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Human DNA Ligase III Recognizes DNA Ends by Dynamic Switching Between Two DNA Bound States
Biology and Chemistry Report
3L2P
  •   Structure Details   Hide

    Structure Keywords

    Keywords LIGASE/DNA
    Text DNA ligase, DNA repair, ATP-binding, Cell cycle, Cell division, DNA damage, DNA recombination, DNA replication, Ligase, Magnesium, Metal-binding, Nucleotide-binding, Nucleus, Phosphoprotein, Zinc-finger, LIGASE-DNA complex

    Polymeric Molecules

    Chain A
    Description DNA ligase 3 
    Fragment UNP residues 257-833 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 65682.4 
    Source Method genetically manipulated  
    Entity Name DNA ligase III, Polydeoxyribonucleotide synthase [ATP] 3 
    Chain B
    Description 5'-D(P*CP*GP*GP*GP*AP*TP*GP*CP*GP*TP*C)-3' 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polydeoxyribonucleotide 
    Formula Weight 3390.2 
    Source Method synthetic  
    Chain C
    Description 5'-D(*GP*TP*CP*GP*GP*AP*CP*TP*G)-3' 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polydeoxyribonucleotide 
    Formula Weight 2771.8 
    Source Method synthetic  
    Chain D
    Description 5'-D(*GP*CP*CP*AP*GP*TP*CP*CP*GP*AP*CP*GP*AP*CP*GP*CP*AP*TP*CP*CP*CP*G)-3' 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polydeoxyribonucleotide 
    Formula Weight 6683.4 
    Source Method synthetic  

    Ligands and Prosthetic Groups

    ID Name Chemical Formula Weight Ligand Structure
    AMP  ADENOSINE MONOPHOSPHATE  C10 H14 N5 O7 P   347.22  View 
     
  •   Protein Details   Hide

    UniProtKB Information

    Chain SWS/UNP ID SWS/UNP Accession(s)
    A DNLI3_HUMAN P49916     

    Keywords and Names

    Chain(s) RCSB Name UniProtKB Name UniProtKB Keywords

    EC, Associated Pathways and Catalytic Sites

    Chain(s) IUBMB KEGG BioCyc
    6.5.1.1      
    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. 
    71897   DNA Biosynthetic Process  The Cellular DNA Metabolic Process Resulting in the Formation of DNA Deoxyribonucleic Acid One of the Two Main Types of Nucleic Acid Consisting of a Long Unbranched Macromolecule Formed From One or Two Strands of Linked Deoxyribonucleotides the 3' Phosphate Group of Each Constituent Deoxyribonucleotide Being Joined in 3' 5' Phosphodiester Linkage to the 5' Hydroxyl Group of the Deoxyribose Moiety of the Next One. 
    3677   DNA Binding  Any Molecular Function by Which a Gene Product Interacts Selectively and Non Covalently with DNA (deoxyribonucleic Acid). 
    3909   DNA Ligase Activity  Catalysis of the Formation of a Phosphodiester Bond Between the 3' Hydroxyl Group At the End of One DNA Chain and the 5' Phosphate Group At the End of Another. This Reaction Requires an Energy Source Such As ATP or Nad+. 
    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 lig3
    Host Scientific Name Escherichia coli  
    Host Strain Bl21(de3)
    Host Vector Type Pet 28


    Genome Information

    Chromosome Locus Gene ID Gene Name Symbol
    17 17q11.2-q12 3980     ligase III, DNA, ATP-dependent LIG3    

    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
    rs149175581 LS-SNP   dbSNP   A 177 R - > Q Helix 54% (Exposed) 17 33316584
    rs141255794 LS-SNP   dbSNP   A 177 R - > W Helix 54% (Exposed) 17 33316583
    rs199806002 LS-SNP   dbSNP   A 204 R - > Q Helix 67% (Exposed) 17 33316665
    rs143227519 LS-SNP   dbSNP   A 219 T - > I Helix 4% (Buried) 17 33318009
    rs148073351 LS-SNP   dbSNP   A 236 D - > N Helix 7% (Buried) 17 33318059
    rs141783152 LS-SNP   dbSNP   A 240 V - > L Helix 8% (Buried) 17 33318071
    rs150154135 LS-SNP   dbSNP   A 253 D - > N Helix 55% (Exposed) 17 33318110
    rs112165510 LS-SNP   dbSNP   A 262 D - > G Coil 18% (Intermediate) 17 33318694
    rs201706144 LS-SNP   dbSNP   A 296 R - > W Helix 39% (Exposed) 17 33318795
    rs192558553 LS-SNP   dbSNP   A 296 R - > Q Helix 39% (Exposed) 17 33318796
    rs142785435 LS-SNP   dbSNP   A 405 V - > I Helix 22% (Intermediate) 17 33321313
    rs148247013 LS-SNP   dbSNP   A 441 R - > S Turn 46% (Exposed) 17 33321421 AMP
    rs145992710 LS-SNP   dbSNP   A 441 R - > H Turn 46% (Exposed) 17 33321422 AMP
    rs147386726 LS-SNP   dbSNP   A 456 D - > N 3/10 Helix 55% (Exposed) 17 33323098
    rs199764227 LS-SNP   dbSNP   A 479 N - > K Turn 52% (Exposed) 17 33323169
    rs200503859 LS-SNP   dbSNP   A 480 K - > Q Turn 44% (Exposed) 17 33323170
    rs149469889 LS-SNP   dbSNP   A 497 A - > G Helix 78% (Exposed) 17 33323600
    rs200267761 LS-SNP   dbSNP   A 521 R - > K Bend 40% (Exposed) 17 33323672
    rs201705066 LS-SNP   dbSNP   A 525 E - > V Helix 51% (Exposed) 17 33324768
    rs188532751 LS-SNP   dbSNP   A 533 N - > S Helix 35% (Intermediate) 17 33324792
    rs1802880 LS-SNP   dbSNP   A 592 D - > V Turn 10% (Intermediate) 17 33325669
    rs146586818 LS-SNP   dbSNP   A 650 T - > M Helix 15% (Intermediate) 17 33326422
    rs145709942 LS-SNP   dbSNP   A 719 R - > H Beta Ladder 26% (Intermediate) 17 33328361
    rs200119021 LS-SNP   dbSNP   A 724 R - > Q Coil 38% (Exposed) 17 33328376
    rs200768752 LS-SNP   dbSNP   A 735 L - > V Helix 23% (Intermediate) 17 33328408