CPLM 1.0 - Compendium of Protein Lysine Modification
TagContent
CPLM ID CPLM-004643
UniProt Accession
Genbank Protein ID
Genbank Nucleotide ID
Protein Name
 TFIIH basal transcription factor complex helicase XPD subunit 
Protein Synonyms/Alias
 Basic transcription factor 2 80 kDa subunit; BTF2 p80; CXPD; DNA excision repair protein ERCC-2; DNA repair protein complementing XP-D cells; TFIIH basal transcription factor complex 80 kDa subunit; TFIIH 80 kDa subunit; TFIIH p80; Xeroderma pigmentosum group D-complementing protein 
Gene Name
 ERCC2 
Gene Synonyms/Alias
 XPD; XPDC 
Created Date
 July 27, 2013 
Organism
 Homo sapiens (Human) 
NCBI Taxa ID
 9606 
Lysine Modification
Position
Peptide
Type
References
35LKRTLDAKGHGVLEMubiquitination[1, 2]
69AYPLEVTKLIYCSRTubiquitination[2]
82RTVPEIEKVIEELRKubiquitination[2]
96KLLNFYEKQEGEKLPubiquitination[1, 2]
101YEKQEGEKLPFLGLAubiquitination[1, 2]
113GLALSSRKNLCIHPEubiquitination[2]
128VTPLRFGKDVDGKCHubiquitination[2]
133FGKDVDGKCHSLTASubiquitination[2]
181IYNLDDLKALGRRQGubiquitination[1, 2, 3]
223KIADLVSKELARKAVubiquitination[2]
268GNLETLQKTVLRIKEubiquitination[2, 4, 5, 6]
507DQVAISSKFETREDIubiquitination[1, 3, 4, 6]
565LENIQRNKLLFIETQubiquitination[2]
603LLSVARGKVSEGIDFubiquitination[1, 2]
671VGRAIRGKTDYGLMVubiquitination[2, 7]
682GLMVFADKRFARGDKubiquitination[1, 2]
751LESEETLKRIEQIAQubiquitination[1, 3]
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] 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]
 [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] 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]
 [6] 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]
 [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] 
Functional Description
 ATP-dependent 5'-3' DNA helicase, component of the core- TFIIH basal transcription factor. Involved in nucleotide excision repair (NER) of DNA by opening DNA around the damage, and in RNA transcription by RNA polymerase II by anchoring the CDK-activating kinase (CAK) complex, composed of CDK7, cyclin H and MAT1, to the core-TFIIH complex. Involved in the regulation of vitamin-D receptor activity. As part of the mitotic spindle-associated MMXD complex it plays a role in chromosome segregation. Might have a role in aging process and could play a causative role in the generation of skin cancers. 
Sequence Annotation
 DOMAIN 7 283 Helicase ATP-binding.
 NP_BIND 42 49 ATP (By similarity).
 REGION 438 637 Mediates interaction with MMS19.
 MOTIF 234 237 DEAH box.
 MOTIF 682 695 Nuclear localization signal (Potential).
 METAL 116 116 Iron-sulfur (4Fe-4S) (By similarity).
 METAL 134 134 Iron-sulfur (4Fe-4S) (By similarity).
 METAL 155 155 Iron-sulfur (4Fe-4S) (By similarity).
 METAL 190 190 Iron-sulfur (4Fe-4S) (Probable).  
Keyword
 4Fe-4S; Alternative splicing; ATP-binding; Cataract; Chromosome partition; Cockayne syndrome; Complete proteome; Cytoplasm; Cytoskeleton; Deafness; Disease mutation; DNA damage; DNA repair; DNA-binding; Dwarfism; Helicase; Host-virus interaction; Hydrolase; Ichthyosis; Iron; Iron-sulfur; Magnesium; Metal-binding; Nucleotide-binding; Nucleus; Polymorphism; Reference proteome; Transcription; Transcription regulation; Ubl conjugation; Xeroderma pigmentosum. 
Sequence Source
 UniProt (SWISSPROT/TrEMBL); GenBank; EMBL 
Protein Length
 760 AA 
Protein Sequence
MKLNVDGLLV YFPYDYIYPE QFSYMRELKR TLDAKGHGVL EMPSGTGKTV SLLALIMAYQ 60
RAYPLEVTKL IYCSRTVPEI EKVIEELRKL LNFYEKQEGE KLPFLGLALS SRKNLCIHPE 120
VTPLRFGKDV DGKCHSLTAS YVRAQYQHDT SLPHCRFYEE FDAHGREVPL PAGIYNLDDL 180
KALGRRQGWC PYFLARYSIL HANVVVYSYH YLLDPKIADL VSKELARKAV VVFDEAHNID 240
NVCIDSMSVN LTRRTLDRCQ GNLETLQKTV LRIKETDEQR LRDEYRRLVE GLREASAARE 300
TDAHLANPVL PDEVLQEAVP GSIRTAEHFL GFLRRLLEYV KWRLRVQHVV QESPPAFLSG 360
LAQRVCIQRK PLRFCAERLR SLLHTLEITD LADFSPLTLL ANFATLVSTY AKGFTIIIEP 420
FDDRTPTIAN PILHFSCMDA SLAIKPVFER FQSVIITSGT LSPLDIYPKI LDFHPVTMAT 480
FTMTLARVCL CPMIIGRGND QVAISSKFET REDIAVIRNY GNLLLEMSAV VPDGIVAFFT 540
SYQYMESTVA SWYEQGILEN IQRNKLLFIE TQDGAETSVA LEKYQEACEN GRGAILLSVA 600
RGKVSEGIDF VHHYGRAVIM FGVPYVYTQS RILKARLEYL RDQFQIREND FLTFDAMRHA 660
AQCVGRAIRG KTDYGLMVFA DKRFARGDKR GKLPRWIQEH LTDANLNLTV DEGVQVAKYF 720
LRQMAQPFHR EDQLGLSLLS LEQLESEETL KRIEQIAQQL 760 
Gene Ontology
 GO:0005737; C:cytoplasm; IDA:UniProtKB.
 GO:0005675; C:holo TFIIH complex; IDA:UniProtKB.
 GO:0071817; C:MMXD complex; IDA:UniProtKB.
 GO:0000441; C:SSL2-core TFIIH complex; IEA:Compara.
 GO:0051539; F:4 iron, 4 sulfur cluster binding; IEA:UniProtKB-KW.
 GO:0043139; F:5'-3' DNA helicase activity; IDA:UniProtKB.
 GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
 GO:0004003; F:ATP-dependent DNA helicase activity; IEA:InterPro.
 GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
 GO:0008094; F:DNA-dependent ATPase activity; TAS:UniProtKB.
 GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
 GO:0006370; P:7-methylguanosine mRNA capping; TAS:Reactome.
 GO:0007568; P:aging; IEA:Compara.
 GO:0006915; P:apoptotic process; IEA:Compara.
 GO:0030282; P:bone mineralization; IEA:Compara.
 GO:0000075; P:cell cycle checkpoint; IMP:UniProtKB.
 GO:0008283; P:cell proliferation; IEA:Compara.
 GO:0032289; P:central nervous system myelin formation; IEA:Compara.
 GO:0007059; P:chromosome segregation; IMP:UniProtKB.
 GO:0040016; P:embryonic cleavage; IEA:Compara.
 GO:0043249; P:erythrocyte maturation; IEA:Compara.
 GO:0030198; P:extracellular matrix organization; IEA:Compara.
 GO:0035315; P:hair cell differentiation; IMP:UniProtKB.
 GO:0048820; P:hair follicle maturation; IEA:Compara.
 GO:0060218; P:hematopoietic stem cell differentiation; IEA:Compara.
 GO:0001701; P:in utero embryonic development; IEA:Compara.
 GO:0006917; P:induction of apoptosis; IMP:UniProtKB.
 GO:0035264; P:multicellular organism growth; IEA:Compara.
 GO:0043066; P:negative regulation of apoptotic process; IEA:Compara.
 GO:0000718; P:nucleotide-excision repair, DNA damage removal; TAS:Reactome.
 GO:0033683; P:nucleotide-excision repair, DNA incision; IMP:UniProtKB.
 GO:0043388; P:positive regulation of DNA binding; IEA:Compara.
 GO:0045944; P:positive regulation of transcription from RNA polymerase II promoter; IDA:UniProtKB.
 GO:0050434; P:positive regulation of viral transcription; TAS:Reactome.
 GO:0009791; P:post-embryonic development; IEA:Compara.
 GO:0006468; P:protein phosphorylation; IDA:GOC.
 GO:0001666; P:response to hypoxia; IEA:Compara.
 GO:0006979; P:response to oxidative stress; IMP:UniProtKB.
 GO:0043588; P:skin development; IEA:Compara.
 GO:0021510; P:spinal cord development; IEA:Compara.
 GO:0006363; P:termination of RNA polymerase I transcription; TAS:Reactome.
 GO:0006362; P:transcription elongation from RNA polymerase I promoter; TAS:Reactome.
 GO:0006368; P:transcription elongation from RNA polymerase II promoter; TAS:Reactome.
 GO:0006361; P:transcription initiation from RNA polymerase I promoter; TAS:Reactome.
 GO:0006367; P:transcription initiation from RNA polymerase II promoter; TAS:Reactome.
 GO:0006283; P:transcription-coupled nucleotide-excision repair; IDA:UniProtKB.
 GO:0009650; P:UV protection; IGI:MGI.
 GO:0022415; P:viral reproductive process; TAS:Reactome.
 GO:0019048; P:virus-host interaction; IEA:UniProtKB-KW. 
Interpro
 IPR006555; ATP-dep_Helicase_C.
 IPR010614; DEAD_2.
 IPR002464; DNA/RNA_helicase_DEAH_CS.
 IPR013020; DNA_helicase_DNA-repair_Rad3.
 IPR010643; DUF1227.
 IPR014013; Helic_SF1/SF2_ATP-bd_DinG/Rad3.
 IPR006554; Helicase-like_DEXD_c2.
 IPR027417; P-loop_NTPase.
 IPR001945; XPGD_DNA_repair. 
Pfam
 PF06733; DEAD_2
 PF06777; DUF1227
 PF13307; Helicase_C_2 
SMART
 SM00488; DEXDc2
 SM00491; HELICc2 
PROSITE
 PS00690; DEAH_ATP_HELICASE
 PS51193; HELICASE_ATP_BIND_2 
PRINTS
 PR00852; XRODRMPGMNTD.