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Protein

Exosome complex component rrp40

Gene

rrp40

Organism
Schizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Protein inferred from homologyi

Functioni

Non-catalytic component of the RNA exosome complex which has 3'->5' exoribonuclease activity and participates in a multitude of cellular RNA processing and degradation events. In the nucleus, the RNA exosome complex is involved in proper maturation of stable RNA species such as rRNA, snRNA and snoRNA, in the elimination of RNA processing by-products and non-coding 'pervasive' transcripts, such as antisense RNA species and cryptic unstable transcripts (CUTs), and of mRNAs with processing defects, thereby limiting or excluding their export to the cytoplasm. In the cytoplasm, the RNA exosome complex is involved in general mRNA turnover and in RNA surveillance pathways, preventing translation of aberrant mRNAs. The catalytic inactive RNA exosome core complex of 9 subunits (Exo-9) is proposed to play a pivotal role in the binding and presentation of RNA for ribonucleolysis, and to serve as a scaffold for the association with catalytic subunits and accessory proteins or complexes. rrp40 as peripheral part of the Exo-9 complex is thought to stabilize the hexameric ring of RNase PH-domain subunits (By similarity).By similarity

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Biological processi

rRNA processing

Keywords - Ligandi

RNA-binding

Enzyme and pathway databases

ReactomeiR-SPO-429958. mRNA decay by 3' to 5' exoribonuclease.
R-SPO-450385. Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA.

Names & Taxonomyi

Protein namesi
Recommended name:
Exosome complex component rrp40
Alternative name(s):
Ribosomal RNA-processing protein 40
Gene namesi
Name:rrp40
ORF Names:SPAC22A12.12c
OrganismiSchizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast)
Taxonomic identifieri284812 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaTaphrinomycotinaSchizosaccharomycetesSchizosaccharomycetalesSchizosaccharomycetaceaeSchizosaccharomyces
Proteomesi
  • UP000002485 Componenti: Chromosome I

Organism-specific databases

EuPathDBiFungiDB:SPAC22A12.12c.
PomBaseiSPAC22A12.12c. rrp40.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Exosome, Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 240240Exosome complex component rrp40PRO_0000352816Add
BLAST

Proteomic databases

MaxQBiO13903.
PRIDEiO13903.

Interactioni

Subunit structurei

Component of the RNA exosome complex. Specifically part of the catalytically inactive RNA exosome core (Exo-9) complex which associates with catalytic subunits dis3 and rrp6 in cytoplasmic- and nuclear-specific RNA exosome complex forms. Exo-9 is formed by a hexameric ring of RNase PH domain-containing subunits and peripheral S1 domain-containing components csl4, rrp4 and rrp40 located on the top of the ring structure (By similarity).By similarity

Protein-protein interaction databases

BioGridi278328. 5 interactions.

Structurei

3D structure databases

ProteinModelPortaliO13903.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini75 – 14470S1 motifAdd
BLAST

Sequence similaritiesi

Belongs to the RRP40 family.Curated
Contains 1 S1 motif domain.Curated

Phylogenomic databases

HOGENOMiHOG000184644.
InParanoidiO13903.
KOiK03681.
OMAiISYLAFE.
OrthoDBiEOG7FJHC7.
PhylomeDBiO13903.

Family and domain databases

InterProiIPR026699. Exosome_RNA_bind1/RRP40/RRP4.
IPR004088. KH_dom_type_1.
IPR012340. NA-bd_OB-fold.
[Graphical view]
PANTHERiPTHR21321. PTHR21321. 1 hit.
PfamiPF15985. KH_6. 1 hit.
[Graphical view]
SUPFAMiSSF50249. SSF50249. 1 hit.
SSF54791. SSF54791. 1 hit.

Sequencei

Sequence statusi: Complete.

O13903-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MAEVEEKGLL SYYFPGERIP DSIISQDGSI RLGPGLVFQK KDREEEIVVS
60 70 80 90 100
KAGRLHQTGK NAMLIDSRTK RYIPATNDQV IGQIISRFAE GYRVDIGSAH
110 120 130 140 150
IAQLNALAFE NVTRKSRPNL NVGSLVYARV SLADRDMEPE LECFDATTGK
160 170 180 190 200
AAGYGELKNG YMITGLSLSH CRKLILPKNT LLQTLGSYIP FEIAVGMNGR
210 220 230 240
VWVNSENLST TVLICTAIRN CEFMSDEEQI KYCKDLIKKL
Length:240
Mass (Da):26,726
Last modified:January 1, 1998 - v1
Checksum:i0E1B3A8A0C132A0A
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CU329670 Genomic DNA. Translation: CAB16582.1.
PIRiT38152.
RefSeqiNP_593242.1. NM_001018639.2.

Genome annotation databases

EnsemblFungiiSPAC22A12.12c.1; SPAC22A12.12c.1:pep; SPAC22A12.12c.
GeneIDi2541837.
KEGGispo:SPAC22A12.12c.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CU329670 Genomic DNA. Translation: CAB16582.1.
PIRiT38152.
RefSeqiNP_593242.1. NM_001018639.2.

3D structure databases

ProteinModelPortaliO13903.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi278328. 5 interactions.

Proteomic databases

MaxQBiO13903.
PRIDEiO13903.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiSPAC22A12.12c.1; SPAC22A12.12c.1:pep; SPAC22A12.12c.
GeneIDi2541837.
KEGGispo:SPAC22A12.12c.

Organism-specific databases

EuPathDBiFungiDB:SPAC22A12.12c.
PomBaseiSPAC22A12.12c. rrp40.

Phylogenomic databases

HOGENOMiHOG000184644.
InParanoidiO13903.
KOiK03681.
OMAiISYLAFE.
OrthoDBiEOG7FJHC7.
PhylomeDBiO13903.

Enzyme and pathway databases

ReactomeiR-SPO-429958. mRNA decay by 3' to 5' exoribonuclease.
R-SPO-450385. Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA.

Miscellaneous databases

NextBioi20802925.
PROiO13903.

Family and domain databases

InterProiIPR026699. Exosome_RNA_bind1/RRP40/RRP4.
IPR004088. KH_dom_type_1.
IPR012340. NA-bd_OB-fold.
[Graphical view]
PANTHERiPTHR21321. PTHR21321. 1 hit.
PfamiPF15985. KH_6. 1 hit.
[Graphical view]
SUPFAMiSSF50249. SSF50249. 1 hit.
SSF54791. SSF54791. 1 hit.
ProtoNetiSearch...

Publicationsi

  1. "The genome sequence of Schizosaccharomyces pombe."
    Wood V., Gwilliam R., Rajandream M.A., Lyne M.H., Lyne R., Stewart A., Sgouros J.G., Peat N., Hayles J., Baker S.G., Basham D., Bowman S., Brooks K., Brown D., Brown S., Chillingworth T., Churcher C.M., Collins M.
    , Connor R., Cronin A., Davis P., Feltwell T., Fraser A., Gentles S., Goble A., Hamlin N., Harris D.E., Hidalgo J., Hodgson G., Holroyd S., Hornsby T., Howarth S., Huckle E.J., Hunt S., Jagels K., James K.D., Jones L., Jones M., Leather S., McDonald S., McLean J., Mooney P., Moule S., Mungall K.L., Murphy L.D., Niblett D., Odell C., Oliver K., O'Neil S., Pearson D., Quail M.A., Rabbinowitsch E., Rutherford K.M., Rutter S., Saunders D., Seeger K., Sharp S., Skelton J., Simmonds M.N., Squares R., Squares S., Stevens K., Taylor K., Taylor R.G., Tivey A., Walsh S.V., Warren T., Whitehead S., Woodward J.R., Volckaert G., Aert R., Robben J., Grymonprez B., Weltjens I., Vanstreels E., Rieger M., Schaefer M., Mueller-Auer S., Gabel C., Fuchs M., Duesterhoeft A., Fritzc C., Holzer E., Moestl D., Hilbert H., Borzym K., Langer I., Beck A., Lehrach H., Reinhardt R., Pohl T.M., Eger P., Zimmermann W., Wedler H., Wambutt R., Purnelle B., Goffeau A., Cadieu E., Dreano S., Gloux S., Lelaure V., Mottier S., Galibert F., Aves S.J., Xiang Z., Hunt C., Moore K., Hurst S.M., Lucas M., Rochet M., Gaillardin C., Tallada V.A., Garzon A., Thode G., Daga R.R., Cruzado L., Jimenez J., Sanchez M., del Rey F., Benito J., Dominguez A., Revuelta J.L., Moreno S., Armstrong J., Forsburg S.L., Cerutti L., Lowe T., McCombie W.R., Paulsen I., Potashkin J., Shpakovski G.V., Ussery D., Barrell B.G., Nurse P.
    Nature 415:871-880(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: 972 / ATCC 24843.

Entry informationi

Entry nameiRRP40_SCHPO
AccessioniPrimary (citable) accession number: O13903
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 4, 2008
Last sequence update: January 1, 1998
Last modified: May 11, 2016
This is version 97 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Schizosaccharomyces pombe
    Schizosaccharomyces pombe: entries and gene names
  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.