CPLM 1.0 - Compendium of Protein Lysine Modification
TagContent
CPLM ID CPLM-005170
UniProt Accession
Genbank Protein ID
Genbank Nucleotide ID
Protein Name
 40S ribosomal protein S3 
Protein Synonyms/Alias
  
Gene Name
 RPS3 
Gene Synonyms/Alias
 OK/SW-cl.26 
Created Date
 July 27, 2013 
Organism
 Homo sapiens (Human) 
NCBI Taxa ID
 9606 
Lysine Modification
Position
Peptide
Type
References
7*MAVQISKKRKFVADubiquitination[1, 2, 3, 4]
8MAVQISKKRKFVADGubiquitination[1, 3, 4]
10VQISKKRKFVADGIFubiquitination[1, 2, 3, 4, 5, 6, 7, 8]
18FVADGIFKAELNEFLsumoylation[9]
18FVADGIFKAELNEFLubiquitination[1, 3, 4, 6, 8, 10, 11]
62TQNVLGEKGRRIRELacetylation[12]
62TQNVLGEKGRRIRELubiquitination[1, 3, 4, 5, 6, 7, 8, 11]
75ELTAVVQKRFGFPEGubiquitination[1, 2, 3, 4, 5, 6, 7, 8, 11]
90SVELYAEKVATRGLCubiquitination[1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 13]
108QAESLRYKLLGGLAVubiquitination[1, 2, 3, 4, 6, 7, 8, 11]
132FIMESGAKGCEVVVSubiquitination[3, 11]
141CEVVVSGKLRGQRAKubiquitination[1, 2, 3, 4, 5, 6, 7, 11]
151GQRAKSMKFVDGLMIubiquitination[1, 3, 4, 6, 7, 8]
185RQGVLGIKVKIMLPWubiquitination[3, 6, 8]
187GVLGIKVKIMLPWDPubiquitination[1, 2, 3, 4, 6, 7, 8]
197LPWDPTGKIGPKKPLubiquitination[1, 2, 3, 4, 5, 6, 7, 8, 10, 11]
201PTGKIGPKKPLPDHVubiquitination[1, 2, 3, 4, 5, 6, 7]
202TGKIGPKKPLPDHVSubiquitination[1, 2, 3, 4, 5, 6, 7, 8, 13]
214HVSIVEPKDEILPTTsumoylation[9]
214HVSIVEPKDEILPTTubiquitination[1, 2, 3, 4, 5, 6, 7, 8]
227TTPISEQKGGKPEPPubiquitination[1, 2, 3, 4, 6, 8]
230ISEQKGGKPEPPAMPsumoylation[9]
230ISEQKGGKPEPPAMPubiquitination[1, 2, 3, 4, 6, 7, 8, 11]
Reference
 [1] A proteome-wide, quantitative survey of in vivo ubiquitylation sites reveals widespread regulatory roles.
 Wagner SA, Beli P, Weinert BT, Nielsen ML, Cox J, Mann M, Choudhary C.
 Mol Cell Proteomics. 2011 Oct;10(10):M111.013284. [PMID: 21890473]
 [2] Methods for quantification of in vivo changes in protein ubiquitination following proteasome and deubiquitinase inhibition.
 Udeshi ND, Mani DR, Eisenhaure T, Mertins P, Jaffe JD, Clauser KR, Hacohen N, Carr SA.
 Mol Cell Proteomics. 2012 May;11(5):148-59. [PMID: 22505724]
 [3] Refined preparation and use of anti-diglycine remnant (K-ε-GG) antibody enables routine quantification of 10,000s of ubiquitination sites in single proteomics experiments.
 Udeshi ND, Svinkina T, Mertins P, Kuhn E, Mani DR, Qiao JW, Carr SA.
 Mol Cell Proteomics. 2013 Mar;12(3):825-31. [PMID: 23266961]
 [4] hCKSAAP_UbSite: improved prediction of human ubiquitination sites by exploiting amino acid pattern and properties.
 Chen Z, Zhou Y, Song J, Zhang Z.
 Biochim Biophys Acta. 2013 Aug;1834(8):1461-7. [PMID: 23603789]
 [5] Mass spectrometric analysis of lysine ubiquitylation reveals promiscuity at site level.
 Danielsen JM, Sylvestersen KB, Bekker-Jensen S, Szklarczyk D, Poulsen JW, Horn H, Jensen LJ, Mailand N, Nielsen ML.
 Mol Cell Proteomics. 2011 Mar;10(3):M110.003590. [PMID: 21139048]
 [6] Systematic and quantitative assessment of the ubiquitin-modified proteome.
 Kim W, Bennett EJ, Huttlin EL, Guo A, Li J, Possemato A, Sowa ME, Rad R, Rush J, Comb MJ, Harper JW, Gygi SP.
 Mol Cell. 2011 Oct 21;44(2):325-40. [PMID: 21906983]
 [7] Systems-wide analysis of ubiquitylation dynamics reveals a key role for PAF15 ubiquitylation in DNA-damage bypass.
 Povlsen LK, Beli P, Wagner SA, Poulsen SL, Sylvestersen KB, Poulsen JW, Nielsen ML, Bekker-Jensen S, Mailand N, Choudhary C.
 Nat Cell Biol. 2012 Oct;14(10):1089-98. [PMID: 23000965]
 [8] Landscape of the PARKIN-dependent ubiquitylome in response to mitochondrial depolarization.
 Sarraf SA, Raman M, Guarani-Pereira V, Sowa ME, Huttlin EL, Gygi SP, Harper JW.
 Nature. 2013 Apr 18;496(7445):372-6. [PMID: 23503661]
 [9] Ribosomal protein S3 is stabilized by sumoylation.
 Jang CY, Shin HS, Kim HD, Kim JW, Choi SY, Kim J.
 Biochem Biophys Res Commun. 2011 Oct 28;414(3):523-7. [PMID: 21968017]
 [10] Global analysis of lysine ubiquitination by ubiquitin remnant immunoaffinity profiling.
 Xu G, Paige JS, Jaffrey SR.
 Nat Biotechnol. 2010 Aug;28(8):868-73. [PMID: 20639865]
 [11] Ubiquitin ligase substrate identification through quantitative proteomics at both the protein and peptide levels.
 Lee KA, Hammerle LP, Andrews PS, Stokes MP, Mustelin T, Silva JC, Black RA, Doedens JR.
 J Biol Chem. 2011 Dec 2;286(48):41530-8. [PMID: 21987572]
 [12] Lysine acetylation targets protein complexes and co-regulates major cellular functions.
 Choudhary C, Kumar C, Gnad F, Nielsen ML, Rehman M, Walther TC, Olsen JV, Mann M.
 Science. 2009 Aug 14;325(5942):834-40. [PMID: 19608861]
 [13] Quantitative analysis of global ubiquitination in HeLa cells by mass spectrometry.
 Meierhofer D, Wang X, Huang L, Kaiser P.
 J Proteome Res. 2008 Oct;7(10):4566-76. [PMID: 18781797] 
Functional Description
  
Sequence Annotation
 DOMAIN 21 92 KH type-2.
 MOD_RES 2 2 N-acetylalanine.
 MOD_RES 62 62 N6-acetyllysine.
 MOD_RES 221 221 Phosphothreonine.
 MOD_RES 224 224 Phosphoserine.
 MOD_RES 242 242 Phosphothreonine.
 CROSSLNK 90 90 Glycyl lysine isopeptide (Lys-Gly)
 CROSSLNK 202 202 Glycyl lysine isopeptide (Lys-Gly)  
Keyword
 3D-structure; Acetylation; Alternative splicing; Complete proteome; Cytoplasm; Direct protein sequencing; Isopeptide bond; Phosphoprotein; Reference proteome; Ribonucleoprotein; Ribosomal protein; RNA-binding; Ubl conjugation. 
Sequence Source
 UniProt (SWISSPROT/TrEMBL); GenBank; EMBL 
Protein Length
 243 AA 
Protein Sequence
MAVQISKKRK FVADGIFKAE LNEFLTRELA EDGYSGVEVR VTPTRTEIII LATRTQNVLG 60
EKGRRIRELT AVVQKRFGFP EGSVELYAEK VATRGLCAIA QAESLRYKLL GGLAVRRACY 120
GVLRFIMESG AKGCEVVVSG KLRGQRAKSM KFVDGLMIHS GDPVNYYVDT AVRHVLLRQG 180
VLGIKVKIML PWDPTGKIGP KKPLPDHVSI VEPKDEILPT TPISEQKGGK PEPPAMPQPV 240
PTA 243 
Gene Ontology
 GO:0022627; C:cytosolic small ribosomal subunit; IDA:UniProtKB.
 GO:0005634; C:nucleus; IDA:UniProtKB.
 GO:0032587; C:ruffle membrane; IDA:UniProtKB.
 GO:0003684; F:damaged DNA binding; IDA:UniProtKB.
 GO:0003906; F:DNA-(apurinic or apyrimidinic site) lyase activity; IDA:UniProtKB.
 GO:0004519; F:endonuclease activity; IMP:UniProtKB.
 GO:0051536; F:iron-sulfur cluster binding; NAS:UniProtKB.
 GO:0003729; F:mRNA binding; IDA:UniProtKB.
 GO:0003735; F:structural constituent of ribosome; IDA:UniProtKB.
 GO:0006919; P:activation of cysteine-type endopeptidase activity involved in apoptotic process; IDA:UniProtKB.
 GO:0045738; P:negative regulation of DNA repair; IMP:UniProtKB.
 GO:0032088; P:negative regulation of NF-kappaB transcription factor activity; IMP:UniProtKB.
 GO:0000184; P:nuclear-transcribed mRNA catabolic process, nonsense-mediated decay; TAS:Reactome.
 GO:1900119; P:positive regulation of execution phase of apoptosis; IDA:UniProtKB.
 GO:0006974; P:response to DNA damage stimulus; IEP:UniProtKB.
 GO:0006614; P:SRP-dependent cotranslational protein targeting to membrane; TAS:Reactome.
 GO:0006414; P:translational elongation; TAS:Reactome.
 GO:0006413; P:translational initiation; NAS:UniProtKB.
 GO:0006415; P:translational termination; TAS:Reactome.
 GO:0019083; P:viral transcription; TAS:Reactome. 
Interpro
 IPR004087; KH_dom.
 IPR015946; 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. 
Pfam
 PF07650; KH_2
 PF00189; Ribosomal_S3_C 
SMART
 SM00322; KH 
PROSITE
 PS50823; KH_TYPE_2
 PS00548; RIBOSOMAL_S3 
PRINTS