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Protein

40S ribosomal protein S3

Gene

Rps3

Organism
Rattus norvegicus (Rat)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Involved in translation as a component of the 40S small ribosomal subunit (By similarity). Has endonuclease activity and plays a role in repair of damaged DNA (PubMed:7775413). Cleaves phosphodiester bonds of DNAs containing altered bases with broad specificity and cleaves supercoiled DNA more efficiently than relaxed DNA (By similarity). Displays high binding affinity for 7,8-dihydro-8-oxoguanine (8-oxoG), a common DNA lesion caused by reactive oxygen species (ROS) (By similarity). Has also been shown to bind with similar affinity to intact and damaged DNA (By similarity). Stimulates the N-glycosylase activity of the base excision protein OGG1 (By similarity). Enhances the uracil excision activity of UNG1 (By similarity). Also stimulates the cleavage of the phosphodiester backbone by APEX1 (By similarity). When located in the mitochondrion, reduces cellular ROS levels and mitochondrial DNA damage. Has also been shown to negatively regulate DNA repair in cells exposed to hydrogen peroxide (By similarity). Plays a role in regulating transcription as part of the NF-kappa-B p65-p50 complex where it binds to the RELA/p65 subunit, enhances binding of the complex to DNA and promotes transcription of target genes (By similarity). Represses its own translation by binding to its cognate mRNA (By similarity). Binds to and protects TP53/p53 from MDM2-mediated ubiquitination (By similarity). Involved in spindle formation and chromosome movement during mitosis by regulating microtubule polymerization (By similarity). Involved in induction of apoptosis through its role in activation of CASP8 (By similarity). Induces neuronal apoptosis by interacting with the E2F1 transcription factor and acting synergistically with it to up-regulate pro-apoptotic proteins BCL2L11/BIM and HRK/Dp5 (By similarity). Interacts with TRADD following exposure to UV radiation and induces apoptosis by caspase-dependent JNK activation (By similarity).By similarity1 Publication

Catalytic activityi

The C-O-P bond 3' to the apurinic or apyrimidinic site in DNA is broken by a beta-elimination reaction, leaving a 3'-terminal unsaturated sugar and a product with a terminal 5'-phosphate.By similarity

GO - Molecular functioni

  • DNA-(apurinic or apyrimidinic site) lyase activity Source: UniProtKB-EC
  • DNA binding Source: UniProtKB-KW
  • kinase binding Source: UniProtKB
  • RNA binding Source: UniProtKB-KW
  • structural constituent of ribosome Source: RGD

GO - Biological processi

  • apoptotic process Source: UniProtKB-KW
  • cell division Source: UniProtKB-KW
  • cellular response to DNA damage stimulus Source: UniProtKB
  • cellular response to nerve growth factor stimulus Source: UniProtKB
  • DNA repair Source: UniProtKB-KW
  • mitotic nuclear division Source: UniProtKB-KW
  • regulation of apoptotic process Source: UniProtKB
  • regulation of transcription, DNA-templated Source: UniProtKB-KW
  • regulation of translation Source: UniProtKB-KW
  • transcription, DNA-templated Source: UniProtKB-KW
  • translation Source: RGD
Complete GO annotation...

Keywords - Molecular functioni

Lyase, Ribonucleoprotein, Ribosomal protein

Keywords - Biological processi

Apoptosis, Cell cycle, Cell division, DNA damage, DNA repair, Mitosis, Transcription, Transcription regulation, Translation regulation

Keywords - Ligandi

DNA-binding, RNA-binding

Enzyme and pathway databases

ReactomeiR-RNO-156827. L13a-mediated translational silencing of Ceruloplasmin expression.
R-RNO-1799339. SRP-dependent cotranslational protein targeting to membrane.
R-RNO-72649. Translation initiation complex formation.
R-RNO-72689. Formation of a pool of free 40S subunits.
R-RNO-72695. Formation of the ternary complex, and subsequently, the 43S complex.
R-RNO-72702. Ribosomal scanning and start codon recognition.
R-RNO-72706. GTP hydrolysis and joining of the 60S ribosomal subunit.
R-RNO-975956. Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC).
R-RNO-975957. Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC).

Names & Taxonomyi

Protein namesi
Recommended name:
40S ribosomal protein S3 (EC:4.2.99.18By similarity)
Gene namesi
Name:Rps3
OrganismiRattus norvegicus (Rat)
Taxonomic identifieri10116 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeRattus
Proteomesi
  • UP000002494 Componenti: Chromosome 1

Organism-specific databases

RGDi619888. Rps3.

Subcellular locationi

  • Cytoplasm By similarity
  • Nucleus By similarity
  • Nucleusnucleolus By similarity
  • Mitochondrion inner membrane By similarity; Peripheral membrane protein By similarity
  • Cytoplasmcytoskeletonspindle By similarity

  • Note: In normal cells, located mainly in the cytoplasm with small amounts in the nucleus but translocates to the nucleus in cells undergoing apoptosis. Nuclear translocation is induced by DNA damaging agents such as hydrogen peroxide. Accumulates in the mitochondrion in response to increased ROS levels. Localizes to the spindle during mitosis. Localized in cytoplasmic mRNP granules containing untranslated mRNAs.By similarity

GO - Cellular componenti

  • cytosolic small ribosomal subunit Source: RGD
  • dendrite Source: RGD
  • endomembrane system Source: RGD
  • intracellular ribonucleoprotein complex Source: UniProtKB
  • mitochondrial inner membrane Source: UniProtKB-SubCell
  • nucleolus Source: UniProtKB-SubCell
  • nucleus Source: UniProtKB
  • spindle Source: UniProtKB-SubCell
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Cytoskeleton, Membrane, Mitochondrion, Mitochondrion inner membrane, Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methionineiRemovedBy similarity
Chaini2 – 24324240S ribosomal protein S3PRO_0000130322Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei2 – 21N-acetylalanineBy similarity
Modified residuei6 – 61Phosphoserine; by PKC/PRKCDBy similarity
Modified residuei42 – 421Phosphothreonine; by MAPKBy similarity
Modified residuei62 – 621N6-acetyllysineBy similarity
Modified residuei64 – 641Asymmetric dimethylarginine; by PRMT1By similarity
Modified residuei65 – 651Asymmetric dimethylarginine; by PRMT1By similarity
Modified residuei67 – 671Asymmetric dimethylarginine; by PRMT1By similarity
Modified residuei70 – 701Phosphothreonine; by PKBBy similarity
Cross-linki90 – 90Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)By similarity
Modified residuei132 – 1321N6-succinyllysineBy similarity
Cross-linki202 – 202Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)By similarity
Modified residuei209 – 2091Phosphoserine; by IKKBBy similarity
Modified residuei221 – 2211Phosphothreonine; by CDK1 and PKC/PRKCDBy similarity
Modified residuei224 – 2241PhosphoserineBy similarity
Modified residuei242 – 2421PhosphothreonineBy similarity

Post-translational modificationi

Methylation by PRMT1 is required for import into the nucleolus and for ribosome assembly.By similarity
Sumoylation by SUMO1 enhances protein stability through increased resistance to proteolysis. Sumoylation occurs at one or more of the three consensus sites, Lys-18, Lys-214 and Lys-230.By similarity
Phosphorylation at Thr-221 by CDK1 occurs mainly in G2/M phase. Phosphorylation by PRKCD occurs on a non-ribosomal-associated form which results in translocation of RPS3 to the nucleus and enhances its endonuclease activity. Phosphorylated on Ser-209 by IKKB in response to activation of the NF-kappa-B p65-p50 complex which enhances the association of RPS3 with importin-alpha and mediates the nuclear translocation of RPS3. Phosphorylation by MAPK is required for translocation to the nucleus following exposure of cells to DNA damaging agents such as hydrogen peroxide. Phosphorylation by PKB/AKT mediates RPS3 nuclear translocation, enhances RPS3 endonuclease activity and suppresses RPS3-induced neuronal apoptosis.By similarity
Ubiquitinated. This is prevented by interaction with HSP90 which stabilizes the protein.By similarity

Keywords - PTMi

Acetylation, Isopeptide bond, Methylation, Phosphoprotein, Ubl conjugation

Proteomic databases

PaxDbiP62909.
PRIDEiP62909.

PTM databases

iPTMnetiP62909.
PhosphoSiteiP62909.

Expressioni

Gene expression databases

GenevisibleiP62909. RN.

Interactioni

Subunit structurei

Component of the 40S small ribosomal subunit. Identified in a IGF2BP1-dependent mRNP granule complex containing untranslated mRNAs. Interacts with HNRPD. Interacts with PRMT1; the interaction methylates RPS3. Interacts with SUMO1; the interaction sumoylates RPS3. Interacts with UBC9. Interacts with CDK1; the interaction phosphorylates RPS3. Interacts with PRKCD; the interaction phosphorylates RPS3. Interacts with PKB/AKT; the interaction phosphorylates RPS3. Interacts with E2F1; the interaction occurs in the absence of nerve growth factor and increases transcription of pro-apoptotic proteins BCL2L11/BIM and HRK/Dp5. Interacts with the base excision repair proteins APEX1 and OGG1; interaction with OGG1 increases OGG1 N-glycosylase activity. Interacts with UNG; the interaction increases the uracil excision activity of UNG1. Interacts with HSP90; the interaction prevents the ubiquitination and proteasome-dependent degradation of RPS3 and is suppressed by increased ROS levels. Interacts with TOM70; the interaction promotes translocation of RPS3 to the mitochondrion. Interacts (via N-terminus) with RELA (via N-terminus); the interaction enhances the DNA-binding activity of the NF-kappa-B p65-p50 complex. Interacts with NFKBIA; the interaction is direct and may bridge the interaction between RPS3 and RELA. Interacts with IKKB; the interaction phosphorylates RPS3 and enhances its translocation to the nucleus. Interacts (via KH domain) with MDM2 and TP53. Interacts with TRADD. Interacts with CRY1.By similarity

GO - Molecular functioni

  • kinase binding Source: UniProtKB

Protein-protein interaction databases

BioGridi250818. 4 interactions.
IntActiP62909. 3 interactions.
MINTiMINT-1863295.
STRINGi10116.ENSRNOP00000023935.

Structurei

3D structure databases

ProteinModelPortaliP62909.
SMRiP62909. Positions 3-227.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini21 – 9272KH type-2PROSITE-ProRule annotationAdd
BLAST

Sequence similaritiesi

Belongs to the ribosomal protein S3P family.Curated
Contains 1 KH type-2 domain.PROSITE-ProRule annotation

Phylogenomic databases

eggNOGiKOG3181. Eukaryota.
COG0092. LUCA.
GeneTreeiENSGT00390000008610.
HOGENOMiHOG000210611.
HOVERGENiHBG002195.
InParanoidiP62909.
KOiK02985.
OMAiQKFTEGY.
OrthoDBiEOG7F7W9M.
PhylomeDBiP62909.
TreeFamiTF300901.

Family and domain databases

Gene3Di3.30.1140.32. 1 hit.
3.30.300.20. 1 hit.
InterProiIPR015946. KH_dom-like_a/b.
IPR004044. KH_dom_type_2.
IPR009019. KH_prok-type.
IPR001351. Ribosomal_S3_C.
IPR018280. Ribosomal_S3_CS.
IPR005703. Ribosomal_S3_euk/arc.
[Graphical view]
PfamiPF07650. KH_2. 1 hit.
[Graphical view]
SUPFAMiSSF54814. SSF54814. 1 hit.
SSF54821. SSF54821. 1 hit.
TIGRFAMsiTIGR01008. uS3_euk_arch. 1 hit.
PROSITEiPS50823. KH_TYPE_2. 1 hit.
PS00548. RIBOSOMAL_S3. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

P62909-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MAVQISKKRK FVADGIFKAE LNEFLTRELA EDGYSGVEVR VTPTRTEIII
60 70 80 90 100
LATRTQNVLG EKGRRIRELT AVVQKRFGFP EGSVELYAEK VATRGLCAIA
110 120 130 140 150
QAESLRYKLL GGLAVRRACY GVLRFIMESG AKGCEVVVSG KLRGQRAKSM
160 170 180 190 200
KFVDGLMIHS GDPVNYYVDT AVRHVLLRQG VLGIKVKIML PWDPSGKIGP
210 220 230 240
KKPLPDHVSI VEPKDEILPT TPISEQKGGK PEPPAMPQPV PTA
Length:243
Mass (Da):26,674
Last modified:August 31, 2004 - v1
Checksum:i6B9BB34FDEE04AAF
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X51536 mRNA. Translation: CAA35916.1.
BC088450 mRNA. Translation: AAH88450.1.
PIRiS13882. R3RT3.
RefSeqiNP_001009239.1. NM_001009239.1.
UniGeneiRn.127805.

Genome annotation databases

EnsembliENSRNOT00000023935; ENSRNOP00000023935; ENSRNOG00000017418.
GeneIDi140654.
KEGGirno:140654.
UCSCiRGD:619888. rat.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X51536 mRNA. Translation: CAA35916.1.
BC088450 mRNA. Translation: AAH88450.1.
PIRiS13882. R3RT3.
RefSeqiNP_001009239.1. NM_001009239.1.
UniGeneiRn.127805.

3D structure databases

ProteinModelPortaliP62909.
SMRiP62909. Positions 3-227.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi250818. 4 interactions.
IntActiP62909. 3 interactions.
MINTiMINT-1863295.
STRINGi10116.ENSRNOP00000023935.

PTM databases

iPTMnetiP62909.
PhosphoSiteiP62909.

Proteomic databases

PaxDbiP62909.
PRIDEiP62909.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSRNOT00000023935; ENSRNOP00000023935; ENSRNOG00000017418.
GeneIDi140654.
KEGGirno:140654.
UCSCiRGD:619888. rat.

Organism-specific databases

CTDi6188.
RGDi619888. Rps3.

Phylogenomic databases

eggNOGiKOG3181. Eukaryota.
COG0092. LUCA.
GeneTreeiENSGT00390000008610.
HOGENOMiHOG000210611.
HOVERGENiHBG002195.
InParanoidiP62909.
KOiK02985.
OMAiQKFTEGY.
OrthoDBiEOG7F7W9M.
PhylomeDBiP62909.
TreeFamiTF300901.

Enzyme and pathway databases

ReactomeiR-RNO-156827. L13a-mediated translational silencing of Ceruloplasmin expression.
R-RNO-1799339. SRP-dependent cotranslational protein targeting to membrane.
R-RNO-72649. Translation initiation complex formation.
R-RNO-72689. Formation of a pool of free 40S subunits.
R-RNO-72695. Formation of the ternary complex, and subsequently, the 43S complex.
R-RNO-72702. Ribosomal scanning and start codon recognition.
R-RNO-72706. GTP hydrolysis and joining of the 60S ribosomal subunit.
R-RNO-975956. Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC).
R-RNO-975957. Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC).

Miscellaneous databases

NextBioi620608.
PROiP62909.

Gene expression databases

GenevisibleiP62909. RN.

Family and domain databases

Gene3Di3.30.1140.32. 1 hit.
3.30.300.20. 1 hit.
InterProiIPR015946. KH_dom-like_a/b.
IPR004044. KH_dom_type_2.
IPR009019. KH_prok-type.
IPR001351. Ribosomal_S3_C.
IPR018280. Ribosomal_S3_CS.
IPR005703. Ribosomal_S3_euk/arc.
[Graphical view]
PfamiPF07650. KH_2. 1 hit.
[Graphical view]
SUPFAMiSSF54814. SSF54814. 1 hit.
SSF54821. SSF54821. 1 hit.
TIGRFAMsiTIGR01008. uS3_euk_arch. 1 hit.
PROSITEiPS50823. KH_TYPE_2. 1 hit.
PS00548. RIBOSOMAL_S3. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "The primary structure of rat ribosomal protein S3."
    Devi K.R.G., Chan Y.-L., Wool I.G.
    Arch. Biochem. Biophys. 283:546-550(1990) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA], PROTEIN SEQUENCE OF 158-172.
    Strain: Sprague-Dawley.
    Tissue: Liver.
  2. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
    The MGC Project Team
    Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Tissue: Kidney.
  3. "Implication of mammalian ribosomal protein S3 in the processing of DNA damage."
    Kim J., Chubatsu L.S., Admon A., Stahl J., Fellous R., Linn S.
    J. Biol. Chem. 270:13620-13629(1995) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.

Entry informationi

Entry nameiRS3_RAT
AccessioniPrimary (citable) accession number: P62909
Secondary accession number(s): P17073, P47933
Entry historyi
Integrated into UniProtKB/Swiss-Prot: August 31, 2004
Last sequence update: August 31, 2004
Last modified: May 11, 2016
This is version 107 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. Ribosomal proteins
    Ribosomal proteins families and list of entries
  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.