

Entry history

Integrated into UniProtKB/Swiss-Prot:	November 1, 1997
Last sequence update:	November 1, 1996
Last modified:	May 1, 2013
This is version 106 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Fungal Protein Annotation Program