CPLM 1.0 - Compendium of Protein Lysine Modification
TagContent
CPLM ID CPLM-008233
UniProt Accession
Genbank Protein ID
Genbank Nucleotide ID
Protein Name
 DNA ligase 3 
Protein Synonyms/Alias
 DNA ligase III; Polydeoxyribonucleotide synthase [ATP] 3 
Gene Name
 LIG3 
Gene Synonyms/Alias
  
Created Date
 July 27, 2013 
Organism
 Homo sapiens (Human) 
NCBI Taxa ID
 9606 
Lysine Modification
Position
Peptide
Type
References
316LLLPGVIKTVYNLNDacetylation[1]
442PNAYEAFKASRNLQDubiquitination[2]
531SYFSRSLKPVLPHKVubiquitination[3]
615RPLCERRKFLHDNMVubiquitination[3]
638SEMKRVTKALDLADMubiquitination[3]
660GLEGLVLKDVKGTYEubiquitination[3]
728QKWCTVTKCAGGHDDubiquitination[3, 4, 5, 6]
765PSWLKVNKIYYPDFIubiquitination[3, 4]
Reference
 [1] 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]
 [2] 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]
 [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] 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] 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]
 [6] 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] 
Functional Description
 Interacts with DNA-repair protein XRCC1 and can correct defective DNA strand-break repair and sister chromatid exchange following treatment with ionizing radiation and alkylating agents. 
Sequence Annotation
 DOMAIN 933 1009 BRCT.
 ZN_FING 93 185 PARP-type.
 ACT_SITE 508 508 N6-AMP-lysine intermediate (By
 METAL 560 560 Magnesium 1 (By similarity).
 METAL 655 655 Magnesium 2 (By similarity).
 BINDING 506 506 ATP (By similarity).
 BINDING 513 513 ATP (By similarity).
 BINDING 528 528 ATP (By similarity).
 BINDING 660 660 ATP (By similarity).
 BINDING 671 671 ATP (By similarity).
 BINDING 675 675 ATP (By similarity).
 MOD_RES 209 209 Phosphothreonine (By similarity).
 MOD_RES 210 210 Phosphoserine.
 MOD_RES 227 227 Phosphoserine.  
Keyword
 3D-structure; Alternative splicing; ATP-binding; Cell cycle; Cell division; Complete proteome; DNA damage; DNA recombination; DNA repair; DNA replication; Ligase; Magnesium; Metal-binding; Nucleotide-binding; Nucleus; Phosphoprotein; Polymorphism; Reference proteome; Zinc; Zinc-finger. 
Sequence Source
 UniProt (SWISSPROT/TrEMBL); GenBank; EMBL 
Protein Length
 1009 AA 
Protein Sequence
MSLAFKIFFP QTLRALSRKE LCLFRKHHWR DVRQFSQWSE TDLLHGHPLF LRRKPVLSFQ 60
GSHLRSRATY LVFLPGLHVG LCSGPCEMAE QRFCVDYAKR GTAGCKKCKE KIVKGVCRIG 120
KVVPNPFSES GGDMKEWYHI KCMFEKLERA RATTKKIEDL TELEGWEELE DNEKEQITQH 180
IADLSSKAAG TPKKKAVVQA KLTTTGQVTS PVKGASFVTS TNPRKFSGFS AKPNNSGEAP 240
SSPTPKRSLS SSKCDPRHKD CLLREFRKLC AMVADNPSYN TKTQIIQDFL RKGSAGDGFH 300
GDVYLTVKLL LPGVIKTVYN LNDKQIVKLF SRIFNCNPDD MARDLEQGDV SETIRVFFEQ 360
SKSFPPAAKS LLTIQEVDEF LLRLSKLTKE DEQQQALQDI ASRCTANDLK CIIRLIKHDL 420
KMNSGAKHVL DALDPNAYEA FKASRNLQDV VERVLHNAQE VEKEPGQRRA LSVQASLMTP 480
VQPMLAEACK SVEYAMKKCP NGMFSEIKYD GERVQVHKNG DHFSYFSRSL KPVLPHKVAH 540
FKDYIPQAFP GGHSMILDSE VLLIDNKTGK PLPFGTLGVH KKAAFQDANV CLFVFDCIYF 600
NDVSLMDRPL CERRKFLHDN MVEIPNRIMF SEMKRVTKAL DLADMITRVI QEGLEGLVLK 660
DVKGTYEPGK RHWLKVKKDY LNEGAMADTA DLVVLGAFYG QGSKGGMMSI FLMGCYDPGS 720
QKWCTVTKCA GGHDDATLAR LQNELDMVKI SKDPSKIPSW LKVNKIYYPD FIVPDPKKAA 780
VWEITGAEFS KSEAHTADGI SIRFPRCTRI RDDKDWKSAT NLPQLKELYQ LSKEKADFTV 840
VAGDEGSSTT GGSSEENKGP SGSAVSRKAP SKPSASTKKA EGKLSNSNSK DGNMQTAKPS 900
AMKVGEKLAT KSSPVKVGEK RKAADETLCQ TKVLLDIFTG VRLYLPPSTP DFSRLRRYFV 960
AFDGDLVQEF DMTSATHVLG SRDKNPAAQQ VSPEWIWACI RKRRLVAPC 1009 
Gene Ontology
 GO:0005694; C:chromosome; IBA:RefGenome.
 GO:0005654; C:nucleoplasm; TAS:Reactome.
 GO:0000795; C:synaptonemal complex; IEA:Compara.
 GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
 GO:0003677; F:DNA binding; TAS:ProtInc.
 GO:0003910; F:DNA ligase (ATP) activity; IBA:RefGenome.
 GO:0008270; F:zinc ion binding; IEA:InterPro.
 GO:0006284; P:base-excision repair; TAS:Reactome.
 GO:0051301; P:cell division; IEA:UniProtKB-KW.
 GO:0051103; P:DNA ligation involved in DNA repair; IEA:InterPro.
 GO:0006303; P:double-strand break repair via nonhomologous end joining; IEA:Compara.
 GO:0006273; P:lagging strand elongation; IBA:RefGenome.
 GO:0043504; P:mitochondrial DNA repair; IEA:Compara.
 GO:0045910; P:negative regulation of DNA recombination; IEA:Compara.
 GO:0006289; P:nucleotide-excision repair; IBA:RefGenome.
 GO:0007131; P:reciprocal meiotic recombination; TAS:ProtInc.
 GO:0007283; P:spermatogenesis; TAS:ProtInc. 
Interpro
 IPR001357; BRCT_dom.
 IPR000977; DNA_ligase_ATP-dep.
 IPR012309; DNA_ligase_ATP-dep_C.
 IPR012310; DNA_ligase_ATP-dep_cent.
 IPR016059; DNA_ligase_ATP-dep_CS.
 IPR012308; DNA_ligase_ATP-dep_N.
 IPR012340; NA-bd_OB-fold.
 IPR001510; Znf_PARP. 
Pfam
 PF04679; DNA_ligase_A_C
 PF01068; DNA_ligase_A_M
 PF04675; DNA_ligase_A_N
 PF00645; zf-PARP 
SMART
 SM00292; BRCT 
PROSITE
 PS50172; BRCT
 PS00697; DNA_LIGASE_A1
 PS00333; DNA_LIGASE_A2
 PS50160; DNA_LIGASE_A3
 PS00347; PARP_ZN_FINGER_1
 PS50064; PARP_ZN_FINGER_2 
PRINTS