CPLM 1.0 - Compendium of Protein Lysine Modification
TagContent
CPLM ID CPLM-012678
UniProt Accession
Genbank Protein ID
Genbank Nucleotide ID
Protein Name
 DNA damage-binding protein 1 
Protein Synonyms/Alias
 DDB p127 subunit; DNA damage-binding protein a; DDBa; Damage-specific DNA-binding protein 1; HBV X-associated protein 1; XAP-1; UV-damaged DNA-binding factor; UV-damaged DNA-binding protein 1; UV-DDB 1; XPE-binding factor; XPE-BF; Xeroderma pigmentosum group E-complementing protein; XPCe 
Gene Name
 DDB1 
Gene Synonyms/Alias
 XAP1 
Created Date
 July 27, 2013 
Organism
 Homo sapiens (Human) 
NCBI Taxa ID
 9606 
Lysine Modification
Position
Peptide
Type
References
60KEVGMYGKIAVMELFubiquitination[1]
70VMELFRPKGESKDLLubiquitination[1, 2, 3, 4, 5]
74FRPKGESKDLLFILTubiquitination[1]
92NACILEYKQSGESIDubiquitination[1, 3, 6]
141RLYDGLFKVIPLDRDubiquitination[1, 2, 3, 4, 5, 7]
150IPLDRDNKELKAFNIubiquitination[1]
153DRDNKELKAFNIRLEacetylation[8]
153DRDNKELKAFNIRLEubiquitination[1, 2, 3, 4, 5]
191DPQGRHVKTYEVSLRubiquitination[1, 2, 3, 4, 5, 9]
200YEVSLREKEFNKGPWubiquitination[1]
204LREKEFNKGPWKQENubiquitination[1, 2, 4, 5]
254AIAPPIIKQSTIVCHubiquitination[1]
287LFMLLLEKEEQMDGTubiquitination[3]
298MDGTVTLKDLRVELLubiquitination[2, 3, 4, 5]
383VTCSGAFKEGSLRIIubiquitination[1, 6, 9]
484RLVSQEPKALVSEWKubiquitination[1, 2, 5]
491KALVSEWKEPQAKNIubiquitination[1, 3, 9]
570DISARILKLPSFELLubiquitination[1, 2, 4, 5]
579PSFELLHKEMLGGEIubiquitination[1, 2, 3, 5, 7]
628GLLSDRKKVTLGTQPubiquitination[1]
723PLYESPRKICYQEVSubiquitination[1]
823LVSCKLGKDPNTYFIubiquitination[1, 3, 7, 9]
844YPEEAEPKQGRIVVFubiquitination[3]
857VFQYSDGKLQTVAEKubiquitination[1, 2, 3, 4, 5, 7]
864KLQTVAEKEVKGAVYubiquitination[1, 3]
867TVAEKEVKGAVYSMVubiquitination[1]
897LYEWTTEKELRTECNubiquitination[1, 3, 7]
915NIMALYLKTKGDFILubiquitination[1]
917MALYLKTKGDFILVGubiquitination[1, 2, 3, 5, 7]
936SVLLLAYKPMEGNFEubiquitination[1, 2, 3, 5, 7]
1067KVIKSVGKIEHSFWRacetylation[8]
1067KVIKSVGKIEHSFWRubiquitination[1, 2, 4, 5]
1081RSFHTERKTEPATGFubiquitination[1, 3, 7]
1104FLDISRPKMQEVVANubiquitination[7]
1121YDDGSGMKREATADDubiquitination[1, 2, 3, 4, 5, 6, 7, 9, 10, 11]
1131ATADDLIKVVEELTRubiquitination[1, 2, 3, 5, 7, 10]
Reference
 [1] 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]
 [2] 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]
 [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] 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]
 [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] 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]
 [8] 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]
 [9] 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]
 [10] Global analysis of lysine ubiquitination by ubiquitin remnant immunoaffinity profiling.
 Xu G, Paige JS, Jaffrey SR.
 Nat Biotechnol. 2010 Aug;28(8):868-73. [PMID: 20639865]
 [11] 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] 
Functional Description
 Required for DNA repair. Binds to DDB2 to form the UV- damaged DNA-binding protein complex (the UV-DDB complex). The UV- DDB complex may recognize UV-induced DNA damage and recruit proteins of the nucleotide excision repair pathway (the NER pathway) to initiate DNA repair. The UV-DDB complex preferentially binds to cyclobutane pyrimidine dimers (CPD), 6-4 photoproducts (6-4 PP), apurinic sites and short mismatches. Also appears to function as a component of numerous distinct DCX (DDB1-CUL4-X-box) E3 ubiquitin-protein ligase complexes which mediate the ubiquitination and subsequent proteasomal degradation of target proteins. The functional specificity of the DCX E3 ubiquitin- protein ligase complex is determined by the variable substrate recognition component recruited by DDB1. DCX(DDB2) (also known as DDB1-CUL4-ROC1, CUL4-DDB-ROC1 and CUL4-DDB-RBX1) may ubiquitinate histone H2A, histone H3 and histone H4 at sites of UV-induced DNA damage. The ubiquitination of histones may facilitate their removal from the nucleosome and promote subsequent DNA repair. DCX(DDB2) also ubiquitinates XPC, which may enhance DNA-binding by XPC and promote NER. DCX(DTL) plays a role in PCNA-dependent polyubiquitination of CDT1 and MDM2-dependent ubiquitination of TP53 in response to radiation-induced DNA damage and during DNA replication. DCX(ERCC8) (the CSA complex) plays a role in transcription-coupled repair (TCR). May also play a role in ubiquitination of CDKN1B/p27kip when associated with CUL4 and SKP2. 
Sequence Annotation
 REGION 2 768 Interaction with CDT1.
 REGION 391 709 Interaction with CUL4A.
 REGION 771 1140 Interaction with CDT1 and CUL4A.
 MOD_RES 2 2 N-acetylserine.
 MOD_RES 8 8 Phosphothreonine (By similarity).
 MOD_RES 757 757 Phosphoserine (By similarity).
 MOD_RES 766 766 Phosphoserine (By similarity).
 MOD_RES 1067 1067 N6-acetyllysine.  
Keyword
 3D-structure; Acetylation; Complete proteome; Cytoplasm; DNA damage; DNA repair; DNA-binding; Host-virus interaction; Nucleus; Phosphoprotein; Polymorphism; Reference proteome; Ubl conjugation; Ubl conjugation pathway. 
Sequence Source
 UniProt (SWISSPROT/TrEMBL); GenBank; EMBL 
Protein Length
 1140 AA 
Protein Sequence
MSYNYVVTAQ KPTAVNGCVT GHFTSAEDLN LLIAKNTRLE IYVVTAEGLR PVKEVGMYGK 60
IAVMELFRPK GESKDLLFIL TAKYNACILE YKQSGESIDI ITRAHGNVQD RIGRPSETGI 120
IGIIDPECRM IGLRLYDGLF KVIPLDRDNK ELKAFNIRLE ELHVIDVKFL YGCQAPTICF 180
VYQDPQGRHV KTYEVSLREK EFNKGPWKQE NVEAEASMVI AVPEPFGGAI IIGQESITYH 240
NGDKYLAIAP PIIKQSTIVC HNRVDPNGSR YLLGDMEGRL FMLLLEKEEQ MDGTVTLKDL 300
RVELLGETSI AECLTYLDNG VVFVGSRLGD SQLVKLNVDS NEQGSYVVAM ETFTNLGPIV 360
DMCVVDLERQ GQGQLVTCSG AFKEGSLRII RNGIGIHEHA SIDLPGIKGL WPLRSDPNRE 420
TDDTLVLSFV GQTRVLMLNG EEVEETELMG FVDDQQTFFC GNVAHQQLIQ ITSASVRLVS 480
QEPKALVSEW KEPQAKNISV ASCNSSQVVV AVGRALYYLQ IHPQELRQIS HTEMEHEVAC 540
LDITPLGDSN GLSPLCAIGL WTDISARILK LPSFELLHKE MLGGEIIPRS ILMTTFESSH 600
YLLCALGDGA LFYFGLNIET GLLSDRKKVT LGTQPTVLRT FRSLSTTNVF ACSDRPTVIY 660
SSNHKLVFSN VNLKEVNYMC PLNSDGYPDS LALANNSTLT IGTIDEIQKL HIRTVPLYES 720
PRKICYQEVS QCFGVLSSRI EVQDTSGGTT ALRPSASTQA LSSSVSSSKL FSSSTAPHET 780
SFGEEVEVHN LLIIDQHTFE VLHAHQFLQN EYALSLVSCK LGKDPNTYFI VGTAMVYPEE 840
AEPKQGRIVV FQYSDGKLQT VAEKEVKGAV YSMVEFNGKL LASINSTVRL YEWTTEKELR 900
TECNHYNNIM ALYLKTKGDF ILVGDLMRSV LLLAYKPMEG NFEEIARDFN PNWMSAVEIL 960
DDDNFLGAEN AFNLFVCQKD SAATTDEERQ HLQEVGLFHL GEFVNVFCHG SLVMQNLGET 1020
STPTQGSVLF GTVNGMIGLV TSLSESWYNL LLDMQNRLNK VIKSVGKIEH SFWRSFHTER 1080
KTEPATGFID GDLIESFLDI SRPKMQEVVA NLQYDDGSGM KREATADDLI KVVEELTRIH 1140 
Gene Ontology
 GO:0031464; C:Cul4A-RING ubiquitin ligase complex; IDA:UniProtKB.
 GO:0031465; C:Cul4B-RING ubiquitin ligase complex; IDA:UniProtKB.
 GO:0005737; C:cytoplasm; IDA:UniProtKB.
 GO:0005654; C:nucleoplasm; TAS:Reactome.
 GO:0003684; F:damaged DNA binding; TAS:ProtInc.
 GO:0000075; P:cell cycle checkpoint; IMP:UniProtKB.
 GO:0000718; P:nucleotide-excision repair, DNA damage removal; TAS:Reactome.
 GO:0043161; P:proteasomal ubiquitin-dependent protein catabolic process; IMP:UniProtKB.
 GO:0042787; P:protein ubiquitination involved in ubiquitin-dependent protein catabolic process; IDA:UniProtKB.
 GO:0019048; P:virus-host interaction; IEA:UniProtKB-KW.
 GO:0016055; P:Wnt receptor signaling pathway; IEA:Compara. 
Interpro
 IPR004871; Cleavage/polyA-sp_fac_asu_C.
 IPR015943; WD40/YVTN_repeat-like_dom. 
Pfam
 PF03178; CPSF_A 
SMART
  
PROSITE
  
PRINTS