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Q9UXC4

- RRP4_SULSO

UniProt

Q9UXC4 - RRP4_SULSO

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Protein

Exosome complex component Rrp4

Gene

rrp4

Organism
Sulfolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)
Status
Reviewed - Annotation score: 3 out of 5- Experimental evidence at protein leveli

Functioni

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.3 PublicationsUniRule annotation

GO - Molecular functioni

  1. RNA binding Source: UniProtKB-HAMAP

GO - Biological processi

  1. RNA catabolic process Source: UniProtKB-HAMAP
Complete GO annotation...

Keywords - Ligandi

RNA-binding

Enzyme and pathway databases

BioCyciSSOL273057:GCH2-697-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Exosome complex component Rrp4UniRule annotation
Gene namesi
Name:rrp4UniRule annotation
Ordered Locus Names:SSO0736
ORF Names:C20_026
OrganismiSulfolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)
Taxonomic identifieri273057 [NCBI]
Taxonomic lineageiArchaeaCrenarchaeotaThermoproteiSulfolobalesSulfolobaceaeSulfolobus
ProteomesiUP000001974: Chromosome

Subcellular locationi

Cytoplasm UniRule annotation

GO - Cellular componenti

  1. cytoplasm Source: UniProtKB-HAMAP
  2. exosome (RNase complex) Source: UniProtKB-KW
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Exosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 249249Exosome complex component Rrp4PRO_0000050156Add
BLAST

Interactioni

Subunit structurei

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.4 PublicationsUniRule annotation

Protein-protein interaction databases

STRINGi273057.SSO0736.

Structurei

Secondary structure

1
249
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi8 – 103Combined sources
Beta strandi15 – 173Combined sources
Beta strandi22 – 265Combined sources
Beta strandi36 – 394Combined sources
Beta strandi42 – 454Combined sources
Beta strandi47 – 548Combined sources
Beta strandi57 – 637Combined sources
Beta strandi75 – 839Combined sources
Beta strandi85 – 917Combined sources
Beta strandi93 – 964Combined sources
Beta strandi98 – 1014Combined sources
Helixi102 – 1065Combined sources
Beta strandi117 – 1193Combined sources
Beta strandi125 – 13410Combined sources
Beta strandi137 – 1426Combined sources
Beta strandi156 – 1583Combined sources
Helixi161 – 1633Combined sources
Helixi164 – 1685Combined sources
Helixi170 – 1723Combined sources
Helixi173 – 1797Combined sources
Beta strandi187 – 1893Combined sources
Beta strandi192 – 1954Combined sources
Turni201 – 2066Combined sources
Helixi208 – 2114Combined sources
Turni212 – 2198Combined sources
Turni224 – 2274Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
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[»]
ProteinModelPortaliQ9UXC4.
SMRiQ9UXC4. Positions 7-221.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ9UXC4.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini73 – 14472S1 motifUniRule annotationAdd
BLAST
Domaini154 – 21158KHUniRule annotationAdd
BLAST

Domaini

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.2 Publications

Sequence similaritiesi

Belongs to the RRP4 family.UniRule annotation
Contains 1 KH domain.UniRule annotation
Contains 1 S1 motif domain.UniRule annotation

Phylogenomic databases

eggNOGiCOG1097.
HOGENOMiHOG000229527.
InParanoidiQ9UXC4.
KOiK03679.
OMAiGSMISML.

Family and domain databases

Gene3Di2.40.50.140. 1 hit.
HAMAPiMF_00623. Exosome_Rrp4.
InterProiIPR023474. 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. S1_dom.
[Graphical view]
PANTHERiPTHR21321. PTHR21321. 1 hit.
PfamiPF00013. KH_1. 1 hit.
PF00575. S1. 1 hit.
[Graphical view]
SMARTiSM00322. KH. 1 hit.
SM00316. S1. 1 hit.
[Graphical view]
SUPFAMiSSF50249. SSF50249. 1 hit.
SSF54791. SSF54791. 1 hit.
PROSITEiPS50126. S1. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q9UXC4-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MNMSQSQKIV LQPRSIVVPG ELLAEGEFQI PWSPYILKIN SKYYSTVVGL
60 70 80 90 100
FDVKDTQFEV IPLEGSFYYP KINDIVIGLV EDVEIYGWVV DIKAPYKAYL
110 120 130 140 150
PASNLLGRSI NVGEDLRRYL DVGDYVIARI ENFDRSIDPV LSVKGKDLGR
160 170 180 190 200
VSNGIVIDIM PVKVPRVIGK NKSMYETLTS KSGCSIFVAN NGRIWATCPS
210 220 230 240
RFSEEILIEA IRKIENESHI KGLTDRIKQF IEEKLGERNA SSGETKTNS
Length:249
Mass (Da):27,998
Last modified:May 1, 2000 - v1
Checksum:iA36AD0CA0363D4B8
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Y18930 Genomic DNA. Translation: CAB57567.1.
AE006641 Genomic DNA. Translation: AAK41032.1.
PIRiA99222.
RefSeqiNP_342242.1. NC_002754.1.
WP_010923058.1. NC_002754.1.

Genome annotation databases

EnsemblBacteriaiAAK41032; AAK41032; SSO0736.
GeneIDi1454999.
KEGGisso:SSO0736.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Y18930 Genomic DNA. Translation: CAB57567.1 .
AE006641 Genomic DNA. Translation: AAK41032.1 .
PIRi A99222.
RefSeqi NP_342242.1. NC_002754.1.
WP_010923058.1. NC_002754.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
2JE6 X-ray 1.60 I 1-249 [» ]
2JEA X-ray 2.33 I 1-249 [» ]
2JEB X-ray 2.40 I 1-249 [» ]
3L7Z X-ray 2.41 C/F/I 1-249 [» ]
4BA1 X-ray 1.80 I 1-249 [» ]
4BA2 X-ray 2.50 I 1-249 [» ]
ProteinModelPortali Q9UXC4.
SMRi Q9UXC4. Positions 7-221.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

STRINGi 273057.SSO0736.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai AAK41032 ; AAK41032 ; SSO0736 .
GeneIDi 1454999.
KEGGi sso:SSO0736.

Phylogenomic databases

eggNOGi COG1097.
HOGENOMi HOG000229527.
InParanoidi Q9UXC4.
KOi K03679.
OMAi GSMISML.

Enzyme and pathway databases

BioCyci SSOL273057:GCH2-697-MONOMER.

Miscellaneous databases

EvolutionaryTracei Q9UXC4.

Family and domain databases

Gene3Di 2.40.50.140. 1 hit.
HAMAPi MF_00623. Exosome_Rrp4.
InterProi IPR023474. 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. S1_dom.
[Graphical view ]
PANTHERi PTHR21321. PTHR21321. 1 hit.
Pfami PF00013. KH_1. 1 hit.
PF00575. S1. 1 hit.
[Graphical view ]
SMARTi SM00322. KH. 1 hit.
SM00316. S1. 1 hit.
[Graphical view ]
SUPFAMi SSF50249. SSF50249. 1 hit.
SSF54791. SSF54791. 1 hit.
PROSITEi PS50126. S1. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 35092 / DSM 1617 / JCM 11322 / P2.
  2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 35092 / DSM 1617 / JCM 11322 / P2.
  3. 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. 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.

Entry informationi

Entry nameiRRP4_SULSO
AccessioniPrimary (citable) accession number: Q9UXC4
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 25, 2003
Last sequence update: May 1, 2000
Last modified: October 29, 2014
This is version 88 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3