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CpG specific methyltransferase in complex with target DNA
DOI:10.2210/pdb4dkj/pdb   NDB ID: NA1572
4DKJ
Primary Citation
 
 
  •   Molecular Description Hide
    Classification: Transferase/dna
    Structure Weight: 56380.77
    Molecule: Cytosine-specific methyltransferase
    Polymer: 1 Type: protein Length: 403
    Chains: A
    EC#: 2.1.1.37   
    Mutation: S295P
    Organism: Mycoplasma penetrans HF-2
    Gene Name: MYPE4940
    UniProtKB: Protein Feature View | Search PDB | Q8EVR5  
    Molecule: DNA (5'-D(*CP*CP*AP*CP*AP*TP*GP*(C37)P*GP*CP*TP*GP*AP*A)-3')
    Polymer: 2 Type: dna Length: 14
    Chains: B
    Molecule: DNA (5'-D(*GP*TP*TP*CP*AP*GP*(5CM)P*GP*CP*AP*TP*GP*TP*G)-3')
    Polymer: 3 Type: dna Length: 14
    Chains: C
     
  •   Structure Validation Hide

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  • MolProbity Ramachandran Plot
     

  •   Related Citations in PDB Entry (REMARK 1) Hide
     
  •   Source Hide
    Polymer: 1
    Scientific Name: Mycoplasma penetrans   Taxonomy   Expression System: Escherichia coli  
    Polymer: 2
    Scientific Name: Synthetic construct   Taxonomy    
    Polymer: 3
    Scientific Name: Synthetic construct   Taxonomy    
     
  •   Related PDB Entries Hide
    Identifier Details
    1MHT  COVALENT TERNARY STRUCTURE OF HHAI METHYLTRANSFERASE, DNA AND S-ADENOSYL-L-HOMOCYSTEINE 
    2C7P  HHAI DNA METHYLTRANSFERASE COMPLEX WITH OLIGONUCLEOTIDE CONTAINING 2-AMINOPURINE OPPOSITE TO THE TARGET BASE (GCGC:GMPC) AND SAH 
    3PT6  Crystal structure of mouse DNMT1(650-1602) in complex with DNA 
    3PT9  Crystal structure of mouse DNMT1(731-1602) in the free state 
    3PTA  Crystal structure of human DNMT1(646-1600) in complex with DNA 
    4DA4  Structure of mouse DNMT1 (731-1602) bound to hemimethylated CpG DNA 
     
  •   Ligand Chemical Component Hide
    Identifier Formula Name View Interactions
    GOL
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    GOL C3 H8 O3
    GLYCEROL
    SAH
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    SAH C14 H20 N6 O5 S
    S-ADENOSYL-L-HOMOCYSTEINE
    SAH:4DKJ
     
  •   Modified Residues Hide
    Identifier Formula Parent Type
    C37
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    C37 C9 H13 F N3 O7 P DC dnaLinking
    5CM
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    5CM C10 H16 N3 O7 P DC dnaLinking
     
  •   External Domain Annotations Hide
     
  •   Structural Biology Knowledgebase Data Hide
     
  • Nucleic Acid Database Hide
    View the NDB ID associated with this structure: NA1572
     
 
Data in orange boxes are gathered from external resources (when available).
 
  Biological Assembly       
Biological assembly 1 assigned by authors and generated by PISA (software)
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  •   MyPDB Personal Annotations Hide
     
  •   Deposition Summary Hide
    Authors:   Wojciechowski, M.,  Czapinska, H.,  Bochtler, M.

    Deposition:   2012-02-03
    Release:   2012-12-05
    Last Modified (REVDAT):   2013-01-16
     
  •   Revision History    Hide
    Mouse over text for details
    2013-01-16
    Citation
    2013-01-02
    Citation
    2012-12-19
    Citation
     
  •   Experimental Details Hide
    Method:   X-RAY DIFFRACTION
    Exp. Data:
      Structure Factors
    EDS  
    Resolution[Å]:   2.15
    R-Value: 0.178 (obs.)
    R-Free: 0.216
    Space Group: P 41 21 2
    Unit Cell:
      Length [Å] Angles [°]
    a = 83.95 α = 90.00 
    b = 83.95 β = 90.00 
    c = 173.84 γ = 90.00