CPLM 1.0 - Compendium of Protein Lysine Modification
TagContent
CPLM ID CPLM-010889
UniProt Accession
Genbank Protein ID
Genbank Nucleotide ID
Protein Name
 DNA repair protein complementing XP-C cells 
Protein Synonyms/Alias
 Xeroderma pigmentosum group C-complementing protein; p125 
Gene Name
 XPC 
Gene Synonyms/Alias
 XPCC 
Created Date
 July 27, 2013 
Organism
 Homo sapiens (Human) 
NCBI Taxa ID
 9606 
Lysine Modification
Position
Peptide
Type
References
44FEDEKPPKKSLLSKVacetylation[1]
45EDEKPPKKSLLSKVSacetylation[1]
50PKKSLLSKVSQGKRKacetylation[1]
161SRSLLPVKPVEIEIEubiquitination[2, 3, 4]
174IETPEQAKTRERSEKubiquitination[2, 3, 4, 5, 6, 7]
183RERSEKIKLEFETYLubiquitination[2, 3, 7]
359QVLENHTKPKTSKGTubiquitination[2, 4, 6, 7]
361LENHTKPKTSKGTKQubiquitination[3]
374KQEETFAKGTCRPSAacetylation[8]
508SSSSSSSKRGKKMCSubiquitination[2]
619SPFMDREKKEDLEFQubiquitination[3]
620PFMDREKKEDLEFQAubiquitination[3]
650NHPLYALKRHLLKYEubiquitination[3]
693SRDTWLKKARVVRLGubiquitination[3]
705RLGEVPYKMVKGFSNubiquitination[3, 9]
708EVPYKMVKGFSNRARubiquitination[3]
750PPVAVDGKVPRNEFGubiquitination[2, 4, 6, 10]
849KRALGNWKLLAKGLLubiquitination[5]
853GNWKLLAKGLLIRERubiquitination[3]
Reference
 [1] Regulation of cellular metabolism by protein lysine acetylation.
 Zhao S, Xu W, Jiang W, Yu W, Lin Y, Zhang T, Yao J, Zhou L, Zeng Y, Li H, Li Y, Shi J, An W, Hancock SM, He F, Qin L, Chin J, Yang P, Chen X, Lei Q, Xiong Y, Guan KL.
 Science. 2010 Feb 19;327(5968):1000-4. [PMID: 20167786]
 [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] 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]
 [4] 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]
 [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]
 [6] 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]
 [7] 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]
 [8] 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]
 [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] 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] 
Functional Description
 Involved in global genome nucleotide excision repair (GG-NER) by acting as damage sensing and DNA-binding factor component of the XPC complex. Has only a low DNA repair activity by itself which is stimulated by RAD23B and RAD23A. Has a preference to bind DNA containing a short single-stranded segment but not to damaged oligonucleotides. This feature is proposed to be related to a dynamic sensor function: XPC can rapidly screen duplex DNA for non-hydrogen-bonded bases by forming a transient nucleoprotein intermediate complex which matures into a stable recognition complex through an intrinsic single-stranded DNA- binding activity. 
Sequence Annotation
 REGION 496 734 Interaction with RAD23B.
 REGION 607 766 Minimal sensor domain involved in damage
 REGION 607 741 DNA-binding; preference for heteroduplex
 REGION 767 831 DNA-binding; preference for single
 REGION 816 940 Interaction with ERCC2 and GTF2H1.
 REGION 847 866 Interaction with CETN2.
 MOTIF 390 395 Nuclear localization signal (Potential).
 MOD_RES 94 94 Phosphoserine.
 MOD_RES 129 129 Phosphoserine.
 MOD_RES 169 169 Phosphothreonine.
 MOD_RES 397 397 Phosphoserine (By similarity).
 MOD_RES 399 399 Phosphoserine (By similarity).
 MOD_RES 876 876 Phosphothreonine.
 MOD_RES 883 883 Phosphoserine.
 MOD_RES 884 884 Phosphoserine.
 MOD_RES 891 891 Phosphoserine.  
Keyword
 3D-structure; Alternative splicing; Complete proteome; Cytoplasm; Direct protein sequencing; Disease mutation; DNA damage; DNA repair; DNA-binding; Nucleus; Phosphoprotein; Polymorphism; Reference proteome; Ubl conjugation; Xeroderma pigmentosum. 
Sequence Source
 UniProt (SWISSPROT/TrEMBL); GenBank; EMBL 
Protein Length
 940 AA 
Protein Sequence
MARKRAAGGE PRGRELRSQK SKAKSKARRE EEEEDAFEDE KPPKKSLLSK VSQGKRKRGC 60
SHPGGSADGP AKKKVAKVTV KSENLKVIKD EALSDGDDLR DFPSDLKKAH HLKRGATMNE 120
DSNEEEEESE NDWEEVEELS EPVLGDVRES TAFSRSLLPV KPVEIEIETP EQAKTRERSE 180
KIKLEFETYL RRAMKRFNKG VHEDTHKVHL LCLLANGFYR NNICSQPDLH AIGLSIIPAR 240
FTRVLPRDVD TYYLSNLVKW FIGTFTVNAE LSASEQDNLQ TTLERRFAIY SARDDEELVH 300
IFLLILRALQ LLTRLVLSLQ PIPLKSATAK GKKPSKERLT ADPGGSSETS SQVLENHTKP 360
KTSKGTKQEE TFAKGTCRPS AKGKRNKGGR KKRSKPSSSE EDEGPGDKQE KATQRRPHGR 420
ERRVASRVSY KEESGSDEAG SGSDFELSSG EASDPSDEDS EPGPPKQRKA PAPQRTKAGS 480
KSASRTHRGS HRKDPSLPAA SSSSSSSKRG KKMCSDGEKA EKRSIAGIDQ WLEVFCEQEE 540
KWVCVDCVHG VVGQPLTCYK YATKPMTYVV GIDSDGWVRD VTQRYDPVWM TVTRKCRVDA 600
EWWAETLRPY QSPFMDREKK EDLEFQAKHM DQPLPTAIGL YKNHPLYALK RHLLKYEAIY 660
PETAAILGYC RGEAVYSRDC VHTLHSRDTW LKKARVVRLG EVPYKMVKGF SNRARKARLA 720
EPQLREENDL GLFGYWQTEE YQPPVAVDGK VPRNEFGNVY LFLPSMMPIG CVQLNLPNLH 780
RVARKLDIDC VQAITGFDFH GGYSHPVTDG YIVCEEFKDV LLTAWENEQA VIERKEKEKK 840
EKRALGNWKL LAKGLLIRER LKRRYGPKSE AAAPHTDAGG GLSSDEEEGT SSQAEAARIL 900
AASWPQNRED EEKQKLKGGP KKTKREKKAA ASHLFPFEQL 940 
Gene Ontology
 GO:0005737; C:cytoplasm; IDA:UniProtKB.
 GO:0005654; C:nucleoplasm; TAS:Reactome.
 GO:0071942; C:XPC complex; IDA:UniProtKB.
 GO:0000405; F:bubble DNA binding; TAS:UniProtKB.
 GO:0003684; F:damaged DNA binding; IDA:UniProtKB.
 GO:0000404; F:loop DNA binding; TAS:UniProtKB.
 GO:0003697; F:single-stranded DNA binding; IDA:UniProtKB.
 GO:0000075; P:cell cycle checkpoint; IMP:UniProtKB.
 GO:0031573; P:intra-S DNA damage checkpoint; IEA:Compara.
 GO:0000715; P:nucleotide-excision repair, DNA damage recognition; IDA:UniProtKB.
 GO:0000718; P:nucleotide-excision repair, DNA damage removal; TAS:Reactome.
 GO:0042493; P:response to drug; IEA:Compara.
 GO:0010224; P:response to UV-B; IEA:Compara. 
Interpro
 IPR004583; DNA_repair_Rad4.
 IPR018026; DNA_repair_Rad4_subgr.
 IPR018325; Rad4/PNGase_transGLS-fold.
 IPR018326; Rad4_beta-hairpin_dom1.
 IPR018327; Rad4_beta-hairpin_dom2.
 IPR018328; Rad4_beta-hairpin_dom3. 
Pfam
 PF10403; BHD_1
 PF10404; BHD_2
 PF10405; BHD_3
 PF03835; Rad4 
SMART
 SM01030; BHD_1
 SM01031; BHD_2
 SM01032; BHD_3 
PROSITE
  
PRINTS