CPLM 1.0 - Compendium of Protein Lysine Modification
TagContent
CPLM ID CPLM-029857
UniProt Accession
Genbank Protein ID
Genbank Nucleotide ID
Protein Name
 Poly(A) binding protein, cytoplasmic 4 (Inducible form), isoform CRA_e 
Protein Synonyms/Alias
 Polyadenylate-binding protein 4 
Gene Name
 PABPC4 
Gene Synonyms/Alias
 hCG_2031827 
Created Date
 July 27, 2013 
Organism
 Homo sapiens (Human) 
NCBI Taxa ID
 9606 
Lysine Modification
Position
Peptide
Type
References
78TMNFDVIKGKPIRIMubiquitination[1, 2, 3, 4, 5, 6]
80NFDVIKGKPIRIMWSubiquitination[4]
95QRDPSLRKSGVGNVFubiquitination[2, 4, 6]
104GVGNVFIKNLDKSIDubiquitination[2, 4, 6]
108VFIKNLDKSIDNKALacetylation[6, 7, 8]
108VFIKNLDKSIDNKALubiquitination[1, 2, 4, 6, 9]
113LDKSIDNKALYDTFSubiquitination[2, 4, 6]
129FGNILSCKVVCDENGubiquitination[2, 10]
157AADKAIEKMNGMLLNubiquitination[1, 4, 6]
167GMLLNDRKVFVGRFKubiquitination[2]
186REAELGAKAKEFTNVubiquitination[2, 4, 5]
188AELGAKAKEFTNVYIubiquitination[1, 3, 4, 6, 11]
196EFTNVYIKNFGEEVDubiquitination[1, 2]
208EVDDESLKELFSQFGubiquitination[2]
216ELFSQFGKTLSVKVMubiquitination[1, 2, 4, 5, 6, 10]
254AVEEMNGKEISGKIIubiquitination[2]
279RQAELKRKFEQLKQEubiquitination[2, 4]
284KRKFEQLKQERISRYubiquitination[2, 4, 5, 6, 10]
299QGVNLYIKNLDDTIDubiquitination[1]
309DDTIDDEKLRKEFSPubiquitination[2, 4]
312IDDEKLRKEFSPFGSubiquitination[1, 2, 4, 6]
333MLEDGRSKGFGFVCFubiquitination[1, 2, 3, 4, 6]
348SSPEEATKAVTEMNGubiquitination[2, 4, 6, 10]
361NGRIVGSKPLYVALAubiquitination[1, 2, 4, 6]
375AQRKEERKAHLTNQYubiquitination[1, 2, 4, 5, 6]
495PRAVAPYKYASSVRSmethylation[12]
606AKKEAAQKVGAVAAAubiquitination[2, 6]
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] 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] 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]
 [7] 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]
 [8] 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]
 [9] 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]
 [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] Proteome-wide identification of ubiquitylation sites by conjugation of engineered lysine-less ubiquitin.
 Oshikawa K, Matsumoto M, Oyamada K, Nakayama KI.
 J Proteome Res. 2012 Feb 3;11(2):796-807. [PMID: 22053931]
 [12] Mass spectrometry-based identification and characterisation of lysine and arginine methylation in the human proteome.
 Bremang M, Cuomo A, Agresta AM, Stugiewicz M, Spadotto V, Bonaldi T.
 Mol Biosyst. 2013 Jul 30;9(9):2231-47. [PMID: 23748837
Functional Description
  
Sequence Annotation
  
Keyword
 Complete proteome; Reference proteome. 
Sequence Source
 UniProt (SWISSPROT/TrEMBL); GenBank; EMBL 
Protein Length
 615 AA 
Protein Sequence
MNAAASSYPM ASLYVGDLHS DVTEAMLYEK FSPAGPVLSI RVCRDMITRR SLGYAYVNFQ 60
QPADAERALD TMNFDVIKGK PIRIMWSQRD PSLRKSGVGN VFIKNLDKSI DNKALYDTFS 120
AFGNILSCKV VCDENGSKGY AFVHFETQEA ADKAIEKMNG MLLNDRKVFV GRFKSRKERE 180
AELGAKAKEF TNVYIKNFGE EVDDESLKEL FSQFGKTLSV KVMRDPNGKS KGFGFVSYEK 240
HEDANKAVEE MNGKEISGKI IFVGRAQKKV ERQAELKRKF EQLKQERISR YQGVNLYIKN 300
LDDTIDDEKL RKEFSPFGSI TSAKVMLEDG RSKGFGFVCF SSPEEATKAV TEMNGRIVGS 360
KPLYVALAQR KEERKAHLTN QYMQRVAGMR ALPANAILNQ FQPAAGGYFV PAVPQAQGRP 420
PYYTPNQLAQ MRPNPRWQQG GRPQGFQGMP SAIRQSGPRP TLRHLAPTGV PTAVQNLAPR 480
AAVAAAAPRA VAPYKYASSV RSPHPAIQPL QAPQPAVHVQ GQEPLTASML AAAPPQEQKQ 540
MLGERLFPLI QTMHSNLAGK ITGMLLEIDN SELLHMLESP ESLRSKVDEA VAVLQAHHAK 600
KEAAQKVGAV AAATS 615 
Gene Ontology
 GO:0000166; F:nucleotide binding; IEA:InterPro.
 GO:0003723; F:RNA binding; IEA:InterPro. 
Interpro
 IPR012677; Nucleotide-bd_a/b_plait.
 IPR006515; PABP_1234.
 IPR002004; PABP_HYD.
 IPR000504; RRM_dom. 
Pfam
 PF00658; PABP
 PF00076; RRM_1 
SMART
 SM00517; PolyA
 SM00360; RRM 
PROSITE
 PS51309; PABC
 PS50102; RRM 
PRINTS