CPLM 1.0 - Compendium of Protein Lysine Modification
TagContent
CPLM ID CPLM-007092
UniProt Accession
Genbank Protein ID
Genbank Nucleotide ID
Protein Name
 60S ribosomal protein L3 
Protein Synonyms/Alias
 HIV-1 TAR RNA-binding protein B; TARBP-B 
Gene Name
 RPL3 
Gene Synonyms/Alias
 OK/SW-cl.32 
Created Date
 July 27, 2013 
Organism
 Homo sapiens (Human) 
NCBI Taxa ID
 9606 
Lysine Modification
Position
Peptide
Type
References
39FPKDDPSKPVHLTAFubiquitination[1, 2]
115EHISDECKRRFYKNWubiquitination[3, 4]
120ECKRRFYKNWHKSKKubiquitination[1, 2]
155KDFSSMKKYCQVIRVubiquitination[4]
224IDVIGVTKGKGYKGVubiquitination[3, 5]
250KTHRGLRKVACIGAWubiquitination[4]
283HRTEINKKIYKIGQGubiquitination[4]
286EINKKIYKIGQGYLIubiquitination[1, 2, 3, 4, 5, 6, 7, 8]
294IGQGYLIKDGKLIKNacetylation[9]
294IGQGYLIKDGKLIKNubiquitination[3, 4, 5, 6, 7, 8]
297GYLIKDGKLIKNNASubiquitination[4]
300IKDGKLIKNNASTDYubiquitination[1, 2, 3, 4, 5, 8]
312TDYDLSDKSINPLGGubiquitination[3]
349KRVLTLRKSLLVQTKubiquitination[3, 4]
356KSLLVQTKRRALEKIubiquitination[4]
362TKRRALEKIDLKFIDubiquitination[1, 2, 4]
366ALEKIDLKFIDTTSKacetylation[9, 10]
366ALEKIDLKFIDTTSKubiquitination[1, 2, 3, 4, 5, 7, 8]
373KFIDTTSKFGHGRFQacetylation[9]
373KFIDTTSKFGHGRFQubiquitination[1, 2, 3, 4, 8]
385RFQTMEEKKAFMGPLubiquitination[3]
386FQTMEEKKAFMGPLKubiquitination[1, 2, 4]
399LKKDRIAKEEGA***sumoylation[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] 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]
 [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] 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]
 [5] 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]
 [6] 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]
 [7] 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]
 [8] 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]
 [9] 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]
 [10] Regulation of cellular metabolism by protein lysine acetylation.
 Zhao S, Xu W, Jiang W, Yu W, Lin Y, Zhang T, Yao J, Zhou L, Zeng Y, Li H, Li Y, Shi J, An W, Hancock SM, He F, Qin L, Chin J, Yang P, Chen X, Lei Q, Xiong Y, Guan KL.
 Science. 2010 Feb 19;327(5968):1000-4. [PMID: 20167786]
 [11] Targeted identification of SUMOylation sites in human proteins using affinity enrichment and paralog-specific reporter ions.
 Lamoliatte F, Bonneil E, Durette C, Caron-Lizotte O, Wildemann D, Zerweck J, Wenschuh H, Thibault P.
 Mol Cell Proteomics. 2013 Jun 7;. [PMID: 23750026
Functional Description
 The L3 protein is a component of the large subunit of cytoplasmic ribosomes. 
Sequence Annotation
 MOD_RES 13 13 Phosphoserine.
 MOD_RES 294 294 N6-acetyllysine.
 MOD_RES 304 304 Phosphoserine.
 MOD_RES 366 366 N6-acetyllysine.  
Keyword
 3D-structure; Acetylation; Complete proteome; Cytoplasm; Direct protein sequencing; Nucleus; Phosphoprotein; Polymorphism; Reference proteome; Ribonucleoprotein; Ribosomal protein. 
Sequence Source
 UniProt (SWISSPROT/TrEMBL); GenBank; EMBL 
Protein Length
 403 AA 
Protein Sequence
MSHRKFSAPR HGSLGFLPRK RSSRHRGKVK SFPKDDPSKP VHLTAFLGYK AGMTHIVREV 60
DRPGSKVNKK EVVEAVTIVE TPPMVVVGIV GYVETPRGLR TFKTVFAEHI SDECKRRFYK 120
NWHKSKKKAF TKYCKKWQDE DGKKQLEKDF SSMKKYCQVI RVIAHTQMRL LPLRQKKAHL 180
MEIQVNGGTV AEKLDWARER LEQQVPVNQV FGQDEMIDVI GVTKGKGYKG VTSRWHTKKL 240
PRKTHRGLRK VACIGAWHPA RVAFSVARAG QKGYHHRTEI NKKIYKIGQG YLIKDGKLIK 300
NNASTDYDLS DKSINPLGGF VHYGEVTNDF VMLKGCVVGT KKRVLTLRKS LLVQTKRRAL 360
EKIDLKFIDT TSKFGHGRFQ TMEEKKAFMG PLKKDRIAKE EGA 403 
Gene Ontology
 GO:0022625; C:cytosolic large ribosomal subunit; IDA:UniProtKB.
 GO:0005730; C:nucleolus; 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
 IPR000597; Ribosomal_L3.
 IPR019926; Ribosomal_L3_CS.
 IPR009000; Transl_elong_init/rib_B-barrel. 
Pfam
 PF00297; Ribosomal_L3 
SMART
  
PROSITE
 PS00474; RIBOSOMAL_L3 
PRINTS