P25359 (RRP43_YEAST) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Exosome complex component RRP43

Alternative name(s):
Ribosomal RNA-processing protein 43

Gene names

Name:	RRP43
Ordered Locus Names:	YCR035C
ORF Names:	YCR35C, YCR522

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	394 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. RRP43 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.5 Ref.8 Ref.9 Ref.14
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 NIP7 and NOP8. Interacts strongly with RRP46. Ref.5 Ref.7 Ref.9 Ref.14
Subcellular location	Cytoplasm. Nucleus › nucleolus Ref.10.
Miscellaneous	Present with 3180 molecules/cell in log phase SD medium.
Sequence similarities	Belongs to the RNase PH family.
Caution	According to Ref.14 and Ref.12, 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 Direct protein sequencing 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.9Ref.5. Source: SGD nonfunctional rRNA decay Inferred by curator Ref.7. 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 PubMed 18940861. 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.7. Source: SGD nuclear-transcribed mRNA catabolic process, non-stop decay Inferred by curator Ref.7. Source: SGD polyadenylation-dependent snoRNA 3'-end processing Inferred by curator Ref.7. Source: SGD
Cellular_component	cytoplasmic exosome (RNase complex) Inferred from direct assay Ref.7PubMed 19046973. Source: SGD nuclear exosome (RNase complex) Inferred from direct assay Ref.7PubMed 19046973. Source: SGD nucleolus Inferred from direct assay PubMed 9891085. Source: SGD nucleoplasm Inferred from direct assay PubMed 9891085. Source: SGD
Molecular_function	RNA binding Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
NIP7	Q08962	3	EBI-1773,EBI-12067
PIH1	P38768	2	EBI-1773,EBI-24499

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 394

394

Exosome complex component RRP43

PRO_0000139970

Amino acid modifications

Modified residue

26

1

Phosphoserine Ref.15

Experimental info

Mutagenesis

162

1

S → F: Interaction with RRP46 abolished; when associated with T-246. Ref.9

Mutagenesis

212

1

V → A: Interaction with RRP46 abolished. Ref.9

Mutagenesis

230

1

C → Y: Interaction with RRP46 abolished; when associated with T-274 and Y-276. Ref.9

Mutagenesis

246

1

A → T: Interaction with RRP46 abolished; when associated with F-162. Ref.9

Mutagenesis

274

1

I → T: Interaction with RRP46 abolished; when associated with Y-230 and Y-276. Ref.9

Mutagenesis

276

1

C → Y: Interaction with RRP46 abolished; when associated with Y-230 and T-274. Ref.9

Sequence conflict

102

1

A → S in CAA40227. Ref.1

Sequence conflict

363

1

V → M in CAA40227. Ref.1

Secondary structure

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394

Helix Strand Turn

Details...

Beta strand

10 – 12

3

Helix

19 – 25

7

Helix

27 – 35

9

Turn

36 – 38

3

Beta strand

48 – 50

3

Beta strand

53 – 60

8

Beta strand

65 – 67

3

Beta strand

76 – 82

7

Beta strand

85 – 98

14

Helix

124 – 126

3

Beta strand

131 – 136

6

Helix

146 – 161

16

Helix

167 – 170

4

Beta strand

175 – 180

6

Turn

181 – 183

3

Beta strand

184 – 188

5

Beta strand

208 – 221

14

Helix

227 – 238

12

Beta strand

242 – 249

8

Beta strand

257 – 260

4

Beta strand

265 – 268

4

Beta strand

275 – 283

9

Turn

288 – 290

3

Beta strand

293 – 301

9

Helix

304 – 306

3

Beta strand

328 – 333

6

Helix

336 – 342

7

Beta strand

345 – 351

7

Beta strand

357 – 367

11

Helix

371 – 391

21

Sequences

	Sequence		Length	Mass (Da)
	P25359 [UniParc]. Last modified June 27, 2003. Version 2. Checksum: 8801837B8184134D	FASTA	394	44,011
	10 20 30 40 50 60 MAESTTLETI EIHPITFPPE VLARISPELS LQRHLSLGIR PCLRKYEEFR DVAIENNTLS 70 80 90 100 110 120 RYADAGNIDT KNNILGSNVL KSGKTIVITS ITGGIIEETS AAIKDLDDFG EEELFEVTKE 130 140 150 160 170 180 EDIIANYASV YPVVEVERGR VGACTDEEMT ISQKLHDSIL HSRILPKKAL KVKAGVRSAN 190 200 210 220 230 240 EDGTFSVLYP DELEDDTLNE TNLKMKRKWS YVLYAKIVVL SRTGPVFDLC WNSLMYALQS 250 260 270 280 290 300 VKLPRAFIDE RASDLRMTIR TRGRSATIRE TYEIICDQTK SVPLMINAKN IAFASNYGIV 310 320 330 340 350 360 ELDPECQLQN SDNSEEEEVD IDMDKLNTVL IADLDTEAEE TSIHSTISIL AAPSGNYKQL 370 380 390 TLVGGGAKIT PEMIKRSLLL SRVRADDLST RFNI

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"The complete sequence of the 8.2 kb segment left of MAT on chromosome III reveals five ORFs, including a gene for a yeast ribokinase." Thierry A., Fairhead C., Dujon B. Yeast 6:521-534(1990) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: ATCC 96604 / S288c / FY1679.
[2]	"The complete DNA sequence of yeast chromosome III." Oliver S.G., van der Aart Q.J.M., Agostoni-Carbone M.L., Aigle M., Alberghina L., Alexandraki D., Antoine G., Anwar R., Ballesta J.P.G., Benit P., Berben G., Bergantino E., Biteau N., Bolle P.-A., Bolotin-Fukuhara M., Brown A., Brown A.J.P., Buhler J.-M. , Carcano C., Carignani G., Cederberg H., Chanet R., Contreras R., Crouzet M., Daignan-Fornier B., Defoor E., Delgado M.D., Demolder J., Doira C., Dubois E., Dujon B., Duesterhoeft A., Erdmann D., Esteban M., Fabre F., Fairhead C., Faye G., Feldmann H., Fiers W., Francingues-Gaillard M.-C., Franco L., Frontali L., Fukuhara H., Fuller L.J., Galland P., Gent M.E., Gigot D., Gilliquet V., Glansdorff N., Goffeau A., Grenson M., Grisanti P., Grivell L.A., de Haan M., Haasemann M., Hatat D., Hoenicka J., Hegemann J.H., Herbert C.J., Hilger F., Hohmann S., Hollenberg C.P., Huse K., Iborra F., Indge K.J., Isono K., Jacq C., Jacquet M., James C.M., Jauniaux J.-C., Jia Y., Jimenez A., Kelly A., Kleinhans U., Kreisl P., Lanfranchi G., Lewis C., van der Linden C.G., Lucchini G., Lutzenkirchen K., Maat M.J., Mallet L., Mannhaupt G., Martegani E., Mathieu A., Maurer C.T.C., McConnell D., McKee R.A., Messenguy F., Mewes H.-W., Molemans F., Montague M.A., Muzi Falconi M., Navas L., Newlon C.S., Noone D., Pallier C., Panzeri L., Pearson B.M., Perea J., Philippsen P., Pierard A., Planta R.J., Plevani P., Poetsch B., Pohl F.M., Purnelle B., Ramezani Rad M., Rasmussen S.W., Raynal A., Remacha M.A., Richterich P., Roberts A.B., Rodriguez F., Sanz E., Schaaff-Gerstenschlaeger I., Scherens B., Schweitzer B., Shu Y., Skala J., Slonimski P.P., Sor F., Soustelle C., Spiegelberg R., Stateva L.I., Steensma H.Y., Steiner S., Thierry A., Thireos G., Tzermia M., Urrestarazu L.A., Valle G., Vetter I., van Vliet-Reedijk J.C., Voet M., Volckaert G., Vreken P., Wang H., Warmington J.R., von Wettstein D., Wicksteed B.L., Wilson C., Wurst H., Xu G., Yoshikawa A., Zimmermann F.K., Sgouros J.G. Nature 357:38-46(1992) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 204508 / S288c.
[3]	Valles G., Volckaerts G. Submitted (JUN-2001) to the EMBL/GenBank/DDBJ databases Cited for: SEQUENCE REVISION TO 102 AND 363.
[4]	Saccharomyces Genome Database Submitted (DEC-2009) to the EMBL/GenBank/DDBJ databases Cited for: GENOME REANNOTATION. Strain: ATCC 204508 / S288c.
[5]	"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: PROTEIN SEQUENCE OF 25-33, FUNCTION, SUBUNIT, MASS SPECTROMETRY.
[6]	"The complete sequence of a 7.5 kb region of chromosome III from Saccharomyces cerevisiae that lies between CRY1 and MAT." Wicksteed B.L., Roberts A.B., Sagliocco F.A., Brown A.J.P. Yeast 7:761-772(1991) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 232-394.
[7]	"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.
[8]	"The exosome subunit Rrp43p is required for the efficient maturation of 5.8S, 18S and 25S rRNA." Zanchin N.I., Goldfarb D.S. Nucleic Acids Res. 27:1283-1288(1999) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION.
[9]	"Temperature-sensitive mutants of the exosome subunit Rrp43p show a deficiency in mRNA degradation and no longer interact with the exosome." Oliveira C.C., Gonzales F.A., Zanchin N.I. Nucleic Acids Res. 30:4186-4198(2002) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, INTERACTION WITH RRP46, MUTAGENESIS OF SER-162; VAL-212; CYS-230; ALA-246; ILE-274 AND CYS-276.
[10]	"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].
[11]	"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].
[12]	"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.
[13]	Erratum Liu Q., Greimann J.C., Lima C.D. Cell 131:188-189(2007)
[14]	"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.
[15]	"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-26, MASS SPECTROMETRY.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

X56909 Genomic DNA. Translation: CAA40227.1.
X59720 Genomic DNA. Translation: CAC42984.1.
S78624 Genomic DNA. Translation: AAB21261.1.
BK006937 Genomic DNA. Translation: DAA07514.1.

PIR

S12917.

RefSeq

NP_009964.2. NM_001178749.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
4IFD	X-ray	2.80	C	2-394	[»]

ProteinModelPortal

P25359.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-5485N.

IntAct

P25359. 18 interactions.

MINT

MINT-564723.

STRING

4932.YCR035C.

Proteomic databases

PaxDb

P25359.

PeptideAtlas

P25359.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblFungi

YCR035C; YCR035C; YCR035C.

GeneID

850401.

KEGG

sce:YCR035C.

Organism-specific databases

CYGD

YCR035c.

SGD

S000000631. RRP43.

Phylogenomic databases

eggNOG

NOG286862.

HOGENOM

HOG000057141.

KO

K12586.

OMA

PTDEEMI.

OrthoDB

EOG4RBTTK.

Enzyme and pathway databases

BioCyc

YEAST:G3O-29348-MONOMER.

Gene expression databases

Genevestigator

P25359.

GermOnline

YCR035C. 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

965938.

Entry information

Entry name

RRP43_YEAST

Accession

Primary (citable) accession number: P25359
Secondary accession number(s): D6VR45, Q8NKJ5

Entry history

Integrated into UniProtKB/Swiss-Prot:	May 1, 1992
Last sequence update:	June 27, 2003
Last modified:	May 29, 2013
This is version 120 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Fungal Protein Annotation Program