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Protein

Exosome complex component Rrp42

Gene

rrp42

Organism
Pyrococcus abyssi (strain GE5 / Orsay)
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...

Names & Taxonomyi

Protein namesi
Recommended name:
Exosome complex component Rrp42UniRule annotation
Gene namesi
Name:rrp42UniRule annotation
Ordered Locus Names:PYRAB06110
ORF Names:PAB0421
OrganismiPyrococcus abyssi (strain GE5 / Orsay)
Taxonomic identifieri272844 [NCBI]
Taxonomic lineageiArchaeaEuryarchaeotaThermococciThermococcalesThermococcaceaePyrococcus
Proteomesi
  • UP000000810 Componenti: Chromosome
  • UP000009139 Componenti: Chromosome

Subcellular locationi

  • Cytoplasm UniRule annotation

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Exosome

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi45 – 451K → A: Does not affect ring assembly, but decreases RNA degradation. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 274274Exosome complex component Rrp42PRO_0000140001Add
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 annotation

Protein-protein interaction databases

STRINGi272844.PAB0421.

Structurei

Secondary structure

1
274
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi10 – 2011Combined sources
Beta strandi36 – 405Combined sources
Beta strandi46 – 549Combined sources
Beta strandi57 – 6812Combined sources
Beta strandi79 – 868Combined sources
Helixi88 – 903Combined sources
Beta strandi96 – 983Combined sources
Helixi101 – 11515Combined sources
Turni116 – 1183Combined sources
Helixi122 – 1254Combined sources
Beta strandi126 – 1283Combined sources
Turni129 – 1313Combined sources
Beta strandi132 – 14413Combined sources
Helixi149 – 16315Combined sources
Beta strandi165 – 1717Combined sources
Turni173 – 1753Combined sources
Beta strandi178 – 1869Combined sources
Beta strandi194 – 2018Combined sources
Beta strandi204 – 2085Combined sources
Helixi211 – 2166Combined sources
Beta strandi218 – 2258Combined sources
Beta strandi231 – 2399Combined sources
Helixi244 – 27229Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2PNZX-ray2.14B1-274[»]
2PO0X-ray2.30B1-274[»]
2PO1X-ray1.94B1-274[»]
2PO2X-ray2.41B1-274[»]
ProteinModelPortaliQ9V118.
SMRiQ9V118. Positions 8-274.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ9V118.

Family & Domainsi

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiarCOG01574. Archaea.
COG2123. LUCA.
HOGENOMiHOG000229504.
KOiK12589.
OMAiMRDHIIN.

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. 2 hits.
SSF55666. SSF55666. 1 hit.

Sequencei

Sequence statusi: Complete.

Q9V118-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSDNEIVAGI MRDHIINLLK EGKRIDDRGF EDYRPIEIEV GVIEKAEGSA
60 70 80 90 100
LVKLGSTQVL VGIKTSLGEP FPDTPNMGVM TTNVELVPLA SPTFEPGPPD
110 120 130 140 150
ERAIELARVI DRGIRESKAL NLEKMVIVPG KIVRVVFIDV HVLDHDGNLM
160 170 180 190 200
DAIGIAAIAA LLNARVPKVR YNEETGEVET LDETEPLPVE KIPVPVTFAK
210 220 230 240 250
IGNILVVDPS LDEELVMDGK ITITTDETGH ISAVQKSEGG AFKLEEVMYA
260 270
VETAFKKAEE IRKLILEAVE KAKQ
Length:274
Mass (Da):29,952
Last modified:May 1, 2000 - v1
Checksum:i01EFAA68DD57CAEF
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AJ248284 Genomic DNA. Translation: CAB49533.1.
HE613800 Genomic DNA. Translation: CCE70003.1.
PIRiF75181.
RefSeqiWP_010867735.1. NC_000868.1.

Genome annotation databases

EnsemblBacteriaiCAB49533; CAB49533; PAB0421.
GeneIDi1495516.
KEGGipab:PAB0421.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AJ248284 Genomic DNA. Translation: CAB49533.1.
HE613800 Genomic DNA. Translation: CCE70003.1.
PIRiF75181.
RefSeqiWP_010867735.1. NC_000868.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2PNZX-ray2.14B1-274[»]
2PO0X-ray2.30B1-274[»]
2PO1X-ray1.94B1-274[»]
2PO2X-ray2.41B1-274[»]
ProteinModelPortaliQ9V118.
SMRiQ9V118. Positions 8-274.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi272844.PAB0421.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiCAB49533; CAB49533; PAB0421.
GeneIDi1495516.
KEGGipab:PAB0421.

Phylogenomic databases

eggNOGiarCOG01574. Archaea.
COG2123. LUCA.
HOGENOMiHOG000229504.
KOiK12589.
OMAiMRDHIIN.

Miscellaneous databases

EvolutionaryTraceiQ9V118.

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. 2 hits.
SSF55666. SSF55666. 1 hit.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: GE5 / Orsay.
  2. "Re-annotation of two hyperthermophilic archaea Pyrococcus abyssi GE5 and Pyrococcus furiosus DSM 3638."
    Gao J., Wang J.
    Curr. Microbiol. 64:118-129(2012) [PubMed] [Europe PMC] [Abstract]
    Cited for: GENOME REANNOTATION.
    Strain: GE5 / Orsay.
  3. "Insights into the mechanism of progressive RNA degradation by the archaeal exosome."
    Navarro M.V., Oliveira C.C., Zanchin N.I., Guimaraes B.G.
    J. Biol. Chem. 283:14120-14131(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.94 ANGSTROMS) IN COMPLEX WITH RRP41, MUTAGENESIS OF LYS-45.

Entry informationi

Entry nameiRRP42_PYRAB
AccessioniPrimary (citable) accession number: Q9V118
Secondary accession number(s): G8ZJ76
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 25, 2003
Last sequence update: May 1, 2000
Last modified: April 13, 2016
This is version 89 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.