Q12149 (RRP6_YEAST) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Exosome complex exonuclease RRP6
EC=3.1.13.-

Alternative name(s):
Ribosomal RNA-processing protein 6

Gene names

Name:	RRP6
Synonyms:	UNC733
Ordered Locus Names:	YOR001W

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	733 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Nuclear-specific 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. 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. RRP6 has 3'-5' exonuclease activity which is not modulated upon association with Exo-9 suggesting that the complex inner RNA-binding path is not used to access its active site. Ref.5 Ref.6 Ref.7 Ref.11
Subunit structure	Component of the RNA exosome complex. The catalytically inactive RNA exosome core (Exo-9) complex 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. RRP6 specifically is part of the nuclear form of the RNA exosome complex; the association appears to be mediated by Exo-9 and not by DIS3. Interacts with LRP1. Interacts with NPL3, NOP53 and PAP1. Ref.6 Ref.7 Ref.8 Ref.11 Ref.15 Ref.17
Subcellular location	Nucleus › nucleolus Ref.6 Ref.7 Ref.9 Ref.11.
Disruption phenotype	Deletion mutant is impaired in growth at all temperatures and is nonviable at 37 degrees Celsius. It is defective in the 3' processing of the 5.8S rRNA and accumulates a discrete species, 5.8S + 30, that is 3' extended by about 30 nucleotides. Deletion also causes an accumulation of 7S RNA and 5' ETS and increases the level of poly(A)+ mRNA. Ref.6 Ref.7 Ref.15
Miscellaneous	Present with 2160 molecules/cell in log phase SD medium.
Sequence similarities	Belongs to the exosome component 10/RRP6 family. Contains 1 HRDC domain.

Ontologies

Keywords
Biological process	rRNA processing
Cellular component	Exosome Nucleus
Ligand	RNA-binding
Molecular function	Exonuclease Hydrolase Nuclease
PTM	Phosphoprotein
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 10508172PubMed 10611222PubMed 16373491. 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.6PubMed 10508172PubMed 18940861Ref.5. Source: SGD histone mRNA catabolic process Inferred from mutant phenotype PubMed 17179095. Source: SGD nuclear polyadenylation-dependent CUT catabolic process Inferred from mutant phenotype PubMed 15935759PubMed 16973436PubMed 18007593. Source: SGD nuclear polyadenylation-dependent antisense transcript catabolic process Inferred from mutant phenotype PubMed 18022365. Source: SGD nuclear polyadenylation-dependent mRNA catabolic process Inferred from mutant phenotype PubMed 16373491PubMed 19369424. Source: SGD nuclear polyadenylation-dependent rRNA catabolic process Inferred from mutant phenotype Ref.6PubMed 15173578PubMed 15572680PubMed 16431988PubMed 18007593PubMed 18940861. Source: SGD nuclear polyadenylation-dependent snRNA catabolic process Inferred from mutant phenotype PubMed 16431988. Source: SGD nuclear polyadenylation-dependent snoRNA catabolic process Inferred from mutant phenotype PubMed 16373491. Source: SGD nuclear polyadenylation-dependent tRNA catabolic process Inferred from direct assay PubMed 15828860. Source: SGD nuclear retention of pre-mRNA with aberrant 3'-ends at the site of transcription Inferred from genetic interaction PubMed 11586364PubMed 12417728. Source: SGD polyadenylation-dependent snoRNA 3'-end processing Inferred from mutant phenotype PubMed 10611222PubMed 16373491PubMed 18951092. Source: SGD posttranscriptional tethering of RNA polymerase II gene DNA at nuclear periphery Inferred from mutant phenotype PubMed 18614049. Source: SGD
Cellular_component	nuclear exosome (RNase complex) Inferred from direct assay Ref.6PubMed 19046973. Source: SGD nucleolus Inferred from direct assay PubMed 16541108. Source: SGD
Molecular_function	3'-5'-exoribonuclease activity Inferred from direct assay Ref.7. Source: SGD RNA binding Inferred from electronic annotation. Source: UniProtKB-KW nucleotide binding Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 733

733

Exosome complex exonuclease RRP6

PRO_0000097456

Regions

Domain

435 – 515

81

HRDC

Amino acid modifications

Modified residue

110

1

Phosphoserine Ref.16 Ref.18

Modified residue

138

1

Phosphoserine Ref.14

Modified residue

406

1

Phosphotyrosine Ref.18

Modified residue

410

1

Phosphothreonine Ref.18

Modified residue

412

1

Phosphoserine Ref.18

Modified residue

520

1

Phosphothreonine Ref.18

Modified residue

640

1

Phosphoserine Ref.18

Modified residue

645

1

Phosphoserine Ref.14 Ref.16 Ref.18

Experimental info

Sequence conflict

402

1

E → G in AAT92869. Ref.4

Secondary structure

1

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733

Helix Strand Turn

Details...

Helix

132 – 135

4

Helix

162 – 165

4

Beta strand

173 – 175

3

Helix

184 – 189

6

Helix

194 – 196

3

Helix

208 – 210

3

Beta strand

214 – 216

3

Helix

219 – 229

11

Beta strand

233 – 242

10

Beta strand

244 – 248

5

Beta strand

250 – 257

8

Beta strand

262 – 266

5

Turn

267 – 273

7

Helix

274 – 277

4

Helix

278 – 281

4

Beta strand

286 – 292

7

Helix

294 – 304

11

Beta strand

309 – 313

5

Helix

314 – 321

8

Helix

328 – 335

8

Turn

343 – 346

4

Helix

356 – 367

12

Helix

369 – 382

14

Helix

386 – 398

13

Helix

404 – 406

3

Beta strand

413 – 416

4

Beta strand

421 – 427

7

Helix

436 – 438

3

Helix

439 – 456

18

Helix

460 – 463

4

Helix

466 – 475

10

Helix

480 – 484

5

Helix

492 – 496

5

Helix

498 – 515

18

Turn

534 – 536

3

Helix

539 – 553

15

Beta strand

570 – 572

3

Turn

573 – 577

5

Beta strand

582 – 585

4

Beta strand

591 – 594

4

Helix

596 – 611

16

Helix

612 – 614

3

Beta strand

617 – 619

3

Sequences

	Sequence		Length	Mass (Da)
	Q12149 [UniParc]. Last modified November 1, 1996. Version 1. Checksum: B19A0B2ED74C6DA7	FASTA	733	84,039
	10 20 30 40 50 60 MTSENPDVLL SRVINVVRAA SSLASQDVDF YKNLDRGFSK DLKSKADKLA DMANEIILSI 70 80 90 100 110 120 DEHHESFELK EEDISDLWNN FGNIMDNLLE MSDHSLDKLN CAINSKSRGS DLQYLGEFSG 130 140 150 160 170 180 KNFSPTKRVE KPQLKFKSPI DNSESHPFIP LLKEKPNALK PLSESLRLVD DDENNPSHYP 190 200 210 220 230 240 HPYEYEIDHQ EYSPEILQIR EEIPSKSWDD SVPIWVDTST ELESMLEDLK NTKEIAVDLE 250 260 270 280 290 300 HHDYRSYYGI VCLMQISTRE RDYLVDTLKL RENLHILNEV FTNPSIVKVF HGAFMDIIWL 310 320 330 340 350 360 QRDLGLYVVG LFDTYHASKA IGLPRHSLAY LLENFANFKT SKKYQLADWR IRPLSKPMTA 370 380 390 400 410 420 YARADTHFLL NIYDQLRNKL IESNKLAGVL YESRNVAKRR FEYSKYRPLT PSSEVYSPIE 430 440 450 460 470 480 KESPWKILMY QYNIPPEREV LVRELYQWRD LIARRDDESP RFVMPNQLLA ALVAYTPTDV 490 500 510 520 530 540 IGVVSLTNGV TEHVRQNAKL LANLIRDALR NIKNTNEEAT PIPSSETKAD GILLETISVP 550 560 570 580 590 600 QIRDVMERFS VLCNSNISKS RAKPVTNSSI LLGKILPREE HDIAYSKDGL PNKVKTEDIR 610 620 630 640 650 660 IRAQNFKSAL ANLEDIIFEI EKPLVVPVKL EEIKTVDPAS APNHSPEIDN LDDLVVLKKK 670 680 690 700 710 720 NIQKKQPAKE KGVTEKDAVD YSKIPNILSN KPGQNNRQQK KRRFDPSSSD SNGPRAAKKR 730 RPAAKGKNLS FKR

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"The sequence of a 30 kb fragment on the left arm of chromosome XV from Saccharomyces cerevisiae reveals 15 open reading frames, five of which correspond to previously identified genes." Sterky F., Holmberg A., Pettersson B., Uhlen M. Yeast 12:1091-1095(1996) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]	"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.
[3]	Saccharomyces Genome Database Submitted (DEC-2009) to the EMBL/GenBank/DDBJ databases Cited for: GENOME REANNOTATION. Strain: ATCC 204508 / S288c.
[4]	"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.
[5]	"Rrp6p, the yeast homologue of the human PM-Scl 100-kDa autoantigen, is essential for efficient 5.8 S rRNA 3' end formation." Briggs M.W., Burkard K.T.D., Butler J.S. J. Biol. Chem. 273:13255-13263(1998) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION.
[6]	"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 RNA EXOSOME COMPLEX BY MASS SPECTROMETRY, SUBCELLULAR LOCATION, DISRUPTION PHENOTYPE.
[7]	"A nuclear 3'-5' exonuclease involved in mRNA degradation interacts with Poly(A) polymerase and the hnRNA protein Npl3p." Burkard K.T.D., Butler J.S. Mol. Cell. Biol. 20:604-616(2000) [PubMed] [Europe PMC] [Abstract] Cited for: CATALYTIC ACTIVITY, FUNCTION, INTERACTION WITH NPL3 AND PAP1, SUBCELLULAR LOCATION, DISRUPTION PHENOTYPE.
[8]	"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.
[9]	"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].
[10]	"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].
[11]	"Genome-wide mRNA surveillance is coupled to mRNA export." Hieronymus H., Yu M.C., Silver P.A. Genes Dev. 18:2652-2662(2004) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, INTERACTION WITH LRP1, SUBCELLULAR LOCATION.
[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, EXONUCLEASE ACTIVITY.
[13]	Erratum Liu Q., Greimann J.C., Lima C.D. Cell 131:188-189(2007)
[14]	"Large-scale phosphorylation analysis of alpha-factor-arrested Saccharomyces cerevisiae." Li X., Gerber S.A., Rudner A.D., Beausoleil S.A., Haas W., Villen J., Elias J.E., Gygi S.P. J. Proteome Res. 6:1190-1197(2007) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-138 AND SER-645, MASS SPECTROMETRY. Strain: ADR376.
[15]	"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, INTERACTION WITH THE RNA EXOSOME, SUBUNIT, DISRUPTION PHENOTYPE.
[16]	"Proteome-wide identification of in vivo targets of DNA damage checkpoint kinases." Smolka M.B., Albuquerque C.P., Chen S.H., Zhou H. Proc. Natl. Acad. Sci. U.S.A. 104:10364-10369(2007) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-110 AND SER-645, MASS SPECTROMETRY.
[17]	"Nop53p interacts with 5.8S rRNA co-transcriptionally, and regulates processing of pre-rRNA by the exosome." Granato D.C., Machado-Santelli G.M., Oliveira C.C. FEBS J. 275:4164-4178(2008) [PubMed] [Europe PMC] [Abstract] Cited for: INTERACTION WITH NOP53.
[18]	"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-110; TYR-406; THR-410; SER-412; THR-520; SER-640 AND SER-645, MASS SPECTROMETRY.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

Z74909 Genomic DNA. Translation: CAA99189.1.
U43491 Genomic DNA. Translation: AAC49480.1.
AY692850 Genomic DNA. Translation: AAT92869.1.
BK006948 Genomic DNA. Translation: DAA10783.1.

PIR

S61984.

RefSeq

NP_014643.1. NM_001183420.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1M0Y	model	-	A	207-382	[»]
2HBJ	X-ray	2.10	A	129-536	[»]
2HBK	X-ray	2.25	A	129-536	[»]
2HBL	X-ray	2.30	A	129-536	[»]
2HBM	X-ray	2.70	A	129-536	[»]
4IFD	X-ray	2.80	K	518-693	[»]

ProteinModelPortal

Q12149.

SMR

Q12149. Positions 129-516.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-4560N.

IntAct

Q12149. 27 interactions.

MINT

MINT-534618.

STRING

4932.YOR001W.

Proteomic databases

PaxDb

Q12149.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblFungi

YOR001W; YOR001W; YOR001W.

GeneID

854162.

KEGG

sce:YOR001W.

Organism-specific databases

CYGD

YOR001w.

SGD

S000005527. RRP6.

Phylogenomic databases

eggNOG

COG0349.

GeneTree

ENSGT00390000015408.

HOGENOM

HOG000196525.

KO

K12591.

OMA

YGIVCLM.

OrthoDB

EOG4SJ8P0.

Enzyme and pathway databases

BioCyc

YEAST:G3O-33552-MONOMER.

Gene expression databases

Genevestigator

Q12149.

GermOnline

YOR001W. Saccharomyces cerevisiae.

Family and domain databases

InterPro

IPR002562. 3'-5'_exonuclease_dom.
IPR012588. Exosome-assoc_fac_Rrp6_N.
IPR010997. HRDC-like.
IPR002121. HRDC_dom.
IPR012337. RNaseH-like_dom.
[Graphical view]

Pfam

PF01612. DNA_pol_A_exo1. 1 hit.
PF00570. HRDC. 1 hit.
PF08066. PMC2NT. 1 hit.
[Graphical view]

SMART

SM00474. 35EXOc. 1 hit.
SM00341. HRDC. 1 hit.
[Graphical view]

SUPFAM

SSF47819. HRDC_like. 1 hit.
SSF53098. RNaseH_fold. 1 hit.

PROSITE

PS50967. HRDC. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

Q12149.

NextBio

975938.

Entry information

Entry name

RRP6_YEAST

Accession

Primary (citable) accession number: Q12149
Secondary accession number(s): D6W267, Q6B280

Entry history

Integrated into UniProtKB/Swiss-Prot:	June 1, 2001
Last sequence update:	November 1, 1996
Last modified:	May 29, 2013
This is version 121 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Fungal Protein Annotation Program