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Q9UXC4

- RRP4_SULSO

UniProt

Q9UXC4 - RRP4_SULSO

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
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    • History
      Entry version 87 (01 Oct 2014)
      Sequence version 1 (01 May 2000)
      Previous versions | rss
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    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

    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-SubCell
    2. exosome (RNase complex) Source: UniProtKB-KW

    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 – 103
    Beta strandi15 – 173
    Beta strandi22 – 265
    Beta strandi36 – 394
    Beta strandi42 – 454
    Beta strandi47 – 548
    Beta strandi57 – 637
    Beta strandi75 – 839
    Beta strandi85 – 917
    Beta strandi93 – 964
    Beta strandi98 – 1014
    Helixi102 – 1065
    Beta strandi117 – 1193
    Beta strandi125 – 13410
    Beta strandi137 – 1426
    Beta strandi156 – 1583
    Helixi161 – 1633
    Helixi164 – 1685
    Helixi170 – 1723
    Helixi173 – 1797
    Beta strandi187 – 1893
    Beta strandi192 – 1954
    Turni201 – 2066
    Helixi208 – 2114
    Turni212 – 2198
    Turni224 – 2274

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    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.
    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. RNA-binding_domain_S1.
    [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

    MNMSQSQKIV LQPRSIVVPG ELLAEGEFQI PWSPYILKIN SKYYSTVVGL    50
    FDVKDTQFEV IPLEGSFYYP KINDIVIGLV EDVEIYGWVV DIKAPYKAYL 100
    PASNLLGRSI NVGEDLRRYL DVGDYVIARI ENFDRSIDPV LSVKGKDLGR 150
    VSNGIVIDIM PVKVPRVIGK NKSMYETLTS KSGCSIFVAN NGRIWATCPS 200
    RFSEEILIEA IRKIENESHI KGLTDRIKQF IEEKLGERNA SSGETKTNS 249
    Length:249
    Mass (Da):27,998
    Last modified:May 1, 2000 - v1
    Checksum:iA36AD0CA0363D4B8
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    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:
    EMBL
    GenBank
    DDBJ
    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:
    PDBe
    RCSB PDB
    PDBj
    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.
    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. RNA-binding_domain_S1.
    [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

    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 1, 2014
    This is version 87 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