CPLM 1.0 - Compendium of Protein Lysine Modification
TagContent
CPLM ID CPLM-005501
UniProt Accession
Genbank Protein ID
Genbank Nucleotide ID
Protein Name
 60S ribosomal protein L13 
Protein Synonyms/Alias
 Breast basic conserved protein 1 
Gene Name
 RPL13 
Gene Synonyms/Alias
 BBC1; OK/SW-cl.46 
Created Date
 July 27, 2013 
Organism
 Homo sapiens (Human) 
NCBI Taxa ID
 9606 
Lysine Modification
Position
Peptide
Type
References
11SRNGMVLKPHFHKDWubiquitination[1]
16VLKPHFHKDWQRRVAacetylation[2]
16VLKPHFHKDWQRRVAubiquitination[1]
88LRVAGIHKKVARTIGubiquitination[3]
105VDPRRRNKSTESLQAubiquitination[1, 3, 4, 5, 6, 7]
123RLKEYRSKLILFPRKacetylation[8, 9]
123RLKEYRSKLILFPRKubiquitination[1, 4, 6, 7, 10]
136RKPSAPKKGDSSAEEubiquitination[1, 3, 7, 10, 11]
145DSSAEELKLATQLTGubiquitination[1, 3, 7, 10, 11]
174RVITEEEKNFKAFASubiquitination[1, 3, 4]
177TEEEKNFKAFASLRMacetylation[2]
177TEEEKNFKAFASLRMubiquitination[1, 4]
200GIRAKRAKEAAEQDVubiquitination[3]
Reference
 [1] 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]
 [2] 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]
 [3] 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]
 [4] 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]
 [5] 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]
 [6] 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]
 [7] 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]
 [8] 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]
 [9] 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]
 [10] 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]
 [11] 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
Functional Description
  
Sequence Annotation
 MOD_RES 16 16 N6-acetyllysine.
 MOD_RES 77 77 Phosphoserine.
 MOD_RES 106 106 Phosphoserine.
 MOD_RES 177 177 N6-acetyllysine.  
Keyword
 3D-structure; Acetylation; Alternative splicing; Complete proteome; Phosphoprotein; Polymorphism; Reference proteome; Ribonucleoprotein; Ribosomal protein. 
Sequence Source
 UniProt (SWISSPROT/TrEMBL); GenBank; EMBL 
Protein Length
 211 AA 
Protein Sequence
MAPSRNGMVL KPHFHKDWQR RVATWFNQPA RKIRRRKARQ AKARRIAPRP ASGPIRPIVR 60
CPTVRYHTKV RAGRGFSLEE LRVAGIHKKV ARTIGISVDP RRRNKSTESL QANVQRLKEY 120
RSKLILFPRK PSAPKKGDSS AEELKLATQL TGPVMPVRNV YKKEKARVIT EEEKNFKAFA 180
SLRMARANAR LFGIRAKRAK EAAEQDVEKK K 211 
Gene Ontology
 GO:0022625; C:cytosolic large ribosomal subunit; IDA:UniProtKB.
 GO:0003723; F:RNA binding; TAS:ProtInc.
 GO:0003735; F:structural constituent of ribosome; NAS:UniProtKB.
 GO:0000184; P:nuclear-transcribed mRNA catabolic process, nonsense-mediated decay; TAS:Reactome.
 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
 IPR001380; Ribosomal_L13e.
 IPR018256; Ribosomal_L13e_CS. 
Pfam
 PF01294; Ribosomal_L13e 
SMART
  
PROSITE
 PS01104; RIBOSOMAL_L13E 
PRINTS