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Protein

Exosome complex component Rrp41

Gene

rrp41

Organism
Pyrococcus abyssi (strain GE5 / Orsay)
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 (Probable).1 Publication

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Exonuclease, Hydrolase, Nuclease

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:PYRAB06100
ORF Names:PAB0420
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
Mutagenesisi89 – 891R → E: Does not affect ring assembly, but abolishes RNA degradation; when associated with E-91. 1 Publication
Mutagenesisi91 – 911K → E: Does not affect ring assembly, but abolishes RNA degradation; when associated with E-89. 1 Publication
Mutagenesisi137 – 1371R → A: Decrease in activity. 1 Publication
Mutagenesisi186 – 1861D → A: Abolishes RNA degradation. 1 Publication
Mutagenesisi204 – 2041D → A: Decrease in activity. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 249249Exosome complex component Rrp41PRO_0000139985Add
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.PAB0420.

Structurei

Secondary structure

1
249
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi11 – 133Combined sources
Beta strandi29 – 335Combined sources
Beta strandi37 – 4711Combined sources
Beta strandi50 – 6112Combined sources
Helixi65 – 673Combined sources
Beta strandi70 – 723Combined sources
Beta strandi74 – 818Combined sources
Helixi83 – 853Combined sources
Beta strandi86 – 883Combined sources
Helixi96 – 10914Combined sources
Helixi110 – 1123Combined sources
Helixi115 – 1173Combined sources
Beta strandi121 – 13111Combined sources
Helixi136 – 15015Combined sources
Beta strandi155 – 1573Combined sources
Beta strandi160 – 1678Combined sources
Beta strandi170 – 1745Combined sources
Helixi177 – 1815Combined sources
Beta strandi184 – 1929Combined sources
Turni193 – 1964Combined sources
Beta strandi197 – 2015Combined sources
Helixi209 – 24133Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2PNZX-ray2.14A1-249[»]
2PO0X-ray2.30A1-249[»]
2PO1X-ray1.94A1-249[»]
2PO2X-ray2.41A1-249[»]
ProteinModelPortaliQ9V119.
SMRiQ9V119. Positions 9-244.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ9V119.

Family & Domainsi

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiarCOG01575. Archaea.
COG0689. LUCA.
HOGENOMiHOG000229515.
KOiK11600.
OMAiFKMYLQQ.

Family and domain databases

Gene3Di3.30.230.70. 1 hit.
HAMAPiMF_00591. Exosome_Rrp41.
InterProiIPR001247. ExoRNase_PH_dom1.
IPR015847. ExoRNase_PH_dom2.
IPR027408. PNPase/RNase_PH_dom.
IPR020568. Ribosomal_S5_D2-typ_fold.
IPR011807. Rrp41.
[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.

Q9V119-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MMEKPEGLKL IDENGRRIDG RKKYELRPIK MEVGVLKNAN GSAYIEWGKN
60 70 80 90 100
KIIAAVYGPR ELHPKHLQRP DRAILRVRYN MAPFSVEERK KPGPDRRSIE
110 120 130 140 150
ISKVIKGALE PALILEMFPR TAIDVFIEVL QADAGTRVAG ITAASLALAD
160 170 180 190 200
AGIPMRDLVA ACAAGKIEGE IVLDLNKEED NYGEADVPVA IMPLKNDITL
210 220 230 240
LQMDGYLTKD EFIEAVKLAI KGAKAVYQKQ REALKEKYLK IAQEVEGSE
Length:249
Mass (Da):27,678
Last modified:May 1, 2000 - v1
Checksum:iACB0748E1BF074A6
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AJ248284 Genomic DNA. Translation: CAB49532.1.
HE613800 Genomic DNA. Translation: CCE70002.1.
PIRiE75181.
RefSeqiWP_010867734.1. NC_000868.1.

Genome annotation databases

EnsemblBacteriaiCAB49532; CAB49532; PAB0420.
GeneIDi1495515.
KEGGipab:PAB0420.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AJ248284 Genomic DNA. Translation: CAB49532.1.
HE613800 Genomic DNA. Translation: CCE70002.1.
PIRiE75181.
RefSeqiWP_010867734.1. NC_000868.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2PNZX-ray2.14A1-249[»]
2PO0X-ray2.30A1-249[»]
2PO1X-ray1.94A1-249[»]
2PO2X-ray2.41A1-249[»]
ProteinModelPortaliQ9V119.
SMRiQ9V119. Positions 9-244.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi272844.PAB0420.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiCAB49532; CAB49532; PAB0420.
GeneIDi1495515.
KEGGipab:PAB0420.

Phylogenomic databases

eggNOGiarCOG01575. Archaea.
COG0689. LUCA.
HOGENOMiHOG000229515.
KOiK11600.
OMAiFKMYLQQ.

Miscellaneous databases

EvolutionaryTraceiQ9V119.

Family and domain databases

Gene3Di3.30.230.70. 1 hit.
HAMAPiMF_00591. Exosome_Rrp41.
InterProiIPR001247. ExoRNase_PH_dom1.
IPR015847. ExoRNase_PH_dom2.
IPR027408. PNPase/RNase_PH_dom.
IPR020568. Ribosomal_S5_D2-typ_fold.
IPR011807. Rrp41.
[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: 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 RRP42, FUNCTION, MUTAGENESIS OF ARG-89; LYS-91; ARG-137; ASP-186 AND ASP-204.

Entry informationi

Entry nameiRRP41_PYRAB
AccessioniPrimary (citable) accession number: Q9V119
Secondary accession number(s): G8ZJ75
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 25, 2003
Last sequence update: May 1, 2000
Last modified: November 11, 2015
This is version 90 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.