CPLM 1.0 - Compendium of Protein Lysine Modification
TagContent
CPLM ID CPLM-002285
UniProt Accession
Genbank Protein ID
Genbank Nucleotide ID
Protein Name
 40S ribosomal protein S3 
Protein Synonyms/Alias
 RP13; YS3 
Gene Name
 RPS3 
Gene Synonyms/Alias
 SUF14; YNL178W; N1653 
Created Date
 July 27, 2013 
Organism
 Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) 
NCBI Taxa ID
 559292 
Lysine Modification
Position
Peptide
Type
References
45EVRVTPTKTEVIIRAacetylation[1]
45EVRVTPTKTEVIIRAubiquitination[2, 3]
75ELTLLVQKRFKYAPGacetylation[1]
75ELTLLVQKRFKYAPGubiquitination[3]
78LLVQKRFKYAPGTIVacetylation[1]
106VAQAESMKFKLLNGLacetylation[1]
106VAQAESMKFKLLNGLubiquitination[3, 4]
108QAESMKFKLLNGLAIacetylation[1]
108QAESMKFKLLNGLAIubiquitination[3]
132YVMESGAKGCEVVVSubiquitination[3, 4]
141CEVVVSGKLRAARAKubiquitination[3, 4]
151AARAKAMKFADGFLIacetylation[1]
151AARAKAMKFADGFLIubiquitination[3, 4]
185RQGVLGIKVKIMRDPubiquitination[3]
200AKSRTGPKALPDAVTubiquitination[3, 4]
212AVTIIEPKEEEPILAacetylation[1]
212AVTIIEPKEEEPILAsumoylation[5]
212AVTIIEPKEEEPILAubiquitination[2, 3, 4, 6, 7, 8, 9]
223PILAPSVKDYRPAEEubiquitination[3]
Reference
 [1] Proteome-wide analysis of lysine acetylation suggests its broad regulatory scope in Saccharomyces cerevisiae.
 Henriksen P, Wagner SA, Weinert BT, Sharma S, Bacinskaja G, Rehman M, Juffer AH, Walther TC, Lisby M, Choudhary C.
 Mol Cell Proteomics. 2012 Nov;11(11):1510-22. [PMID: 22865919]
 [2] A perturbed ubiquitin landscape distinguishes between ubiquitin in trafficking and in proteolysis.
 Ziv I, Matiuhin Y, Kirkpatrick DS, Erpapazoglou Z, Leon S, Pantazopoulou M, Kim W, Gygi SP, Haguenauer-Tsapis R, Reis N, Glickman MH, Kleifeld O.
 Mol Cell Proteomics. 2011 May;10(5):M111.009753. [PMID: 21427232]
 [3] Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.
 Swaney DL, Beltrao P, Starita L, Guo A, Rush J, Fields S, Krogan NJ, Villén J.
 Nat Methods. 2013 Jul;10(7):676-82. [PMID: 23749301]
 [4] Sites of ubiquitin attachment in Saccharomyces cerevisiae.
 Starita LM, Lo RS, Eng JK, von Haller PD, Fields S.
 Proteomics. 2012 Jan;12(2):236-40. [PMID: 22106047]
 [5] Identification of sumoylated proteins by systematic immunoprecipitation of the budding yeast proteome.
 Wykoff DD, O'Shea EK.
 Mol Cell Proteomics. 2005 Jan;4(1):73-83. [PMID: 15596868]
 [6] A proteomics approach to understanding protein ubiquitination.
 Peng J, Schwartz D, Elias JE, Thoreen CC, Cheng D, Marsischky G, Roelofs J, Finley D, Gygi SP.
 Nat Biotechnol. 2003 Aug;21(8):921-6. [PMID: 12872131]
 [7] Systematic approach for validating the ubiquitinated proteome.
 Seyfried NT, Xu P, Duong DM, Cheng D, Hanfelt J, Peng J.
 Anal Chem. 2008 Jun 1;80(11):4161-9. [PMID: 18433149]
 [8] Computational identification of ubiquitylation sites from protein sequences.
 Tung CW, Ho SY.
 BMC Bioinformatics. 2008 Jul 15;9:310. [PMID: 18625080]
 [9] Identification, analysis, and prediction of protein ubiquitination sites.
 Radivojac P, Vacic V, Haynes C, Cocklin RR, Mohan A, Heyen JW, Goebl MG, Iakoucheva LM.
 Proteins. 2010 Feb 1;78(2):365-80. [PMID: 19722269] 
Functional Description
  
Sequence Annotation
 DOMAIN 21 92 KH type-2.
 MOD_RES 44 44 Phosphothreonine.
 MOD_RES 70 70 Phosphothreonine.
 MOD_RES 97 97 Phosphoserine.
 MOD_RES 129 129 Phosphoserine.
 MOD_RES 221 221 Phosphoserine.
 MOD_RES 231 231 Phosphothreonine.
 CROSSLNK 212 212 Glycyl lysine isopeptide (Lys-Gly)  
Keyword
 3D-structure; 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
 240 AA 
Protein Sequence
MVALISKKRK LVADGVFYAE LNEFFTRELA EEGYSGVEVR VTPTKTEVII RATRTQDVLG 60
ENGRRINELT LLVQKRFKYA PGTIVLYAER VQDRGLSAVA QAESMKFKLL NGLAIRRAAY 120
GVVRYVMESG AKGCEVVVSG KLRAARAKAM KFADGFLIHS GQPVNDFIDT ATRHVLMRQG 180
VLGIKVKIMR DPAKSRTGPK ALPDAVTIIE PKEEEPILAP SVKDYRPAEE TEAQAEPVEA 240 
Gene Ontology
 GO:0030686; C:90S preribosome; IDA:SGD.
 GO:0022627; C:cytosolic small ribosomal subunit; IDA:SGD.
 GO:0030688; C:preribosome, small subunit precursor; IDA:SGD.
 GO:0003906; F:DNA-(apurinic or apyrimidinic site) lyase activity; IDA:SGD.
 GO:0003723; F:RNA binding; IEA:UniProtKB-KW.
 GO:0003735; F:structural constituent of ribosome; IDA:SGD.
 GO:0002181; P:cytoplasmic translation; IC:SGD.
 GO:0000056; P:ribosomal small subunit export from nucleus; IGI:SGD.
 GO:0006407; P:rRNA export from nucleus; IMP:SGD. 
Interpro
 IPR004087; KH_dom.
 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