An Information Portal to 108124 Biological Macromolecular Structures

Human TDG in a post-reactive complex with 5-hydroxymethyluracil (5hmU)
Biology and Chemistry Report
  •   Structure Details   Hide

    Structure Keywords

    Keywords HYDROLASE/DNA
    Text base excision repair, HYDROLASE-DNA complex

    Polymeric Molecules

    Chain A
    Description G/T mismatch-specific thymine DNA glycosylase 
    Fragment human TDG glycosylase domain, UNP residues 111-308 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 23070.8 
    Source Method genetically manipulated  
    Entity Name Thymine-DNA glycosylase 
    Chain C
    Description DNA (28-MER) 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polydeoxyribonucleotide 
    Formula Weight 8646.6 
    Source Method synthetic  
    Chain D
    Description DNA (29-MER) 
    Nonstandard Linkage no 
    Nonstandard Monomers yes 
    Polymer Type polydeoxyribonucleotide 
    Formula Weight 8777.7 
    Source Method synthetic  

    Ligands and Prosthetic Groups

    ID Name Chemical Formula Weight Ligand Structure
    HMU  5-HYDROXYMETHYL URACIL  C5 H6 N2 O3   142.11  View 
  •   Protein Details   Hide

    UniProtKB Information

    Chain SWS/UNP ID SWS/UNP Accession(s)
    A TDG_HUMAN Q13569     

    Keywords and Names

    Chain(s) RCSB Name UniProtKB Name UniProtKB Keywords

    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. 
    6298   Mismatch Repair  A System For the Correction of Errors in Which an Incorrect Base Which Cannot Form Hydrogen Bonds with the Corresponding Base in the Parent Strand Is Incorporated Into the Daughter Strand. the Mismatch Repair System Promotes Genomic Fidelity by Repairing Base Base Mismatches Insertion Deletion Loops and Heterologies Generated During DNA Replication and Recombination. 
    16798   Hydrolase Activity Acting On Glycosyl Bonds  Catalysis of the Hydrolysis of Any Glycosyl Bond. 
    16799   Hydrolase Activity Hydrolyzing N Glycosyl Compounds  Catalysis of the Hydrolysis of Any N Glycosyl Bond. 
    30983   Mismatched DNA Binding  Interacting Selectively and Non Covalently with Double Stranded DNA Containing One or More Mismatches. 

  •   Gene Details   Hide

    Genetic Source

    Chain A
    Common Name Human
    Scientific Name Homo sapiens  
    Gene tdg
    Host Scientific Name Escherichia coli  
    Host Plasmid Name pXC1056

    Genome Information

    Chromosome Locus Gene ID Gene Name Symbol
    12 12q24.1 6996     thymine-DNA glycosylase TDG    

    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
    rs149084574 LS-SNP   dbSNP   A 126 D - > N Coil 34% (Intermediate) 12 104373818
    rs71466288 LS-SNP   dbSNP   A 134 I - > M Beta Ladder 1% (Buried) 12 104373844
    rs140436257 LS-SNP   dbSNP   A 176 M - > V 3/10 Helix 62% (Exposed) 12 104376624
    rs4135113 LS-SNP   dbSNP   A 199 G - > S Bend 25% (Intermediate) 12 104376693
    rs61937630 LS-SNP   dbSNP   A 201 K - > T 3/10 Helix 96% (Exposed) 12 104376700
    rs17853764 LS-SNP   dbSNP   A 268 V - > G Beta Ladder 0% (Buried) 12 104378537
    rs138856428 LS-SNP   dbSNP   A 279 F - > L Bend 21% (Intermediate) 12 104378569
    rs140103994 LS-SNP   dbSNP   A 292 L - > P Helix 1% (Buried) 12 104378609
    rs78938744 LS-SNP   dbSNP   A 300 K - > R Helix 34% (Intermediate) 12 104378633