CPLM 1.0 - Compendium of Protein Lysine Modification
TagContent
CPLM ID CPLM-001532
UniProt Accession
Genbank Protein ID
Genbank Nucleotide ID
Protein Name
 Ubiquitin conjugation factor E4 B 
Protein Synonyms/Alias
 Homozygously deleted in neuroblastoma 1; Ubiquitin fusion degradation protein 2 
Gene Name
 UBE4B 
Gene Synonyms/Alias
 HDNB1; KIAA0684; UFD2 
Created Date
 July 27, 2013 
Organism
 Homo sapiens (Human) 
NCBI Taxa ID
 9606 
Lysine Modification
Position
Peptide
Type
References
442DRVGIEEKKAPKMCSubiquitination[1, 2]
443RVGIEEKKAPKMCSQubiquitination[2]
558LCETKFGKTHPVCNLubiquitination[3]
575SLRLWLPKSLSPGCGubiquitination[2, 3]
610DDVKVVEKYFSGPAIubiquitination[1, 4, 5]
702QQLSTKIKLETVDPTubiquitination[1, 2]
794NRTVEDLKNNESQWKubiquitination[1, 2, 4, 5, 6]
801KNNESQWKDSPLATRubiquitination[1, 2, 4, 5, 6, 7]
827LKKLVRCKACADAGLubiquitination[2, 3]
951AVQPRTQKFFEMIENubiquitination[1, 2, 3, 4, 5, 8]
964ENHPLSTKLLVPSLMubiquitination[1, 4, 5, 9]
972LLVPSLMKFYTDVEHubiquitination[1]
989ATSEFYDKFTIRYHIubiquitination[4, 5]
1056HEVQEEMKNKEQWDQubiquitination[1, 2]
1058VQEEMKNKEQWDQLPubiquitination[1, 2]
1106ILTKQVQKPFLRPELubiquitination[2, 4, 5]
1132LQQLCGPKCRDLKVEubiquitination[2]
1143LKVENPEKYGFEPKKubiquitination[2]
1150KYGFEPKKLLDQLTDubiquitination[2]
1169LDCARFAKAIADDQRubiquitination[2]
1180DDQRSYSKELFEEVIubiquitination[2]
1189LFEEVISKMRKAGIKubiquitination[1, 2, 3, 4, 5]
1203KSTIAIEKFKLLAEKubiquitination[2, 4, 5]
1205TIAIEKFKLLAEKVEubiquitination[2]
1210KFKLLAEKVEEIVAKubiquitination[2, 3]
1217KVEEIVAKNARAEIDubiquitination[1, 2]
Reference
 [1] 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]
 [2] 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]
 [3] 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]
 [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] 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]
 [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] 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]
 [9] 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
 Binds to the ubiquitin moieties of preformed conjugates and catalyzes ubiquitin chain assembly in conjunction with E1, E2, and E3 (By similarity). 
Sequence Annotation
 DOMAIN 1231 1293 U-box.
 MOD_RES 31 31 Phosphoserine.
 MOD_RES 84 84 Phosphoserine.
 MOD_RES 88 88 Phosphoserine.
 MOD_RES 90 90 Phosphoserine.
 MOD_RES 101 101 Phosphoserine.
 MOD_RES 103 103 Phosphoserine.
 MOD_RES 105 105 Phosphoserine (By similarity).
 MOD_RES 803 803 Phosphoserine.
 MOD_RES 1265 1265 Phosphoserine.  
Keyword
 3D-structure; Alternative splicing; Complete proteome; Cytoplasm; Phosphoprotein; Polymorphism; Reference proteome; Ubl conjugation pathway. 
Sequence Source
 UniProt (SWISSPROT/TrEMBL); GenBank; EMBL 
Protein Length
 1302 AA 
Protein Sequence
MEELSADEIR RRRLARLAGG QTSQPTTPLT SPQRENPPGP PIAASAPGPS QSLGLNVHNM 60
TPATSPIGAS GVAHRSQSSE GVSSLSSSPS NSLETQSQSL SRSQSMDIDG VSCEKSMSQV 120
DVDSGIENME VDENDRREKR SLSDKEPSSG PEVSEEQALQ LVCKIFRVSW KDRDRDVIFL 180
SSLSAQFKQN PKEVFSDFKD LIGQILMEVL MMSTQTRDEN PFASLTATSQ PIAAAARSPD 240
RNLLLNTGSN PGTSPMFCSV ASFGASSLSS LYESSPAPTP SFWSSVPVMG PSLASPSRAA 300
SQLAVPSTPL SPHSAASGTA AGSQPSSPRY RPYTVTHPWA SSGVSILSSS PSPPALASSP 360
QAVPASSSRQ RPSSTGPPLP PASPSATSRR PSSLRISPSL GASGGASNWD SYSDHFTIET 420
CKETDMLNYL IECFDRVGIE EKKAPKMCSQ PAVSQLLSNI RSQCISHTAL VLQGSLTQPR 480
SLQQPSFLVP YMLCRNLPYG FIQELVRTTH QDEEVFKQIF IPILQGLALA AKECSLDSDY 540
FKYPLMALGE LCETKFGKTH PVCNLVASLR LWLPKSLSPG CGRELQRLSY LGAFFSFSVF 600
AEDDVKVVEK YFSGPAITLE NTRVVSQSLQ HYLELGRQEL FKILHSILLN GETREAALSY 660
MAAVVNANMK KAQMQTDDRL VSTDGFMLNF LWVLQQLSTK IKLETVDPTY IFHPRCRITL 720
PNDETRVNAT MEDVNDWLTE LYGDQPPFSE PKFPTECFFL TLHAHHLSIL PSCRRYIRRL 780
RAIRELNRTV EDLKNNESQW KDSPLATRHR EMLKRCKTQL KKLVRCKACA DAGLLDESFL 840
RRCLNFYGLL IQLLLRILDP AYPDITLPLN SDVPKVFAAL PEFYVEDVAE FLFFIVQYSP 900
QALYEPCTQD IVMFLVVMLC NQNYIRNPYL VAKLVEVMFM TNPAVQPRTQ KFFEMIENHP 960
LSTKLLVPSL MKFYTDVEHT GATSEFYDKF TIRYHISTIF KSLWQNIAHH GTFMEEFNSG 1020
KQFVRYINML INDTTFLLDE SLESLKRIHE VQEEMKNKEQ WDQLPRDQQQ ARQSQLAQDE 1080
RVSRSYLALA TETVDMFHIL TKQVQKPFLR PELGPRLAAM LNFNLQQLCG PKCRDLKVEN 1140
PEKYGFEPKK LLDQLTDIYL QLDCARFAKA IADDQRSYSK ELFEEVISKM RKAGIKSTIA 1200
IEKFKLLAEK VEEIVAKNAR AEIDYSDAPD EFRDPLMDTL MTDPVRLPSG TIMDRSIILR 1260
HLLNSPTDPF NRQTLTESML EPVPELKEQI QAWMREKQNS DH 1302 
Gene Ontology
 GO:0005737; C:cytoplasm; ISS:UniProtKB.
 GO:0005634; C:nucleus; IEA:Compara.
 GO:0000151; C:ubiquitin ligase complex; TAS:UniProtKB.
 GO:0019899; F:enzyme binding; ISS:UniProtKB.
 GO:0034450; F:ubiquitin-ubiquitin ligase activity; IEA:Compara.
 GO:0008626; P:granzyme-mediated apoptotic signaling pathway; IDA:UniProtKB.
 GO:0031175; P:neuron projection development; IEA:Compara.
 GO:0000209; P:protein polyubiquitination; IEA:Compara.
 GO:0042787; P:protein ubiquitination involved in ubiquitin-dependent protein catabolic process; TAS:UniProtKB.
 GO:0034976; P:response to endoplasmic reticulum stress; IEA:Compara.
 GO:0009411; P:response to UV; IDA:UniProtKB.
 GO:0003222; P:ventricular trabecula myocardium morphogenesis; IEA:Compara. 
Interpro
 IPR019474; Ub_conjug_fac_E4_core.
 IPR003613; Ubox_domain.
 IPR013083; Znf_RING/FYVE/PHD. 
Pfam
 PF04564; U-box
 PF10408; Ufd2P_core 
SMART
 SM00504; Ubox 
PROSITE
  
PRINTS