1YF3

T4Dam in Complex with AdoHcy and 13-mer Oligonucleotide Making Non- and Semi-specific (~1/4) Contact


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.29 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.221 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Transition from Nonspecific to Specific DNA Interactions along the Substrate-Recognition Pathway of Dam Methyltransferase.

Horton, J.R.Liebert, K.Hattman, S.Jeltsch, A.Cheng, X.

(2005) Cell 121: 349-361

  • DOI: 10.1016/j.cell.2005.02.021
  • Primary Citation of Related Structures:  
    1YF3, 1YFL, 1YFJ

  • PubMed Abstract: 
  • DNA methyltransferases methylate target bases within specific nucleotide sequences. Three structures are described for bacteriophage T4 DNA-adenine methyltransferase (T4Dam) in ternary complexes with partially and fully specific DNA and a methyl-donor analog ...

    DNA methyltransferases methylate target bases within specific nucleotide sequences. Three structures are described for bacteriophage T4 DNA-adenine methyltransferase (T4Dam) in ternary complexes with partially and fully specific DNA and a methyl-donor analog. We also report the effects of substitutions in the related Escherichia coli DNA methyltransferase (EcoDam), altering residues corresponding to those involved in specific interaction with the canonical GATC target sequence in T4Dam. We have identified two types of protein-DNA interactions: discriminatory contacts, which stabilize the transition state and accelerate methylation of the cognate site, and antidiscriminatory contacts, which do not significantly affect methylation of the cognate site but disfavor activity at noncognate sites. These structures illustrate the transition in enzyme-DNA interaction from nonspecific to specific interaction, suggesting that there is a temporal order for formation of specific contacts.


    Related Citations: 
    • Structure of the bacteriophage T4 DNA adenine methyltransferase
      Yang, Z., Horton, J.R., Zhou, L., Zhang, X.J., Dong, A., Zhang, X., Schlagman, S.L., Kossykh, V., Cheng, X.
      (2003) Nat Struct Mol Biol 10: 849

    Organizational Affiliation

    Department of Biochemistry, Emory University School of Medicine, 1510 Clifton Road, Atlanta, GA 30322, USA.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
DNA adenine methylaseC [auth A], D [auth B]259Escherichia virus T4Mutation(s): 0 
Gene Names: DAM
EC: 2.1.1.72
Find proteins for P04392 (Enterobacteria phage T4)
Explore P04392 
Go to UniProtKB:  P04392
Protein Feature View
Expand
  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    5'-D(*AP*CP*CP*AP*TP*GP*AP*TP*CP*TP*GP*AP*C)-3'A [auth C]13N/A
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 2
      MoleculeChainsLengthOrganismImage
      5'-D(*TP*GP*TP*CP*AP*GP*AP*TP*CP*AP*TP*GP*G)-3'B [auth D]13N/A
      Small Molecules
      Ligands 2 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      SAH
      Query on SAH

      Download Ideal Coordinates CCD File 
      E [auth A], G [auth B]S-ADENOSYL-L-HOMOCYSTEINE
      C14 H20 N6 O5 S
      ZJUKTBDSGOFHSH-WFMPWKQPSA-N
       Ligand Interaction
      GOL
      Query on GOL

      Download Ideal Coordinates CCD File 
      F [auth A], H [auth B]GLYCEROL
      C3 H8 O3
      PEDCQBHIVMGVHV-UHFFFAOYSA-N
       Ligand Interaction
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 2.29 Å
      • R-Value Free: 0.270 
      • R-Value Work: 0.214 
      • R-Value Observed: 0.221 
      • Space Group: P 1 21 1
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 38.9α = 90
      b = 125.8β = 104.7
      c = 73.2γ = 90
      Software Package:
      Software NamePurpose
      XDSdata scaling
      SCALEPACKdata scaling
      GLRFphasing
      CNSrefinement
      XDSdata reduction

      Structure Validation

      View Full Validation Report



      Entry History 

      Deposition Data

      Revision History  (Full details and data files)

      • Version 1.0: 2005-05-17
        Type: Initial release
      • Version 1.1: 2008-04-30
        Changes: Version format compliance
      • Version 1.2: 2011-07-13
        Changes: Non-polymer description, Version format compliance
      • Version 1.3: 2017-10-11
        Changes: Refinement description