CPLM 1.0 - Compendium of Protein Lysine Modification
TagContent
CPLM ID CPLM-010618
UniProt Accession
Genbank Protein ID
Genbank Nucleotide ID
Protein Name
 DNA-dependent protein kinase catalytic subunit 
Protein Synonyms/Alias
 DNA-PK catalytic subunit; DNA-PKcs; p460 
Gene Name
 Prkdc 
Gene Synonyms/Alias
 Xrcc7 
Created Date
 July 27, 2013 
Organism
 Mus musculus (Mouse) 
NCBI Taxa ID
 10090 
Lysine Modification
Position
Peptide
Type
References
2000VPMERKKKYIEIRKEacetylation[1]
2746KLSLLYAKRGLMEQKacetylation[1]
2746KLSLLYAKRGLMEQKubiquitination[2]
2971SDYCQAAKLYDEALNacetylation[3, 4]
3260SLSMKLLKEMHKESKacetylation[1]
3593KDWVSDTKDELGKNPacetylation[3, 4]
Reference
 [1] Label-free quantitative proteomics of the lysine acetylome in mitochondria identifies substrates of SIRT3 in metabolic pathways.
 Rardin MJ, Newman JC, Held JM, Cusack MP, Sorensen DJ, Li B, Schilling B, Mooney SD, Kahn CR, Verdin E, Gibson BW.
 Proc Natl Acad Sci U S A. 2013 Apr 16;110(16):6601-6. [PMID: 23576753]
 [2] Proteomic analyses reveal divergent ubiquitylation site patterns in murine tissues.
 Wagner SA, Beli P, Weinert BT, Schölz C, Kelstrup CD, Young C, Nielsen ML, Olsen JV, Brakebusch C, Choudhary C.
 Mol Cell Proteomics. 2012 Dec;11(12):1578-85. [PMID: 22790023]
 [3] Proteomic investigations of lysine acetylation identify diverse substrates of mitochondrial deacetylase sirt3.
 Sol EM, Wagner SA, Weinert BT, Kumar A, Kim HS, Deng CX, Choudhary C.
 PLoS One. 2012;7(12):e50545. [PMID: 23236377]
 [4] SIRT5-Mediated Lysine Desuccinylation Impacts Diverse Metabolic Pathways.
 Park J, Chen Y, Tishkoff DX, Peng C, Tan M, Dai L, Xie Z, Zhang Y, Zwaans BM, Skinner ME, Lombard DB, Zhao Y.
 Mol Cell. 2013 Jun 27;50(6):919-30. [PMID: 23806337] 
Functional Description
 Serine/threonine-protein kinase that acts as a molecular sensor for DNA damage. Involved in DNA nonhomologous end joining (NHEJ) required for double-strand break (DSB) repair and V(D)J recombination. Must be bound to DNA to express its catalytic properties. Promotes processing of hairpin DNA structures in V(D)J recombination by activation of the hairpin endonuclease artemis (DCLRE1C). The assembly of the DNA-PK complex at DNA ends is also required for the NHEJ ligation step. Required to protect and align broken ends of DNA. May also act as a scaffold protein to aid the localization of DNA repair proteins to the site of damage. Found at the ends of chromosomes, suggesting a further role in the maintenance of telomeric stability and the prevention of chromosomal end fusion. Also involved in modulation of transcription. Recognizes the substrate consensus sequence [ST]-Q. Phosphorylates 'Ser-139' of histone variant H2AX/H2AFX, thereby regulating DNA damage response mechanism. Phosphorylates DCLRE1C, C1D, c-Abl/ABL1, histone H1, HSPCA, c-jun/JUN, p53/TP53, PARP1, POU2F1, DHX9, SRF, XRCC1, XRCC4, XRCC5, XRCC6, WRN, MYC and RFA2. Can phosphorylate C1D not only in the presence of linear DNA but also in the presence of supercoiled DNA. Ability to phosphorylate p53/TP53 in the presence of supercoiled DNA is dependent on C1D (By similarity). 
Sequence Annotation
 REPEAT 288 323 HEAT 1.
 REPEAT 1001 1037 HEAT 2.
 REPEAT 1050 1086 HEAT 3.
 REPEAT 1720 1753 TPR 1.
 DOMAIN 2884 3539 FAT.
 REPEAT 2921 2954 TPR 2.
 REPEAT 2956 2983 TPR 3.
 DOMAIN 3747 4015 PI3K/PI4K.
 DOMAIN 4096 4128 FATC.
 REGION 1501 1536 Interaction with C1D (By similarity).
 REGION 1501 1536 Leucine-zipper.
 REGION 2432 3213 KIP-binding (By similarity).
 MOD_RES 117 117 N6-acetyllysine (By similarity).
 MOD_RES 891 891 Phosphoserine (By similarity).
 MOD_RES 1206 1206 N6-acetyllysine (By similarity).
 MOD_RES 1967 1967 N6-acetyllysine (By similarity).
 MOD_RES 2255 2255 N6-acetyllysine (By similarity).
 MOD_RES 2605 2605 Phosphothreonine; by autocatalysis (By
 MOD_RES 2608 2608 Phosphoserine; by autocatalysis (By
 MOD_RES 2634 2634 Phosphothreonine; by autocatalysis (By
 MOD_RES 2643 2643 Phosphothreonine; by autocatalysis (By
 MOD_RES 3206 3206 Phosphoserine (By similarity).
 MOD_RES 3241 3241 N6-acetyllysine (By similarity).
 MOD_RES 3260 3260 N6-acetyllysine (By similarity).
 MOD_RES 3638 3638 N6-acetyllysine (By similarity).
 MOD_RES 3642 3642 N6-acetyllysine (By similarity).
 MOD_RES 4026 4026 Phosphoserine (By similarity).  
Keyword
 Acetylation; Alternative splicing; ATP-binding; Complete proteome; Disease mutation; DNA damage; DNA repair; Kinase; Nucleotide-binding; Nucleus; Phosphoprotein; Polymorphism; Reference proteome; Repeat; S-nitrosylation; SCID; Serine/threonine-protein kinase; TPR repeat; Transferase. 
Sequence Source
 UniProt (SWISSPROT/TrEMBL); GenBank; EMBL 
Protein Length
 4128 AA 
Protein Sequence
MAEEGTGVRC WLLQLQEFLS AADRCSAAGA SYQLIRSLGQ ECVLSTSSAV QALQISLVFS 60
RDFGLLVFIR KSLSIEDFRD CREEALKFLC VFLEKIDQKV MHYSLDIKNT CTSVYTKDRT 120
AKCKIPALDL LIKLLQILRS TRLMDEFKIG ELFNKFYGEL ASKSKLPDTV LEKVYELLGV 180
LGEVHPSEMI NHSENLFRAF LGELKTQMTS TVREPKFPVL AGCLKGLSSL LCNFTKSMEE 240
DPQTSKEIFG FTFKAIRPQI EMKRYAVPLA GLRLLTLHAS QFTACLLDNY ITLFEVLSKW 300
CSHTNVELKK AAHSALESFL RQISFTVAED AELHKSRLKY FMEQFYGIIR NTDSNNKELA 360
IAIRGYGLFA GPCKVINAKD VDFMYVELIQ RCKQMFLTHA DASEDHVYQM PSFLQSIASV 420
LLYLDTVPEV YTPVLEHLMV VQIDSFPQYS PKMQLVCCKA IIKLFLALSE KGPVHWNCIS 480
AVVHQGLIRI CSKPVVLQKD VESRSDNRSA SEEVRTGRWK VPTYKDYVDL FQHLLGCDQM 540
EDFILGDETF LFVNSSLKSL NHLLYDEFIR SVLKIVEKLD LTLEKQTVGE QEDGSTADVW 600
VIPTSDPAAN LHPAKPSDFS ALINLVEFCR EILPRKHVGF FEPWVYSFAY ELILQSTRLP 660
LISGFYKLLS IAVKNARKIK YFEGISPKSL KHSPEDTEKY SCFALFAKFG KEVSVKMKQY 720
KDELLASCLT FVLSLPHDII ELDVRAYVPA LQMAFKLGLS HMPLAEIGLH ALKEWSVHID 780
KSILQPYYKD ILPCLDGYLN TSTLSDETKS HWGLSALSRA AQKGFNRHVV KHLKRTRNSS 840
PDEALSLEEI RIKVVQILGS LGGQINKSLV TATSGERMKK YVAWDAERRL SFAVPFREMK 900
PVIYLDVFLP RVTELALSAS DRQTKVAACE LLHSMVMFML GRATQMPEGQ GLPPMYQLYK 960
HTFPVLLQLA CDVDQVTRQL YEPLVMQLIH WLTNNKKFES QDTVALLEAI LDGIVDPVDS 1020
TLRDFCGRCV QEFLKWSIKQ TTPQQQEKSP VNSKSLFKRL YSLALHPNAF KRLGAALAFN 1080
HIYKEFREEG SLVEQFVFEA LVTYMESLAL AHEDEKSLGT VQQCCDAIDH LRRIIEKKHV 1140
SLNKAKKRRL PQGFPPLTSL CLLDLVEWLL AHCGRPQTEC RHKSMELFYK FVPLLPGNKS 1200
PSLWLKDLIK KKGISFLINT FEGGASSSDQ PAGILAQPTL VYLQGPISLR GVLQWLDLLL 1260
AALECYNTFI EKETVQGQEV LGAEVQSSLL KSVAFFLESI ATHSARAVEQ RFGSGAPGPP 1320
SLHEEEKYNY SKCTVLVRIM EFTTTLLIAS PEDCKLLEKD LCNTNLMQVL VKMICEPMSL 1380
GFNIGDVQVM NHLPSICVNL LKALRKSPYR DMLETHLKEK VTVQSVEELC SINLCSSGAR 1440
QERSKLLSIL SACKQLHKAG FSHVISPSQS TALNHSVGMR LLSLVYKGIV PAEERQCLQS 1500
LDPSCKSLAN GLLELAFGFG GLCDHLVSLL LNSAMLSTQY LGSSQRNISF SHGEYFYSLF 1560
SEVINSELLK NLDIAVSRLM ESSSDNPKMV STVLNGMLDT SFRDRAVQKH QGLKLATAIL 1620
QNWRKCDSWW APDSAPESKT TVLSLLAKML QIDSALSFDT NHSSFSEIFT TYASLLADTK 1680
LGLHLKGQAI ILLPFFTSLR EGSLENLKHI LEKLIVCNFP MKSDEFPPDS LKYNNYVDCM 1740
KKFLDALELS QSPMLFQLMT DILCREQRHI MEELFQTTFK RIARQSPCVT QLNLLESVYT 1800
MFRKADLPSN VTRQAFVDRS LLTLLWHCDL DTLKEFFSRI VVDAIDVLKS RFTKLNEFTF 1860
DTQITKKMCY YKMLAVMYSR LLKDDVHSKE AKINQAFHGS RVAEGNELTK TLLKLCHDAF 1920
TENMVGESQL LEKRRLYHCA AYNCAISLIS CVFNELKFYQ GFLFNEKPEK NLFIFENLID 1980
LKRCYTFPIE VEVPMERKKK YIEIRKEARD AANGASGSPH YMSSLSYLTD SSLSEEMSQF 2040
DFSTGVQSYS YSSQDRKPTT GHFQRREHQD SMTQDDIMEL EMDELNQHEC MAPMIALIKH 2100
MQRNVIAPKG EEGSIPKDLP PWMKFLHDKL GNASVSLNIR LFLAKLVINT EEVFRPYAKH 2160
WLSPLLQLAV CENNREGIHY MMVEIVATIL SWTGLATPTG VPKDEVLANR LLRFLMKHVF 2220
HPKRAVFRHN LEIIKTLVEC WKECLSIPYR LIFEKFSHKD PNSKDNSVGI QLLGIVIANN 2280
LPPYDPNCDI TSAMYFEALV NNMSFVKYKE VYAAAAEVLG LILQYITERK HVIAELVCEL 2340
VIKQLKQHQN TMEDKFIVCL NKIAKGFPPL ADRFLNALFF LLPKFHGVMK TLCLEVVLCR 2400
AEEITGLYLQ LKSKDFLQVM RHRDDERQKV CLDIVYKMVA KLKPIELREL LNPVVEFVSH 2460
PSPTCREQMY NILMWIHDNY RDQESQNDED SQEIFKLAKD VLIQGLIDEN VGLQLIIRNF 2520
WSHETRLPSN TLDRLLALNS LYSPKIEVHF LSLATNFLLE MTRMSPDYLN PIFEHPLSEC 2580
EFQEYTIDPD WRFRSTVLTP MFIETQASPS ILHTQTQEGP LSDQRQKPGQ VRATQQQYDF 2640
TPTQASVERS SFDWLTGSSI DLLADHTVFS SETLSSSLLF SHKRTEKSQR MSCKSVGPDF 2700
GTKKLGLPDD EVDNQVKSGT PSQADILRLR RRFLKDREKL SLLYAKRGLM EQKLEKDIKS 2760
EFKMKQDAQV VLYRSYRHGD LPDIQIQHSG LITPLQAVAQ KDPIIAKQLF SSLFSGILKE 2820
MNKFKTTSEK NIITQNLLQD FNRFLNTTFL FFPPFVSCIQ EISCQHPDFL TLDPASVRVG 2880
CLASLQQPGG IRLLEEALLR LMPKEPPTKR VRGKTCLPPD VLRWMELAKL YRSIGEYDVL 2940
RGIFSSELGT TQDTQNALLA EARSDYCQAA KLYDEALNKL EWVDGEPTEA EKEFWELASL 3000
DCYNNLSKWK ELEYCSTVNI VSENSLDLSK MWSEPFYQET YLPYVIRSKL KLLLQGEGNQ 3060
SLLTFVDEAM NKELQKTVLE LQYSQELSLL YILQDDIDRA TYYIKNGIQI FMQNYSSIDV 3120
LLYRSRLAKL QSVQTLAEIE EFLSFICKHG DLSSLGPLRR LLKTWTSRYP DVVTDPMHIW 3180
DDIITNRCFF LSKIEERLTA PSGDHSMSVD EDEESIDREV YEPKEDVRCM LQSCRFTMKM 3240
KMIESAWKQS NFSLSMKLLK EMHKESKTRE IWRVQWLHSY SQLNHCRSHT QSPREQVLNM 3300
LKTITLLDES DISNYLNKNI QASCDQSILL GTTCRIMADA LSREPACLSD LEENKVNSIL 3360
TLSGSNAENT ETVITGLYQR AFHHLSKAVQ SAEEETQLSC WGHEAAAERA HAYMTLVGFC 3420
DQQLRKVEES ASQKTSAEME AYPALVVEKM LRALKLNSSE ARLKFPRLLQ IIEQYSEETL 3480
NIMTKEISSI PCWQFIGWIS HMMALLDKEE AIAVQHTVEE IADNYPQAII YPFIISSESY 3540
SFKNTSSGHN NKAFVERIKS KLDHGEVIHS FINALDQLSN PDLLFKDWVS DTKDELGKNP 3600
VNKKNIEKLY ERMYAALGDL RAPGLGPFRR RFIQAFGKEF VKSFGNGGSK LLTMKVDDFC 3660
KITGSLLVRM KKDSKLPGNL KEYSPWMSEF KAQFLKNELE IPGQYDGKSK PLPEYHVRIS 3720
GFDERVKVML SLRKPKRIVI RGHDEKEYPF LVKGGEDLRQ DQRIEQIFEV MNAILSQDAA 3780
CSQRNMQLRT YRVVPMTSRL GLIEWIENTM TLKDLLLSNM SQEEKVANNS DPKAPIRDYK 3840
DWLMKVSGKS DAGAYVLMYS RANRTETVVA FRRRESQVPP DLLKRAFVKM STSPEAFLAL 3900
RSHFASSHAL LCISHWLLGI GDRHLNNFMV AMETGSVIGI DFGHAFGSAT QFLPVPELMP 3960
FRLTRQFVSL MLPMKETGLM CTVMVHALRA FRSCAGLLTD TMEIFVKEPS FDWKSFEQTM 4020
LRKGGSWIQE INVTEKNWYP QHKIRYAKRK LAGANPAVIT CDELYLGHEA SSAFRSYTAV 4080
ARGNRDYNIR AQEPESGLSE ETQVKCLVDQ ATDPNILGRT WEGWEPWM 4128 
Gene Ontology
 GO:0005958; C:DNA-dependent protein kinase-DNA ligase 4 complex; IEA:Compara.
 GO:0070419; C:nonhomologous end joining complex; ISS:UniProtKB.
 GO:0005730; C:nucleolus; IEA:UniProtKB-SubCell.
 GO:0005634; C:nucleus; IDA:MGI.
 GO:0005667; C:transcription factor complex; IEA:Compara.
 GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
 GO:0003677; F:DNA binding; IEA:InterPro.
 GO:0004677; F:DNA-dependent protein kinase activity; IEA:Compara.
 GO:0002326; P:B cell lineage commitment; IMP:MGI.
 GO:0007420; P:brain development; IGI:MGI.
 GO:0032869; P:cellular response to insulin stimulus; IEA:Compara.
 GO:0006302; P:double-strand break repair; IMP:MGI.
 GO:0006303; P:double-strand break repair via nonhomologous end joining; IEA:InterPro.
 GO:0035234; P:germ cell programmed cell death; IMP:MGI.
 GO:0007507; P:heart development; IGI:MGI.
 GO:0033152; P:immunoglobulin V(D)J recombination; IMP:MGI.
 GO:0008630; P:intrinsic apoptotic signaling pathway in response to DNA damage; IMP:MGI.
 GO:0018105; P:peptidyl-serine phosphorylation; IEA:Compara.
 GO:0043065; P:positive regulation of apoptotic process; IMP:MGI.
 GO:0045944; P:positive regulation of transcription from RNA polymerase II promoter; IEA:Compara.
 GO:0002328; P:pro-B cell differentiation; IMP:MGI.
 GO:0031648; P:protein destabilization; IDA:MGI.
 GO:0010332; P:response to gamma radiation; IMP:MGI.
 GO:0001756; P:somitogenesis; IGI:MGI.
 GO:0033077; P:T cell differentiation in thymus; IMP:MGI.
 GO:0002360; P:T cell lineage commitment; IMP:MGI.
 GO:0033153; P:T cell receptor V(D)J recombination; IMP:MGI.
 GO:0000723; P:telomere maintenance; IMP:MGI. 
Interpro
 IPR011989; ARM-like.
 IPR016024; ARM-type_fold.
 IPR003152; FATC.
 IPR011009; Kinase-like_dom.
 IPR012582; NUC194.
 IPR000403; PI3/4_kinase_cat_dom.
 IPR018936; PI3/4_kinase_CS.
 IPR003151; PIK-rel_kinase_FAT.
 IPR014009; PIK_FAT. 
Pfam
 PF02259; FAT
 PF02260; FATC
 PF08163; NUC194
 PF00454; PI3_PI4_kinase 
SMART
 SM00146; PI3Kc 
PROSITE
 PS51189; FAT
 PS51190; FATC
 PS50077; HEAT_REPEAT
 PS00915; PI3_4_KINASE_1
 PS00916; PI3_4_KINASE_2
 PS50290; PI3_4_KINASE_3
 PS50005; TPR
 PS50293; TPR_REGION 
PRINTS