Q08285 (RRP40_YEAST) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Exosome complex component RRP40

Alternative name(s):
Ribosomal RNA-processing protein 40

Gene names

Name:	RRP40
Ordered Locus Names:	YOL142W

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	240 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. RRP40 as peripheral part of the Exo-9 complex is thought to stabilize the hexameric ring of RNase PH-domain subunits. Ref.4 Ref.9 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. Ref.4 Ref.9
Subcellular location	Cytoplasm. Nucleus › nucleolus Ref.5.
Miscellaneous	Present with 6050 molecules/cell in log phase SD medium.
Sequence similarities	Belongs to the RRP40 family. Contains 1 S1 motif domain.
Caution	According to Ref.9 and Ref.7, only DIS3/RRP44 subunit of the exosome core has exonuclease activity.

Ontologies

Keywords
Biological process	rRNA processing
Cellular component	Cytoplasm Exosome Nucleus
Ligand	RNA-binding
PTM	Phosphoprotein
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 by curator Ref.4. 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 direct assay PubMed 17391830. Source: SGD manganese ion binding Inferred from direct assay PubMed 17159918. Source: SGD
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 240

240

Exosome complex component RRP40

PRO_0000097453

Regions

Domain

67 – 137

71

S1 motif

Amino acid modifications

Modified residue

16

1

Phosphothreonine Ref.10

Experimental info

Sequence conflict

160

1

L → F in CAA99163. Ref.1

Secondary structure

1

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240

Helix Strand Turn

Details...

Beta strand

19 – 21

3

Beta strand

25 – 27

3

Turn

29 – 31

3

Beta strand

34 – 36

3

Beta strand

40 – 44

5

Beta strand

53 – 59

7

Beta strand

71 – 79

9

Beta strand

81 – 89

9

Beta strand

95 – 98

4

Beta strand

107 – 109

3

Beta strand

118 – 125

8

Beta strand

133 – 137

5

Turn

139 – 141

3

Beta strand

148 – 150

3

Beta strand

154 – 157

4

Helix

160 – 168

9

Helix

174 – 179

6

Beta strand

185 – 189

5

Turn

190 – 192

3

Beta strand

193 – 197

5

Helix

201 – 217

17

Helix

220 – 222

3

Helix

223 – 230

8

Turn

231 – 233

3

Sequences

	Sequence		Length	Mass (Da)
	Q08285 [UniParc]. Last modified September 21, 2011. Version 2. Checksum: 62B3A30348BBAA7C	FASTA	240	26,556
	10 20 30 40 50 60 MSTFIFPGDS FPVDPTTPVK LGPGIYCDPN TQEIRPVNTG VLHVSAKGKS GVQTAYIDYS 70 80 90 100 110 120 SKRYIPSVND FVIGVIIGTF SDSYKVSLQN FSSSVSLSYM AFPNASKKNR PTLQVGDLVY 130 140 150 160 170 180 ARVCTAEKEL EAEIECFDST TGRDAGFGIL EDGMIIDVNL NFARQLLFNN DFPLLKVLAA 190 200 210 220 230 240 HTKFEVAIGL NGKIWVKCEE LSNTLACYRT IMECCQKNDT AAFKDIAKRQ FKEILTVKEE

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"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. , 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 96604 / S288c / FY1679.
[2]	Saccharomyces Genome Database Submitted (MAR-2011) to the EMBL/GenBank/DDBJ databases Cited for: GENOME REANNOTATION, SEQUENCE REVISION TO 160. Strain: ATCC 204508 / S288c.
[3]	"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. , 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.
[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]	"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].
[6]	"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].
[7]	"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.
[8]	Erratum Liu Q., Greimann J.C., Lima C.D. Cell 131:188-189(2007)
[9]	"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, INTERACTION OF THE EXOSOME WITH RRP6 AND SKI7, SUBUNIT.
[10]	"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-16, MASS SPECTROMETRY.
[11]	"The exosome contains domains with specific endoribonuclease, exoribonuclease and cytoplasmic mRNA decay activities." Schaeffer D., Tsanova B., Barbas A., Reis F.P., Dastidar E.G., Sanchez-Rotunno M., Arraiano C.M., van Hoof A. Nat. Struct. Mol. Biol. 16:56-62(2009) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION IN RNA EXOSOME COMPLEX STABILITY.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

Z74884 Genomic DNA. Translation: CAA99163.1.
AY692926 Genomic DNA. Translation: AAT92945.1.
BK006948 Genomic DNA. Translation: DAA10643.2.

PIR

S61872.

RefSeq

NP_014499.2. NM_001183396.2.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
2JA9	X-ray	2.20	A	62-236	[»]
4IFD	X-ray	2.80	G	1-240	[»]

ProteinModelPortal

Q08285.

SMR

Q08285. Positions 62-236.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-5330N.

IntAct

Q08285. 17 interactions.

MINT

MINT-530842.

STRING

4932.YOL142W.

Proteomic databases

PaxDb

Q08285.

PeptideAtlas

Q08285.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblFungi

YOL142W; YOL142W; YOL142W.

GeneID

854023.

KEGG

sce:YOL142W.

Organism-specific databases

CYGD

YOL142w.

SGD

S000005502. RRP40.

Phylogenomic databases

eggNOG

COG1097.

GeneTree

ENSGT00390000012042.

HOGENOM

HOG000184644.

KO

K03681.

OMA

SYMAFPN.

OrthoDB

EOG45QMPG.

Gene expression databases

Genevestigator

Q08285.

GermOnline

YOL142W. Saccharomyces cerevisiae.

Family and domain databases

InterPro

IPR026699. Exosome_RNA_bind1/RRP40/RRP4.
IPR022967. RNA-binding_domain_S1.
[Graphical view]

PANTHER

PTHR21321. PTHR21321. 1 hit.

SMART

SM00316. S1. 1 hit.
[Graphical view]

PROSITE

PS50126. S1. False negative.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

Q08285.

NextBio

975559.

Entry information

Entry name

RRP40_YEAST

Accession

Primary (citable) accession number: Q08285
Secondary accession number(s): D6W1S7, E9P8Z4

Entry history

Integrated into UniProtKB/Swiss-Prot:	June 1, 2001
Last sequence update:	September 21, 2011
Last modified:	May 1, 2013
This is version 106 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Fungal Protein Annotation Program