P38792 (RRP4_YEAST) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Exosome complex component RRP4

Alternative name(s):
Ribosomal RNA-processing protein 4

Gene names

Name:	RRP4
Ordered Locus Names:	YHR069C

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	359 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. RRP4 as peripheral part of the Exo-9 complex is thought to stabilize the hexameric ring of RNase PH-domain subunits. Ref.1 Ref.4 Ref.10 Ref.12
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/RRP47. Ref.1 Ref.5 Ref.6 Ref.10
Subcellular location	Cytoplasm. Nucleus › nucleolus Ref.5 Ref.7.
Miscellaneous	Present with 4840 molecules/cell in log phase SD medium.
Sequence similarities	Belongs to the exosome component 2/RRP4 family. Contains 1 S1 motif domain.
Caution	Was originally (Ref.1 and Ref.4) thought to have exonuclease activity but it was later shown (Ref.10 and Ref.9) that only DIS3/RRP44 subunit of the exosome core has this activity.

Ontologies

Keywords
Biological process	rRNA processing
Cellular component	Cytoplasm Exosome Nucleus
Ligand	RNA-binding
PTM	Phosphoprotein
Technical term	3D-structure Complete proteome Direct protein sequencing Reference proteome
Gene Ontology (GO)
Biological_process	U4 snRNA 3'-end processing Inferred from mutant phenotype PubMed 10611222. 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.5PubMed 10508172Ref.4Ref.1. 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 rRNA catabolic process Inferred from mutant phenotype Ref.5. Source: SGD nuclear polyadenylation-dependent tRNA catabolic process Inferred from direct assay PubMed 15828860PubMed 17643380. Source: SGD nuclear retention of pre-mRNA with aberrant 3'-ends at the site of transcription Inferred from genetic interaction PubMed 11586364. 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 from mutant phenotype PubMed 10611222. 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...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 359

359

Exosome complex component RRP4

PRO_0000097455

Regions

Domain

107 – 187

81

S1 motif

Amino acid modifications

Modified residue

28

1

Phosphoserine Ref.11

Modified residue

268

1

Phosphoserine Ref.11

Natural variations

Natural variant

136

1

L → P in RRP4-1; temperature-sensitive(ts) lethal mutation.

Secondary structure

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359

Helix Strand Turn

Details...

Beta strand

7 – 12

6

Beta strand

60 – 62

3

Beta strand

67 – 69

3

Beta strand

73 – 76

4

Beta strand

79 – 91

13

Beta strand

94 – 101

8

Beta strand

111 – 120

10

Beta strand

123 – 127

5

Beta strand

129 – 132

4

Beta strand

134 – 137

4

Helix

138 – 140

3

Helix

146 – 148

3

Turn

153 – 157

5

Helix

159 – 161

3

Beta strand

168 – 176

9

Beta strand

178 – 180

3

Beta strand

182 – 185

4

Beta strand

188 – 193

6

Beta strand

196 – 201

6

Helix

204 – 206

3

Beta strand

214 – 217

4

Turn

218 – 220

3

Beta strand

221 – 225

5

Beta strand

229 – 235

7

Helix

238 – 242

5

Helix

276 – 278

3

Beta strand

279 – 281

3

Helix

291 – 309

19

Helix

316 – 325

10

Helix

326 – 328

3

Beta strand

329 – 331

3

Helix

332 – 336

5

Helix

338 – 356

19

Sequences

	Sequence		Length	Mass (Da)
	P38792 [UniParc]. Last modified February 1, 1995. Version 1. Checksum: 0718A7ABF42E9B9B	FASTA	359	39,427
	10 20 30 40 50 60 MSEVITITKR NGAFQNSSNL SYNNTGISDD ENDEEDIYMH DVNSASKSES DSQIVTPGEL 70 80 90 100 110 120 VTDDPIWMRG HGTYFLDNMT YSSVAGTVSR VNRLLSVIPL KGRYAPETGD HVVGRIAEVG 130 140 150 160 170 180 NKRWKVDIGG KQHAVLMLGS VNLPGGILRR KSESDELQMR SFLKEGDLLN AEVQSLFQDG 190 200 210 220 230 240 SASLHTRSLK YGKLRNGMFC QVPSSLIVRA KNHTHNLPGN ITVVLGVNGY IWLRKTSQMD 250 260 270 280 290 300 LARDTPSANN SSSIKSTGPT GAVSLNPSIT RLEEESSWQI YSDENDPSIS NNIRQAICRY 310 320 330 340 350 ANVIKALAFC EIGITQQRIV SAYEASMVYS NVGELIEKNV MESIGSDILT AEKMRGNGN

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"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: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 94-101; 256-271 AND 306-318, FUNCTION, SUBUNIT, MASS SPECTROMETRY.
[2]	"Complete nucleotide sequence of Saccharomyces cerevisiae chromosome VIII." Johnston M., Andrews S., Brinkman R., Cooper J., Ding H., Dover J., Du Z., Favello A., Fulton L., Gattung S., Geisel C., Kirsten J., Kucaba T., Hillier L.W., Jier M., Johnston L., Langston Y., Latreille P. , Louis E.J., Macri C., Mardis E., Menezes S., Mouser L., Nhan M., Rifkin L., Riles L., St Peter H., Trevaskis E., Vaughan K., Vignati D., Wilcox L., Wohldman P., Waterston R., Wilson R., Vaudin M. Science 265:2077-2082(1994) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 204511 / S288c / AB972.
[3]	Saccharomyces Genome Database Submitted (DEC-2009) to the EMBL/GenBank/DDBJ databases Cited for: GENOME REANNOTATION. Strain: ATCC 204508 / S288c.
[4]	"The 3' end of yeast 5.8S rRNA is generated by an exonuclease processing mechanism." Mitchell P., Petfalski E., Tollervey D. Genes Dev. 10:502-513(1996) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, VARIANT RRP4-1.
[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 RNA EXOSOME COMPLEX BY MASS SPECTROMETRY, SUBCELLULAR LOCATION.
[6]	"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.
[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]	"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.
[11]	"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 SER-28 AND SER-268, MASS SPECTROMETRY.
[12]	"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

U00061 Genomic DNA. Translation: AAB68393.1.
BK006934 Genomic DNA. Translation: DAA06762.1.

PIR

S46714.

RefSeq

NP_011936.1. NM_001179199.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
4IFD	X-ray	2.80	H	1-359	[»]

ProteinModelPortal

P38792.

SMR

P38792. Positions 53-238.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-5888N.

IntAct

P38792. 21 interactions.

MINT

MINT-649511.

STRING

4932.YHR069C.

Proteomic databases

PaxDb

P38792.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblFungi

YHR069C; YHR069C; YHR069C.

GeneID

856466.

KEGG

sce:YHR069C.

Organism-specific databases

CYGD

YHR069c.

SGD

S000001111. RRP4.

Phylogenomic databases

eggNOG

COG1097.

GeneTree

ENSGT00440000033656.

HOGENOM

HOG000193685.

KO

K03679.

OMA

GNKRWKV.

OrthoDB

EOG4G1QRD.

Gene expression databases

Genevestigator

P38792.

GermOnline

YHR069C. Saccharomyces cerevisiae.

Family and domain databases

InterPro

IPR025721. Exosome_cplx_N_dom.
IPR026699. Exosome_RNA_bind1/RRP40/RRP4.
IPR022967. RNA-binding_domain_S1.
[Graphical view]

PANTHER

PTHR21321. PTHR21321. 1 hit.

Pfam

PF14382. ECR1_N. 1 hit.
[Graphical view]

SMART

SM00316. S1. 1 hit.
[Graphical view]

PROSITE

PS50126. S1. False negative.
[Graphical view]

ProtoNet

Search...

Other

NextBio

982123.

Entry information

Entry name

RRP4_YEAST

Accession

Primary (citable) accession number: P38792
Secondary accession number(s): D3DL18

Entry history

Integrated into UniProtKB/Swiss-Prot:	February 1, 1995
Last sequence update:	February 1, 1995
Last modified:	May 1, 2013
This is version 109 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Fungal Protein Annotation Program