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Protein

Exosome complex component Rrp42

Gene

rrp42

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

Non-catalytic component of the exosome, which is a complex involved in RNA degradation. Contributes to the structuring of the Rrp41 active site.UniRule annotation2 Publications

GO - Molecular functioni

  1. 3'-5' exonuclease activity Source: InterPro

GO - Biological processi

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

Enzyme and pathway databases

BioCyciSSOL273057:GCH2-695-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Exosome complex component Rrp42UniRule annotation
Gene namesi
Name:rrp42UniRule annotation
Ordered Locus Names:SSO0732
ORF Names:C20_023
OrganismiSulfolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)
Taxonomic identifieri273057 [NCBI]
Taxonomic lineageiArchaeaCrenarchaeotaThermoproteiSulfolobalesSulfolobaceaeSulfolobus
ProteomesiUP000001974 Componenti: 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
Mutagenesisi112 – 1121R → E: Abolishes exoribonuclease activity of the complex; when associated with E-116. 1 Publication
Mutagenesisi116 – 1161R → E: Abolishes exoribonuclease activity of the complex; when associated with E-112. 1 Publication
Mutagenesisi218 – 2181E → A: Does not change activity. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 275275Exosome complex component Rrp42PRO_0000140006Add
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-60492N.
STRINGi273057.SSO0732.

Structurei

Secondary structure

1
275
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi13 – 197Combined sources
Turni20 – 223Combined sources
Helixi23 – 253Combined sources
Beta strandi29 – 313Combined sources
Beta strandi40 – 445Combined sources
Beta strandi50 – 589Combined sources
Beta strandi61 – 7212Combined sources
Beta strandi76 – 783Combined sources
Beta strandi79 – 813Combined sources
Beta strandi83 – 908Combined sources
Turni92 – 943Combined sources
Beta strandi100 – 1023Combined sources
Helixi105 – 12016Combined sources
Helixi126 – 1294Combined sources
Beta strandi130 – 1323Combined sources
Turni133 – 1353Combined sources
Beta strandi136 – 14813Combined sources
Helixi153 – 16614Combined sources
Beta strandi169 – 1746Combined sources
Beta strandi181 – 19010Combined sources
Beta strandi193 – 1953Combined sources
Beta strandi198 – 2058Combined sources
Beta strandi208 – 2125Combined sources
Helixi215 – 2206Combined sources
Beta strandi222 – 2298Combined sources
Turni231 – 2333Combined sources
Beta strandi235 – 24410Combined sources
Helixi248 – 27326Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2BR2X-ray2.80A/C/E/G/I/K/M/O/Q/S/U/W1-275[»]
2C37X-ray2.80A/C/E/G/I/K/M/O/Q/S/U/W1-275[»]
2C38X-ray3.10A/C/E/G/I/K/M/O/Q/S/U/W1-275[»]
2C39X-ray3.30A/C/E/G/I/K/M/O/Q/S/U/W1-275[»]
2JE6X-ray1.60A1-275[»]
2JEAX-ray2.33A1-275[»]
2JEBX-ray2.40A1-275[»]
3L7ZX-ray2.41A/D/G1-275[»]
4BA1X-ray1.80A1-275[»]
4BA2X-ray2.50A1-275[»]
ProteinModelPortaliQ9UXC0.
SMRiQ9UXC0. Positions 1-275.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ9UXC0.

Family & Domainsi

Sequence similaritiesi

Belongs to the RNase PH family. Rrp42 subfamily.UniRule annotation

Phylogenomic databases

eggNOGiCOG2123.
HOGENOMiHOG000229504.
InParanoidiQ9UXC0.
KOiK12589.
OMAiVWIVFID.

Family and domain databases

Gene3Di3.30.230.70. 1 hit.
HAMAPiMF_00622. Exosome_Rrp42.
InterProiIPR001247. ExoRNase_PH_dom1.
IPR015847. ExoRNase_PH_dom2.
IPR020869. Exosome_complex_exonuc_2_prob.
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. 2 hits.
SSF55666. SSF55666. 1 hit.

Sequencei

Sequence statusi: Complete.

Q9UXC0-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSSTPSNQNI IPIIKKESIV SLFEKGIRQD GRKLTDYRPL SITLDYAKKA
60 70 80 90 100
DGSALVKLGT TMVLAGTKLE IDKPYEDTPN QGNLIVNVEL LPLAYETFEP
110 120 130 140 150
GPPDENAIEL ARVVDRSLRD SKALDLTKLV IEPGKSVWTV WLDVYVLDYG
160 170 180 190 200
GNVLDACTLA SVAALYNTKV YKVEQHSNGI SVNKNEVVGK LPLNYPVVTI
210 220 230 240 250
SVAKVDKYLV VDPDLDEESI MDAKISFSYT PDLKIVGIQK SGKGSMSLQD
260 270
IDQAENTARS TAVKLLEELK KHLGI
Length:275
Mass (Da):30,194
Last modified:May 1, 2000 - v1
Checksum:i4188C9D6928A144C
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Y18930 Genomic DNA. Translation: CAB57571.1.
AE006641 Genomic DNA. Translation: AAK41030.1.
PIRiG90221.
RefSeqiNP_342240.1. NC_002754.1.
WP_009991305.1. NC_002754.1.

Genome annotation databases

EnsemblBacteriaiAAK41030; AAK41030; SSO0732.
GeneIDi1454997.
KEGGisso:SSO0732.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Y18930 Genomic DNA. Translation: CAB57571.1.
AE006641 Genomic DNA. Translation: AAK41030.1.
PIRiG90221.
RefSeqiNP_342240.1. NC_002754.1.
WP_009991305.1. NC_002754.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2BR2X-ray2.80A/C/E/G/I/K/M/O/Q/S/U/W1-275[»]
2C37X-ray2.80A/C/E/G/I/K/M/O/Q/S/U/W1-275[»]
2C38X-ray3.10A/C/E/G/I/K/M/O/Q/S/U/W1-275[»]
2C39X-ray3.30A/C/E/G/I/K/M/O/Q/S/U/W1-275[»]
2JE6X-ray1.60A1-275[»]
2JEAX-ray2.33A1-275[»]
2JEBX-ray2.40A1-275[»]
3L7ZX-ray2.41A/D/G1-275[»]
4BA1X-ray1.80A1-275[»]
4BA2X-ray2.50A1-275[»]
ProteinModelPortaliQ9UXC0.
SMRiQ9UXC0. Positions 1-275.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

DIPiDIP-60492N.
STRINGi273057.SSO0732.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAK41030; AAK41030; SSO0732.
GeneIDi1454997.
KEGGisso:SSO0732.

Phylogenomic databases

eggNOGiCOG2123.
HOGENOMiHOG000229504.
InParanoidiQ9UXC0.
KOiK12589.
OMAiVWIVFID.

Enzyme and pathway databases

BioCyciSSOL273057:GCH2-695-MONOMER.

Miscellaneous databases

EvolutionaryTraceiQ9UXC0.

Family and domain databases

Gene3Di3.30.230.70. 1 hit.
HAMAPiMF_00622. Exosome_Rrp42.
InterProiIPR001247. ExoRNase_PH_dom1.
IPR015847. ExoRNase_PH_dom2.
IPR020869. Exosome_complex_exonuc_2_prob.
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. 2 hits.
SSF55666. SSF55666. 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(2005) [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(2009) [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(2011) [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(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.80 ANGSTROMS) IN COMPLEX WITH RRP41, SUBUNIT, MUTAGENESIS OF ARG-112 AND ARG-116.
  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(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.80 ANGSTROMS) IN COMPLEX WITH RRP41, FUNCTION, SUBUNIT, MUTAGENESIS OF GLU-218.
  9. Cited for: X-RAY CRYSTALLOGRAPHY (1.60 ANGSTROMS) IN COMPLEX WITH RRP41 AND RRP4, 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(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.41 ANGSTROMS) IN COMPLEX WITH RRP41 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(2011) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.80 ANGSTROMS) IN COMPLEX WITH RRP41 AND RRP4, SUBUNIT.

Entry informationi

Entry nameiRRP42_SULSO
AccessioniPrimary (citable) accession number: Q9UXC0
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 25, 2003
Last sequence update: May 1, 2000
Last modified: April 1, 2015
This is version 84 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.