P53256 (RRP46_YEAST) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Exosome complex component RRP46

Alternative name(s):
Ribosomal RNA-processing protein 46

Gene names

Name:	RRP46
Ordered Locus Names:	YGR095C

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	223 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. RRP46 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.11
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. Interacts with LRP1. Ref.4 Ref.5 Ref.11
Subcellular location	Cytoplasm. Nucleus › nucleolus Ref.7.
Miscellaneous	Present with 10800 molecules/cell in log phase SD medium.
Sequence similarities	Belongs to the RNase PH family.
Caution	According to Ref.11 and Ref.9, only DIS3/RRP44 subunit of the exosome core has exonuclease activity.
Sequence caution	The sequence CAA97098.1 differs from that shown. Reason: Erroneous initiation.

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 Ref.4PubMed 10508172. Source: SGD nonfunctional rRNA decay Inferred by curator Ref.4. Source: SGD nuclear polyadenylation-dependent mRNA catabolic process Inferred from mutant phenotype PubMed 19369424. Source: SGD nuclear polyadenylation-dependent rRNA catabolic process Inferred from mutant phenotype Ref.4. 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.4. Source: SGD nuclear-transcribed mRNA catabolic process, non-stop decay Inferred by curator Ref.4. Source: SGD polyadenylation-dependent snoRNA 3'-end processing Inferred by curator Ref.4. Source: SGD
Cellular_component	cytoplasmic exosome (RNase complex) Inferred from direct assay Ref.4PubMed 19046973. Source: SGD nuclear exosome (RNase complex) Inferred from direct assay Ref.4PubMed 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...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 223

223

Exosome complex component RRP46

PRO_0000139978

Secondary structure

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223

Helix Strand Turn

Details...

Beta strand

4 – 7

4

Beta strand

11 – 21

11

Beta strand

24 – 34

11

Turn

38 – 40

3

Beta strand

43 – 53

11

Beta strand

55 – 57

3

Helix

61 – 77

17

Helix

80 – 82

3

Beta strand

86 – 96

11

Turn

101 – 103

3

Helix

106 – 123

18

Beta strand

127 – 139

13

Turn

140 – 142

3

Beta strand

145 – 148

4

Helix

151 – 155

5

Beta strand

157 – 168

12

Turn

169 – 172

4

Beta strand

173 – 186

14

Helix

188 – 217

30

Turn

218 – 220

3

Sequences

	Sequence		Length	Mass (Da)
	P53256 [UniParc]. Last modified October 31, 2006. Version 2. Checksum: F1307E0EE4FC3133	FASTA	223	24,407
	10 20 30 40 50 60 MSVQAEIGIL DHVDGSSEFV SQDTKVICSV TGPIEPKARQ ELPTQLALEI IVRPAKGVAT 70 80 90 100 110 120 TREKVLEDKL RAVLTPLITR HCYPRQLCQI TCQILESGED EAEFSLRELS CCINAAFLAL 130 140 150 160 170 180 VDAGIALNSM CASIPIAIIK DTSDIIVDPT AEQLKISLSV HTLALEFVNG GKVVKNVLLL 190 200 210 220 DSNGDFNEDQ LFSLLELGEQ KCQELVTNIR RIIQDNISPR LVV

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"The nucleotide sequence of Saccharomyces cerevisiae chromosome VII." Tettelin H., Agostoni-Carbone M.L., Albermann K., Albers M., Arroyo J., Backes U., Barreiros T., Bertani I., Bjourson A.J., Brueckner M., Bruschi C.V., Carignani G., Castagnoli L., Cerdan E., Clemente M.L., Coblenz A., Coglievina M., Coissac E. , Defoor E., Del Bino S., Delius H., Delneri D., de Wergifosse P., Dujon B., Durand P., Entian K.-D., Eraso P., Escribano V., Fabiani L., Fartmann B., Feroli F., Feuermann M., Frontali L., Garcia-Gonzalez M., Garcia-Saez M.I., Goffeau A., Guerreiro P., Hani J., Hansen M., Hebling U., Hernandez K., Heumann K., Hilger F., Hofmann B., Indge K.J., James C.M., Klima R., Koetter P., Kramer B., Kramer W., Lauquin G., Leuther H., Louis E.J., Maillier E., Marconi A., Martegani E., Mazon M.J., Mazzoni C., McReynolds A.D.K., Melchioretto P., Mewes H.-W., Minenkova O., Mueller-Auer S., Nawrocki A., Netter P., Neu R., Nombela C., Oliver S.G., Panzeri L., Paoluzi S., Plevani P., Portetelle D., Portillo F., Potier S., Purnelle B., Rieger M., Riles L., Rinaldi T., Robben J., Rodrigues-Pousada C., Rodriguez-Belmonte E., Rodriguez-Torres A.M., Rose M., Ruzzi M., Saliola M., Sanchez-Perez M., Schaefer B., Schaefer M., Scharfe M., Schmidheini T., Schreer A., Skala J., Souciet J.-L., Steensma H.Y., Talla E., Thierry A., Vandenbol M., van der Aart Q.J.M., Van Dyck L., Vanoni M., Verhasselt P., Voet M., Volckaert G., Wambutt R., Watson M.D., Weber N., Wedler E., Wedler H., Wipfli P., Wolf K., Wright L.F., Zaccaria P., Zimmermann M., Zollner A., Kleine K. Nature 387:81-84(1997) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 96604 / S288c / FY1679.
[2]	Saccharomyces Genome Database Submitted (DEC-2009) to the EMBL/GenBank/DDBJ databases Cited for: GENOME REANNOTATION. Strain: ATCC 204508 / S288c.
[3]	Kennedy M.C., Dietrich F.S. Submitted (SEP-2003) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [MRNA] OF 1-67. Strain: ATCC 204511 / S288c / AB972.
[4]	"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 EXOSOME COMPLEX BY MASS SPECTROMETRY.
[5]	"A panoramic view of yeast noncoding RNA processing." Peng W.-T., Robinson M.D., Mnaimneh S., Krogan N.J., Cagney G., Morris Q.D., Davierwala A.P., Grigull J., Yang X., Zhang W., Mitsakakis N., Ryan O.W., Datta N., Jojic V., Pal C., Canadien V., Richards D.P., Beattie B. , Wu L.F., Altschuler S.J., Roweis S., Frey B.J., Emili A., Greenblatt J.F., Hughes T.R. Cell 113:919-933(2003) [PubMed] [Europe PMC] [Abstract] Cited for: INTERACTION WITH LRP1.
[6]	"Sequencing and comparison of yeast species to identify genes and regulatory elements." Kellis M., Patterson N., Endrizzi M., Birren B.W., Lander E.S. Nature 423:241-254(2003) [PubMed] [Europe PMC] [Abstract] Cited for: IDENTIFICATION OF PROBABLE INITIATION SITE.
[7]	"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].
[8]	"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].
[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: RECONSTITUTION OF THE RNA EXOSOME COMPLEX, LACK OF EXONUCLEASE ACTIVITY.
[10]	Erratum Liu Q., Greimann J.C., Lima C.D. Cell 131:188-189(2007)
[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, FUNCTION OF THE RNA EXOSOME COMPLEX, SUBUNIT.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

Z72880 Genomic DNA. Translation: CAA97098.1. Different initiation.
AY389297 mRNA. Translation: AAQ97229.1.
BK006941 Genomic DNA. Translation: DAA08188.1.

PIR

S64390.

RefSeq

NP_011609.2. NM_001181224.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
4IFD	X-ray	2.80	D	1-223	[»]

ProteinModelPortal

P53256.

SMR

P53256. Positions 6-214.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-6838N.

IntAct

P53256. 23 interactions.

MINT

MINT-2732969.

STRING

4932.YGR095C.

Proteomic databases

PaxDb

P53256.

PeptideAtlas

P53256.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblFungi

YGR095C; YGR095C; YGR095C.

GeneID

852987.

KEGG

sce:YGR095C.

Organism-specific databases

CYGD

YGR095c.

SGD

S000003327. RRP46.

Phylogenomic databases

eggNOG

COG0689.

GeneTree

ENSGT00550000075002.

HOGENOM

HOG000248419.

KO

K12590.

OMA

YPRQLIQ.

OrthoDB

EOG4HDX3Z.

Enzyme and pathway databases

BioCyc

YEAST:G3O-30805-MONOMER.

Gene expression databases

Genevestigator

P53256.

GermOnline

YGR095C. Saccharomyces cerevisiae.

Family and domain databases

Gene3D

3.30.230.70. 1 hit.

InterPro

IPR001247. ExoRNase_PH_dom1.
IPR015847. ExoRNase_PH_dom2.
IPR027408. PNPase/RNase_PH_dom.
IPR020568. Ribosomal_S5_D2-typ_fold.
[Graphical view]

Pfam

PF01138. RNase_PH. 1 hit.
PF03725. RNase_PH_C. 1 hit.
[Graphical view]

SUPFAM

SSF55666. 3_ExoRNase. 1 hit.
SSF54211. Ribosomal_S5_D2-typ_fold. 1 hit.

ProtoNet

Search...

Other

NextBio

972806.

Entry information

Entry name

RRP46_YEAST

Accession

Primary (citable) accession number: P53256
Secondary accession number(s): D6VUM7, Q6TQU1

Entry history

Integrated into UniProtKB/Swiss-Prot:	October 1, 1996
Last sequence update:	October 31, 2006
Last modified:	May 29, 2013
This is version 107 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Fungal Protein Annotation Program