POP-OUT | CLOSE
CpG specific methyltransferase in complex with target DNA
DOI:10.2210/pdb4dkj/pdb   NDB ID: NA1572
4DKJ
Primary Citation

CpG underrepresentation and the bacterial CpG-specific DNA methyltransferase M.MpeI.

Wojciechowski, M.,  Czapinska, H.,  Bochtler, M.

Journal: (2013) Proc.Natl.Acad.Sci.USA 110: 105-110

PubMed: 23248272  
PubMedCentral: PMC3538198  
DOI: 10.1073/pnas.1207986110  
Search Related Articles in PubMed  
PubMed Abstract:
Cytosine methylation promotes deamination. In eukaryotes, CpG methylation is thought to account for CpG underrepresentation. Whether scarcity of CpGs in prokaryotic genomes is diagnostic for methylation is not clear. Here, we report that Mycoplasms tend to be CpG depleted and... [ Read More & Search PubMed Abstracts ]
 
  •   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  
    Q8EVR5UniProtKBPDB SitesSecstruc4DKJ.APDBPDB ID 4DKJ chain A - Cytosine-specific methyltransferase (72-294) - 2.15 Å - Wed Dec 05 2012
    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
     
  •   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 Interactions
    GOL
    Search 
    Download      		GOL C3 H8 O3
    GLYCEROL
    SAH
    Search 
    Download      		SAH C14 H20 N6 O5 S
    S-ADENOSYL-L-HOMOCYSTEINE
    		SAH:4DKJ
     
  •   Modified Residues Hide
    Identifier Formula Parent Type
    C37
    Search      		C37 C9 H13 F N3 O7 P DC dnaLinking
    5CM
    Search      		5CM C10 H16 N3 O7 P 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: NA1572
     
 
Data in orange boxes are gathered from external resources (when available).
Reset Layout
 
  Biological Assembly       
Biological assembly 1 assigned by authors and generated by PISA (software)
Downloadable viewers:
 
 
 
  •   MyPDB Personal Annotations Hide

    To save personal annotations, please login to your MyPDB account.

     
  •   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