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Structure of mouse DNMT1 (731-1602) bound to hemimethylated CpG DNA
DOI:10.2210/pdb4da4/pdb   NDB ID: NA1539
4DA4
Primary Citation

Structure-based mechanistic insights into DNMT1-mediated maintenance DNA methylation.

Song, J.,  Teplova, M.,  Ishibe-Murakami, S.,  Patel, D.J.

Journal: (2012) Science 335: 709-712

PubMed: 22323818  
DOI: 10.1126/science.1214453  
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PubMed Abstract:
DNMT1, the major maintenance DNA methyltransferase in animals, helps to regulate gene expression, genome imprinting, and X-chromosome inactivation. We report on the crystal structure of a productive covalent mouse DNMT1(731-1602)-DNA complex containing a central hemimethylated CpG site. The methyl group... [ Read More & Search PubMed Abstracts ]
 
  •   Molecular Description Hide
    Classification: Transferase/dna
    Structure Weight: 213998.92
    Molecule: DNA (cytosine-5)-methyltransferase 1
    Polymer: 1 Type: protein Length: 873
    Chains: A, B
    EC#: 2.1.1.37   
    Fragment: UNP residues 731-1602
    Organism Mus musculus
    Gene Names Dnmt1 Dnmt Met1 Uim
    UniProtKB:   Protein Feature View | Search PDB | P13864  
    P13864Molec. ProcessingDNA (cytosine-5)-methyltransferase 1MotifBAH 1BAH 2CXInteraction withAuCatalyticInteraIntInteraction wiInterInteraction with the PRInterDNA replicaNE.C.2.1.1.37: DNA (cytosine-5-)-methyltransferaseUP SitesUniProtKBPDB SitesSecstruc4DA4.A4DA4.BPDBTooltip
    Molecule: DNA_UPPER_STRAND
    Polymer: 2 Type: dna Length: 12
    Chains: C, E
    Molecule: DNA_LOWER_STRAND
    Polymer: 3 Type: dna Length: 12
    Chains: D, F
     
  •   Source Hide
    Polymer: 1
    Scientific Name: Mus musculus   Taxonomy   Common Name: Mouse Expression System: Escherichia coli  
    Polymer: 2
    Scientific Name: Synthetic construct   Taxonomy    
    Polymer: 3
    Scientific Name: Synthetic construct   Taxonomy    
     
  •   Ligand Chemical Component Hide
    Identifier Formula Name Interactions
    CIT
    Search 
    Download      		CIT C6 H8 O7
    CITRIC ACID
    SAH
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    Download      		SAH C14 H20 N6 O5 S
    S-ADENOSYL-L-HOMOCYSTEINE
    		SAH:4DA4
    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 (85) - data from BindingDB  
    N/Ain BindingMoad
    N/Ain PDBbind
     
  •   Modified Residues Hide
    Identifier Formula Parent Type
    5CM
    Search      		5CM C10 H16 N3 O7 P DC dnaLinking
    C49
    Search      		C49 C10 H15 F N3 O7 P S DC dnaLinking
     
  •   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: NA1539
     
 
Data in orange boxes are gathered from external resources (when available).
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  Biological Assembly 1       
Biological assembly 1 assigned by authors and generated by PISA (software)
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  •   MyPDB Personal Annotations Hide

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  •   Deposition Summary Hide
    Authors:   Song, J.,  Patel, D.J.

    Deposition:   2012-01-12
    Release:   2012-02-22
     
  •   Revision History    Hide
    No revisions since initial release
     
  •   Experimental Details Hide
    Method:   X-RAY DIFFRACTION
    Exp. Data:
      Structure Factors
    Resolution[Å]:   2.60
    R-Value: 0.198 (obs.)
    R-Free: 0.246
    Space Group: P 21
    Unit Cell:
      Length [Å] Angles [°]
    a = 89.68 α = 90.00 
    b = 152.04 β = 94.54 
    c = 96.05 γ = 90.00