1G38

ADENINE-SPECIFIC METHYLTRANSFERASE M. TAQ I/DNA COMPLEX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.208 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Structure of the N6-adenine DNA methyltransferase M.TaqI in complex with DNA and a cofactor analog.

Goedecke, K.Pignot, M.Goody, R.S.Scheidig, A.J.Weinhold, E.

(2001) Nat Struct Biol 8: 121-125

  • DOI: 10.1038/84104
  • Primary Citation of Related Structures:  
    1G38

  • PubMed Abstract: 
  • The 2.0 A crystal structure of the N6-adenine DNA methyltransferase M.TaqI in complex with specific DNA and a nonreactive cofactor analog reveals a previously unrecognized stabilization of the extrahelical target base. To catalyze the transfer of the ...

    The 2.0 A crystal structure of the N6-adenine DNA methyltransferase M.TaqI in complex with specific DNA and a nonreactive cofactor analog reveals a previously unrecognized stabilization of the extrahelical target base. To catalyze the transfer of the methyl group from the cofactor S-adenosyl-l-methionine to the 6-amino group of adenine within the double-stranded DNA sequence 5'-TCGA-3', the target nucleoside is rotated out of the DNA helix. Stabilization of the extrahelical conformation is achieved by DNA compression perpendicular to the DNA helix axis at the target base pair position and relocation of the partner base thymine in an interstrand pi-stacked position, where it would sterically overlap with an innerhelical target adenine. The extrahelical target adenine is specifically recognized in the active site, and the 6-amino group of adenine donates two hydrogen bonds to Asn 105 and Pro 106, which both belong to the conserved catalytic motif IV of N6-adenine DNA methyltransferases. These hydrogen bonds appear to increase the partial negative charge of the N6 atom of adenine and activate it for direct nucleophilic attack on the methyl group of the cofactor.


    Related Citations: 
    • DIFFERENTIAL BINDING OF S-ADENOSYLMETHIONINE, S-ADENOSYLHOMOCYSTEINE AND SINEFUNGIN TO THE ADENINE-SPECIFIC DNA METHYLTRANSFERASE M. TAQ I
      Schluckebier, G., Kozak, M., Bleimling, N., Weinhold, E., Saenger, W.
      (1997) J Mol Biol 265: 56

    Organizational Affiliation

    Max-Planck-Institut für molekulare Physiologie, Abteilung Physikalische Biochemie, Otto-Hahn-Str. 11, D-44227 Dortmund, Germany.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
MODIFICATION METHYLASE TAQIAD393Thermus aquaticusMutation(s): 0 
Gene Names: taqIM
EC: 2.1.1.72
Find proteins for P14385 (Thermus aquaticus)
Explore P14385 
Go to UniProtKB:  P14385
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    5'-D(*GP*TP*TP*CP*GP*AP*TP*GP*TP*C)-3'B, E10N/A
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 2
      MoleculeChainsLengthOrganismImage
      5'-D(*GP*AP*CP*AP*TP*CP*GP*(6MA)P*AP*C)-3'C, F10N/A
      Small Molecules
      Ligands 1 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      NEA
      Query on NEA

      Download CCD File 
      A, D
      5'-DEOXY-5'-[2-(AMINO)ETHYLTHIO]ADENOSINE
      C12 H18 N6 O3 S
      APAPOJUCRZTCHD-WOUKDFQISA-N
       Ligand Interaction
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 2.00 Å
      • R-Value Free: 0.234 
      • R-Value Work: 0.196 
      • R-Value Observed: 0.208 
      • Space Group: P 1 21 1
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 59.5α = 90
      b = 68.65β = 92.2
      c = 114.43γ = 90
      Software Package:
      Software NamePurpose
      MAR345data collection
      XDSdata reduction
      AMoREphasing
      CNSrefinement
      XDSdata scaling

      Structure Validation

      View Full Validation Report



      Entry History 

      Deposition Data

      Revision History 

      • Version 1.0: 2001-03-05
        Type: Initial release
      • Version 1.1: 2008-04-27
        Changes: Version format compliance
      • Version 1.2: 2011-07-13
        Changes: Version format compliance
      • Version 1.3: 2013-08-28
        Changes: Atomic model
      • Version 1.4: 2017-10-04
        Changes: Advisory, Refinement description