Q05636 (RRP45_YEAST) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Exosome complex component RRP45

Alternative name(s):
Ribosomal RNA-processing protein 45

Gene names

Name:	RRP45
Ordered Locus Names:	YDR280W
ORF Names:	D9954.1

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	305 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. RRP45 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. Interacts with LRP1. Ref.4 Ref.5 Ref.10
Subcellular location	Cytoplasm. Nucleus › nucleolus Ref.6.
Miscellaneous	Present with 4800 molecules/cell in log phase SD medium.
Sequence similarities	Belongs to the RNase PH family.
Caution	According to Ref.10 and Ref.8, 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
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	U1 snRNA 3'-end processing Inferred from mutant phenotype PubMed 10508172. Source: SGD U4 snRNA 3'-end processing Inferred from mutant phenotype PubMed 10508172. Source: SGD U5 snRNA 3'-end processing Inferred from mutant phenotype PubMed 10508172. 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.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 direct assay PubMed 16541108. Source: SGD
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 – 305

305

Exosome complex component RRP45

PRO_0000139974

Secondary structure

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305

Helix Strand Turn

Details...

Helix

9 – 20

12

Beta strand

36 – 40

5

Beta strand

46 – 51

6

Beta strand

54 – 65

12

Beta strand

76 – 80

5

Helix

85 – 87

3

Helix

99 – 111

13

Turn

112 – 116

5

Helix

120 – 123

4

Beta strand

124 – 126

3

Turn

127 – 129

3

Beta strand

130 – 142

13

Helix

147 – 161

15

Beta strand

167 – 170

4

Beta strand

173 – 176

4

Turn

179 – 181

3

Beta strand

194 – 201

8

Helix

206 – 210

5

Beta strand

218 – 222

5

Helix

225 – 228

4

Beta strand

232 – 240

9

Turn

241 – 243

3

Beta strand

244 – 250

7

Beta strand

252 – 254

3

Helix

258 – 299

42

Sequences

	Sequence		Length	Mass (Da)
	Q05636 [UniParc]. Last modified November 1, 1996. Version 1. Checksum: 65C9DB5A63678F2D	FASTA	305	33,962
	10 20 30 40 50 60 MAKDIEISAS ESKFILEALR QNYRLDGRSF DQFRDVEITF GKEFGDVSVK MGNTKVHCRI 70 80 90 100 110 120 SCQIAQPYED RPFEGLFVIS TEISPMAGSQ FENGNITGED EVLCSRIIEK SVRRSGALDV 130 140 150 160 170 180 EGLCIVAGSK CWAVRADVHF LDCDGGFIDA SCIAVMAGLM HFKKPDITVH GEQIIVHPVN 190 200 210 220 230 240 EREPVPLGIL HIPICVTFSF FNPQDTEENI KGETNSEISI IDATLKEELL RDGVLTVTLN 250 260 270 280 290 300 KNREVVQVSK AGGLPMDALT LMKCCHEAYS IIEKITDQIL QLLKEDSEKR NKYAAMLTSE NAREI

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"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 204511 / S288c / AB972.
[2]	Saccharomyces Genome Database Submitted (DEC-2009) to the EMBL/GenBank/DDBJ databases Cited for: GENOME REANNOTATION. 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, SUBUNIT.
[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]	"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.
[11]	"The yeast exosome functions as a macromolecular cage to channel RNA substrates for degradation." Bonneau F., Basquin J., Ebert J., Lorentzen E., Conti E. Cell 139:547-559(2009) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (3.0 ANGSTROMS) IN COMPLEX WITH SKI6 AND DIS3.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

U51030 Genomic DNA. Translation: AAB64446.1.
AY557748 Genomic DNA. Translation: AAS56074.1.
BK006938 Genomic DNA. Translation: DAA12120.1.

PIR

S70136.

RefSeq

NP_010566.1. NM_001180588.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
2WP8	X-ray	3.00	A	1-305	[»]
4IFD	X-ray	2.80	A	2-305	[»]

ProteinModelPortal

Q05636.

SMR

Q05636. Positions 7-303.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-2084N.

IntAct

Q05636. 27 interactions.

MINT

MINT-555570.

STRING

4932.YDR280W.

Proteomic databases

PaxDb

Q05636.

PeptideAtlas

Q05636.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblFungi

YDR280W; YDR280W; YDR280W.

GeneID

851874.

KEGG

sce:YDR280W.

Organism-specific databases

CYGD

YDR280w.

SGD

S000002688. RRP45.

Phylogenomic databases

eggNOG

COG2123.

GeneTree

ENSGT00530000063093.

HOGENOM

HOG000229504.

KO

K03678.

OMA

LIDASCI.

OrthoDB

EOG4X0R2H.

Gene expression databases

Genevestigator

Q05636.

GermOnline

YDR280W. Saccharomyces cerevisiae.

Family and domain databases

InterPro

IPR001247. ExoRNase_PH_dom1.
IPR015847. ExoRNase_PH_dom2.
IPR020568. Ribosomal_S5_D2-typ_fold.
[Graphical view]

Pfam

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

SUPFAM

SSF54211. Ribosomal_S5_D2-typ_fold. 1 hit.

ProtoNet

Search...

Other

EvolutionaryTrace

Q05636.

NextBio

969829.

Entry information

Entry name

RRP45_YEAST

Accession

Primary (citable) accession number: Q05636
Secondary accession number(s): D6VSR0

Entry history

Integrated into UniProtKB/Swiss-Prot:	June 1, 2001
Last sequence update:	November 1, 1996
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