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Protein

Exosome complex component Rrp42

Gene

rrp42

Organism
Archaeoglobus fulgidus (strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126)
Status
Reviewed-Annotation score: Annotation score: 2 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 annotation

GO - Biological processi

Complete GO annotation...

Enzyme and pathway databases

BioCyciAFUL224325:GJBC-507-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Exosome complex component Rrp42UniRule annotation
Gene namesi
Name:rrp42UniRule annotation
Ordered Locus Names:AF_0494
OrganismiArchaeoglobus fulgidus (strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126)
Taxonomic identifieri224325 [NCBI]
Taxonomic lineageiArchaeaEuryarchaeotaArchaeoglobiArchaeoglobalesArchaeoglobaceaeArchaeoglobus
Proteomesi
  • UP000002199 Componenti: Chromosome

Subcellular locationi

  • Cytoplasm UniRule annotation

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Exosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 259259Exosome complex component Rrp42PRO_0000139996Add
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 annotation2 Publications

Protein-protein interaction databases

STRINGi224325.AF0494.

Structurei

Secondary structure

1
259
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi5 – 1915Combined sources
Beta strandi35 – 395Combined sources
Beta strandi45 – 539Combined sources
Beta strandi56 – 6712Combined sources
Beta strandi78 – 847Combined sources
Beta strandi91 – 933Combined sources
Beta strandi95 – 984Combined sources
Helixi100 – 11516Combined sources
Helixi121 – 1244Combined sources
Beta strandi125 – 1273Combined sources
Turni128 – 1303Combined sources
Beta strandi131 – 14313Combined sources
Helixi148 – 16114Combined sources
Helixi168 – 1703Combined sources
Beta strandi172 – 1743Combined sources
Beta strandi185 – 1928Combined sources
Beta strandi195 – 1995Combined sources
Helixi204 – 2074Combined sources
Beta strandi211 – 2166Combined sources
Beta strandi222 – 2309Combined sources
Helixi235 – 25420Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2BA0X-ray2.70G/H/I1-259[»]
2BA1X-ray2.70G/H/I1-259[»]
3M7NX-ray2.40G/H/I1-259[»]
3M85X-ray3.00G/H/I1-259[»]
ProteinModelPortaliO29756.
SMRiO29756. Positions 3-258.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiO29756.

Family & Domainsi

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiarCOG01574. Archaea.
COG2123. LUCA.
KOiK12589.
OMAiVWIVFID.

Family and domain databases

Gene3Di3.30.230.70. 1 hit.
HAMAPiMF_00622. Exosome_Rrp42.
InterProiIPR001247. ExoRNase_PH_dom1.
IPR015847. ExoRNase_PH_dom2.
IPR027408. PNPase/RNase_PH_dom.
IPR020568. Ribosomal_S5_D2-typ_fold.
IPR020869. Rrp42_archaea.
[Graphical view]
PfamiPF01138. RNase_PH. 1 hit.
PF03725. RNase_PH_C. 1 hit.
[Graphical view]
SUPFAMiSSF54211. SSF54211. 1 hit.
SSF55666. SSF55666. 1 hit.

Sequencei

Sequence statusi: Complete.

O29756-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MPEDILVDIK RDYVLSKLRD NERIDGRGFD EFRKVEIIPN VIEKAEGSAL
60 70 80 90 100
VKLGDTQVVV GVKMQPGEPY PDTPDRGVII VNAELVPLAS PTFEPGPPDE
110 120 130 140 150
NSIELARVVD RGIRESEAVD LSKLVIEEGE KVWIVFVDIH ALDDDGNLLD
160 170 180 190 200
ASALAAIAAL MNTKVPAERF DLGEDYLLPV RDLPVSVTSL IVGNKYLVDP
210 220 230 240 250
SREEMSVGDT TLTITTDKDD NVVAMQKSGG YLLDEKLFDE LLDVSINCAR

KLREKFKEI
Length:259
Mass (Da):28,647
Last modified:January 1, 1998 - v1
Checksum:iE8289D46F9DDCCB3
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE000782 Genomic DNA. Translation: AAB90743.1.
PIRiF69311.
RefSeqiWP_010878001.1. NC_000917.1.

Genome annotation databases

EnsemblBacteriaiAAB90743; AAB90743; AF_0494.
GeneIDi24794034.
KEGGiafu:AF_0494.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE000782 Genomic DNA. Translation: AAB90743.1.
PIRiF69311.
RefSeqiWP_010878001.1. NC_000917.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2BA0X-ray2.70G/H/I1-259[»]
2BA1X-ray2.70G/H/I1-259[»]
3M7NX-ray2.40G/H/I1-259[»]
3M85X-ray3.00G/H/I1-259[»]
ProteinModelPortaliO29756.
SMRiO29756. Positions 3-258.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi224325.AF0494.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAB90743; AAB90743; AF_0494.
GeneIDi24794034.
KEGGiafu:AF_0494.

Phylogenomic databases

eggNOGiarCOG01574. Archaea.
COG2123. LUCA.
KOiK12589.
OMAiVWIVFID.

Enzyme and pathway databases

BioCyciAFUL224325:GJBC-507-MONOMER.

Miscellaneous databases

EvolutionaryTraceiO29756.

Family and domain databases

Gene3Di3.30.230.70. 1 hit.
HAMAPiMF_00622. Exosome_Rrp42.
InterProiIPR001247. ExoRNase_PH_dom1.
IPR015847. ExoRNase_PH_dom2.
IPR027408. PNPase/RNase_PH_dom.
IPR020568. Ribosomal_S5_D2-typ_fold.
IPR020869. Rrp42_archaea.
[Graphical view]
PfamiPF01138. RNase_PH. 1 hit.
PF03725. RNase_PH_C. 1 hit.
[Graphical view]
SUPFAMiSSF54211. SSF54211. 1 hit.
SSF55666. SSF55666. 1 hit.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "The complete genome sequence of the hyperthermophilic, sulphate-reducing archaeon Archaeoglobus fulgidus."
    Klenk H.-P., Clayton R.A., Tomb J.-F., White O., Nelson K.E., Ketchum K.A., Dodson R.J., Gwinn M.L., Hickey E.K., Peterson J.D., Richardson D.L., Kerlavage A.R., Graham D.E., Kyrpides N.C., Fleischmann R.D., Quackenbush J., Lee N.H., Sutton G.G.
    , Gill S.R., Kirkness E.F., Dougherty B.A., McKenney K., Adams M.D., Loftus B.J., Peterson S.N., Reich C.I., McNeil L.K., Badger J.H., Glodek A., Zhou L., Overbeek R., Gocayne J.D., Weidman J.F., McDonald L.A., Utterback T.R., Cotton M.D., Spriggs T., Artiach P., Kaine B.P., Sykes S.M., Sadow P.W., D'Andrea K.P., Bowman C., Fujii C., Garland S.A., Mason T.M., Olsen G.J., Fraser C.M., Smith H.O., Woese C.R., Venter J.C.
    Nature 390:364-370(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126.
  2. "Structural framework for the mechanism of archaeal exosomes in RNA processing."
    Buttner K., Wenig K., Hopfner K.P.
    Mol. Cell 20:461-471(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.70 ANGSTROMS) IN COMPLEX WITH RRP41; RRP4 AND CSL4, SUBUNIT.
  3. "Quantitative analysis of processive RNA degradation by the archaeal RNA exosome."
    Hartung S., Niederberger T., Hartung M., Tresch A., Hopfner K.P.
    Nucleic Acids Res. 38:5166-5176(2010) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.40 ANGSTROMS) IN COMPLEX WITH RRP41 AND CSL4, SUBUNIT.

Entry informationi

Entry nameiRRP42_ARCFU
AccessioniPrimary (citable) accession number: O29756
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 25, 2003
Last sequence update: January 1, 1998
Last modified: April 13, 2016
This is version 93 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

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 one 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.