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Crystal structure of methyl CpG binding domain of MBD4 in complex with the 5mCG/hmCG sequence
Biology and Chemistry Report
3VYB
  •   Structure Details   Hide

    Structure Keywords

    Keywords HYDROLASE/DNA
    Text methyl CpG binding domain, protein-DNA complex, versatile base recognition, HYDROLASE-DNA complex

    Polymeric Molecules

    Chain A
    Description Methyl-CpG-binding domain protein 4 
    Fragment methyl CpG binding domain, UNP residues 69-136 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 7829.2 
    Source Method genetically manipulated  
    Entity Name Methyl-CpG-binding protein MBD4, Mismatch-specific DNA N-glycosylase 
    Chain B
    Description DNA (5'-D(*GP*TP*CP*AP*CP*TP*AP*CP*(5CM)P*GP*GP*AP*CP*A)-3') 
    Nonstandard Linkage no 
    Nonstandard Monomers yes 
    Polymer Type polydeoxyribonucleotide 
    Formula Weight 4263.8 
    Source Method synthetic  
    Chain C
    Description DNA (5'-D(*GP*TP*CP*(5HC)P*GP*GP*TP*AP*GP*TP*GP*AP*CP*T)-3') 
    Nonstandard Linkage no 
    Nonstandard Monomers yes 
    Polymer Type polydeoxyribonucleotide 
    Formula Weight 4341.9 
    Source Method synthetic  

    Ligands and Prosthetic Groups

    ID Name Chemical Formula Weight Ligand Structure
    ACT  ACETATE ION  C2 H3 O2   59.04  View 
    EDO  1,2-ETHANEDIOL  C2 H6 O2   62.07  View 
     
  •   Protein Details   Hide

    UniProtKB Information

    Chain SWS/UNP ID SWS/UNP Accession(s)
    A MBD4_MOUSE Q9Z2D7     

    EC, Associated Pathways and Catalytic Sites

    Chain(s) IUBMB KEGG BioCyc
    3.2.2      
    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. 
    5634   Nucleus  A Membrane Bounded Organelle of Eukaryotic Cells in Which Chromosomes Are Housed and Replicated. in Most Cells the Nucleus Contains All of the Cell's Chromosomes Except the Organellar Chromosomes and Is the Site of RNA Synthesis and Processing. in Some Species or in Specialized Cell Types RNA Metabolism or DNA Replication May Be Absent. 
    3677   DNA Binding  Any Molecular Function by Which a Gene Product Interacts Selectively and Non Covalently with DNA (deoxyribonucleic Acid). 
    8263   Pyrimidine Specific Mismatch Base Pair DNA N Glycosylase Activity  Catalysis of the Removal of Mismatched Pyrimidine Bases in Dna. Enzymes with This Activity Recognize and Remove Pyrimidines Present in Mismatches by Cleaving the N C1' Glycosidic Bond Between the Target Damaged DNA Base and the Deoxyribose Sugar. the Reaction Releases a Free Base and Leaves an Apyrimidinic (ap) Site. 


     
  •   Gene Details   Hide

    Genetic Source

    Chain A
    Common Name Mouse
    Scientific Name Mus musculus  
    Gene mbd4
    Host Scientific Name Escherichia coli  
    Host Strain Bl21(de3)
    Host Vector Type Plasmid


    Genome Information

    Chromosome Locus Gene ID Gene Name Symbol
    6 6 E3|6 53.72 cM 17193     methyl-CpG binding domain protein 4 MBD4