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Protein

Exosome complex component Rrp4

Gene

rrp4

Organism
Aeropyrum pernix (strain ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1)
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. Increases the RNA binding and the efficiency of RNA degradation. Confers strong poly(A) specificity to the exosome.UniRule annotation

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Ligandi

RNA-binding

Enzyme and pathway databases

BioCyciAPER272557:GJD6-984-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Exosome complex component Rrp4UniRule annotation
Gene namesi
Name:rrp4UniRule annotation
Ordered Locus Names:APE_1448
OrganismiAeropyrum pernix (strain ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1)
Taxonomic identifieri272557 [NCBI]
Taxonomic lineageiArchaeaCrenarchaeotaThermoproteiDesulfurococcalesDesulfurococcaceaeAeropyrum
Proteomesi
  • UP000002518 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 – 235235Exosome complex component Rrp4PRO_0000050144Add
BLAST

Interactioni

Subunit structurei

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

Protein-protein interaction databases

STRINGi272557.APE_1448.

Structurei

Secondary structure

1
235
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi70 – 778Combined sources
Beta strandi79 – 857Combined sources
Beta strandi87 – 904Combined sources
Beta strandi92 – 954Combined sources
Helixi96 – 1005Combined sources
Turni106 – 1094Combined sources
Beta strandi120 – 1289Combined sources
Beta strandi134 – 1374Combined sources
Beta strandi140 – 1423Combined sources
Beta strandi148 – 1536Combined sources
Helixi156 – 1583Combined sources
Helixi160 – 1623Combined sources
Helixi165 – 1673Combined sources
Helixi168 – 17710Combined sources
Beta strandi180 – 1845Combined sources
Turni185 – 1873Combined sources
Beta strandi188 – 1925Combined sources
Helixi196 – 21116Combined sources
Helixi219 – 23214Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2Z0SX-ray3.20A1-235[»]
ProteinModelPortaliQ9YC02.
SMRiQ9YC02. Positions 60-234.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ9YC02.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini67 – 13973S1 motifUniRule annotationAdd
BLAST
Domaini149 – 20557KHUniRule annotationAdd
BLAST

Sequence similaritiesi

Belongs to the RRP4 family.UniRule annotation
Contains 1 KH domain.UniRule annotation
Contains 1 S1 motif domain.UniRule annotation

Phylogenomic databases

eggNOGiarCOG00678. Archaea.
COG1097. LUCA.
HOGENOMiHOG000229527.
KOiK03679.
OMAiPYDGLLH.

Family and domain databases

Gene3Di2.40.50.140. 1 hit.
3.30.1370.10. 1 hit.
HAMAPiMF_00623. Exosome_Rrp4. 1 hit.
InterProiIPR026699. Exosome_RNA_bind1/RRP40/RRP4.
IPR004087. KH_dom.
IPR004088. KH_dom_type_1.
IPR012340. NA-bd_OB-fold.
IPR023474. Rrp4.
IPR022967. S1_dom.
IPR003029. S1_domain.
[Graphical view]
PANTHERiPTHR21321. PTHR21321. 1 hit.
PfamiPF00013. KH_1. 1 hit.
[Graphical view]
SMARTiSM00322. KH. 1 hit.
SM00316. S1. 1 hit.
[Graphical view]
SUPFAMiSSF50249. SSF50249. 1 hit.
SSF54791. SSF54791. 1 hit.
PROSITEiPS50126. S1. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q9YC02-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSSERQLAGR IVVPGEPLPE EVEASPPYVI DYKGVKRATV VGLLREKGDG
60 70 80 90 100
GGRAFVKLKE IYVPQAGDVV IGLIQSVGIM NWFVDINSPY VAVLSVQDFL
110 120 130 140 150
GRPFNPAVDD MQSLLKVGDY IKAKVVAFDK TRSPLLTVQG EGLGRIVRGK
160 170 180 190 200
IVEISPAKVP RVIGRKMSML KTLEEKTECK IFVARNGRIH LECPNEDLEA
210 220 230
IAVMAIKIID EEAYTSGLTK RIIKFIEEER RIREV
Length:235
Mass (Da):26,061
Last modified:November 1, 1999 - v1
Checksum:i70A79A5EB0BF8CE7
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BA000002 Genomic DNA. Translation: BAA80446.1.
PIRiH72623.

Genome annotation databases

EnsemblBacteriaiBAA80446; BAA80446; APE_1448.
KEGGiape:APE_1448.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BA000002 Genomic DNA. Translation: BAA80446.1.
PIRiH72623.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2Z0SX-ray3.20A1-235[»]
ProteinModelPortaliQ9YC02.
SMRiQ9YC02. Positions 60-234.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi272557.APE_1448.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiBAA80446; BAA80446; APE_1448.
KEGGiape:APE_1448.

Phylogenomic databases

eggNOGiarCOG00678. Archaea.
COG1097. LUCA.
HOGENOMiHOG000229527.
KOiK03679.
OMAiPYDGLLH.

Enzyme and pathway databases

BioCyciAPER272557:GJD6-984-MONOMER.

Miscellaneous databases

EvolutionaryTraceiQ9YC02.

Family and domain databases

Gene3Di2.40.50.140. 1 hit.
3.30.1370.10. 1 hit.
HAMAPiMF_00623. Exosome_Rrp4. 1 hit.
InterProiIPR026699. Exosome_RNA_bind1/RRP40/RRP4.
IPR004087. KH_dom.
IPR004088. KH_dom_type_1.
IPR012340. NA-bd_OB-fold.
IPR023474. Rrp4.
IPR022967. S1_dom.
IPR003029. S1_domain.
[Graphical view]
PANTHERiPTHR21321. PTHR21321. 1 hit.
PfamiPF00013. KH_1. 1 hit.
[Graphical view]
SMARTiSM00322. KH. 1 hit.
SM00316. S1. 1 hit.
[Graphical view]
SUPFAMiSSF50249. SSF50249. 1 hit.
SSF54791. SSF54791. 1 hit.
PROSITEiPS50126. S1. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiRRP4_AERPE
AccessioniPrimary (citable) accession number: Q9YC02
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 25, 2003
Last sequence update: November 1, 1999
Last modified: September 7, 2016
This is version 94 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.