CPLM 1.0 - Compendium of Protein Lysine Modification
TagContent
CPLM ID CPLM-003705
UniProt Accession
Genbank Protein ID
Genbank Nucleotide ID
Protein Name
 Polyubiquitin-C 
Protein Synonyms/Alias
 Ubiquitin 
Gene Name
 UBC 
Gene Synonyms/Alias
  
Created Date
 July 27, 2013 
Organism
 Homo sapiens (Human) 
NCBI Taxa ID
 9606 
Lysine Modification
Position
Peptide
Type
References
6**MQIFVKTLTGKTIubiquitination[1, 2, 3]
11FVKTLTGKTITLEVEubiquitination[1, 2, 3]
27SDTIENVKAKIQDKEubiquitination[2]
29TIENVKAKIQDKEGIubiquitination[1, 2, 3]
33VKAKIQDKEGIPPDQubiquitination[1, 2]
48QRLIFAGKQLEDGRTubiquitination[1, 2, 3]
63LSDYNIQKESTLHLVubiquitination[1, 2, 3]
82GGMQIFVKTLTGKTIubiquitination[2]
671LSDYNIQKESTLHLVsumoylation[4]
Reference
 [1] 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]
 [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] 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]
 [4] 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
 Ubiquitin exists either covalently attached to another protein, or free (unanchored). When covalently bound, it is conjugated to target proteins via an isopeptide bond either as a monomer (monoubiquitin), a polymer linked via different Lys residues of the ubiquitin (polyubiquitin chains) or a linear polymer linked via the initiator Met of the ubiquitin (linear polyubiquitin chains). Polyubiquitin chains, when attached to a target protein, have different functions depending on the Lys residue of the ubiquitin that is linked: Lys-6-linked may be involved in DNA repair; Lys-11-linked is involved in ERAD (endoplasmic reticulum-associated degradation) and in cell-cycle regulation; Lys-29-linked is involved in lysosomal degradation; Lys-33-linked is involved in kinase modification; Lys-48-linked is involved in protein degradation via the proteasome; Lys-63-linked is involved in endocytosis, DNA-damage responses as well as in signaling processes leading to activation of the transcription factor NF-kappa-B. Linear polymer chains formed via attachment by the initiator Met lead to cell signaling. Ubiquitin is usually conjugated to Lys residues of target proteins, however, in rare cases, conjugation to Cys or Ser residues has been observed. When polyubiquitin is free (unanchored-polyubiquitin), it also has distinct roles, such as in activation of protein kinases, and in signaling. 
Sequence Annotation
 DOMAIN 1 76 Ubiquitin-like 1.
 DOMAIN 77 152 Ubiquitin-like 2.
 DOMAIN 153 228 Ubiquitin-like 3.
 DOMAIN 229 304 Ubiquitin-like 4.
 DOMAIN 305 380 Ubiquitin-like 5.
 DOMAIN 381 456 Ubiquitin-like 6.
 DOMAIN 457 532 Ubiquitin-like 7.
 DOMAIN 533 608 Ubiquitin-like 8.
 DOMAIN 609 684 Ubiquitin-like 9.
 BINDING 54 54 Activating enzyme.
 BINDING 72 72 Activating enzyme.
 CROSSLNK 6 6 Glycyl lysine isopeptide (Lys-Gly)
 CROSSLNK 11 11 Glycyl lysine isopeptide (Lys-Gly)
 CROSSLNK 27 27 Glycyl lysine isopeptide (Lys-Gly)
 CROSSLNK 29 29 Glycyl lysine isopeptide (Lys-Gly)
 CROSSLNK 33 33 Glycyl lysine isopeptide (Lys-Gly)
 CROSSLNK 48 48 Glycyl lysine isopeptide (Lys-Gly)
 CROSSLNK 63 63 Glycyl lysine isopeptide (Lys-Gly)
 CROSSLNK 76 76 Glycyl lysine isopeptide (Gly-Lys)  
Keyword
 3D-structure; Complete proteome; Cytoplasm; Direct protein sequencing; Isopeptide bond; Nucleus; Reference proteome; Repeat; Ubl conjugation. 
Sequence Source
 UniProt (SWISSPROT/TrEMBL); GenBank; EMBL 
Protein Length
 685 AA 
Protein Sequence
MQIFVKTLTG KTITLEVEPS DTIENVKAKI QDKEGIPPDQ QRLIFAGKQL EDGRTLSDYN 60
IQKESTLHLV LRLRGGMQIF VKTLTGKTIT LEVEPSDTIE NVKAKIQDKE GIPPDQQRLI 120
FAGKQLEDGR TLSDYNIQKE STLHLVLRLR GGMQIFVKTL TGKTITLEVE PSDTIENVKA 180
KIQDKEGIPP DQQRLIFAGK QLEDGRTLSD YNIQKESTLH LVLRLRGGMQ IFVKTLTGKT 240
ITLEVEPSDT IENVKAKIQD KEGIPPDQQR LIFAGKQLED GRTLSDYNIQ KESTLHLVLR 300
LRGGMQIFVK TLTGKTITLE VEPSDTIENV KAKIQDKEGI PPDQQRLIFA GKQLEDGRTL 360
SDYNIQKEST LHLVLRLRGG MQIFVKTLTG KTITLEVEPS DTIENVKAKI QDKEGIPPDQ 420
QRLIFAGKQL EDGRTLSDYN IQKESTLHLV LRLRGGMQIF VKTLTGKTIT LEVEPSDTIE 480
NVKAKIQDKE GIPPDQQRLI FAGKQLEDGR TLSDYNIQKE STLHLVLRLR GGMQIFVKTL 540
TGKTITLEVE PSDTIENVKA KIQDKEGIPP DQQRLIFAGK QLEDGRTLSD YNIQKESTLH 600
LVLRLRGGMQ IFVKTLTGKT ITLEVEPSDT IENVKAKIQD KEGIPPDQQR LIFAGKQLED 660
GRTLSDYNIQ KESTLHLVLR LRGGV 685 
Gene Ontology
 GO:0005829; C:cytosol; TAS:Reactome.
 GO:0030666; C:endocytic vesicle membrane; TAS:Reactome.
 GO:0010008; C:endosome membrane; TAS:Reactome.
 GO:0005654; C:nucleoplasm; TAS:Reactome.
 GO:0000187; P:activation of MAPK activity; TAS:Reactome.
 GO:0031145; P:anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process; TAS:Reactome.
 GO:0002479; P:antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent; TAS:Reactome.
 GO:0097190; P:apoptotic signaling pathway; TAS:Reactome.
 GO:0016044; P:cellular membrane organization; TAS:Reactome.
 GO:0019221; P:cytokine-mediated signaling pathway; TAS:Reactome.
 GO:0006977; P:DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest; TAS:Reactome.
 GO:0006281; P:DNA repair; TAS:Reactome.
 GO:0046788; P:egress of virus within host cell; TAS:Reactome.
 GO:0016197; P:endosomal transport; TAS:Reactome.
 GO:0007173; P:epidermal growth factor receptor signaling pathway; TAS:Reactome.
 GO:0008543; P:fibroblast growth factor receptor signaling pathway; TAS:Reactome.
 GO:0000082; P:G1/S transition of mitotic cell cycle; TAS:Reactome.
 GO:0007249; P:I-kappaB kinase/NF-kappaB cascade; TAS:Reactome.
 GO:0045087; P:innate immune response; TAS:Reactome.
 GO:0034220; P:ion transmembrane transport; TAS:Reactome.
 GO:0007254; P:JNK cascade; TAS:Reactome.
 GO:0016071; P:mRNA metabolic process; TAS:Reactome.
 GO:0002755; P:MyD88-dependent toll-like receptor signaling pathway; TAS:Reactome.
 GO:0043066; P:negative regulation of apoptotic process; TAS:Reactome.
 GO:0042059; P:negative regulation of epidermal growth factor receptor signaling pathway; TAS:Reactome.
 GO:0000122; P:negative regulation of transcription from RNA polymerase II promoter; TAS:Reactome.
 GO:0030512; P:negative regulation of transforming growth factor beta receptor signaling pathway; TAS:Reactome.
 GO:0032480; P:negative regulation of type I interferon production; TAS:Reactome.
 GO:0051436; P:negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle; TAS:Reactome.
 GO:0048011; P:neurotrophin TRK receptor signaling pathway; TAS:Reactome.
 GO:0007220; P:Notch receptor processing; TAS:Reactome.
 GO:0007219; P:Notch signaling pathway; TAS:Reactome.
 GO:0070423; P:nucleotide-binding oligomerization domain containing signaling pathway; TAS:Reactome.
 GO:0043123; P:positive regulation of I-kappaB kinase/NF-kappaB cascade; TAS:Reactome.
 GO:0051092; P:positive regulation of NF-kappaB transcription factor activity; TAS:Reactome.
 GO:0045944; P:positive regulation of transcription from RNA polymerase II promoter; TAS:Reactome.
 GO:0032481; P:positive regulation of type I interferon production; TAS:Reactome.
 GO:0051437; P:positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle; TAS:Reactome.
 GO:0000209; P:protein polyubiquitination; TAS:Reactome.
 GO:0061418; P:regulation of transcription from RNA polymerase II promoter in response to hypoxia; TAS:Reactome.
 GO:0050852; P:T cell receptor signaling pathway; TAS:Reactome.
 GO:0034166; P:toll-like receptor 10 signaling pathway; TAS:Reactome.
 GO:0034134; P:toll-like receptor 2 signaling pathway; TAS:Reactome.
 GO:0034138; P:toll-like receptor 3 signaling pathway; TAS:Reactome.
 GO:0034142; P:toll-like receptor 4 signaling pathway; TAS:Reactome.
 GO:0034146; P:toll-like receptor 5 signaling pathway; TAS:Reactome.
 GO:0034162; P:toll-like receptor 9 signaling pathway; TAS:Reactome.
 GO:0038123; P:toll-like receptor TLR1:TLR2 signaling pathway; TAS:Reactome.
 GO:0038124; P:toll-like receptor TLR6:TLR2 signaling pathway; TAS:Reactome.
 GO:0006367; P:transcription initiation from RNA polymerase II promoter; TAS:Reactome.
 GO:0007179; P:transforming growth factor beta receptor signaling pathway; TAS:Reactome.
 GO:0035666; P:TRIF-dependent toll-like receptor signaling pathway; TAS:Reactome.
 GO:0019082; P:viral protein processing; TAS:Reactome.
 GO:0019068; P:virion assembly; TAS:Reactome. 
Interpro
 IPR000626; Ubiquitin.
 IPR019954; Ubiquitin_CS.
 IPR019956; Ubiquitin_subgr.
 IPR019955; Ubiquitin_supergroup. 
Pfam
 PF00240; ubiquitin 
SMART
 SM00213; UBQ 
PROSITE
 PS00299; UBIQUITIN_1
 PS50053; UBIQUITIN_2 
PRINTS
 PR00348; UBIQUITIN.