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Crystal structure of the DBD domain of human DNA ligase IV Apo form
Biology and Chemistry Report
  •   Structure Details   Hide

    Structure Keywords

    Keywords LIGASE, DNA binding protein
    Text Helical domain, DNA binding domain, LIGASE, DNA binding protein

    Polymeric Molecules

    Chain A
    Description DNA ligase 4 
    Fragment DNA binding domain 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 27345.8 
    Source Method genetically manipulated  
    Entity Name DNA ligase IV, Polydeoxyribonucleotide synthase [ATP] 4 

    Ligands and Prosthetic Groups

    ID Name Chemical Formula Weight Ligand Structure
    PO4  PHOSPHATE ION  O4 P   94.97  View 
  •   Protein Details   Hide

    UniProtKB Information

    Chain SWS/UNP ID SWS/UNP Accession(s)
    A DNLI4_HUMAN P49917     

    EC, Associated Pathways and Catalytic Sites

    Chain(s) IUBMB KEGG BioCyc      
    C: Cellular Location | F: Molecular Function | P: Biological Process
    Chain A
    GO ID   Ontology GO Term Definition
    6281   DNA Repair  The Process of Restoring DNA After Damage. Genomes Are Subject to Damage by Chemical and Physical Agents in the Environment (e.g. Uv and Ionizing Radiations Chemical Mutagens Fungal and Bacterial Toxins Etc.) and by Free Radicals or Alkylating Agents Endogenously Generated in Metabolism. DNA Is Also Damaged Because of Errors During Its Replication. a Variety of Different DNA Repair Pathways Have Been Reported That Include Direct Reversal Base Excision Repair Nucleotide Excision Repair Photoreactivation Bypass Double Strand Break Repair Pathway and Mismatch Repair Pathway. 
    6310   DNA Recombination  Any Process in Which a New Genotype Is Formed by Reassortment of Genes Resulting in Gene Combinations Different From Those That Were Present in the Parents. in Eukaryotes Genetic Recombination Can Occur by Chromosome Assortment Intrachromosomal Recombination or Nonreciprocal Interchromosomal Recombination. Intrachromosomal Recombination Occurs by Crossing Over. in Bacteria It May Occur by Genetic Transformation Conjugation Transduction or F Duction. 
    51103   DNA Ligation Involved in DNA Repair  The Re Formation of a Broken Phosphodiester Bond in the DNA Backbone Carried Out by DNA Ligase That Contributes to DNA Repair. 
    3677   DNA Binding  Any Molecular Function by Which a Gene Product Interacts Selectively and Non Covalently with DNA (deoxyribonucleic Acid). 
    3910   DNA ligase (ATP) activity  Catalysis of the Reaction: ATP + Deoxyribonucleotide(n) + Deoxyribonucleotide(m) = AMP + Diphosphate + Deoxyribonucleotide(n+m). 
    5524   ATP Binding  Interacting Selectively and Non Covalently with ATP Adenosine 5' Triphosphate a Universally Important Coenzyme and Enzyme Regulator. 

  •   Gene Details   Hide

    Genetic Source

    Chain A
    Common Name Human
    Scientific Name Homo sapiens  
    Gene lig4
    Host Scientific Name Escherichia coli  
    Host Strain Bl21(de3) Cp Ripl
    Host Vector Type Plasmid
    Host Plasmid Name pET15b

    Genome Information

    Chromosome Locus Gene ID Gene Name Symbol
    13 13q33-q34 3981     ligase IV, DNA, ATP-dependent LIG4    

    Single Nucleotide Polymorphisms (from LS-SNP database)

    SNP ID LsSnp Link dbSNP Link Chain PDB position Amino acid changes Secondary structure Solvent Accessibility Chromosome Chromosome position Ligand
    rs1805388 LS-SNP   dbSNP   A 9 T - > I Beta 20% (Intermediate) 13 108863591
    rs111480660 LS-SNP   dbSNP   A 14 V - > IL Bend 1% (Buried) 13 108863577
    rs201433057 LS-SNP   dbSNP   A 15 P - > S Beta 34% (Intermediate) 13 108863574
    rs3093763 LS-SNP   dbSNP   A 62 D - > H Coil 45% (Exposed) 13 108863433
    rs199707115 LS-SNP   dbSNP   A 77 R - > K Coil 91% (Exposed) 13 108863387
    rs143897303 LS-SNP   dbSNP   A 98 N - > S Turn 48% (Exposed) 13 108863324
    rs61752350 LS-SNP   dbSNP   A 127 M - > I Helix 36% (Exposed) 13 108863236
    rs142013741 LS-SNP   dbSNP   A 160 S - > Y Helix 58% (Exposed) 13 108863138
    rs138021217 LS-SNP   dbSNP   A 167 I - > R Helix 1% (Buried) 13 108863117
    rs199854013 LS-SNP   dbSNP   A 187 I - > T Helix 5% (Buried) 13 108863057
    rs151152559 LS-SNP   dbSNP   A 198 V - > I Bend 19% (Intermediate) 13 108863025 PO4
    rs142957638 LS-SNP   dbSNP   A 229 H - > R Coil 66% (Exposed) 13 108862931