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Crystal Structure of Human DNA Ligase I bound to 5'-adenylated, nicked DNA
Biology and Chemistry Report
1X9N
  •   Structure Details   Hide

    Structure Keywords

    Keywords Ligase/DNA
    Text DNA ligase, 5'-adenylated nicked DNA, protein-DNA complex, Ligase-DNA COMPLEX

    Polymeric Molecules

    Chain B
    Description dideoxy terminated DNA 
    Nonstandard Linkage no 
    Nonstandard Monomers yes 
    Polymer Type polydeoxyribonucleotide 
    Formula Weight 3982.6 
    Source Method synthetic  
    Chain C
    Description 5'-phosphorylated DNA 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polydeoxyribonucleotide 
    Formula Weight 4641.1 
    Source Method synthetic  
    Chain D
    Description template DNA 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polydeoxyribonucleotide 
    Formula Weight 8529.6 
    Source Method synthetic  
    Chain A
    Description DNA ligase I 
    Nonstandard Linkage no 
    Nonstandard Monomers yes 
    Polymer Type polypeptide(L) 
    Formula Weight 76610.0 
    Source Method genetically manipulated  
    Entity Name Polydeoxyribonucleotide synthase [ATP] 
    Entity Name Sys 6.5.1.1 

    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 DNLI1_HUMAN P18858     

    EC, Associated Pathways and Catalytic Sites

    Chain(s) IUBMB KEGG BioCyc Catalytic Site(s)
    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. 
    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). 
    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  
    Genus Homo
    Gene lig1
    Host Scientific Name Escherichia coli  
    Host Genus Escherichia
    Host Strain Bl21(de3)rp
    Host Vector Type Plasmid
    Host Plasmid Name pET24a


    Genome Information

    Chromosome Locus Gene ID Gene Name Symbol
    19 19q13.2-q13.3 3978     ligase I, DNA, ATP-dependent LIG1    

    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
    rs180771242 LS-SNP   dbSNP   A 265 G - > V 3/10 Helix 67% (Exposed) 19 48647203
    rs3730933 LS-SNP   dbSNP   A 267 N - > S Coil 36% (Exposed) 19 48647197
    rs201846395 LS-SNP   dbSNP   A 269 A - > T Turn 29% (Intermediate) 19 48647192
    rs111846131 LS-SNP   dbSNP   A 289 Y - > F Helix 0% (Buried) 19 48646848
    rs111507847 LS-SNP   dbSNP   A 318 S - > F Helix 0% (Buried) 19 48643362
    rs144552403 LS-SNP   dbSNP   A 335 L - > F Helix 14% (Intermediate) 19 48643312
    rs201228692 LS-SNP   dbSNP   A 337 H - > R Coil 59% (Exposed) 19 48643305
    rs3730947 LS-SNP   dbSNP   A 349 V - > M Coil 13% (Intermediate) 19 48643270
    rs202150273 LS-SNP   dbSNP   A 355 L - > F Helix 7% (Buried) 19 48643252
    rs3730966 LS-SNP   dbSNP   A 369 V - > I Helix 0% (Buried) 19 48640928
    rs201504571 LS-SNP   dbSNP   A 409 R - > C Helix 19% (Intermediate) 19 48640808
    rs4987068 LS-SNP   dbSNP   A 409 R - > H Helix 19% (Intermediate) 19 48640807
    rs148171804 LS-SNP   dbSNP   A 413 R - > S Helix 50% (Exposed) 19 48640794
    rs143797790 LS-SNP   dbSNP   A 424 I - > T Helix 9% (Intermediate) 19 48640325
    rs139908769 LS-SNP   dbSNP   A 448 G - > R Turn 68% (Exposed) 19 48639372
    rs3730980 LS-SNP   dbSNP   A 480 M - > V Coil 43% (Exposed) 19 48639022
    rs112555243 LS-SNP   dbSNP   A 487 K - > R Bend 42% (Exposed) 19 48639000
    rs150334649 LS-SNP   dbSNP   A 494 T - > M Helix 42% (Exposed) 19 48638979
    rs74929288 LS-SNP   dbSNP   A 497 E - > G Helix 60% (Exposed) 19 48638970
    rs201483928 LS-SNP   dbSNP   A 519 V - > L Helix 18% (Intermediate) 19 48637292
    rs141215260 LS-SNP   dbSNP   A 524 G - > S Helix 19% (Intermediate) 19 48637277
    rs199848958 LS-SNP   dbSNP   A 545 A - > G Beta Ladder 20% (Intermediate) 19 48636330
    rs200550314 LS-SNP   dbSNP   A 549 R - > W Bend 79% (Exposed) 19 48636319
    rs121434560 LS-SNP   dbSNP   A 566 E - > K Beta Ladder 3% (Buried) 19 48636268
    rs3731003 LS-SNP   dbSNP   A 614 T - > I Coil 44% (Exposed) 19 48631258
    rs201804541 LS-SNP   dbSNP   A 639 T - > A Turn 56% (Exposed) 19 48631184
    rs34087182 LS-SNP   dbSNP   A 641 R - > L Bend 11% (Intermediate) 19 48631177
    rs56105837 LS-SNP   dbSNP   A 647 D - > N Coil 34% (Intermediate) 19 48630599
    rs151010868 LS-SNP   dbSNP   A 648 A - > V 3/10 Helix 46% (Exposed) 19 48630595
    rs200049505 LS-SNP   dbSNP   A 672 R - > H Turn 58% (Exposed) 19 48626565
    rs55950593 LS-SNP   dbSNP   A 672 R - > C Turn 58% (Exposed) 19 48626566
    rs3731008 LS-SNP   dbSNP   A 677 R - > L Helix 44% (Exposed) 19 48626550
    rs140821248 LS-SNP   dbSNP   A 705 E - > K Helix 72% (Exposed) 19 48626467
    rs140087554 LS-SNP   dbSNP   A 708 A - > T Helix 31% (Intermediate) 19 48626458
    rs201550323 LS-SNP   dbSNP   A 716 K - > E Helix 67% (Exposed) 19 48626434
    rs199651528 LS-SNP   dbSNP   A 737 K - > E Turn 60% (Exposed) 19 48626214
    rs146309259 LS-SNP   dbSNP   A 753 V - > M Bend 62% (Exposed) 19 48624555
    rs121434561 LS-SNP   dbSNP   A 771 R - > W Bend 24% (Intermediate) 19 48624501
    rs201073563 LS-SNP   dbSNP   A 774 R - > W Bend 38% (Exposed) 19 48624492
    rs201362120 LS-SNP   dbSNP   A 774 R - > Q Bend 38% (Exposed) 19 48624491
    rs201184227 LS-SNP   dbSNP   A 798 T - > S Coil 56% (Exposed) 19 48622440
    rs142509098 LS-SNP   dbSNP   A 813 K - > R Helix 54% (Exposed) 19 48622395
    rs11668325 LS-SNP   dbSNP   A 839 S - > N Coil 45% (Exposed) 19 48620962
    rs145821638 LS-SNP   dbSNP   A 845 K - > N Beta Ladder 8% (Buried) 19 48620943
    rs201176712 LS-SNP   dbSNP   A 884 P - > L 3/10 Helix 11% (Intermediate) 19 48619155
    rs11666150 LS-SNP   dbSNP   A 892 Q - > H Helix 49% (Exposed) 19 48619130
    rs201890024 LS-SNP   dbSNP   A 898 R - > W Helix 56% (Exposed) 19 48618974