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Crystal structure of human DNMT1(646-1600) in complex with DNA
DOI:10.2210/pdb3pta/pdb   NDB ID: NA0855
3PTA
Primary Citation

Structure of DNMT1-DNA complex reveals a role for autoinhibition in maintenance DNA methylation.

Song, J.,  Rechkoblit, O.,  Bestor, T.H.,  Patel, D.J.

Journal: (2011) Science 331: 1036-1040

PubMed: 21163962  
DOI: 10.1126/science.1195380  
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PubMed Abstract:
Maintenance of genomic methylation patterns is mediated primarily by DNA methyltransferase-1 (DNMT1). We have solved structures of mouse and human DNMT1 composed of CXXC, tandem bromo-adjacent homology (BAH1/2), and methyltransferase domains bound to DNA-containing unmethylated CpG sites. The CXXC specifically... [ Read More & Search PubMed Abstracts ]
 
  •   Molecular Description Hide
    Classification: Transferase/dna
    Structure Weight: 120361.53
    Molecule: DNA (cytosine-5)-methyltransferase 1
    Polymer: 1 Type: protein Length: 956
    Chains: A
    EC#: 2.1.1.37   
    Fragment: UNP residues 646-1600
    Organism Homo sapiens
    Gene Names DNMT1 AIM CXXC9 DNMT
    UniProtKB:   Protein Feature View | Search PDB | P26358  
    P26358Molec. ProcessingDNA (cytosine-5)-methyltransferase 1MotifBAH 1BAH 2CInteraction wiAuInteraction with theInteraInInteraction RCatalyticInterHomodimeNDNA repliE.C.2.1.1.37: DNA (cytosine-5-)-methyltransferaseUP SitesUniProtKBPDB SitesSecstruc3PTA.APDBTooltip
    Molecule: DNA (5'-D(*TP*CP*CP*CP*GP*TP*GP*AP*GP*CP*CP*TP*CP*CP*GP*CP*AP*GP*G)-3')
    Polymer: 2 Type: dna Length: 19
    Chains: B
    Molecule: DNA (5'-D(*CP*CP*TP*GP*CP*GP*GP*AP*GP*GP*CP*TP*CP*AP*CP*GP*GP*GP*A)-3')
    Polymer: 3 Type: dna Length: 19
    Chains: C
     
  •   Source Hide
    Polymer: 1
    Scientific Name: Homo sapiens   Taxonomy   Common Name: Human Expression System: Escherichia coli  
    Polymer: 2
    Scientific Name: Synthetic construct   Taxonomy    
    Polymer: 3
    Scientific Name: Synthetic construct   Taxonomy    
     
  •   Related PDB Entries Hide
    Identifier Details
    3PT6   
    3PT9   
     
  •   Ligand Chemical Component Hide
    Identifier Formula Name Interactions
    SAH
    Search 
    Download      		SAH C14 H20 N6 O5 S
    S-ADENOSYL-L-HOMOCYSTEINE
    		SAH:3PTA
    ZN
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    Download      		ZN Zn
    ZINC ION
     
  •   External Ligand Annotations Hide
    Identifier   Binding Affinity (Sequence Identity %)
    SAH
    Search 
    Download      		SAH
    IC50: 800 - 900 nM (100) - data from BindingDB  
    N/Ain BindingMoad
    N/Ain PDBbind
     
  •   External Domain Annotations Hide
     
  •   Structural Biology Knowledgebase Data Hide

    Information from the Structural Biology Knowledgebase  

     
  • Nucleic Acid Database Hide
    View the NDB ID associated with this structure: NA0855
     
 
Data in orange boxes are gathered from external resources (when available).
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  Biological Assembly       
Biological assembly 1 assigned by authors and generated by PISA (software)
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  •   Deposition Summary Hide
    Authors:   Song, J.,  Patel, D.J.

    Deposition:   2010-12-02
    Release:   2010-12-29
    Last Modified (REVDAT):   2011-03-30
     
  •   Revision History    Hide
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    2011-07-13
    Version format compliance
     
  •   Experimental Details Hide
    Method:   X-RAY DIFFRACTION
    Exp. Data:
      Structure Factors
    EDS  
    Resolution[Å]:   3.60
    R-Value: 0.257 (obs.)
    R-Free: 0.291
    Space Group: C 2
    Unit Cell:
      Length [Å] Angles [°]
    a = 162.80 α = 90.00 
    b = 87.90 β = 97.20 
    c = 113.90 γ = 90.00