CPLM 1.0 - Compendium of Protein Lysine Modification
TagContent
CPLM ID CPLM-009522
UniProt Accession
Genbank Protein ID
Genbank Nucleotide ID
Protein Name
 40S ribosomal protein S4, X isoform 
Protein Synonyms/Alias
 SCR10; Single copy abundant mRNA protein 
Gene Name
 RPS4X 
Gene Synonyms/Alias
 CCG2; RPS4; SCAR 
Created Date
 July 27, 2013 
Organism
 Homo sapiens (Human) 
NCBI Taxa ID
 9606 
Lysine Modification
Position
Peptide
Type
References
16LKRVAAPKHWMLDKLubiquitination[1]
22PKHWMLDKLTGVFAPubiquitination[1]
53IFLRNRLKYALTGDEubiquitination[1, 2, 3]
62ALTGDEVKKICMQRFubiquitination[1, 2]
63LTGDEVKKICMQRFIubiquitination[1]
75RFIKIDGKVRTDITYubiquitination[2]
94MDVISIDKTGENFRLubiquitination[1, 2, 4, 5, 6]
106FRLIYDTKGRFAVHRubiquitination[1, 2, 5, 6]
120RITPEEAKYKLCKVRacetylation[7, 8]
120RITPEEAKYKLCKVRubiquitination[2, 5, 8]
122TPEEAKYKLCKVRKIubiquitination[5]
128YKLCKVRKIFVGTKGubiquitination[1, 5, 8]
134RKIFVGTKGIPHLVTacetylation[7, 8, 9, 10]
134RKIFVGTKGIPHLVTubiquitination[1, 2, 5, 6, 8, 11]
155RYPDPLIKVNDTIQIubiquitination[2, 11]
168QIDLETGKITDFIKFubiquitination[2, 11]
211SFDVVHVKDANGNSFubiquitination[1, 2, 3]
230SNIFVIGKGNKPWISubiquitination[1, 5, 6, 8]
233FVIGKGNKPWISLPRubiquitination[1, 5, 11]
259RDKRLAAKQSSG***ubiquitination[2]
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] 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]
 [3] 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]
 [4] 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]
 [5] 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]
 [6] 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]
 [7] 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]
 [8] Integrated proteomic analysis of post-translational modifications by serial enrichment.
 Mertins P, Qiao JW, Patel J, Udeshi ND, Clauser KR, Mani DR, Burgess MW, Gillette MA, Jaffe JD, Carr SA.
 Nat Methods. 2013 Jul;10(7):634-7. [PMID: 23749302]
 [9] Proteomic investigations reveal a role for RNA processing factor THRAP3 in the DNA damage response.
 Beli P, Lukashchuk N, Wagner SA, Weinert BT, Olsen JV, Baskcomb L, Mann M, Jackson SP, Choudhary C.
 Mol Cell. 2012 Apr 27;46(2):212-25. [PMID: 22424773]
 [10] Proteomic investigations of lysine acetylation identify diverse substrates of mitochondrial deacetylase sirt3.
 Sol EM, Wagner SA, Weinert BT, Kumar A, Kim HS, Deng CX, Choudhary C.
 PLoS One. 2012;7(12):e50545. [PMID: 23236377]
 [11] Global identification of modular cullin-RING ligase substrates.
 Emanuele MJ, Elia AE, Xu Q, Thoma CR, Izhar L, Leng Y, Guo A, Chen YN, Rush J, Hsu PW, Yen HC, Elledge SJ.
 Cell. 2011 Oct 14;147(2):459-74. [PMID: 21963094] 
Functional Description
  
Sequence Annotation
 DOMAIN 42 104 S4 RNA-binding.  
Keyword
 3D-structure; Complete proteome; Cytoplasm; Direct protein sequencing; Reference proteome; Ribonucleoprotein; Ribosomal protein; RNA-binding; rRNA-binding. 
Sequence Source
 UniProt (SWISSPROT/TrEMBL); GenBank; EMBL 
Protein Length
 263 AA 
Protein Sequence
MARGPKKHLK RVAAPKHWML DKLTGVFAPR PSTGPHKLRE CLPLIIFLRN RLKYALTGDE 60
VKKICMQRFI KIDGKVRTDI TYPAGFMDVI SIDKTGENFR LIYDTKGRFA VHRITPEEAK 120
YKLCKVRKIF VGTKGIPHLV THDARTIRYP DPLIKVNDTI QIDLETGKIT DFIKFDTGNL 180
CMVTGGANLG RIGVITNRER HPGSFDVVHV KDANGNSFAT RLSNIFVIGK GNKPWISLPR 240
GKGIRLTIAE ERDKRLAAKQ SSG 263 
Gene Ontology
 GO:0022627; C:cytosolic small ribosomal subunit; IDA:UniProtKB.
 GO:0005844; C:polysome; IDA:UniProtKB.
 GO:0019843; F:rRNA binding; IEA:UniProtKB-KW.
 GO:0003735; F:structural constituent of ribosome; IMP:UniProtKB.
 GO:0007275; P:multicellular organismal development; IMP:UniProtKB.
 GO:0000184; P:nuclear-transcribed mRNA catabolic process, nonsense-mediated decay; TAS:Reactome.
 GO:0008284; P:positive regulation of cell proliferation; IMP:UniProtKB.
 GO:0045727; P:positive regulation of translation; IMP: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; TAS:Reactome.
 GO:0006415; P:translational termination; TAS:Reactome.
 GO:0019083; P:viral transcription; TAS:Reactome. 
Interpro
 IPR005824; KOW.
 IPR000876; Ribosomal_S4e.
 IPR013845; Ribosomal_S4e_central_region.
 IPR013843; Ribosomal_S4e_N.
 IPR018199; Ribosomal_S4e_N_CS.
 IPR002942; S4_RNA-bd. 
Pfam
 PF00467; KOW
 PF00900; Ribosomal_S4e
 PF08071; RS4NT
 PF01479; S4 
SMART
 SM00363; S4 
PROSITE
 PS00528; RIBOSOMAL_S4E
 PS50889; S4 
PRINTS