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Protein

Exosome complex component Rrp41

Gene

rrp41

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

Functioni

Catalytic component of the exosome, which is a complex involved in RNA degradation. Has 3'->5' exoribonuclease activity. Can also synthesize heteropolymeric RNA-tails. Binds RNA.UniRule annotation3 Publications

GO - Molecular functioni

  1. 3'-5'-exoribonuclease activity Source: UniProtKB-HAMAP

GO - Biological processi

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

Keywords - Molecular functioni

Exonuclease, Hydrolase, Nuclease

Enzyme and pathway databases

BioCyciSSOL273057:GCH2-696-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Exosome complex component Rrp41UniRule annotation (EC:3.1.13.-UniRule annotation)
Gene namesi
Name:rrp41UniRule annotation
Ordered Locus Names:SSO0735
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
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Exosome

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi98 – 981R → E: Abolishes exoribonuclease activity; when associated with E-99. 1 Publication
Mutagenesisi99 – 991R → E: Abolishes exoribonuclease activity; when associated with E-98. 1 Publication
Mutagenesisi182 – 1821D → A: Abolishes both exoribonuclease and polyadenylation activities. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 248248Exosome complex component Rrp41PRO_0000139991Add
BLAST

Interactioni

Subunit structurei

Component of the archaeal exosome complex. Forms a hexameric ring-like arrangement composed of 3 Rrp41-Rrp42 heterodimers. The hexameric ring associates with a trimer of Rrp4 and/or Csl4 subunits.UniRule annotation6 Publications

Protein-protein interaction databases

DIPiDIP-58154N.
IntActiQ9UXC2. 1 interaction.
MINTiMINT-7891191.
STRINGi273057.SSO0735.

Structurei

Secondary structure

1
248
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi15 – 173Combined sources
Beta strandi31 – 366Combined sources
Beta strandi39 – 4911Combined sources
Beta strandi52 – 6312Combined sources
Helixi67 – 693Combined sources
Beta strandi72 – 743Combined sources
Beta strandi76 – 838Combined sources
Beta strandi87 – 904Combined sources
Helixi98 – 11215Combined sources
Helixi117 – 1193Combined sources
Beta strandi123 – 13311Combined sources
Helixi138 – 15215Combined sources
Beta strandi157 – 1593Combined sources
Beta strandi162 – 1698Combined sources
Beta strandi172 – 1765Combined sources
Helixi179 – 1846Combined sources
Beta strandi185 – 19410Combined sources
Helixi195 – 1973Combined sources
Beta strandi199 – 2079Combined sources
Helixi211 – 23727Combined sources
Helixi238 – 2403Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2BR2X-ray2.80B/D/F/H/J/L/N/P/R/T/V/X1-248[»]
2C37X-ray2.80B/D/F/H/J/L/N/P/R/T/V/X1-248[»]
2C38X-ray3.10B/D/F/H/J/L/N/P/R/T/V/X1-248[»]
2C39X-ray3.30B/D/F/H/J/L/N/P/R/T/V/X1-248[»]
2JE6X-ray1.60B1-248[»]
2JEAX-ray2.33B1-248[»]
2JEBX-ray2.40B1-248[»]
3L7ZX-ray2.41B/E/H4-248[»]
4BA1X-ray1.80B1-248[»]
4BA2X-ray2.50B1-248[»]
ProteinModelPortaliQ9UXC2.
SMRiQ9UXC2. Positions 1-248.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ9UXC2.

Family & Domainsi

Sequence similaritiesi

Belongs to the RNase PH family. Rrp41 subfamily.UniRule annotation

Phylogenomic databases

eggNOGiCOG0689.
HOGENOMiHOG000229515.
InParanoidiQ9UXC2.
KOiK11600.
OMAiDITLLQM.

Family and domain databases

Gene3Di3.30.230.70. 1 hit.
HAMAPiMF_00591. Exosome_Rrp41.
InterProiIPR011807. ExoRNase_exosome_complex.
IPR001247. ExoRNase_PH_dom1.
IPR015847. ExoRNase_PH_dom2.
IPR027408. PNPase/RNase_PH_dom.
IPR020568. Ribosomal_S5_D2-typ_fold.
[Graphical view]
PfamiPF01138. RNase_PH. 1 hit.
PF03725. RNase_PH_C. 1 hit.
[Graphical view]
SUPFAMiSSF54211. SSF54211. 1 hit.
SSF55666. SSF55666. 1 hit.
TIGRFAMsiTIGR02065. ECX1. 1 hit.

Sequencei

Sequence statusi: Complete.

Q9UXC2-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MREMLQVERP KLILDDGKRT DGRKPDELRS IKIELGVLKN ADGSAIFEMG
60 70 80 90 100
NTKAIAAVYG PKEMHPRHLS LPDRAVLRVR YHMTPFSTDE RKNPAPSRRE
110 120 130 140 150
IELSKVIREA LESAVLVELF PRTAIDVFTE ILQADAGSRL VSLMAASLAL
160 170 180 190 200
ADAGIPMRDL IAGVAVGKAD GVIILDLNET EDMWGEADMP IAMMPSLNQV
210 220 230 240
TLFQLNGSMT PDEFRQAFDL AVKGINIIYN LEREALKSKY VEFKEEGV
Length:248
Mass (Da):27,578
Last modified:May 1, 2000 - v1
Checksum:iEAB2C2C89DD5854C
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Y18930 Genomic DNA. Translation: CAB57569.1.
AE006641 Genomic DNA. Translation: AAK41031.1.
PIRiH90221.
RefSeqiNP_342241.1. NC_002754.1.
WP_010923057.1. NC_002754.1.

Genome annotation databases

EnsemblBacteriaiAAK41031; AAK41031; SSO0735.
GeneIDi1454998.
KEGGisso:SSO0735.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Y18930 Genomic DNA. Translation: CAB57569.1.
AE006641 Genomic DNA. Translation: AAK41031.1.
PIRiH90221.
RefSeqiNP_342241.1. NC_002754.1.
WP_010923057.1. NC_002754.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2BR2X-ray2.80B/D/F/H/J/L/N/P/R/T/V/X1-248[»]
2C37X-ray2.80B/D/F/H/J/L/N/P/R/T/V/X1-248[»]
2C38X-ray3.10B/D/F/H/J/L/N/P/R/T/V/X1-248[»]
2C39X-ray3.30B/D/F/H/J/L/N/P/R/T/V/X1-248[»]
2JE6X-ray1.60B1-248[»]
2JEAX-ray2.33B1-248[»]
2JEBX-ray2.40B1-248[»]
3L7ZX-ray2.41B/E/H4-248[»]
4BA1X-ray1.80B1-248[»]
4BA2X-ray2.50B1-248[»]
ProteinModelPortaliQ9UXC2.
SMRiQ9UXC2. Positions 1-248.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

DIPiDIP-58154N.
IntActiQ9UXC2. 1 interaction.
MINTiMINT-7891191.
STRINGi273057.SSO0735.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAK41031; AAK41031; SSO0735.
GeneIDi1454998.
KEGGisso:SSO0735.

Phylogenomic databases

eggNOGiCOG0689.
HOGENOMiHOG000229515.
InParanoidiQ9UXC2.
KOiK11600.
OMAiDITLLQM.

Enzyme and pathway databases

BioCyciSSOL273057:GCH2-696-MONOMER.

Miscellaneous databases

EvolutionaryTraceiQ9UXC2.

Family and domain databases

Gene3Di3.30.230.70. 1 hit.
HAMAPiMF_00591. Exosome_Rrp41.
InterProiIPR011807. ExoRNase_exosome_complex.
IPR001247. ExoRNase_PH_dom1.
IPR015847. ExoRNase_PH_dom2.
IPR027408. PNPase/RNase_PH_dom.
IPR020568. Ribosomal_S5_D2-typ_fold.
[Graphical view]
PfamiPF01138. RNase_PH. 1 hit.
PF03725. RNase_PH_C. 1 hit.
[Graphical view]
SUPFAMiSSF54211. SSF54211. 1 hit.
SSF55666. SSF55666. 1 hit.
TIGRFAMsiTIGR02065. ECX1. 1 hit.
ProtoNetiSearch...

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: INTERACTION WITH EXOSOME.
  5. "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, SUBUNIT.
  6. "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: INTERACTION WITH EXOSOME.
    Strain: ATCC 35092 / DSM 1617 / JCM 11322 / P2.
  7. "Structural basis of 3' end RNA recognition and exoribonucleolytic cleavage by an exosome RNase PH core."
    Lorentzen E., Conti E.
    Mol. Cell 20:473-481(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.80 ANGSTROMS) IN COMPLEX WITH RRP42, SUBUNIT, MUTAGENESIS OF ARG-98 AND ARG-99.
  8. "The archaeal exosome core is a hexameric ring structure with three catalytic subunits."
    Lorentzen E., Walter P., Fribourg S., Evguenieva-Hackenberg E., Klug G., Conti E.
    Nat. Struct. Mol. Biol. 12:575-581(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.80 ANGSTROMS) IN COMPLEX WITH RRP42, FUNCTION, SUBUNIT, MUTAGENESIS OF ASP-182.
  9. Cited for: X-RAY CRYSTALLOGRAPHY (1.60 ANGSTROMS) IN COMPLEX WITH RRP42 AND RRP4, FUNCTION, RNA-BINDING, SUBUNIT.
  10. "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) OF 4-248 IN COMPLEX WITH RRP42 AND RRP4.
  11. "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) OF MUTANT ALA-182 IN COMPLEX WITH RRP42 AND RRP4, SUBUNIT.

Entry informationi

Entry nameiRRP41_SULSO
AccessioniPrimary (citable) accession number: Q9UXC2
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 25, 2003
Last sequence update: May 1, 2000
Last modified: February 4, 2015
This is version 86 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

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.