CPLM 1.0 - Compendium of Protein Lysine Modification
TagContent
CPLM ID CPLM-008234
UniProt Accession
Genbank Protein ID
Genbank Nucleotide ID
Protein Name
 DNA ligase 4 
Protein Synonyms/Alias
 DNA ligase IV; Polydeoxyribonucleotide synthase [ATP] 4 
Gene Name
 LIG4 
Gene Synonyms/Alias
  
Created Date
 July 27, 2013 
Organism
 Homo sapiens (Human) 
NCBI Taxa ID
 9606 
Lysine Modification
Position
Peptide
Type
References
85ERMAYGIKETMLAKLubiquitination[1]
164SNNSAKRKDLIKKSLubiquitination[1]
283GERMQMHKDGDVYKYubiquitination[1]
289HKDGDVYKYFSRNGYubiquitination[1]
411QKTQAHTKNEVIDALubiquitination[1]
424ALNEAIDKREEGIMVubiquitination[1]
513VGSGCTMKELYDLGLubiquitination[1]
626GDDEPQEKKRKAAPKubiquitination[1]
645IGIIEHLKAPNLTNVubiquitination[1]
733LLECFKTKSFVPWQPubiquitination[1]
841EGTRLAIKALELRFHubiquitination[1]
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] 
Functional Description
 Efficiently joins single-strand breaks in a double- stranded polydeoxynucleotide in an ATP-dependent reaction. Involved in DNA non-homologous end joining (NHEJ) required for double-strand break repair and V(D)J recombination. The LIG4-XRCC4 complex is responsible for the NHEJ ligation step, and XRCC4 enhances the joining activity of LIG4. Binding of the LIG4-XRCC4 complex to DNA ends is dependent on the assembly of the DNA- dependent protein kinase complex DNA-PK to these DNA ends. 
Sequence Annotation
 DOMAIN 654 743 BRCT 1.
 DOMAIN 808 911 BRCT 2.
 ACT_SITE 273 273 N6-AMP-lysine intermediate (By
 METAL 331 331 Magnesium 1 (Potential).
 METAL 427 427 Magnesium 2 (Potential).
 BINDING 271 271 ATP (By similarity).
 BINDING 278 278 ATP (By similarity).
 BINDING 293 293 ATP (By similarity).
 BINDING 432 432 ATP (By similarity).
 BINDING 443 443 ATP (By similarity).
 BINDING 449 449 ATP (By similarity).  
Keyword
 3D-structure; ATP-binding; Cell cycle; Cell division; Complete proteome; Direct protein sequencing; Disease mutation; DNA damage; DNA recombination; DNA repair; DNA replication; Ligase; Magnesium; Metal-binding; Nucleotide-binding; Nucleus; Polymorphism; Reference proteome; Repeat; SCID. 
Sequence Source
 UniProt (SWISSPROT/TrEMBL); GenBank; EMBL 
Protein Length
 911 AA 
Protein Sequence
MAASQTSQTV ASHVPFADLC STLERIQKSK GRAEKIRHFR EFLDSWRKFH DALHKNHKDV 60
TDSFYPAMRL ILPQLERERM AYGIKETMLA KLYIELLNLP RDGKDALKLL NYRTPTGTHG 120
DAGDFAMIAY FVLKPRCLQK GSLTIQQVND LLDSIASNNS AKRKDLIKKS LLQLITQSSA 180
LEQKWLIRMI IKDLKLGVSQ QTIFSVFHND AAELHNVTTD LEKVCRQLHD PSVGLSDISI 240
TLFSAFKPML AAIADIEHIE KDMKHQSFYI ETKLDGERMQ MHKDGDVYKY FSRNGYNYTD 300
QFGASPTEGS LTPFIHNAFK ADIQICILDG EMMAYNPNTQ TFMQKGTKFD IKRMVEDSDL 360
QTCYCVFDVL MVNNKKLGHE TLRKRYEILS SIFTPIPGRI EIVQKTQAHT KNEVIDALNE 420
AIDKREEGIM VKQPLSIYKP DKRGEGWLKI KPEYVSGLMD ELDILIVGGY WGKGSRGGMM 480
SHFLCAVAEK PPPGEKPSVF HTLSRVGSGC TMKELYDLGL KLAKYWKPFH RKAPPSSILC 540
GTEKPEVYIE PCNSVIVQIK AAEIVPSDMY KTGCTLRFPR IEKIRDDKEW HECMTLDDLE 600
QLRGKASGKL ASKHLYIGGD DEPQEKKRKA APKMKKVIGI IEHLKAPNLT NVNKISNIFE 660
DVEFCVMSGT DSQPKPDLEN RIAEFGGYIV QNPGPDTYCV IAGSENIRVK NIILSNKHDV 720
VKPAWLLECF KTKSFVPWQP RFMIHMCPST KEHFAREYDC YGDSYFIDTD LNQLKEVFSG 780
IKNSNEQTPE EMASLIADLE YRYSWDCSPL SMFRRHTVYL DSYAVINDLS TKNEGTRLAI 840
KALELRFHGA KVVSCLAEGV SHVIIGEDHS RVADFKAFRR TFKRKFKILK ESWVTDSIDK 900
CELQEENQYL I 911 
Gene Ontology
 GO:0000793; C:condensed chromosome; IDA:UniProtKB.
 GO:0005737; C:cytoplasm; IDA:HPA.
 GO:0032807; C:DNA ligase IV complex; IMP:UniProtKB.
 GO:0005958; C:DNA-dependent protein kinase-DNA ligase 4 complex; ISS:UniProtKB.
 GO:0005925; C:focal adhesion; IDA:HPA.
 GO:0005654; C:nucleoplasm; TAS:Reactome.
 GO:0005886; C:plasma membrane; IDA:HPA.
 GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
 GO:0003677; F:DNA binding; IDA:UniProtKB.
 GO:0003910; F:DNA ligase (ATP) activity; IDA:UniProtKB.
 GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
 GO:0007049; P:cell cycle; IEA:UniProtKB-KW.
 GO:0051301; P:cell division; IEA:UniProtKB-KW.
 GO:0008283; P:cell proliferation; ISS:UniProtKB.
 GO:0071285; P:cellular response to lithium ion; IEA:Compara.
 GO:0007417; P:central nervous system development; ISS:UniProtKB.
 GO:0051276; P:chromosome organization; ISS:UniProtKB.
 GO:0051102; P:DNA ligation involved in DNA recombination; ISS:UniProtKB.
 GO:0051103; P:DNA ligation involved in DNA repair; IDA:UniProtKB.
 GO:0006303; P:double-strand break repair via nonhomologous end joining; IDA:UniProtKB.
 GO:0075713; P:establishment of integrated proviral latency; TAS:Reactome.
 GO:0033152; P:immunoglobulin V(D)J recombination; IEA:Compara.
 GO:0001701; P:in utero embryonic development; ISS:UniProtKB.
 GO:0045190; P:isotype switching; ISS:UniProtKB.
 GO:0006273; P:lagging strand elongation; IBA:RefGenome.
 GO:0043524; P:negative regulation of neuron apoptotic process; ISS:UniProtKB.
 GO:0051402; P:neuron apoptotic process; ISS:UniProtKB.
 GO:0006297; P:nucleotide-excision repair, DNA gap filling; IDA:UniProtKB.
 GO:0048146; P:positive regulation of fibroblast proliferation; ISS:UniProtKB.
 GO:0050769; P:positive regulation of neurogenesis; ISS:UniProtKB.
 GO:0002328; P:pro-B cell differentiation; ISS:UniProtKB.
 GO:0010332; P:response to gamma radiation; ISS:UniProtKB.
 GO:0010165; P:response to X-ray; IMP:UniProtKB.
 GO:0000012; P:single strand break repair; IDA:UniProtKB.
 GO:0035019; P:somatic stem cell maintenance; ISS:UniProtKB.
 GO:0033077; P:T cell differentiation in thymus; ISS:UniProtKB.
 GO:0033153; P:T cell receptor V(D)J recombination; ISS:UniProtKB. 
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.
 IPR021536; DNA_ligase_IV.
 IPR012340; NA-bd_OB-fold. 
Pfam
 PF00533; BRCT
 PF04679; DNA_ligase_A_C
 PF01068; DNA_ligase_A_M
 PF04675; DNA_ligase_A_N
 PF11411; DNA_ligase_IV 
SMART
 SM00292; BRCT 
PROSITE
 PS50172; BRCT
 PS00697; DNA_LIGASE_A1
 PS00333; DNA_LIGASE_A2
 PS50160; DNA_LIGASE_A3 
PRINTS