CPLM 1.0 - Compendium of Protein Lysine Modification
TagContent
CPLM ID CPLM-009642
UniProt Accession
Genbank Protein ID
Genbank Nucleotide ID
Protein Name
 Ubiquitin-60S ribosomal protein L40 
Protein Synonyms/Alias
 CEP52; Ubiquitin A-52 residue ribosomal protein fusion product 1; Ubiquitin; 60S ribosomal protein L40 
Gene Name
 UBA52 
Gene Synonyms/Alias
 UBCEP2 
Created Date
 July 27, 2013 
Organism
 Homo sapiens (Human) 
NCBI Taxa ID
 9606 
Lysine Modification
Position
Peptide
Type
References
6**MQIFVKTLTGKTIubiquitination[1, 2]
11FVKTLTGKTITLEVEsumoylation[3]
11FVKTLTGKTITLEVEubiquitination[1, 2]
27SDTIENVKAKIQDKEubiquitination[1]
29TIENVKAKIQDKEGIubiquitination[2]
33VKAKIQDKEGIPPDQubiquitination[1]
48QRLIFAGKQLEDGRTubiquitination[1, 2]
63LSDYNIQKESTLHLVubiquitination[1, 2]
88SLRQLAQKYNCDKMIacetylation[4]
88SLRQLAQKYNCDKMIubiquitination[2, 5]
93AQKYNCDKMICRKCYubiquitination[1]
Reference
 [1] 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]
 [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] A novel proteomics approach to identify SUMOylated proteins and their modification sites in human cells.
 Galisson F, Mahrouche L, Courcelles M, Bonneil E, Meloche S, Chelbi-Alix MK, Thibault P.
 Mol Cell Proteomics. 2011 Feb;10(2):M110.004796. [PMID: 21098080]
 [4] 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]
 [5] 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] 
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.
 BINDING 54 54 Activating enzyme.
 BINDING 72 72 Activating enzyme.
 MOD_RES 6 6 N6-acetyllysine; alternate (By
 MOD_RES 48 48 N6-acetyllysine; alternate (By
 MOD_RES 57 57 Phosphoserine (By similarity).
 MOD_RES 65 65 Phosphoserine (By similarity).
 MOD_RES 88 88 N6-acetyllysine.
 MOD_RES 98 98 N6,N6,N6-trimethyllysine (By similarity).
 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; Acetylation; Complete proteome; Cytoplasm; Direct protein sequencing; Isopeptide bond; Methylation; Nucleus; Phosphoprotein; Reference proteome; Ribonucleoprotein; Ribosomal protein; Ubl conjugation. 
Sequence Source
 UniProt (SWISSPROT/TrEMBL); GenBank; EMBL 
Protein Length
 128 AA 
Protein Sequence
MQIFVKTLTG KTITLEVEPS DTIENVKAKI QDKEGIPPDQ QRLIFAGKQL EDGRTLSDYN 60
IQKESTLHLV LRLRGGIIEP SLRQLAQKYN CDKMICRKCY ARLHPRAVNC RKKKCGHTNN 120
LRPKKKVK 128 
Gene Ontology
 GO:0005829; C:cytosol; TAS:Reactome.
 GO:0022625; C:cytosolic large ribosomal subunit; IDA:UniProtKB.
 GO:0030666; C:endocytic vesicle membrane; TAS:Reactome.
 GO:0010008; C:endosome membrane; TAS:Reactome.
 GO:0005654; C:nucleoplasm; TAS:Reactome.
 GO:0005840; C:ribosome; IEA:UniProtKB-KW.
 GO:0003735; F:structural constituent of ribosome; IEA:InterPro.
 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: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:0000184; P:nuclear-transcribed mRNA catabolic process, nonsense-mediated decay; 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:0006614; P:SRP-dependent cotranslational protein targeting to membrane; 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:0006412; P:translation; NAS:UniProtKB.
 GO:0006414; P:translational elongation; TAS:Reactome.
 GO:0006413; P:translational initiation; TAS:Reactome.
 GO:0006415; P:translational termination; TAS:Reactome.
 GO:0035666; P:TRIF-dependent toll-like receptor signaling pathway; TAS:Reactome.
 GO:0019082; P:viral protein processing; TAS:Reactome.
 GO:0019083; P:viral transcription; TAS:Reactome.
 GO:0019068; P:virion assembly; TAS:Reactome. 
Interpro
 IPR001975; Ribosomal_L40e.
 IPR000626; Ubiquitin.
 IPR019954; Ubiquitin_CS.
 IPR019956; Ubiquitin_subgr.
 IPR019955; Ubiquitin_supergroup. 
Pfam
 PF01020; Ribosomal_L40e
 PF00240; ubiquitin 
SMART
 SM00213; UBQ 
PROSITE
 PS00299; UBIQUITIN_1
 PS50053; UBIQUITIN_2 
PRINTS
 PR00348; UBIQUITIN.