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Q9UXC4 (RRP4_SULSO) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 85. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (2) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Exosome complex component Rrp4
Gene names
Name:rrp4
Ordered Locus Names:SSO0736
ORF Names:C20_026
OrganismSulfolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2) [Reference proteome] [HAMAP]
Taxonomic identifier273057 [NCBI]
Taxonomic lineageArchaeaCrenarchaeotaThermoproteiSulfolobalesSulfolobaceaeSulfolobus

Protein attributes

Sequence length249 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Non-catalytic component of the exosome, which is a complex involved in RNA degradation. Increases the RNA binding and the efficiency of RNA degradation. Confers strong poly(A) specificity to the exosome. Ref.4 Ref.5 Ref.6

Subunit structure

Component of the archaeal exosome complex. Forms a trimer of Rrp4 and/or Csl4 subunits. The trimer associates with an hexameric ring-like arrangement composed of 3 Rrp41-Rrp42 heterodimers. Ref.7 Ref.8 Ref.9

Subcellular location

Cytoplasm Potential HAMAP-Rule MF_00623.

Domain

Contains an N-terminal domain that mediates interactions with the hexameric ring, a central S1 domain and a C-terminal KH domain. The KH domain is required for efficient RNA degradation, but is not responsible for poly(A) preference. Ref.7 Ref.8

Sequence similarities

Belongs to the RRP4 family.

Contains 1 KH domain.

Contains 1 S1 motif domain.

Ontologies

Keywords
   Cellular componentCytoplasm
Exosome
   LigandRNA-binding
   Technical term3D-structure
Complete proteome
Reference proteome
Gene Ontology (GO)
   Biological_processRNA catabolic process

Inferred from electronic annotation. Source: UniProtKB-HAMAP

   Cellular_componentcytoplasm

Inferred from electronic annotation. Source: UniProtKB-SubCell

exosome (RNase complex)

Inferred from electronic annotation. Source: UniProtKB-KW

   Molecular_functionRNA binding

Inferred from electronic annotation. Source: UniProtKB-HAMAP

Complete GO annotation...

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 249249Exosome complex component Rrp4 HAMAP-Rule MF_00623
PRO_0000050156

Regions

Domain73 – 14472S1 motif
Domain154 – 21158KH

Secondary structure

................................................. 249
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
Q9UXC4 [UniParc].

Last modified May 1, 2000. Version 1.
Checksum: A36AD0CA0363D4B8

FASTA24927,998
        10         20         30         40         50         60 
MNMSQSQKIV LQPRSIVVPG ELLAEGEFQI PWSPYILKIN SKYYSTVVGL FDVKDTQFEV 

        70         80         90        100        110        120 
IPLEGSFYYP KINDIVIGLV EDVEIYGWVV DIKAPYKAYL PASNLLGRSI NVGEDLRRYL 

       130        140        150        160        170        180 
DVGDYVIARI ENFDRSIDPV LSVKGKDLGR VSNGIVIDIM PVKVPRVIGK NKSMYETLTS 

       190        200        210        220        230        240 
KSGCSIFVAN NGRIWATCPS RFSEEILIEA IRKIENESHI KGLTDRIKQF IEEKLGERNA 


SSGETKTNS 

« Hide

References

« Hide 'large scale' references
[1]"Gene content and organization of a 281-kbp contig from the genome of the extremely thermophilic archaeon, Sulfolobus solfataricus P2."
Charlebois R.L., Singh R.K., Chan-Weiher C.C.-Y., Allard G., Chow C., Confalonieri F., Curtis B., Duguet M., Erauso G., Faguy D., Gaasterland T., Garrett R.A., Gordon P., Jeffries A.C., Kozera C., Kushwaha N., Lafleur E., Medina N. expand/collapse author list , Peng X., Penny S.L., She Q., St Jean A., van der Oost J., Young F., Zivanovic Y., Doolittle W.F., Ragan M.A., Sensen C.W.
Genome 43:116-136(2000) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: ATCC 35092 / DSM 1617 / JCM 11322 / P2.
[2]"The complete genome of the crenarchaeon Sulfolobus solfataricus P2."
She Q., Singh R.K., Confalonieri F., Zivanovic Y., Allard G., Awayez M.J., Chan-Weiher C.C.-Y., Clausen I.G., Curtis B.A., De Moors A., Erauso G., Fletcher C., Gordon P.M.K., Heikamp-de Jong I., Jeffries A.C., Kozera C.J., Medina N., Peng X. expand/collapse author list , Thi-Ngoc H.P., Redder P., Schenk M.E., Theriault C., Tolstrup N., Charlebois R.L., Doolittle W.F., Duguet M., Gaasterland T., Garrett R.A., Ragan M.A., Sensen C.W., Van der Oost J.
Proc. Natl. Acad. Sci. U.S.A. 98:7835-7840(2001) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: ATCC 35092 / DSM 1617 / JCM 11322 / P2.
[3]"An exosome-like complex in Sulfolobus solfataricus."
Evguenieva-Hackenberg E., Walter P., Hochleitner E., Lottspeich F., Klug G.
EMBO Rep. 4:889-893(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: INTERACTION WITH EXOSOME.
Strain: ATCC 35092 / DSM 1617 / JCM 11322 / P2.
[4]"Characterization of native and reconstituted exosome complexes from the hyperthermophilic archaeon Sulfolobus solfataricus."
Walter P., Klein F., Lorentzen E., Ilchmann A., Klug G., Evguenieva-Hackenberg E.
Mol. Microbiol. 62:1076-1089(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION, INTERACTION WITH EXOSOME.
[5]"Rrp4 and Csl4 are needed for efficient degradation but not for polyadenylation of synthetic and natural RNA by the archaeal exosome."
Evguenieva-Hackenberg E., Roppelt V., Finsterseifer P., Klug G.
Biochemistry 47:13158-13168(2008) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION.
Strain: ATCC 35092 / DSM 1617 / JCM 11322 / P2.
[6]"The evolutionarily conserved subunits Rrp4 and Csl4 confer different substrate specificities to the archaeal exosome."
Roppelt V., Klug G., Evguenieva-Hackenberg E.
FEBS Lett. 584:2931-2936(2010) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION.
[7]"Heterogeneous complexes of the RNA exosome in Sulfolobus solfataricus."
Witharana C., Roppelt V., Lochnit G., Klug G., Evguenieva-Hackenberg E.
Biochimie 94:1578-1587(2012) [PubMed] [Europe PMC] [Abstract]
Cited for: SUBUNIT, DOMAIN.
Strain: ATCC 35092 / DSM 1617 / JCM 11322 / P2.
[8]"RNA channelling by the archaeal exosome."
Lorentzen E., Dziembowski A., Lindner D., Seraphin B., Conti E.
EMBO Rep. 8:470-476(2007) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (1.60 ANGSTROMS) IN COMPLEX WITH RRP41 AND RRP42, SUBUNIT, DOMAIN.
[9]"Crystal structure of the S. solfataricus archaeal exosome reveals conformational flexibility in the RNA-binding ring."
Lu C., Ding F., Ke A.
PLoS ONE 5:E8739-E8739(2010) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.41 ANGSTROMS) IN COMPLEX WITH RRP41 AND RRP42, SUBUNIT.
[10]"Crystal structure of a 9-subunit archaeal exosome in pre-catalytic states of the phosphorolytic reaction."
Lorentzen E., Conti E.
Archaea 2012:721869-721869(2012) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (1.80 ANGSTROMS) IN COMPLEX WITH RRP41 AND RRP42.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
Y18930 Genomic DNA. Translation: CAB57567.1.
AE006641 Genomic DNA. Translation: AAK41032.1.
PIRA99222.
RefSeqNP_342242.1. NC_002754.1.

3D structure databases

PDBe
RCSB-PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
2JE6X-ray1.60I1-249[»]
2JEAX-ray2.33I1-249[»]
2JEBX-ray2.40I1-249[»]
3L7ZX-ray2.41C/F/I1-249[»]
4BA1X-ray1.80I1-249[»]
4BA2X-ray2.50I1-249[»]
ProteinModelPortalQ9UXC4.
SMRQ9UXC4. Positions 7-221.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

STRING273057.SSO0736.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaAAK41032; AAK41032; SSO0736.
GeneID1454999.
KEGGsso:SSO0736.

Phylogenomic databases

eggNOGCOG1097.
HOGENOMHOG000229527.
KOK03679.
OMAGSMISML.

Enzyme and pathway databases

BioCycSSOL273057:GCH2-697-MONOMER.

Family and domain databases

Gene3D2.40.50.140. 1 hit.
HAMAPMF_00623. Exosome_Rrp4.
InterProIPR023474. Exosome_RNA_bind1.
IPR026699. Exosome_RNA_bind1/RRP40/RRP4.
IPR004087. KH_dom.
IPR004088. KH_dom_type_1.
IPR012340. NA-bd_OB-fold.
IPR003029. Rbsml_prot_S1_RNA-bd_dom.
IPR022967. RNA-binding_domain_S1.
[Graphical view]
PANTHERPTHR21321. PTHR21321. 1 hit.
PfamPF00013. KH_1. 1 hit.
PF00575. S1. 1 hit.
[Graphical view]
SMARTSM00322. KH. 1 hit.
SM00316. S1. 1 hit.
[Graphical view]
SUPFAMSSF50249. SSF50249. 1 hit.
SSF54791. SSF54791. 1 hit.
PROSITEPS50126. S1. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceQ9UXC4.

Entry information

Entry nameRRP4_SULSO
AccessionPrimary (citable) accession number: Q9UXC4
Entry history
Integrated into UniProtKB/Swiss-Prot: March 25, 2003
Last sequence update: May 1, 2000
Last modified: July 9, 2014
This is version 85 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references